File: ChangeLog

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bow 19991122-4
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1999-11-22  Andrew McCallum  <mccallum@justresearch.com>

	* Makefile.in (STANDARD_RAINBOW_METHOD_C_FILES): Added dirk.c.
	* dirk.c (log_gamma): Cache 100 integer x's.
	(bow_dirk_log_kernel): Take vocab size as argument instead of barrel.
	(bow_dirk_score): Add exponentiated log-densities, instead of log
	densities.  Do this by finding the max and subtracting.

1999-11-16  Andrew McCallum  <mccallum@justresearch.com>

	* cdm.c (cdm_options): New command-line options
	"cdm-print-smallest-alphas" and "cdm-print-largest-alphas".
	(cdm_parse_opt): Handle them.
	(bow_cdm_initialize_ct): New code allows this to be called more than
	once.  This way you can add new document (and hence words) and
	re-calculate the infogain.
	(bow_cdm_ct_set_alphas): Added structure ALPHA_RECORD for printing
	largest and smallest alphas.  Added, but commented out, code for
	smoothing the counts before fitting the Dirichlet, using
	log(alpha) in place of alpha, smoothing the alphas.  Print the
	largest and smallest alphas.
	(CDM_SCORE_ANNEAL_TEMPERATURE): New macro, currently defined not to be
	used.
	(bow_cdm_score): Handle it.

1999-11-10  Andrew McCallum  <mccallum@justresearch.com>

	* svm_base.c (sqrtf): New macro, necessary on some non-Linux
	machines.  Bug reported by Chuck Rosenberg.

1999-11-08  Andrew McCallum  <mccallum@justresearch.com>

	* readme.texi: Add simple usage examples for arrow.

	* arrow.c (arrow_serve2): Implement the 'query' command.  Change
	XML labels from "archer" to "arrow".
	(main): Change default number of hits on a query from 1 to 10.

	* libbow-desc.texi: Update descriptions.
	* svm_base.c: Surround many condition man printf's on the
	bow_verbosity_level, so that by default rainbow-stats will still
	work.

	* array.c (cdocs_iterator_count_for_doc): Replace NAN macro with
	arithmetic equivalent.
	* barrel.c (barrel_iterator_count_for_doc): Likewise.

	* wv.c (bow_wv_weight_sum): New function.
	* bow/libbow.h: Declare new function.

	* train_dirichlet.c (moment_match_mccallum): Separate
	implementation of moment matching that determines the variance by
	averaging the variance of all dimentions.
	(train_dirichlet_mom_sparse): New function.
	* bow/train_dirichlet.h: Declare new function.

	* tfidf.c (TFIDF_METHOD): Use
	bow_wv_set_weights_to_count_times_idf() instead of
	bow_wv_set_weights_to_count(), as is correct for TFIDF.  This was
	previously corrected in the scoring function.
	(bow_tfidf_params_tfidf): Change parameter settings for "tfidf"
	method.  Previously it was identical to the "tfidf_log_words"
	method, now it is identical to the "tfidf_log_occur" method.  In
	other words, previously it calculated IDF using the number of
	times the word occurred in the training data; now it uses the
	number of training documents in which the word occurs.

	* split.c (bow_split_options): Remove documentation for 'r'
	suffix.  It's confusing and shouldn't be used unawares.
	(bow_split_parse_opt): Add a 'pcr' suffix, but its not implemented
	yet.
	(bow_set_doc_types_randomly_by_count_per_class): Count the number of
	untagged documents in each class, and if this function is trying
	to tag more than are available, simply have this function tag
	less.

	* rainbow.c (bow_print_log_odds_ratio): Handle words that are not
	in the vocabulary.

	* ddf.c: Implement ddfmm classification method.  This method fits
	the Dirichlet by moment matching only.

	* arrow.c (arrow_serve2): New function.  Now call this instead of
	arrow_serve.  It provides output in XML, like archer does.  Only
	the rank command is implemented.

1999-11-02  Andrew McCallum  <mccallum@justresearch.com>

	* int4str.c (bow_int2str): Assert that INDEX argument is
	non-negative.

1999-10-28  Gregory C Schohn  <gcs@cmu.edu>

	* svm_base.c (svm_vpc_merge): fixed bug for svml-basename - all
 	the docs still need to be output, so that the other data (like
 	word weights can be properly extracted).

1999-10-28  Andrew McCallum  <mccallum@justresearch.com>

	* cdmem.c (cdmem_options): New command-line option
	"cdmem-dist-data".
	(cdmem_parse_opt): Handle it.
	(bow_cdmem_new_vpc_with_weights): Let the command-line option
	determine what documents are used to learn the distance metric.

	* README-SVM (Outputing data): Added new section describing how to
	produce files ready for input into SVM^light.

1999-10-27  Gregory C Schohn  <gcs@cmu.edu>

	* svm_base.c (svm_vpc_merge): fixed svml bugs
	* svm_base.c fixed outdated documentation for parse info.
	* svm_smo.c (smo): fixed a parse error

1999-10-26  Gregory C Schohn  <gcs@cmu.edu>

	* rainbow.c (rainbow_test): added a line for svms.  When svmlight
 	output is being generated, rainbow_test prints the label (only
 	works for binary barrels) so that svm_score can append the data
 	for that example.

	* svm_base.c (svm_options[]): removed some of the single character
 	switches.  Added arguments for tsvms & added svml-basename arg.
	(svm_permute_data, svm_unpermute_data): added.
	(infogain): should have made infogain compatible with sets with
	unlabeled data (it ignore those docs with y = 0). 
	(svm_vpc_merge): added support for using unlabeled docs for
	transduction.  Also added code to spit out svmlight friendly
	files. 
	(svm_score): added code to write svmlight files.
	* svm_trans.c: initial version - pretty much empty now.
	* bow/svm.h: added svm_*permute_data declarations & the
 	transduce_svm declaration.
	* svm_al.c (al_svm_test_wrapper): replaced permutation code with
 	calls to svm_permute_data & svm_unpermute_data.
	* svm_smo.c (smo): removed srandom(1) - was only there for
 	debugging.
	* README-SVM (Bugs): removed section about smo being broken (was
 	fixed).

	* Makefile.in: added svm_trans.c (transductive svms) to the
 	svm_files.

1999-10-25  Andrew McCallum  <mccallum@justresearch.com>

	* .cvsignore: Add automatically-generated archer files, and a few
	others.

1999-10-21  Andrew McCallum  <mccallum@justresearch.com>

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Don't set the
	NUM_WORDS_TO_KEEP to be the WI2IG_SIZE (which is the total number
	of words).  Set it to the MIN of this and the original
	NUM_WORDS_TO_KEEP.  Before this fix, no words were ever getting
	removed.  What a bug!  I wonder how long this has been in there?
	Reported by Carsten Lanquillon <lanqui@cs.cmu.edu>.

1999-10-20  Andrew McCallum  <mccallum@justresearch.com>

	* ddf.c (bow_ddf_dirichlet_from_doc_word_counts): Only print the
	diagnostics for 10 sampled words, not 50.
	* bpe.c (bow_bpe_set_cdoc_word_count_from_wi2dvf_weights): Print
	the alphas for only 10 sampled words intead of 20.

1999-10-19  Andrew McCallum  <mccallum@justresearch.com>

	* svm_base.c: Check verbosity level before printing to stdout.
	Only print if above bow_progress.

1999-10-19  Gregory C Schohn  <gcs@cmu.edu>

	* svm_base.c (svm_score): removed cnt variable (useless) & fixed a
 	typo-bug (sub_model[i] -> barrel).

	* svm_smo.c (smo): changed the printf for information of where
 	opt_pair failed to an fprintf.

1999-10-19  Gregory C Schohn  <gcs@justresearch.com>

	* Makefile.local (DIST_ALL_FILES): added -DGCSJPRC (turn local
 	pedantic debugging) to DEFS.

	* Makefile.in (ALL_CPPFLAGS): added -Ibow (so that pr_loqo.h is
 	found by pr_loqo.c even though they aren't in the same directory
 	[since we can't change pr_loqo.*]).
	(DEFS): Changed from _DEFS & now using += instead of the temporary.

	* svm_base.c: the epsilon_crit is now /2 for SMO (since the actual
 	eps is 2x the variable).  fixed some printfs.

	* svm_loqo.c (build_svm_guts): added code to remember previous KKT
 	epsilon (even though nobody sets the initial value to anything
 	different than the macro).
	(build_svm_guts): added local define (GCSJPRC) for debugging stuff
 	which includes stopping the proc & sending mail.

	* svm_smo.c: commented #DEBUG.  added kcache_ages to appropriate
 	spots across the file.  removed some print statements that weren't
 	to useful anymore.
	(opt_pair): changed an optimality check - used to use (a2+ao2)*eps 
	to detrmine if something moved far enough, now just using eps_a 
	(may not be right, but its more correct than before) - we need it 
	to prevent inf. looping.
	(opt_pair): Removed some unreachable in if statements.
	(opt_pair): Fixed calculations of bup & blow - they were backwards
	(smo): the threshold, b is now (bup+blow)/2 instead of blow (which 
	is at most epsilon_crit different).

1999-10-16  Gregory C Schohn <gcs@justresearch.com>

	* svm_base.c: Added #ifdef HAVE_LOQO around calls to build_svm_guts
	* svm_al.c: Added #ifdef HAVE_LOQO around calls to build_svm_guts
	* Makefile.in: Re-enabled svm code.  Made the pr_loqo checks look 
	./bow/pr_loqo.h

1999-10-16  Andrew McCallum  <mccallum@justresearch.com>

	* README-SVM (Obtaining sources): File renamed from README_SVM.
	Clarify directions for where to put pr_loqo.h.

1999-10-15  Andrew McCallum  <mccallum@justresearch.com>

	* Version (BOW_MINOR_VERSION): Changed from 9 to 95.
	* bow/libbow.h (BOW_MINOR_VERSION): Changed from 9 to 95.

	Bug fixes for distribution.
	* .cvsignore: Added rainbow-rank and rainbow-ts.
	* Makefile.in: Temporarily disable SVM from rainbow.
	(ARCHER_GENERATED_C_FILES): New variable.  Remove this files from
	those distributed, because they should be generated.
	(ARCHER_DIST_FILES): Added archer.c and archer_query.c
	* Makefile.in (DEMO_EXECUTABLES): New variable.
	(ARCHER_DIST_FILES): Added dirichlet.c.
	(DIST_FILES): Added archer.el
	* multiclass.c: Comment out unused variables.

	Odd assortment of clean-ups.
	* bow/libbow.h (bow_random_reset_seed): Declare function.
	* train_dirichlet.c (MOMENT_MATCH_ONLY): New macro.
	(SPARSE): Change macro value from 0 to 1.  This only effects running
	train_dirichlet's main() directly.
	(main): comment out the printing of the gammaln() tests.  New local
	variable COUNTS_SIZE, increased from 100 to 10000.  Print more
	diagnostics at the end.
	* readme.texi: Update for new front-ends and fix command-line
	options so they work.
	* rainbow.c (rainbow_options): Clean up wording in several places.
	(rainbow_query): Change behavior of repeated queries.
	(bow_print_log_odds_ratio): Add a new FILE* argument.  All callers
	changed.
	* nbshrinkage.c: Allow different lambda hierarchical mixture
	weights for different classes.
	* mix.c (mix_options): New command-line option for setting the
	number of EM iterations.
	(mix_new_vpc): Don't allow initial random class_probs to be zero.
	* libbow-desc.texi: Update for new front-ends and MSWin.
	* lex-gram.c (bow_lexer_gram_open_text_fp): Properly save the
	return value of bow_realloc().  This fixes a nasty crash.
	* emsimple.c (bow_emsimple_new_vpc_with_weights): Print
	diagnostics using odds_ratio.
	* dirichlet.c (main): New command-line argument -I.  Handle it.
	* dice.c (print_usage): Expand help statement.
	* ddf.c (ddf_force_large_alphas): New variable.
	(bow_ddf_dirichlet_from_doc_word_counts): Handle it.
	(ddfla): New method.
	* cdmm.c (CDMM_PRINT_ALPHAS_KEY): Change value to not conflict
	with the cdm method.
	* bpe.c (bpe_prior_alpha): Change default prior "ghost count" from
	1 to 0.
	(bow_bpe_set_cdoc_word_count_from_wi2dvf_weights): Make the verbosity
	work even when the vocabulary size is less than 20.
	(bow_bpe_score): Print more information when BOW_PRINT_WORD_SCORES.
	Print more digits of precision of BOW_PRINT_WORD_SCORES for
	individual words.
	* Makefile.local (RAINBOW_METHOD_C_FILES): Move some of these to
	the Makefile.in.

1999-10-15  Gregory C Schohn  <gcs@cmu.edu>

	* svm_base.c: fixed some preprocessing bugs - also mildly cleaned
 	up the code...

	* svm_smo.c: started fixing bugs (the definition of the error
 	vector changed - the modified code did not also change in some
 	spots)- there is still 1 left

	* README_SVM: up to date - ready for release.

1999-10-13  Andrew McCallum  <mccallum@justresearch.com>

	* Makefile.in: Fix errors from last check-in.
	
1999-10-13  Gregory C Schohn  <gcs@cmu.edu>

	* Makefile.in (SVM_FILES): Added a check for pr_loqo.[ch] - if
 	they are there the svm parts of bow are built with it, otherwise
 	they parts of the code that use pr_loqo are turned off.  The
 	conditional sets necessary files & defines.
	
	(STANDARD_LIBBOW_H_FILES): added bow/svm.h
	(STANDARD_LIBBOW_C_FILES): added $(SVM_FILES) (4-5 files,
	replacing svm.c) 

	* configure.in: removed checks for pr_loqo.* - that's now done in
 	the makefile.
	
	added a check for the fpsetmask macro (which is necessary on at
 	least freebsd boxes to turn ieee math on).

1999-10-07  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: (al_svm_test_wrapper) added printing of documents added
	& the # of bound support vectors.

1999-10-06  Dayne Freitag  <dayne@tweed.jprc.com>

	* tagged.lex: HTML entities now recognized by lex, rather than
	function is_entity.  Parser returns when label is lexed; return
	value indicates word, begin label, or end label.
	* opts.c (parse_bow_opt): Conditional removal of code creating the
	bow data directory which is not appropriate for DART and FDART.
	* labels.c (bow_last_label): New function.
        * archer_query_index.c: Major re-write of previous code.
	* archer_query_array.c: Major re-write of previous code, much of
	which was buggy.
	* archer_query.y: Deleted the "term >N term" syntax as
	superfluous.  Added the "term < term" syntax.  Added the "word"
	type and "WORD" terminal to distinguish from NUMBER.
	* archer_query.c: Code to free allocated structures.
	* archer-server.c (archer_query_socket_init): Now releases socket
	on failure.  Unix socket support.  Streamlined code by changing
	code under archer_query_serve_one_query.  New functions:
	archer_query_serve_one_admin_command,
	archer_query_serve_admin_commands,
	archer_query_server_command_loop,
	archer_query_serve_regular_query,
	archer_query_server_process_commands.  Added security features.
	New functions: archer_remote_host_matches_spec,
	archer_query_password_ok.
	(archer_server_index): Call archer_archive after indexing.
	(archer_server_index_with_markup): New function.
	(archer_server_query_new): Fixed output.  Decomposed, adding new
	functions archer_server_print_hitlist and
	archer_server_print_hit.  Added ndump command and new functions
	archer_server_dump_new, archer_server_dump_preamble, and
	archer_server_do_dump.  Added fields command and new function
	archer_server_fields.
        * archer_query_execute.c: Fixed many memory leaks, and rewrote
	large sections.
	* annotation.c (annotation_sarray_reread): New function.
	* archer.c: Allow mark-up spoofing of the indexer, batch
	incremental indexing, passwords and IP-based client restriction.
	New executables
	(conditionally compiled) DART, FDART, and IDART.
	(archer_get_fp_from_filename): New function.
	(flush_labels): New function.
	(archer_index_term): New function.
	(archer_index_label): New function.
	(archer_index_filename_flex): Some code removed to above functions.
	(archer_index): Changed to prevent re-opening/re-construction of
	already opened files and existing data structures (needed for
	batch incremental indexing).

	
1999-10-06  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: (svm_vpc_merge) fixed preprocessing bug that caused big
 	problems when no weighting was being used in conjunction with
 	pairwise voting.
	
	* also changed all of the options *, to svm-*.

1999-10-05  Andrew McCallum  <mccallum@justresearch.com>

	* TODO: Remove and few items that were done.
	* NEWS: Describe some new features.
	* HACKING: Update to remove no-longer-available CVS server
	description.

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Fix verbosity
	message for vocabulary sizes under 5.

1999-10-05  Andrew McCallum  <mccallum@justresearch.com>

	* docnames.c (bow_map_filenames_from_dir): Fix printf argument.

1999-09-29  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: a lot of minor small changes (like printing stuff), no
 	bug fixes - make sure to suppress the score matrix (which is
 	hundred's of MB large) if test-in-train is used with active
 	learning in the active learning stuff if you don't want it!

1999-09-24  Andrew McCallum  <mccallum@justresearch.com>

	* dirichlet.c: Added ability to do simple classification.  For
	example: (echo 2 ; cat
	~/research/projects/dicefactory/synth1/bar.counts ) | ./dirichlet
	-c 2 18.4738 26.1034 2.49099 2.04999

1999-09-22  Andrew McCallum  <mccallum@justresearch.com>

	* docnames.c (bow_map_filenames_from_dir): When a directory can't
	be opened, simply skip it instead of trying to open it as a file.
	(This works around Linux bug whereby directories seem to
	disappear.)

1999-09-20  Kamal Nigam  <knigam@zeno.jprc.com>

	* maxent.c: New code for options maxent-vary-prior-by-count
	maxent-gaussian-prior-no-zero-constraints
	maxent-prune-features-by-count
	maxent-vary-prior-by-count-linearly.

1999-09-19  Gregory C Schohn  <gcs@cmu.edu>

	* configure.in: added check for srandom - which was & still is
 	necessary for libbow.h

	* bow/libbow.h: changed the defines for srandom & random so that
 	both get redefined if one is missing.

1999-09-09  Andrew McCallum  <mccallum@justresearch.com>

	* train_dirichlet.c: Allow the main() test driver to be compiled
	in by simply defining TD_MAIN on the gcc command-line.
	* random.c (bow_random_reset_seed): New function.
	(bow_random_set_seed): Make it work with the above function.
	* multiclass.c (multiclass_iterated_mixture_given_doc_and_cis):
	New function.
	(multiclass_mixture_given_doc): Allow this to be called with a test
	document too.
	(multiclass_log_prob_of_classes_given_doc): Add commented-out code to
	implement BIC.
	(multiclass_explore_cis_greedy1): Bug fixes.
	* cdmem.c (cdmem_parse_opt): Allow printing of the accuracy on the
	unlabeled set.
	(bow_cdmem_class_wi2dvf): New function.
	(bow_cdmem_new_vpc_with_weights): Save original document types and
	classes.  Using new macro SET_CASCADE_TREE_WITH_ALL_DATA, allow
	three different options for training the distance function.  Allow
	multiple rounds of CDM distance metric learning.
	* cdm.c: Include <bow/train_dirichlet.h> instead of defining
	train_dirichlet() extern here.
	(bow_cdm_initialize_ct): Make it safe to call this function more than
	once.
	(bow_cdm_ct_set_alphas): Define COUNTS as double* instead of unsigned*.
	Print the bottom-most word in the cascade tree.  Don't assert DV.
	* barrel.c (bow_barrel_add_from_text_dir): Instead of crashing
	when failing to open a file, simply print warning.

1999-09-03  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: checkpoint - some bitrotting code may not work...
	
	* svm.c: updated SMO to work with Keerthi, et al's modifications - 
	the heuristic is much better, but the running time on 20 newsgroups
	is still slower than Thorsten's methods.
	
	* svm.c: added a lot of active learning logging.

1999-08-18  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c, bow/train_dirichlet.h: Added train_sum_alpha 
	  global variable.

1999-08-18  Andrew McCallum  <mccallum@justresearch.com>

	* bow/libbow.h: Declare new functions.
	* bow/cdm.h: Update function prototypes to match.
	* wv.c (bow_wv_copy): New function.
	* wi2dvf.c (bow_wi2dvf_set_idf_to_count): New function.
	(bow_wi2dvf_dv_hidden): New function.
	* wa.c (bow_wa_remove): New function.
	* vpc.c (bow_wi2dvf_sum): New function.
	(bow_barrel_new_vpc): Move the updating of the CDOC->WORD_COUNT to
	earlier in the function.
	* rainbow.c (rainbow_test): In the test documents include words
	that were previously removed from the training set by, for
	example, feature selection.
	* heap.c (bow_make_dv_heap_from_wi2dvf_hidden): New function.
	* naivebayes.c (bow_naivebayes_pr_wi_ci): All m_est_m to be zero,
	if set as such explicitly on the command-line.
	(bow_naivebayes_total_word_count_for_ci): New function.
	* ddf.c: Add ADDITIONAL_COUNT.
	* dice.c: Add many command-line options.
	* ctdf.c: Add handling for zerotons and unknown words.
	* bpe.c: Include bpe_prior_alpha, and various other bug fixes.
	* barrel.c: Clean up some verbosity messages.
	(bow_barrel_set_idf_to_count_in_train): New function.
	* train_dirichlet.c: Change name from gammaln_fast to gammaln, so
	this function can be used, depending on the #define.
	* cdm.c: Many completions and bug fixes.
	* cdmem.c (SET_CASCADE_TREE_WITH_ALL_DATA): New macro.
	(bow_cdmem_new_vpc_with_weights): Depending on above macro, use all
	labels to set the distance metric.

1999-08-13  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: added active learning stuff - has a pretty bad selection
 	heuristic (subject to pathological cases), had to change
 	(modularize) different sections of the code...

1999-08-09  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: the removal of inconsistent examples (for the
 	Thorsten-like algorithm) is working, it still needs to be extended
 	for SMO.

1999-08-01  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: 3 bug fixes - one in the lagrange multiplier check, one
 	in the loop to call pr_loqo (the maximum number of iterations
 	wasn't increasing when pr_loqo could not converge), & a bug that
 	caused the equality constraint to fall apart when the working set
 	size was less than the maximum working set size (actually, rewrote
 	that block to be way more efficient).
	
	* svm.c Also played with the kernel cache in a lot of different
	ways, a	simple (but not to simple) solution that is committed 
	yields the best times (when the kernel cache is not grossly
	smaller than the number of support vectors squared).

1999-07-28  William Morgan  <wmorgan@jprc.com>

        * archer_query_array.c: added
        * archer_query_array.h: added
        * archer_query_execute.c: added
        * archer_query_execute.h: added
        * archer_query_index.c: added
        * archer_query_index.h: added
	
	* pv.c (bow_pv_read_next_di_li_pi): removed useless assert()

	* archer_query.c: reformatted for better GNU style

	* archer_query.h: ditto

	* archer.c (mem_error): added, as well as other stuff surrounded
 	by ARCHER_USE_MCHECK defines for optional memory checking

	* archer-server.c (archer_server_query_new): made nquery command
 	call new query engine. right now this dumps core.

	* Makefile.in (ARCHER_C_FILES): added archer_query_ files
	(ARCHER_H_FILES): ditto

1999-07-19  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c (train_dirichlet_nr): Added the option to not
	train the sum of alphas, only their ratios.

1999-07-16  Andrew McCallum  <mccallum@justresearch.com>

	* ddf.c: Debug and add smoothing.  It smooths in the same
	proportion that adding a pseudo-count of 1 would do for
	naivebayes.

1999-07-16  William Morgan  <wmorgan@jprc.com>

	* Makefile.in: fixed small bug that occasionally caused make to
 	overwrite archer_query.c

1999-07-16  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: new version - about 3 times as fast thanks to re-using
 	error-cache values for the kkt conditions instead of
 	re-calculating them each time.  A valid cache bitmap was also
 	added...

	* svm.c: made semi-small bug fixes, like precision checks, the
 	removal of a bogus heuristic check & some small coding bugs...

1999-07-16  William Morgan  <wmorgan@jprc.com>

	* bow/archer.h: removed ARCHER_MAX_LABEL_PARAMS (cruft)

	* flex_mail.lex: modified function naming scheme to work with the
 	new way archer lex files are handled

	* configure.in: added AC_PROG_LEX to configure lexer generator

	* archer_query.y: added

	* archer_query.lex: added

	* archer_query.h: added

	* archer_query.c: added

	* archer.c (archer_query_hits_matching_sequence): fixed bug that
 	caused archer to hang
	* Makefile.in: added rules for .lex and .y files for archer
	* archer-server.c (archer_server_query_new): added
	(archer_server_query_hits_matching_sequence): fixed bug that
 	caused archer to hang
	
1999-07-15  Jason Reed  <jcreed@cyclone.jprc.com>

	* archer.c (archer_index_filename_flex): Don't write redundant
 	wi2pv information.

1999-07-13  Jason Reed  <jcreed@cyclone.jprc.com>

	* archer-server.c (archer_server_query): Include terms matched in
 	query results.

	* archer-server.c: Added 'hits' command to select a range of hits
 	to show.
	(No need to send N tens of thousands of hits over the
	socket when someone searches for 'artificial intelligence' or
 	something equally general)

1999-07-13  Gregory C Schohn  <gcs@cmu.edu>

	* svm.c: includes smo, which works fine, but is slower than
 	thorsten's algorithm... for now.

1999-07-13  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c (newton_step): Don't try to change an alpha
	which is zero, because its gradient will always be negative.

1999-07-12  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c (gammaln,digamma,trigamma): Changed to a
	higher precision algorithm.  No effect on Dirichlet fitting,
	however.

1999-07-12  Jason Reed  <jcreed@cyclone.jprc.com>

	* lex-suffixing.c (bow_lexer_suffixing_postprocess_word): Fixed
 	off-by-one bug, I think.

	* archer.c: Does incremental writes in query server. (Does *not*
	do pure incremental writes if we are just doing an --index)
	Removed label name and document name fields from archer_labels
	and archer_docs entries, since they made entries variable length.

	* archer-server.c: Added indexing capability. (on second socket)
	Always use simple lexer for query lexing, independent of
	data lexing.
	Do 'xxx' suffixing iff appropriate.
	
	* wi2pv.c: Made incremental.

	* int4str.c: Added incremental functions.
	* int4word.c: likewise.
	* sarray.c: likewise.
	* array.c: likewise.
	
	* bow/archer.h: likewise.
	* bow/libbow.h: likewise.
	
1999-07-09  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c (train_dirichlet_sparse, train_dirichlet_nr,
	logProb, moment_match): Added extra_count parameter.

1999-07-08  William Morgan  <wmorgan@jprc.com>

        * archer-server.c (archer_query_socket_init): added SIGPIPE
	handling; archer server mode now no longer crashes as easily

1999-07-08  Kamal Nigam  <knigam@server5.jprc.com>

	* Makefile.local (RAINBOW_METHOD_C_FILES): Added emsimple.c.

1999-07-08  Andrew McCallum  <mccallum@justresearch.com>

	* Makefile.local (RAINBOW_METHOD_C_FILES): Added nbsimple.c
	* naivebayes.c (bow_naivebayes_score): Initialize NUM_SCORES to
	get rid of GCC warning.

	* crossbow.c (crossbow_options): New option --use-vocab-in-file.
	(struct crossbow_arg_state): New element VOCAB_MAP.
	(crossbow_doc_read): Read the DOC->CIS.
	(crossbow_index_multiclass_list): Implement
	BOW_PRUNE_VOCAB_BY_OCCUR_COUNT_N.
	(crossbow_index): Handle the VOCAB_MAP.
	* hem.c (crossbow_hem_em_one_iteration): Print the perplexity
	before returning.

1999-07-02  Andrew McCallum  <mccallum@justresearch.com>

	* ddf.c: Random bug fixes.  Added option --ddf-prior-alpha.

1999-07-08  Gregory C Schohn  <gcs@cmu.edu>

	* tfidf.c (tfidf): changed cdocs->length to ndocs so that only
	those documents which could change the df value are considered.

	* svm.c: added support for tfidf scoring for each submodel 
	(could easily be extended to any type of scoring...)
	
1999-07-02  Gregory C Schohn  <gcs@cmu.edu>

	* Makefile.in: added rules for svm.c & pr_loqo.c which are 
	filled in by configure, if they exist...
	
	* configure.in: added a check for pr_loqo.h & pr_loqo.c, if they
 	are there, the makefile will build libbow with its complete svm
 	package, otherwise, svm.c is ignored.

	* rainbow.c (main): added support for build-and-save &
 	test-from-saved	(allowing the user to build a model, 
	then reuse it on succesive runs).  Also added support
	for svm.c.

	* wi2dvf.c (bow_wi2dvf_add_di_wv): bow_dv_add_di_count_weight
	now adds the weight value to the dv.

	* naivebayes.c (bow_naivebayes_score): added 
	naivebayes_score_returns_doc_pr flag so that P(X|C) is returned
 	instead of P(C|X).  Added naivebayes_score_unsorted so that the
	array is returned in unsorted (ie. each ith index is for the 
	ith class).

	* bow/naivebayes.h: added naivebayes_score_returns_doc_pr &
 	naivebayes_score_unsorted globals so that naivebayes.c can be
 	extended for the fisher kernel in svm.
	
	* svm.c: fixed a couple of typos & changed some outdated code.

	* bow/svm.h: Initial check-in.

1999-07-02  William Morgan  <wmorgan@jprc.com>

	* Makefile.in (ARCHER_C_FILES): added required files for
	archer compilation that had been lost previously; added
	lex -> c rule
	
	* Makefile.local: removed unnecessary lexing rule (now in 
	Makefile.in)

	* annotation.c: added GPL header
	
	* labels.c: ditto
	
	* server.c: moved to archer-server.c

	* tagged.lex: moved to tagged_lex.lex

1999-07-01  Thomas P. Minka  <minka@jprc.com>

	* train_dirichlet.c: Changed several functions to use the new
	sparse iterator scheme.
	(moment_match): Uses n_group_by_key instead of n_group.

1999-07-01  Andrew McCallum  <mccallum@justresearch.com>

	* ddf.c: Fix argument types for train_dirichlet_sparse, and call
	with correct types.

	* bow/libbow.h (bow_iterator_double): New type.
	* barrel.c: Added an iterator for the columns of a barrel that
	match a class.
	(bow_barrel_iterator_for_ci_new): New function.
	* array.c: Added (commented-out) code for an iterator over a cdoc.
	* train_dirichlet.c (train_dirichlet_nr): Initialize old_logProb
	to 0 to get rid of gcc warning.

	* ddf.c: Use new iterator.

	* Makefile.in: Drastically rearranged to make different sections
	for different libbow front-ends.
	* Makefile.local: Updated to handle new Makefile.in organization.
	Removed rules for Pete Su's old archer query parser.
	* Makefile.preamble: Emptied.  I think this file is no longer
	necessary.

1999-07-01  Thomas P. Minka  <minka@jprc.com>

        * train_dirichlet.c (train_dirichlet): Changed to call
        train_dirichlet_nr for the work.
        (train_dirichlet_sparse): Same as train_dirichlet but for sparse 
        counts.
        (train_dirichlet_nr): General Newton-Raphson with option for
        sparse counts.
        (moment_match): Changed to save memory.  Added option for sparse 
        counts.
        (logProb): Added option for sparse counts.

1999-06-30  William Morgan  <wmorgan@jprc.com>

	* annotation.c: new file

	* bow/archer.h: added annotation function interfaces and structs

	* server.c (archer_query_socket_init): added annotation handling
 	code
	(archer_server_query): ditto

	* opts.c (bow_options): added ANNOTATION_KEY option

	* Makefile.local (ARCHER_C_FILES): added annotation.c

1999-06-29  William Morgan  <wmorgan@jprc.com>

	* bow/libbow.h: added USE_TAGGED_FLEXER

	* bow/archer.h: changed lexer interfaces slightly, and moved a few
 	things from archer.c

	* tagged.lex: created

	* flex_mail.lex (flex_mail_get_word_extended): added

	* opts.c (bow_options): added FLEX_TAGGED_KEY

	* archer.c (archer_index_filename_flex): added tagged flexer
 	option
	(archer_query_hits_matching_wi): fixed small bug
	(archer_query_hits_matching_sequence): fixed another small bug
	(archer_query_socket_init): removed (to server.c)
	(archer_query_server_process_commands): ditto
	(archer_query_serve_one_query): ditto
	(archer_query_serve): ditto

	* Makefile.local (ARCHER_C_FILES): added flex_mail.c,
 	tagged_lex.c and server.c

	* server.c: created. moved all server code from archer.c to here.

1999-06-28  Andrew McCallum  <mccallum@justresearch.com>

	* ddf.c (bow_ddf_dirichlet_from_doc_word_counts): Make it use the
	train_dirichlet_sparse().
	* ddf.c: New file.
	
1999-06-15  Thomas P. Minka  <minka@jprc.com>

        * train_dirichlet.c (train_dirichlet): Changed to always be
        conservative.

1999-06-11  Thomas P. Minka  <minka@jprc.com>

        * train_dirichlet.c (train_dirichlet): Handles the all zero case
        properly.
        * train_dirichlet.c (main): Reads count data from stdin.

1999-06-11  Kamal Nigam  <knigam@zeno.jprc.com>

	* cdm.c (bow_cdm_ct_set_alphas): change asserts to allow 0 alphas
	* cdmem.c (bow_cdmem_new_vpc_with_weights): Fix word count = 0
	case

1999-06-11  Kamal Nigam  <knigam@server6.jprc.com>

	* train_dirichlet.c (train_dirichlet): changes from Tom.
	* naivebayes.c (bow_naivebayes_score): Fixed memory trashing bug.
	* em.c (bow_em_score): cosmetic fixes only.
	* cdmem.c (bow_cdmem_new_vpc_with_weights): Fixed invocation of
	bow_barrel_score.
	* cdm.c (bow_cdm_word_probs_using_ct_alphas): Removed some code at
	Andrew's request.  Changed assert to allow some roundoff error.
	(bow_cdm_score): Fixed memory-trashing bug.

1999-06-10  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/libbow.h (bow_barrel_set_weights): checked for null function

	* Makefile.preamble (EXTRA_METHOD_C_FILES): added cdmem.c

	* cdm.c (bow_cdm_word_probs_using_ct_alphas): added assert to
	check for NaN
	(bow_cdm_print_word_probs): Removed superfluous exit.
	(bow_cdm_new_vpc): Removed diagnositc.

1999-06-10  Andrew McCallum  <mccallum@justresearch.com>

	* train_dirichlet.c: Use new improved method with iteration.  It
	also now works for Dirichlet densities of arbitrary size, not just
	Betas.  (From Tom Minka.)

	* cdm.c (bow_cdm_word_probs_using_ct_alphas): Fix the setting of
	the bottom-most word in the cascade tree.

	* cdm.c: Several bug fixes.  Now runs.
	* Makefile.preamble (EXTRA_METHOD_C_FILES): Added bpe.c, cdm.c and
	train_dirichlet.c.
	* train_dirichlet.c (train_dirichlet): For now, don't do newton
	iterations.

	* rainbow.c (rainbow_unarchive): Handle the case in which the
	OUTPUTNAME_FILENAME doesn't exist in the model directory.
	* opts.c (parse_bow_opt): Add "dw" as an alias for
	"document-then-word".
	(MAX_NUM_CHILDREN): Upped from 10 to 100.
	(bow_argp_add_child): Fix assertion to complain if we overrun again.
	* int4word.c (bow_words_add_occurrences_from_file): New function.
	(bow_words_add_occurrences_from_text_dir): Use it.
	* info_gain.c (bow_infogain_wa): New function.
	* barrel.c (bow_barrel_add_document): Add comment questioning
	assert().
	* bow/libbow.h: Declare new functions.

	* multiclass.c: Changed total_num_mixtures_possible calculation.
	Changed palpha from 1.0 to 0.01.  Changed malpha from 0 to 1.
	Changed pruning class set size from 4 to 3.  Print a warning if
	the correct class vector was never evaluated.

1999-06-10  Andrew McCallum  <mccallum@justresearch.com>

	* cdm.c: Implemented but not tested.

1999-06-10  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/em.h (bow_em_set_priors_using_class_probs): New prototype.

	* cdm.c (bow_cdm_score): Implemented.

1999-06-09  Andrew McCallum  <mccallum@justresearch.com>

	* lex-suffixing.c (bow_lexer_suffixing_postprocess_word): Before
	rewinding to the beginning of the file (in order to lex without
	adding suffixes), not only check for two newlines in a row, but
	also check for the end of the file, so that files without \n\n and
	without a trailing \n get processed both with and without suffixes
	added.

1999-05-15  Andrew McCallum  <mccallum@justresearch.com>

	* multiclass.c: Backoff the per-class-set mixture distribution in
	a way loosely based on shrinkage.  More bug fixes.

1999-05-14  Andrew McCallum  <mccallum@justresearch.com>

	* multiclass.c: Many bug fixes and enhancements to class set
	search.

	* lex-japanese.c (bow_lexer_japanese_get_word): Minor bug fixes.

	* multiclass.c: Overhauled version with better search in class
	vector space.

	* Makefile.preamble: Instead of conditioning on "ifdef unix",
	condition on "ifndef WIN32", since "unix" wasn't defined on UNIX.
	Fix this properly later.
	(EXTRA_LIBBOW_H_FILES): Add more.

	* Makefile.local (DIST_ALL_FILES): Add extra Makefiles.

1999-06-01  Jason Reed  <jcreed@cyclone.jprc.com>

	* archer.c (archer_index_filename_old_lex): removed erroneous
 	redundant code

1999-05-28  Jason Reed  <jcreed@cyclone.jprc.com>

	* flex_mail.lex: Fixed archer.h include directive

	* Makefile.local (flex_mail.o): Added.
	(archer): Removed redundant target.

1999-05-27  William Morgan  <wmorgan@jprc.com>

	* bow/libbow.h (bow_flex_type): new enumeration
	
	* bow/archer.h (BOW_MAX_WORD_LABELS): new #define
	(archer_label): new typedef

	* pv.c (PV_WRITE_SIZE_INT): fixed off-by-one bug (I think)
	(bow_pv_write_size_di_li_pi): new function
	(bow_pv_write_next_di_li_pi): likewise
	(bow_pv_read_next_di_li_pi): likewise
	(bow_pv_add_di_li_pi): likewise
	(bow_pv_next_di_li_pi): likewise

	* opts.c (bow_options): added flex-mail option
	(parse_bow_opt): likewise

	* labels.c: new file

	* flex_mail.lex: new file

	* deflexer.c (bow_flex_option): new variable

	* archer.c (archer_label_write): new function
	(archer_label_read): new function
	(archer_label_free): new function
	(archer_label_write): new function
	(archer_archive): added label data files
	(archer_unarchive): likewise
	(archer_index_filename_flex): new function
	(archer_query_hits_matching_sequence): added support for labels
	(archer_print_all): likewise

	* wi2pv.c (bow_wi2pv_wi_next_di_li_pi): new function
	(bow_wi2pv_wi_add_di_li_pi): new function

1999-05-13  Andrew McCallum  <mccallum@justresearch.com>

	* Makefile.local (snapshot-all): Fix typo.

	* lex-japanese.c (bow_lexer_japanese_get_word): Better handle
	mixed English and Japanese by doing extra handling for the
	English: downcase, include only alphabetics and postprocess with
	the simple lexer.

	* crossbow.c (crossbow_doc_read): Initialize CIS_MIXTURE.
	(crossbow_unarchive): Use bow_array_new_with_entry_size_from_data_fp
	so that it will work with old models that don't have the
	CIS_MIXTURE.

	* rainbow.c (rainbow_test): Add error messages warning that -O and
	-D are not implemented here.

	* bow/crossbow.h (crossbow_doc): Add element CIS_MIXTURE.
	* array.c (bow_array_new_with_entry_size_from_data_fp): New
	function.
	* bow/libbow.h: Declare new function.

	* Makefile.preamble: Put file names in EXTRA_* variables.
	* Makefile.local (snapshot-all): New target, and support for this
	target.

1999-05-06  Kamal Nigam  <knigam@zeno.jprc.com>

	* maxent.c (maxent_gaussian_prior): New variable for gaussian
	prior option.
	(maxent_prior_variance): Likewise.
	(maxent_halt_accuracy_docs): New variable for new option
	--maxent-halt-by-accuracy
	(maxent_options,maxent_parse_opt,maxent_newton,
	maxent_calculate_accuracy,
	bow_maxent_new_vpc_with_weights_doc_then_word,
	bow_maxent_new_vpc_with_weights):
	Code for new options --maxent-halt-by-accuracy and
	--maxent-gaussian-prior and --maxent-prior-variance

1999-05-03  Robert Stockton  <rgs@jprc.com>
	
	Updated to run under GNU on win32
	* Makefile.preamble [WINNT]: Conditionalized Makefile.preamble to
	specify different switches and libraries for Win32.  This includes
	turning off the "hdb" support which requires unavailable libraries,
	and adding -liberty (sic) to enable deprecated features of the gnu
	command line parser. 
	* archer.c (archer_archive, archer_unarchive):  updated bow_fopen
	calls for data files to specify "binary" mode.  This should have no
	effect under UNIX, but is necessary for proper operation under win32.
	* arrow.c (arrow_archive, arrow_unarchive): likewise
	* barrel.c (bow_barrel_new_from_data_file): likewise
	* crossbow.c (crossbow_archive, crossbow_unarchive,
	  crossbow_index_multiclass_list, crossbow_index): likewise
	* int4word.c (bow_words_write_to_file, bow_words_read_from_fp,
	  bow_words_read_from_file, bow_words_reread_from_file): likewise
	* rainbow-h.c (hier_barrel_write_to_file, hier_barrel_new_from_file,
	  set_vocabulary_from_file): likewise
	* rainbow.c (rainbow_archive, rainbow_unarchive): likewise
	* wi2dvf.c (bow_wi2dvf_write_data_file,
	  bow_wi2dvf_new_from_data_file): likewise
	* wi2pv.c (bow_wi2pv_new, bow_wi2pv_write_to_filename,
	  bow_wi2pv_new_from_filename, bow_wi2pv_reopen_pv): likewise
	* arrow.c [WINNT] (#includes, arrow_socket_init):  Conditionalized
	socket code to deal with the lack of unix sockets under win32. 
	* rainbow.c [WINNT] (#includes, rainbow_socket_init): likewise
        * lex-gram.c (bow_lexer_gram_get_word): Fixed the BOW_MCHECK option so
	that it doesn't try to call "mprove" if the option is disabled.

	Fixed up demo script
	* demo-script: Rainbow no longer defaults to --test-set=0.30, so I
	explicitly added --test-set=0.34 to the command line.  (The value
	was changed to "1/3 of the data" to correspond to the print
	statements.)  
	* demo-script [WINNT]: Explicitly invoke perl for "rainbow-stats" so
	that the script should run better under win32 (while still working
	properly under unix). 
	
1999-04-29  Andrew McCallum  <mccallum@justresearch.com>

	* vpc.c (bow_barrel_new_vpc): Reset the word counts in the
	document barrel based on the (possibly reduced) vocabulary in
	training set, not in the training+test set.  This change has no
	effect on naive Bayes classification.

1999-04-27  Andrew McCallum  <mccallum@justresearch.com>

	* multiclass.c: New overhauled version that represents class sets
	sparsely.

1999-04-26  Andrew McCallum  <mccallum@justresearch.com>

	* hem.c (crossbow_hem_create_children_for_node): Copy word counts
	into WORDS, not NEW_WORDS, because then
	set_new_words_from_perturbed_words() will fill in NEW_WORDS by
	perturbing WORDS.  This was previously causing children to be set
	completely randomly!  (Bug reported by Doug Baker.)

	* bow/treenode.h (treenode): Add variables for holding LOO data in
	a file, but leave them commented out for now.

	* Makefile.local (CROSSBOW_C_FILES): Add lex-japanese.c.
	* Makefile.preamble (METHOD_C_FILES): Add lex-japanese.c and
	maxent.c.

	* istext.c (bow_is_text_always_yes): New global variable.
	(bow_fp_is_text): Obey it.
	* bow/libbow.h (bow_is_text_always_yes): Declare variable.

	* treenode.c (bow_treenode_set_leaf_prior_from_new_prior_all):
	Handle "/Misc/" nodes.

	* hem.c (crossbow_hem_lambdas_from_validation): New static
	variable.
	(crossbow_hem_options): New command-line option
	"hem-lambdas-from-validation".
	(crossbow_hem_parse_opt): Handle it.
	(crossbow_hem_em_one_iteration): Don't skip docs with validation tag
	and use them for setting lambda if
	CROSSBOW_HEM_LAMBDAS_FROM_VALIDATION.  Skip nodes named "Misc".
	Fix the end of the M-step so it works even if vertical word
	movement is turned off.
	(crossbow_hem_full_em): Set some of the unlabeled documents to
	validation documents if CROSSBOW_HEM_LAMBDAS_FROM_VALIDATION.
	(crossbow_hem_full_em): Print the leaf prior.
	(hem_cluster_method): Fix ordering.

1999-04-08  Kamal Nigam  <knigam@server8.jprc.com>

	* maxent.c (maxent_options): Added options --maxent-iterations,
	--maxent-keep-features-by-mi, --maxent-halt-by-logprob,
	--maxent-logprob-constraints, --maxent-smooth-counts,
	--maxent-scoring-hack.
	(maxent_parse_opt): Likewise
	(maxent_calculate_accuracy): takes extra argument; calculates accuracy
	or logprob.
	(maxent_prune_vocab_by_mutual_information): New function.
	(maxent_newton): New function.
	(bow_maxent_new_vpc_with_weights_doc_then_word): New function for
	document-then-word event model.  Code for new features.
	(bow_maxent_new_vpc_with_weights): Code for new features.
	(bow_maxent_score): Code for scoring hack option.
	(bow_method_maxent): changed prior function.

1999-03-30  Andrew McCallum  <mccallum@justresearch.com>

	Fix --gram-size so it works again.
	* opts.c (parse_bow_opt): Use the correct type to sizeof when
	allocating a lex for --gram-size.
	* lex-gram.c (bow_lexer_gram_open_text_fp): Realloc the LEX,
	making it big enough that we don't overrun the buffer malloced by
	bow_lexer_next_open_text_fp().  Note that this function passing
	SELF->NEXT, and thus uses the wrong SIZEOF_LEX when mallocing the
	lex it returns.  (In order to be properly object-oriented, we
	would need to separate object data from object methods a little
	more.)

	* crossbow.c (crossbow_classify_docs_in_dirname): Remove unused
	local variables.

1999-03-29  Andrew McCallum  <mccallum@justresearch.com>

	* hem.c (crossbow_hem_em_one_iteration): Calculate WORD_DEPOSIT
	and LAMBDA_DEPOSIT separately, and always deposit probability in
	the leaves and ancestors, even if we don't expect those
	distributions to change as a result.  Use or don't use
	ANCESTOR_MEMBERSHIP to ensure the right thing here, depending on
	CROSSBOW_HEM_VERTICAL_WORD_MOVEMENT.  Set NEW_LAMBDAS even if
	there is no shrinkge.  Always set WORDS from NEW_WORDS,
	independent of various CROSSBOW_HEM_* flag settings.  Don't ever
	use smoothing to set the lambdas.

	* crossbow.c (crossbow_classify_doc): Remove DI variable, and get
	WV more straightforwardly.

1999-03-29  Kamal Nigam  <knigam@server4.jprc.com>

	* crossbow.c (crossbow_classify_doc): initialize di to bogus
	value. Return a value.
	(crossbow_classify_tagged_docs): Count documents tested correctly.
	(crossbow_classify_docs_in_dirname): have classify_filename return
	a value. 

	* hem.c (iteration_limit): Removed.
	(crossbow_hem_em_one_iteration): Set words from new_words no matter
	what.  If no shrinkage, use prior.
	(crossbow_hem_full_em): If no shrinkage, initialize words using a
	prior, and set lambdas all at the leaves.  Use
	crossbow_hem_max_num_iterations to stop EM iterating.

1999-03-19  Kamal Nigam  <knigam@server4.jprc.com>

	* vpc.c (bow_barrel_new_vpc): added comment about setting
	cdoc->word_count.
	* maxent.c (maxent_num_iterations): new variable and code for
	option --maxent-iterations.
	(maxent_options): Likewise.
	(maxent_parse_opt): Likewise.
	(bow_maxent_new_vpc_with_weights): Likewise.  Also added correct
	normalization of step size (1/doc-length) when calculating
	delta_i.

1999-03-19  Kamal Nigam  <knigam@zeno.jprc.com>

	* maxent.c: initial checkin.

1999-03-17  Kamal Nigam  <knigam@server4.jprc.com>

	* em.c (em_parse_opt): change bow_cdoc_is_model to
	bow_cdoc_is_train

1999-03-19  Andrew McCallum  <mccallum@justresearch.com>

	* lex-suffixing.c (suffixing_snarf_suffix): Only include
	alphabetic characters in the prefix.  This way they can be
	included in queries.
	(bow_lexer_suffixing_postprocess_word): Exclude from the general
	non-suffixing indexing all lines with suffixes beginning with
	"reference"; not just the ones that match "reference" exactly.
	This way "Reference-contexts:" will also be excluded.

	* hem.c (crossbow_hem_max_num_iterations): New static variable.
	(crossbow_hem_options): New command-line option
	"hem-max-num-iterations". 
	(crossbow_hem_parse_opt): Handle it.
	(crossbow_hem_cluster): Obey it.

	* crossbow.c (crossbow_classify_doc): Correctly index WA->ENTRY
	when VERBOSE is 1.

1999-03-18  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_index_filename): Close FP before returning 0 if
	LEX is NULL.  Otherwise we leave too many files open.

	* crossbow.c (crossbow_print_matrix): New function.
	(crossbow_options): New command-line option "print-matrix".
	(crossbow_parse_opt): Handle it.

1999-03-17  Andrew McCallum  <mccallum@justresearch.com>

	* opts.c (parse_bow_opt) [LEX_SUFFIXING_KEY]: Set the ULEX->NEXT
	*after* we do the memcpy so it doesn't get overridden.
	* lex-suffixing.c (bow_lexer_suffixing_open_text_fp): Return 0 if
	the first line doesn't have a header.
	(bow_lexer_suffixing_postprocess_word): Make an initial attempt at
	handling multi-line email headers in which the second line begins
	with a tab.
	(bow_lexer_suffixing_get_word): Explicitly check the DOCUMENT_POSITION
	to see if we are at the end of the file.

	* treenode.c (bow_treenode_set_lambdas_from_new_lambdas): If macro
	MISC_STAYS_FLAT is non-zero, then if the tree contains "/Misc/",
	set the lambdas to uniform.

1999-03-17  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/naivebayes.h (bow_naivebayes_pr_wi_ci): Made public

	* bow/libbow.h (bow_dv_set_di_count_weight): New prototype.
	(bow_wi2dvf_set_wi_di_count_weight): New prototype.

	* wi2dvf.c (bow_wi2dvf_set_wi_di_count_weight): New function.
	Like add_wi_di_count_weight but sets the value directly.
	* dv.c (bow_dv_set_di_count_weight): New function.  Like
	add_di_count_weight, but sets it directly.

	* em.c (em_print_correct): Removed.  Generalized this to
	em_halt_using_accuracy and em_accuracy_docs and em_accuracy_loo,
	to allow for arbitrary sets of documents to be used for halting by
	accuracy.  Added options (--em-halt-using-accuracy and
	--em-print-accuracy) and code for this.  Also generalized
	em-halt-using-perplexity in a similar fashion.  Generalized
	em_test_accuracy to em_calculate_accuracy.
	(em_halt_using_accuracy): Likewise
	(em_accuracy_docs): Likewise.
	(em_accuracy_loo): Likewise.
	(em_options): Likewise.
	(em_parse_opt): Likewise.
	(bow_em_new_vpc_with_weights): Likewise.
	(em_calculate_accuracy): Likewise.
	(em_test_accuracy): Likewise.
	(bow_em_score): Likewise.   Changed for accuracy-loo

1999-03-16  Andrew McCallum  <mccallum@justresearch.com>

	* treenode.c (bow_treenode_set_words_from_new_words): Change logic
	around setting TN->NEW_WORDS_NORMALIZER.  Obey MISC_STAYS_FLAT
	macro.

	* multiclass.c (multiclass_score): New type.
	(multiclass_classify_doc): Use it.  Sort scores after evaluating
	class sets of size one.  Potentially use this to prune the set
	tried with larger combinations.
	(multiclass_classify_doc_into_single_class): New function.  Unused.
	(multiclass_cis_is_in_top): New function.  Unused.
	(compare_multiclass_scores): Renamed from nested function.

	* hem.c (crossbow_hem_garbage_collection): New static variable.
	(crossbow_hem_options): New command-line option
	"hem-garbage-collection". 
	(crossbow_hem_parse_opt): Handle it.
	(crossbow_hem_full_em): Add /Misc/ nodes if doing statistical garbage
	collection.

1999-03-13  Andrew McCallum  <mccallum@justresearch.com>

	* multiclass.c (MAX_CLASSES): Increase from 20+1 to 100+1.
	(multiclass_log_prob_of_classes_given_doc): Backoff MIXTURE if there
	is no local data available.
	(multiclass_classify_doc): Malloc score instead of alloca'ing, because
	it can now be bigger than the stack.

1999-03-12  Andrew McCallum  <mccallum@justresearch.com>

	* rainbow.c (rainbow_options): Command-line option
	"index-printed-barrel" name changed to "index-matrix", to match
	"print-matrix".  (Reported by Doug Baker.)

1999-03-06  Andrew McCallum  <mccallum@justresearch.com>

	* bow/treenode.h: Fix typo in #ifndef at top of file.  Include
	<bow/libbow.h>.  Declare new functions.

	* bow/libbow.h (BOW_DEFAULT_FILE_FORMAT_VERSION): Bumped from 6 to
	7.  Crossbow now writes multiclass "CIS" information, and also
	explicitly writes the CROSSBOW_CLASSES_COUNT.

	* bow/crossbow.h (crossbow_doc): Add elements CIS_SIZE and CIS to
	hold multiclass information.
	(crossbow_method):  Add index and clasify_doc functions.

	* treenode.c: Replace free() with bow_free().
	(bow_treenode_realloc_words_all): New function.
	(bow_treenode_free_loo_and_new_loo): New function.
	(bow_treenode_free_loo_and_new_loo_all): New function.
	(bow_treenode_set_words_from_new_words): Comment out part of
	MISC_STAYS_FLAT code that was zero'ing NEW_WORDS_NORMALIZER.  This
	was messing up LOO processing, and I didn't understand why it was
	done in the first place.
	(bow_treenode_set_prior_from_new_prior_all): New function.
	(bow_treenode_set_prior_and_extra_from_new_prior_all): New function.
	(bow_treenode_pr_wi_loo_local): Add more assertions.

	* rainbow.c (rainbow_test): Use bow_cdoc_is_train instead of old
	bow_cdoc_is_model.

	* hem.c: Use new crossbow_classify_tagged_docs arguments.  Add
	elements to crossbow_method instances.

	* crossbow.c (struct crossbow_arg_state): New member
	MULTICLASS_LIST_FILENAME.
	(crossbow_doc_write): If BOW_FILE_FORMAT_VERSION >= 7, write the CIS
	information.
	(crossbow_doc_read): Likewise for reading.
	(crossbow_archive): Explicitly write the CROSSBOW_CLASSES_COUNT.
	(crossbow_unarchive): If available, read it.
	(crossbow_index_filename): New function, split out from
	crossbow_index().
	and its embedded function write_wv_to_fp().
	(crossbow_index_multiclass_list): New function.
	(crossbow_index): Use crossbow_index_filename.
	(crossbow_classify_doc): New function, split out from
	crossbow_classify_tagged_docs().
	(crossbow_classify_tagged_docs): Use it.
	(crossbow_classify_docs_in_dirname): Likewise.
	(crossbow_classify): Use the method's TRAIN_CLASSIFIER.
	(crossbow_options): New command-line argument "index-multiclass-list".
	(crossbow_parse_opt): Handle it.
	(main): Don't unarchive if doing crossbow_index_multiclass_list.

	* Makefile.local (CROSSBOW_C_FILES): Added multiclass.c.

1999-02-25  Andrew McCallum  <mccallum@justresearch.com>

	* bow/crossbow.h (crossbow_method): Removed classify function,
	added cluster function

	* hem.c: Various bow_doc fixes.
	(hem_cluster_method, hem_classify_method, hem_fienberg_method): New
	method structures.
	(_register_method_hem): Implemented.

	* crossbow.c (crossbow_classify_all_docs): Deleted function.
	(crossbow_classify_tagged_docs): Add new argument FILE *out.
	(crossbow_cluster): Use new method function.
	(crossbow_classify): Likewise.
	(main): Fix for new lexer organization.

	* next.c (bow_cdoc_is_train): Renamed from bow_cdoc_is_model.  All
	callers changed.

	* active.c: Use renamed function bow_cdoc_is_train instead of
	bow_cdoc_is_model.

	* mix.c: Use renamed function bow_cdoc_is_train instead of
	bow_cdoc_is_model.

	* em.c (em_parse_opt): Use renamed function bow_cdoc_is_train.

	* methods.c (bow_method_register_with_name): Add new parameter
	SIZE.  All callers changed.

	* readme.texi: Add required --test-set=0.5

1999-02-23  Sean Slattery  <jslttery@rote.learning.cs.cmu.edu>

        * rainbow-ac.pl: As with rainbow-pr.pl. Binning is going to work
        interestingly here....

	* rainbow-pr.pl: Updated so that points are not output in the
	middle of a run of predictions with the same confidence.

1999-02-21  Jason Rennie  <jrennie@data.jprc.com>

	* rainbow.c: don't seg fault if the rainbow_doc_barrel is NULL

1999-02-20  Sean Slattery  <jslttery@rote.learning.cs.cmu.edu>

        * knn.c (bow_knn_normalise_weights): Cosine normalisation is by
        vector length and not by summing. The query normalisation was fine.

        * knn.c: Added lots more documentation. Made the weight entry of
        each term in each document have the required IDF factored
        in. Needed to do this so the cosine normalisation would do the
        right thing. Much happier that this implementation is closer to
        correct. Also took out the score normalisation at the end.

1999-02-18  Andrew McCallum  <mccallum@justresearch.com>

	Lexer's reorganized.  bow_lexer_simple and bow_lexer_indirect
	removed.  bow_lexer now has NEXT pointer, so all lexer's can be
	chained.  Many lexing parameters now in global variables
	bow_lexer_* declared in lex-simple.c; this way when --lex-white
	follows --skip-headers, the default DOCUMENT_START_PATTERN in
	--lex-white doesn't override the --skip-headers option.  Order of
	lexer's still matters when chaining, like: --lex-white --skip-html
	--lex-suffixing.

	* Makefile.in (STANDARD_LIBBOW_C_FILES): Remove lex-indirect.c.
	Add lex-next.c.

	* opts.c (bow_options): New command-line options "shortest-word"
	and "lex-alphanum".
	(parse_bow_opt): Handle them, and update to new lexer organization.

	* lex-suffixing.c: Updated for new lexer organization.
	* lex-simple.c: Likewise.
	* lex-html.c: Likewise.
	* lex-gram.c: Likewise.
	* deflexer.c: Likewise.
	* rainbow.c: Likewise.
	* arrow.c: Likewise.
	* lex-indirect.c: Half-way updated, and then deleted in favor of
	lex-next.c.

	* bow/libbow.h: Updated for new lexer organization.
	(bow_realloc_hook): Declared new function pointer.
	(bow_realloc): Call new hook instead of malloc's hook.
	* bmalloc.c (_bow_realloc_hook): New function.
	(bow_realloc_hook): New global variable.

	* methods.c (bow_method_register_with_name): When creating the
	sarray, allow space of size rainbow_method, not bow_method.  This
	needs to be fixed further to make any size possible.

	* barrel.c (bow_barrel_new_from_data_fp): Use bow_free() instead
	of free().

	* archer.c (struct archer_arg_state): New element
	SCORE_IS_RAW_COUNT.
	(archer_index_lines): New function.
	(archer_query_hits_matching_sequence): Use new stoplist global
	variable. 
	Only scale if SCORE_IS_RAW_COUNT is non-zero.
	(archer_options): New command-line options "index-lines" and
	"score-is-raw-count".
	(archer_parse_opt): Handle them.
	(main): Likewise.

1999-02-12  Andrew McCallum  <mccallum@justresearch.com>

	* active.c, archer.c, arrow.c, barrel.c, crossbow.c, em.c, evi.c,
	goodturing.c, hem.c, kl.c, knn.c, methods.c, mix.c, naivebayes.c,
	prind.c, rainbow-h.c, rainbow.c, split.c, tfidf.c, crossbow.h,
	em.h, kl.h, knn.h, libbow.h, naivebayes.h, prind.h, tfidf.h,
	treenode.h: Separate bow_method from rainbow_method.  New
	structure rainbow_method.  New structure crossbow_method.

1999-02-01  Andrew McCallum  <mccallum@justresearch.com>

	* hem.c (crossbow_hem_consider_splitting): Fix memory leak by
	freeing the GRANDPARENTS array.

1998-12-17  Andrew McCallum  <mccallum@justresearch.com>

	* naivebayes.c
	(bow_naivebayes_set_cdoc_word_count_from_wi2dvf_weights):
	Initialize num_words_per_ci[] to zero.

1998-11-29  Andrew McCallum  <mccallum@justresearch.com>

	* crossbow.c (struct crossbow_arg_state): Add members PRINTING_TAG
	and CLASSIFY_FILES_DIRNAME.
	(crossbow_classify_tagged_docs): Renamed from
	crossbow_classify_test_docs.
	(crossbow_classify_docs_in_dirname): New function.
	(crossbow_classify): Insist on either restricted or deterministic
	horizontal.  Handle CLASSIFY_FILES_DIRNAME.
	(crossbow_print_doc_names): New function.
	(crossbow_options): New command-line options "classify-files" and
	"print-doc-names".
	(crossbow_parse_opt): Handle them.

	* hem.c (SHRINK_WITH_UNIFORM_ONLY): Change from 1 to 0; i.e. set
	back to default.
	(iteration_limit): Change from 3 to 999.
	(crossbow_hem_options): Add command-line options for
	"hem-deterministic-horizontal" and "hem-restricted-horizontal".
	(crossbow_hem_parse_opt): Handle them.
	(crossbow_hem_unlabeled_perplexity): Add a test for -Inf.
	(crossbow_hem_em_one_iteration): Handle both labeled and unlabeled
	documents.  Handle "resticted-horizontal" case.  Verbosify how
	many documents were incorporated.
	(crossbow_hem_cluster): Handle both labeled and unlabeled documents.
	(crossbow_hem_full_em): Add "Misc" children.  Add commented-out code
	for semi-labeled data.
	(crossbow_hem_fienberg_treenode): Add #if'ed code for
	SHRINK_WITH_UNIFORM_ONLY.

	* treenode.c (bow_treenode_add_misc_child_all): New function.
	(bow_treenode_set_words_from_new_words): Add special case for
	"Misc" nodes.

	* split.c (bow_tag_docs): New function.
	(bow_tag_change_tags): New function.
	* bow/libbow.h (bow_tag_docs): Declare new function.
	(bow_tag_change_tags): Likewise.

1998-11-14  Jason Rennie  <jrennie@cyclone.jprc.com>

	* rainbow.c (bow_print_log_odds_ratio): print to stdout

	* rainbow.c (bow_print_log_odds_ratio): new function
	(rainbow_parse_opt): add --print-log-odds-ratio option

1998-11-13  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_query_server_process_commands): Use different
	prefix for pre-fork and post-fork commands, so we don't try to
	handle a post-fork as a pre-fork.
	(archer_query): Fix bug that caused crash when a +term was the only
	term.

1998-11-12  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_query): Print commas between query terms.

	* lex-suffixing.c (bow_lexer_suffixing_postprocess_word): Skip the
	Reference: words the second time through.

1998-11-11  Jason Rennie  <jrennie@cyclone.jprc.com>

	* rainbow.c (rainbow_query): check rainbow_doc_barrel; free query
	word vector

1998-11-09  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_docs): Change from a bow_array to a bow_sarray,
	so we can keep track of filenames.  All relevant functions
	changed.
	(archer_archive): Flush archer_wi2pv's FP.
	(archer_index_filename): New function, moved out of archer_index.
	Don't raise an error if the file doesn't exist.
	(archer_index): Call it.
	(archer_delete_filename): New function.
	(archer_query_server_process_commands): New argument
	DOING_PRE_FORK_COMMANDS.  Add new commands for adding and removing
	files.
	(archer_query_serve_one_query): Process commands before and after
	forking.

	* sarray.c (bow_sarray_entry_at_keystr): If the KEYSTR is not
	present, don't raise an error, just return NULL.

1998-11-05  Andrew McCallum  <mccallum@justresearch.com>

	* pv.c (bow_pv_max_sizeof_di_pi): Redefined for smaller number of
	bits, since we are now using 7 bits in the IS_MORE bytes, instead
	of just 6.
	(bow_pv_write_unsigned_int): Updated to write 7 bits in the secondary
	"IS_MORE" bytes.
	(bow_pv_read_unsigned_int): Likewise for reading.
	(PV_WRITE_SIZE_INT): New macro.  Unused.
	(bow_pv_write_size_di_pi): New function.  Unused.
	(bow_pv_read_size_di_pi): Likewise.
	* bow/archer.h: Remove declaration of functions that are now
	defined static in pv.c.
	(bow_pe): Add entry BITS_MORE.

	* wi2pv.c (bow_wi2pv_print_stats): Rename COUNT_HISTOGRAM to
	WORD_COUNT_HISTOGRAM, in anticipation of histogramming the number
	of bytes per pv entry also.

	* rainbow.c (main): Fix handling of TAG in doc name printing.

	* split.c (bow_files_source_type): Added two new types:
	bow_files_source_fraction_remaining, and
	bow_files_source_number_remaining.
	(bow_split_options): Update documentation.
	(bow_split_parse_opt): Handle new source types.
	(bow_set_doc_types_randomly_by_count): New option
	TAKE_PROPORTION_FROM_REMAINING.  Revert to pre-1998-10-21 behavior
	if this is zero.
	(bow_set_doc_types_randomly_by_fraction_remaining): New function.
	(bow_set_doc_types): Change the order of operations slightly.  Instead
	of doing all non-filename options together, do first the options
	that specify the number of documents per class, then do the ones
	that select the number of documents per class randomly according
	to some proportion.

1998-11-01  Andrew McCallum  <mccallum@justresearch.com>

	* pv.c (bow_pv_write_unsigned_int): Make it a static inline
	function, for speed.
	(bow_pv_read_unsigned_int): Likewise.
	(bow_pv_write_next_di_pi): Likewise.
	(bow_pv_read_next_di_pi): Likewise.

	* archer.c (archer_index): Pass just a filename, not a directory
	name to bow_wi2pv_new().
	(archer_query_hits_matching_sequence): New argument SUFFIX_STRING.
	All callers changed.  Properly tell the difference between a word
	that doesn't appear and a stopword.  Make a little more efficient.
	(archer_query): Parse things like `title:foo'.
	(archer_query_serve_one_query): Process special comands like ,HITS
	before any query, not just the first.
	(archer_options): Remove "compare" option.

1998-10-21  Andrew McCallum  <mccallum@justresearch.com>

	* split.c (bow_set_doc_types_randomly_by_count): When determining
	how many documents are available, instead of skipping only the
	ignore documents, skip all the non-untagged documents.  This fixes
	a bug whereby there are not enough documents left to label.  Don't
	arbitrarily add one to the number of document to be tagged when
	the ratio-indicated number is zero.  When adding more documents to
	the per-class counts to be tagged, make sure there are untagged
	documents available in that class.

1998-10-16  Andrew McCallum  <mccallum@justresearch.com>

	* rainbow-h.c: All these changes actually made on or before Jun 26
	1998.
	(hier_barrel): Add di4filename.  Change CLASS_WORD_COUNT and
	DOC_WORD_COUNTS from ints to floats.
	(hier_barrel_new): Initialize di4filename.
	(hier_barrel_set_class_word_count): Use the CDOC->NORMALIZER instead
	of the CDOC->WORD_COUNT.
	(hier_barrel_set_class_word_count): New function.  Commented out.
	(hier_barrel_set_class_barrel_cdoc_normalizer_to_word_count): New
	function. 
	(hier_barrel_total_of_cdoc_word_counts): Function removed.
	(hier_barrel_correct_cdoc_prior): Set the CDOC->NORMALIZER in the
	class barrel, so we can use them to reset the WORD_COUNT's.  Do it
	by calling new function.
	(hier_barrel_set_class_model_from_new_class_wi2dvf): Call new function.
	(hier_barrel_free): Free HBARREL->NEW_CLASS_WI2DVF.
	(rainbowh_set_total_num_words): Remove function.
	(hier_barrel_prob_wi_in_ci_local): Make some changes for full_em.
	(hier_barrel_prob_wi_local): Likewise.
	(hier_barrel_calc_lambda_one_iteration): Add #error.
	(hier_barrel_all_reset_doc_word_count_from_loo_doc_wi2dvf): New
	function. 
	(hier_barrel_calc_lambdas_all_nodes): Do more updates at top of
	while() loop and add comments.
	(rainbowh_unarchive): Deal with di4filename.

1998-10-15  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_query_serve_one_query): When forking, in the
	child, reopen the wi2pv PV FILE* so we get our own lseek()
	position.
	* bow/archer.h (bow_wi2pv_reopen_pv): Declare new function.
	* wi2pv.c (bow_wi2pv_reopen_pv): New function.

	* dice.c: New file.

	* hem.c (SHRINK_WITH_UNIFORM_ONLY): New macro.
	(PRINT_WORD_DISTS): New macro.
	(iteration_limit): New variable.  (temporary).
	(crossbow_hem_full_em): Use SHRINK_WITH_UNIFORM_ONLY and
	PRINT_WORD_DISTS.  Use iteration_limit.
	(crossbow_hem_fienberg_treenode): Use SHRINK_WITH_UNIFORM_ONLY and
	PRINT_WORD_DISTS.  Also print results with several fixed lambdas.

	* crossbow.c (struct crossbow_arg_state): New member
	PRINT_FILE_PREFIX.
	(main): Initialize new member.
	(crossbow_print_word_probabilities): New function (not complete).
	(crossbow_options): New option "print-word-probabilities".
	(crossbow_parse_opt): Handle it.

	* treenode.c (bow_treenode_free_loo): No longer declared static.
	(bow_treenode_free_loo_all): New function.
	(bow_treenode_set_new_words_to_zero): New function.
	(bow_treenode_print_all_word_probabilities_all): New function.
	* bow/treenode.h: Declare new functions.

	* kl-div.c (main): Handle new command-line argument -l, for "Larry
	Wasserman's Loss function".  Implement it.

	* archer.c (archer_query_hits_matching_sequence): Change scaler.
	(archer_query): Make a local copy of ARCHER_ARG_STATE.QUERY_STRING and
	replace the trailing newline and carriage return with \0.

	* archer.c (archer_query_hits_matching_sequence): Add 1 to avoid
	dividing by zero.

1998-10-15  Jason Rennie  <jrennie@cyclone.jprc.com>

	* Makefile.preamble (-DVPC_ONLY): new define

	* vpc.c (bow_barrel_new_vpc): set IS_VPC to 1

	* rainbow.c (rainbow_index): allow possibility of building only
	class barrel in order to reduce memory consumption; add checks to
	make sure that rainbow_doc_barrel is not NULL before we try to use it
	(rainbow_options): add vpc-only option

	* hdb-bow.c (bow_barrel_add_from_hdb): if barrel has is_vpc set,
	build a multinomial class barrel instead of a document barrel

	* barrel.c (bow_barrel_add_from_text_dir): if barrel has is_vpc
	set, build a multinomial class barrel instead of a document barrel
	(bow_barrel_new): set IS_VPC to 0

1998-10-14  Andrew McCallum  <mccallum@justresearch.com>

	* hem.c (crossbow_hem_unlabeled_perplexity): New function.
	(crossbow_hem_labeled_perplexity): New function.
	(crossbow_hem_place_labeled_data): Clear old data and LOO info before
	placing the new.  Use new functions.

	* archer.c (archer_query_hits_matching_wi): New function.
	(archer_query_hits_matching_sequence): Use it.  Improve efficiency of
	wi2pv searching.  Use new bow_wa function.
	(archer_query): Remove trailing \n from query terms.
	* wa.c (bow_wa_add_to_end): New function.
	* bow/libbow.h: Declare new function.

	* archer.c (archer_query_hits_matching_sequence): Change the
	weight-setting method to encourage documents that have all query
	term to be ranked above documents that have many repetitions of a
	few terms.
	(archer_query): Fix it so it works with queries that don't have a
	+term.  Free all the temporary space that was allocated.  Print
	the +terms as well as the others.

	* wi2pv.c (bow_wi2pv_new): Instead of saving an absolute pathname
	(and allowing the PV_FILENAME argument to contain '/'s), expect
	PV_FILENAME to be just a filename, and save it only.  Use
	BOW_DATA_DIR as the directory location in which to place the
	PV_FILENAME.
	(bow_wi2pv_new_from_filename): Support the new behavior of
	bow_wi2pv_new.  (Although old models are temporarily supported by
	use of a hack.)

	* naivebayes.c (bow_naivebayes_set_weights): Remove restriction
	that we have less than 200 classes.

	* archer.c (archer_query): Combine results of query terms more
	efficiently.  Print the words that occur in each hit.  Currently
	only works if there is a +term.

1998-10-13  Andrew McCallum  <mccallum@justresearch.com>

	* archer.c (archer_query_hits_matching_sequence): Remove yyparse
	code.  Add code to parse +, - and "" in C.  Gather results in
	various bow_wa arrays, and combine them with the correct
	semantics.
	* Makefile.local (archer): Remove dependence on query* files.

	* wa.c (bow_wa_weight): New function.
	(bow_wa_union): New function.
	(bow_wa_intersection): New function.
	(bow_wa_overlay): New function.
	(bow_wa_diff): New function.
	* bow/libbow.h: Declare new functions.

	* lex-suffixing.c: Whenever calling *lexer_simple_* functions,
	pass BOW_DEFAULT_LEXER_SIMPLE instead of SELF.
	(HEADER_TWICE): New macro.  When this macro is non-zero, read the
	headers twice, once adding the suffixes, once not.

1998-10-13  Jason Rennie  <jrennie@cyclone.jprc.com>

	* configure.in: AC_HAVE_LIBRARY(socket) changed to
	AC_CHECK_LIB(socket,main)

1998-10-09  Peter Su  <Peter Su <psu@jprc.com>

	* configure.in: added check for YACC
	* query.h: New file. header file for query demo.
	* Makefile.in: Added rules for building query demo
	* query_main.c: New file, short demo for parser
	* query_lex.l: New file
	* query_parse.y: New file for parsing boolean queries

1998-10-08  Jason Rennie  <jrennie@cyclone.jprc.com>

	* Makefile.in: define ALL_LIBS before Makefile.preamble is
	included
	* Makefile.in (kl-div): don't use ALL_LIBS; kl-div doesn't depend
	on libargp
	* Makefile.in: do STANDARD_ trick with LIBBOW_C_FILES and
	LIBBOW_H_FILES to exclude HDB stuff from distribution
	* configure.in: Add check for -lsocket.  Needed for Solaris
	* opts.c: add #if HAVE_HDB checks
	* rainbow.c: add #if HAVE_HDB checks
	* arrow.c: add #if HAVE_HDB checks
	* Makefile.in: Remove all mentionings of HDB
	* int4word.c (bow_words_add_occurrences_from_hdb): moved to
	hdb-bow.c
	* docnames.c (bow_map_filenames_from_hdb): moved to hdb-bow.c
	* hdb-bow.c: new file
	* barrel.c (bow_barrel_add_from_hdb): move to hdb-bow.c
	* Makefile.preamble: add HDB-specific compilation definitions

1998-10-08  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_random_seed): Renamed from bow_split_seed.
	* random.c (bow_random_set_seed): Rename bow_split_seed to
	bow_random_seed.
	* opts.c (parse_bow_opt): Rename bow_split_seed to
	bow_random_seed.

	* hem.c (crossbow_hem_create_children_for_node): Use
	bow_treenode_set_new_words_from_perturbed_words() instead of the
	previous direct use of bow_random_double.
	(crossbow_hem_classification_perplexity): New function.
	(crossbow_hem_em_one_iteration): When calculating perplexity, and
	adding the contribution from this leaf, don't add it if
	LEAF_MEMBERSHIP[LI] is zero.  This avoid adding infinity.
	(crossbow_hem_cluster): After perturbing the leaves (which happens
	after EM convergence), don't smooth the new WORDS distribution.
	Previously called ...set_words_from_new_words_all() with alpha=1.
	(crossbow_hem_full_em): When printing "pp", use "classification
	perplexity" instead of "perplexity".

1998-10-07  Andrew McCallum  <mccallum@jprc.com>

	* archer.c (archer_print_word_stats): New function.
	(archer_options): New command-line argument "print-word-stats".
	(archer_parse_opt): Handle it.
	(main): Check to see if WHAT_DOING is NULL, and complain if so.
	* wi2pv.c (bow_wi2pv_print_stats): New function.
	* bow/archer.h: Declare new function.

	* wi2pv.c (bow_wi2pv_new): Convert PV_FILENAME to an absolute
	pathname before saving it.  This way, an archived model can be
	used when running archer from a different CWD from which the index
	was built.

	* stopwords.c (_bow_builtin_stopwords_shorter): New global
	variable.

1998-10-06  Andrew McCallum  <mccallum@jprc.com>

	* wa.c (bow_wa_add): New function.
	(bow_wa_add_wa): New function.
	* bow/libbow.h: Declare new functions.

	* wi2pv.c (bow_wi2pv_wi_count): New function.
	* bow/archer.h: Declare new functions.

	* pv.c (bow_pv_next_di_pi): Exchange the order of "end of PV
	checking" and "unnext checking" to fix bug whereby BOW_PV_REWIND()
	wasn't working.

	* archer.c: Make is work as a server over a socket, like arrow.
	Separate the query handling into two functions, in preparation for
	having a query parser.

	* Makefile.local (archer): New target.
	* pv.c, wi2pv.c, archer.c, bow/archer.h: New files.  Wow, all this
	code written in just 4 hours.

1998-09-30  Jason Rennie  <jrennie@cyclone.jprc.com>

	* configure.in: new compatibility checks
	* split.c (bow_split_parse_opt): use strchr instead of index
	(STANDARDS suggests strchr)
	* em.c, mix.c, active.c: change "//" to "/* */" (some older compilers
	don't know about //)
	* split.c (bow_split_parse_opt): use hack if index() doesn't exist
	* em.c (random01): removed; replaced calls with bow_random_01
	(random_double): removed; replaced calls with bow_random_double
	* active.c (active_select_stream_kl): use bow_random_double where
	appropriate.
	* random.c: check for gettimeofday() and RAND_MAX.  Use simple
	workarounds if not defined
	* lex-simple.c (bow_lexer_simple_open_text_fp) [!HAVE_SETENV]:
	complain and die.
	* bow/libbow.h [__linux__]: redefine assert (re-definition
	on SunOS causes problems)
	(assert): insert comma bettween __STRING(expr) and __FILE__
	to prevent nastiness.  Must have been inadvertently removed earlier.
	[!HAVE_STRCHR, !HAVE_STRRCHR]: redefine as index, rindex
	[!HAVE_RANDOM, !HAVE_SRANDOM]: redefine as rand, srand.
	
1998-09-29  Jason Rennie  <jrennie@cyclone.jprc.com>

	* hdb.c [!HAVE_STRERROR]: redefine as ""
	* configure.in: check for strerror

1998-09-28  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_options): Add optional argument to
	"print-doc-names" that specifies the document type (tag = train,
	test,..) to print.
	(rainbow_parse_opt): Handle it.
	(main): Likewise.

	* bow/libbow.h (bow_str2type): New macro.

	* Makefile.in: Undo changes that added crossbow to the snapshot
	distribution.  It's not yet ready to go out.
	(LIBBOW_H_FILES): Remove bow/crossbow.h and bow/treenode.h.
	(CROSSBOW_C_FILES): Remove variable.
	(OTHER_C_FILES): Remove crossbow.c.
	(all): Remove crossbow.
	(DIST_FILES): Remove $(CROSSBOW_C_FILES).

1998-09-28  Jason Rennie  <jrennie@cyclone.jprc.com>

	* knn.c (bow_knn_score): calculate and return class scores (same
	as before last modification)

	* rainbow.c (rainbow_query): always print class names instead of
	relying on cdoc names

1998-09-25  Andrew McCallum  <mccallum@jprc.com>

	* int4str.c (_str2id): Fix bug whereby returned value may be
	negative or zero! (Reported by Jason Rennie.)

	* hem.c (crossbow_hem_full_em): Print the train- and test-pp for
	the "No Shrinkage" case also.
	(LOG_LOSS): New macro.
	(crossbow_hem_fienberg_treenode): Conditioned on above macro,
	implement lambda-calculation with a log log function.

1998-09-24  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (CLASSES_FROM_DIRS): New macro.
	(crossbow_index): In embedded function write_wv_to_fp() extract the
	directory name from the FILENAME, and use it to determine the
	class index of the DOC.  Count the number of classes from the
	number of different dir names found in the embedded function.
	(crossbow_classify): Temporarily use crossbow_hem_fienberg() instead
	of crossbow_hem_full_em().

	* hem.c (crossbow_hem_full_em): Instead of printing "Initial Flat
	Distribution", print the more precise message "No Shrinkage".
	(crossbow_hem_fienberg_treenode): New function.
	(crossbow_hem_fienberg): New function.

	* treenode.c (bow_treenode_set_lambdas_leaf_only): New function.
	(bow_treenode_set_lambdas_leaf_only_all): New function.
	* bow/treenode.h: Declare new functions.

	* split.c (bow_set_doc_types_randomly_by_count_per_class): Print
	the total number of documents tagged.

1998-09-21  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_doc_type): Reorder the enumeration so that the
	numbers match those of old archived barrels.  (Bug reported by
	Kamal Nigam and Jason Rennie.)

1998-09-18  Andrew McCallum  <mccallum@jprc.com>

	* hem.c (crossbow_hem_options): Explain more defaults.

	* rainbow.c (rainbow_options): Rename "print-barrel" to
	"print-matrix".  Leave "print-barrel" as a hidden alias.

1998-09-17  Andrew McCallum  <mccallum@jprc.com>

	* Makefile.in: Add crossbow the the snapshot distribution.
	(OTHER_C_FILES): Add crossbow.c.
	(LIBBOW_H_FILES): Add bow/crossbow.h and bow/treenode.h.
	(DIST_FILES): Add $(CROSSBOW_C_FILES).
	(all): Add crossbow.

	* bow/libbow.h (bow_cdoc): Reorder the variables so that the order
	of the first three matches that of crossbow_doc.
	(bow_doc): Add CLASS and FILENAME elements.
	* bow/crossbow.h (crossbow_doc): Reorder the variables so that the
	order of the first three matches that of bow_cdoc.

	* crossbow.c (main): Call bow_set_doc_types() only if not
	indexing.
	* hem.c: Turn of MN.  Use new bow_doc types instead of old
	crossbow tags.
	* mn.c (crossbow_hem_em_one_mn_iteration): Don't reset classes
	distribution unless CROSSBOW_CLASSES_COUNT is greater than 1.

	* rainbow.c: Fix some typos in calls to
	bow_set_doc_types_for_barrel().
	(rainbow_query): Remove use of knn_k.

	* crossbow.c (crossbow_classnames): New global variable.
	(crossbow_archive): Write it.
	(crossbow_unarchive): Read it.
	(crossbow_index): Initialize it.
	(struct crossbow_arg_state): Remove test_fraction.
	(crossbow_docs_split): Function removed.
	(crossbow_classify): Don't call removed function.
	(crossbow_options): "test-percentage" option removed.
	(crossbow_parse_opt): No longer handle it.
	(main): Call bow_set_doc_types() to do the test train splits.

	* em.c (bow_em_new_vpc_with_weights): Comment out unused variables
	to avoid warning.

	* split.c: All function names with bow_set_files_, changed to
	bow_set_doc_.  All functions that previously took a bow_barrel as
	an argument now take only the pieces of the barrel they need---so
	that crossbow can use these functions too.
	(bow_set_doc_types_for_barrel): New function that works like old
	bow_set_doc_types() function.
	* bow/libbow.h (bow_set_doc_types): New function declaration.
	(bow_set_doc_types_for_barrel): New function declaration.
	* rainbow.c (main): Call bow_set_doc_types_for_barrel() instead
	of set_doc_types().

1998-09-17  Jason Rennie  <jrennie@cyclone.jprc.com>

	* knn.c: make KNN_K static (local); need to change bow_knn_score
	so that it returns classes instead of k nearest documents

	* rainbow.c (rainbow_query): set NUM_HITS_TO_SHOW to KNN_K if
	method is "knn"

	* knn.c (bow_knn_get_k_best): fixed a bug in document shifting
	schema; return document score in bow_score array
	(bow_knn_score): clear away lots 'o unnecessary junk; expect
	calling function to allocate BSCORES; initialize BSCORES

1998-09-15  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_doc): New typedef.

1998-09-14  Andrew McCallum  <mccallum@jprc.com>

	* hem.c: Replace hem_ with crossbow_hem_.

	* Makefile.in (CROSSBOW_C_FILES): Renamed hac.c to hem.c.
	* hem.c: File renamed from hac.c.
	* crossbow.c: Replaced hac_ with hem_.

	* rainbow.c (rainbow_options): Changed "infogain-vector" to
	"print-word-infogain".  Changed "infogain-pair-vector" to
	"print-word-pair-infogain".  Changed "weight-vector" to
	"print-word-weights".  Changed "foilgain-vector" to
	"print-word-foilgain".
	(main): Call set_doc_types() once at beginning, unless doing
	RAINBOW_TESTING, which does its own call of this function.

	* libbow.texi (Overview): Added rough notes from Devika
	Subramanian.

	* bow/libbow.h (BOW_MINOR_VERSION): Updated from 8 to 9.

	* treenode.c hac.c crossbow.c bow/treenode.h: Changed treenode_ to
	bow_treenode_ in all function names.

1998-09-14  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/libbow.h (bow_wv_set_weights_to_count): Changed prototype.
	(bow_doc_type): Removed unused doc types and added validation type.
	(bow_method): Change prototype so set weights takes two arguments.
	(bow_wv_set_weights): Change prototype
	(bow_wv_set_weights_to_count): Likewise.
	(bow_wv_set_weights_by_event_model): New function.
	(bow_cdoc_is_ignored_model): Removed.
	(bow_cdoc_is_validation): New function.

	* em.c (bow_em_event_model_type): Removed.  Superceded by libbow
	event models.
	(M_EST_M): Removed.
	(M_EST_P): Removed.
	(WORD_PRIOR_COUNT): Removed.
	(bow_em_event_model): Removed.
	(bow_em_calculating_perplexity): New global for perplexity calculating
	hack.
	(binary_pos_ci): New global for binary classification hack.
	(em_halt_using_perplexity): New option variable.
	(em_perplexity_docs): Likewise.
	(em_perplexity_loo): Likewise.
	(bow_em_anneal_normalizer): Likewise.
	(em_options): Removed option --em-event-model.  New code for options
	em-halt-using-perplexity em-anneal-normalizer em-print-perplexity.
	(em_parse_opt): Likewise.
	(bow_cdoc_is_multi_hump_doc): New function.
	(bow_cdoc_is_train_or_unlabeled): New function.
	(bow_em_perturb_weights): Set the random seed.
	(bow_em_perturb_weights): Use the  real word_count in normalizer, not
	the integral one.
	(bow_em_new_vpc_with_weights): num_classes removed. binary_pos_ci
	moved to be a global.  *_class_map variables removed.  Use the
	real word_count in normalizer, not the integral one.  Remove
	infogain pruning; do this in rainbow.c.  Change calculation of
	word_count for documents to be correct.  Do not allow zero class
	probs when randomly choosing them for the EM starting point.  Add
	EM halting when the perplexity of some documents plateaus.  Create
	dv's for all words in the vocabulary so perplexity calculation
	does not get confused if words appear in only the doc barrel and
	not the class barrel.  Use libbow document event model and
	doc-then-word document length.  Use bow_em_set_weights (like
	bow_naivebayes_set_weights).  Calculate and print perplexity if
	necessary or requested.  Implement normalizer annealing.  Add
	multi-hump EM more naturally into the code.  Don't free the
	class_probs; may be used by LOO doc testing.  Update call to
	bow_em_score.
	(em_calculate_perplexity): New function.
	(bow_em_test_accuracy): Update call to bow_em_score.
	(bow_em_print_log_odds_ratio): Disable while normalizer is holding
	word_count info.
	(bow_em_set_priors_using_class_probs): Prime each class's count with
	1.
	(bow_em_pr_wi_ci): New function.
	(bow_em_set_weights): New function.
	(bow_em_score): New calling prototype to send loo class_probs pointer
	as an int.  Use bow_em_pr_wi_ci with loo functionality.  Add
	perplexity calculation hack to return perplexity of each class.
	Use libbow event models implicitly through bow_em_pr_wi_ci
	(bow_method_em): Change wv_set_weights to explicitly use the event
	model.
	
	* naivebayes.c (naivebayes_argp_m_est_m): Remove static so em.c
	can see.
	(M_EST_M): Removed.
	(M_EST_P): Removed.
	(bow_naivebayes_pr_wi_ci): Changed loo_wi_count and loo_w_count to
	floats to handle the document_then_word event model correctly.

	* bow/naivebayes.h (naivebayes_argp_m_est_m): Add prototype so
	em.c can use.

	* wv.c (bow_wv_set_weights_to_count): Add argument to match method
	prototype.
	(bow_wv_set_weights_by_event_model): New function.

	* split.c (bow_validation_files_source): New variable.
	(bow_validation_fraction): New variable.
	(bow_validation_number): New variable.
	(bow_validation_filename): New variable.
	(bow_validation_fancy_counts): New variable.
	(bow_split_options): New option --validation-set
	(bow_split_parse_opt): New option --validation-set
	(bow_split_parse_opt): New format for fancy counts: all ',' as
	delimiters.
	(bow_set_file_types_randomly_by_count_per_class): Print nice message
	to stderr.
	(bow_set_file_types_randomly_by_count): Ensure get at least document
	per class of training.
	(bow_set_files_to_type): Update nice message for stderr.
	(bow_set_file_types_of_remaining): Print nice message to stderr.
	(set_doc_types): handle validation set also.

	* rainbow.c (rainbow_test): Added special call for EM method to
	correctly handle EM-style LOO scoring.

	* next.c (bow_cdoc_is_ignored_model): Removed.
	(bow_cdoc_is_validation): New function.

	* knn.c (bow_knn_query_set_weights): Added argument to procedure
	to be compliant with new prototype for method

	* arrow.c (arrow_compare): Add argument to calls to
	bow_wv_set_weights_to_count.

1998-09-13  Andrew McCallum  <mccallum@jprc.com>

	* NEWS: Update with some new features in version 0.9.
	* Version (BOW_MINOR_VERSION): Changed from 8 to 9.
	* readme.texi: Update list of coming rainbow improvements.  Update
	web address for more information.
	* HACKING: Update GNU URL's and add parens to argp autoconf
	command.
	* install.texi: Remove unnecessary copyright notice.

	* Makefile.in (LIBBOW_H_FILES): Added bow/hdb.h.

1998-09-12  Andrew McCallum  <mccallum@jprc.com>

	* opts.c (bow_options): Changed the name of command-line option
	"split-seed" to "random-seed".

1998-09-08  Jason Rennie  <jrennie@cyclone.jprc.com>

	* wi2dvf.c (bow_wi2dvf_add_di_text_str): add lexer->close call to
	patch memory leak

1998-09-07  Jason Rennie  <jrennie@cyclone.jprc.com>

	* docnames.c, barrel.c, int4word.c: fix memory leak associated with
	HDB.

	* Change instances of "char" in function names to "str" for
	better description of functionality.

1998-09-04  Andrew McCallum  <mccallum@jprc.com>

	* opts.c (bow_options): Make the "lex-for-usenet" option hidden,
	since it is currently broken.

1998-09-03  Andrew McCallum  <mccallum@jprc.com>

	* Makefile.in (snapshot): Make ourselves more Y2K compliant :-) by
	including the first two digits of the year in the snapshot file
	name.

1998-08-24  Jason Rennie  <jrennie@cyclone.jprc.com>

	* bow/hdb.h: new file

	* bow/libbow.h: Added lots of function declarations

	* wi2dvf.c (bow_wi2dvf_add_di_text_char): new function

	* scan.c (bow_scan_char_for_string): new function

	* rainbow.c (rainbow_test_files): Split test_file into test_file,
	test_hdb_file and process_wv; call HDB functions when BOW_HDB is
	set.
	(rainbow_index): Call HDB functions when BOW_HDB is set.

	* opts.c (parse_bow_opt): Added --hdb option with key HDB_KEY

	* lex-suffixing.c (bow_lexer_suffixing_open_char): new function
	(_bow_suffixing_lexer): new field: bow_lexer_suffixing_open_char

	* lex-simple.c (bow_lexer_simple_open_char): new function
	(_bow_white_lexer, bow_alpha_only_lexer, bow_alpha_lexer):
	new field: bow_lexer_simple_open_char

	* lex-indirect.c (bow_lexer_indirect_open_char): new function

	* lex-html.c (_bow_html_lexer): new field:
	bow_lexer_simple_open_char

	* lex-gram.c (bow_lexer_gram_open_char): new function
	(_bow_gram_lexer): new field: bow_lexer_gram_open_char

	* lex-email.c (_bow_email_lexer): new field:
	bow_lexer_simple_open_char

	* istext.c (bow_char_is_text): new function

	* int4word.c (bow_words_add_occurrences_from_hdb): new function

	* hdb.c: new file
	(hdb_open): new function
	(hdb_close): new function
	(hdb_put): new function
	(hdb_get): new function
	(hdb_each): new function

	* docnames.c (bow_map_filenames_from_hdb): new function

	* barrel.c (bow_barrel_add_from_hdb): new function

	* arrow.c (arrow_index): Call HDB functions if BOW_HDB is set

	* Makefile.in: Added stuff necessary to compile with HDB code
	(Hash DataBase - simple file system-like database)

1998-08-19  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h: Fix comment descriptions of event models.

	* opts.c (bow_event_document_then_word_document_length): New
	global variable.
	(bow_options): New command-line option
	"event-document-then-word-document-length".
	(parse_bow_opt): Handle it.
	* bow/libbow.h: Declare new global variable.

	* naivebayes.c (bow_naivebayes_score): Use
	BOW_EVENT_DOCUMENT_THEN_WORD_DOCUMENT_LENGTH.  When multiplying by
	the number of occurrences in the QUERY_WV, use .weight, not
	.count.

	* vpc.c (bow_barrel_new_vpc): Use
	BOW_EVENT_DOCUMENT_THEN_WORD_DOCUMENT_LENGTH.

1998-08-19  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/libbow.h (bow_set_file_types_preprocess): Removed.
	(bow_set_all_files_untagged): Removed.
	(bow_set_file_types_randomly_by_count_per_class): Removed.
	(bow_set_file_types_randomly_by_count): Removed.
	(bow_set_file_types_randomly_fraction): Removed.
	(bow_set_files_to_type): Removed.
	(bow_set_file_types_postprocess): Removed.
	(set_doc_types): New prototype.
	(bow_ignore_next_wv): Removed.
	(bow_ignored_model_next_wv): Removed.
	(bow_cdoc_is_unlabeled): New prototype.

	* split.c (test_files_count): Removed.
	(train_files_count): Removed.
	(untagged_files_count): Removed.
	(bow_files_source_type): New type.
	(bow_split_fancy_count): New type.
	(bow_{test,train,unlabeled,ignore}_{files_source,fraction,number,filename,fancy_counts):
	New variables.
	(bow_test_set_files_use_basename): New variable from opts.c
	(bow_split_options): Code for handling split options.
	(bow_split_parse_opt): Likewise.
	(bow_split_argp): Likewise.
	(bow_split_argp_child): Likewise.
	(bow_set_all_files_untagged): Don't use removed global variables.
	(bow_set_file_types_randomly_by_count_per_class): Likewise.
	(bow_set_file_types_randomly_by_fraction): Likewise.
	(bow_set_files_to_type): Likewise.
	(bow_set_file_types_preprocess): Removed.
	(bow_set_file_types_randomly_by_count): Calculate per class nums by
	converting to floats to avoid integer roundoff error.
	(bow_set_file_types_postprocess): Removed.
	(bow_set_file_types_of_remaining): New function.
	(set_doc_types): New function.
	(_register_split_args): New function.

	* rainbow.c (rainbow_options): Removed options
	prind-non-uniform-priors prind-no-foilgain-weight-scaling
	prind-no-score-normalization and moved to prind.c.  Removed
	test-percentage set-test-files testing-files
	set-files-use-basename testing-files-use-basename set-train-files
	and moved functionality to split.c.
	(struct rainbow_arg_state): Likewise.
	(rainbow_parse_opt): Likewise.
	(rainbow_lisp_setup): Likewise.
	(main): Likewise.
	(rainbow_test): Removed test/train split code into split.c.

	* prind.c (prind_options): New for options.  Taken from rainbow.c
	(prind_parse_opt): Likewise.
	(prind_argp): Likewise.
	(prind_argp_child): Likewise.
	(_register_method_prind): Added option registration.

	* opts.c (bow_test_set_files_use_basename): Removed to split.c

	* next.c (bow_cdoc_is_model): Updated to new document types.
	(bow_cdoc_is_test): Likewise.
	(bow_cdoc_is_nontest): Likewise.
	(bow_cdoc_is_ignore): Likewise.
	(bow_cdoc_is_ignored_model): Likewise.
	(bow_cdoc_is_unlabeled): New function.
	(bow_ignore_next_wv): Removed.
	(bow_ignored_model_next_wv): Removed.

	* naivebayes.c (naivebayes_options): Changed argument priority.

	* mix.c (mix_options): Changed priority number of the options.
	(mix_new_vpc): Updated to new document types.

	* knn.c (knn_options): Changed priority number of the options.

	* em.c (use_unknown_percent): Removed.
	(bow_em_binary_model_counts): Removed.
	(unknown_percent): Removed.
	(not_unknown_num_by_class): Removed.
	(bow_em_unlabeled_num): Removed.
	(em_no_splitting): Removed.
	(bow_em_fancy_counts): Removed.
	(em_no_reset_doc_types): Removed.
	(em_options): Removed options em-unlabeled-percent
	em-labeled-num-by-class em-unlabeled-num em-no-splitting
	em-no-reset-doc-types.
	(em_parse_opt): Likewise.
	(bow_em_new_vpc_with_weights): Remove all code to do train/unlabeled
	splits.  This is now handled by libbow.  Changed call to
	bow_ignore_next_wv to be a call to bow_heap_next_wv.

	* active.c (active_initial_known): Removed.
	(active_num_unlabeled): Removed.
	(active_options): Removed options --active-initial-known and
	--active-num-unlabeled.  Now handled by libbow.
	(active_parse_opt): Likewise.
	(active_select_qbc): Update document types so unlabeled docs are now
	of type bow_doc_unlabeled.  Change other document types to the new
	ones.
	(active_select_weighted_kl): Likewise.
	(active_select_dkl): Likewise.
	(active_select_vote_entropy): Likewise.
	(active_select_uncertain): Liekwise.
	(active_select_relevant): Likewise.
	(active_select_length): Likewise.
	(active_select_random): Likewise.
	(active_select_stream_ve): Likewise.
	(active_select_stream_kl): Likewise.
	(active_learn): Likewise.  Also removed all code to handle
	test/train/ignore split here.  Now done in libbow.  Don't change
	doc types at end of active_learn.

1998-08-18  Andrew McCallum  <mccallum@jprc.com>

	* treenode.c (treenode_keywords_print): Instead of contintionally
	printing keywords, and sometimes printing "alias" (depending on kl
	value), always print the keywords, AND print the kl divergence
	value, so that a later post-processing program can decide for
	itself which keywords and aliases it wants to use.

1998-08-17  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h: Declare new split.c functions.
	(bow_doc_type): Add bow_doc_untagged.

	* rainbow.c (rainbow_options): New command-line options
	"set-test-files", "set-train-files", "set-files-use-basename".
	Not all are yet handled.
	(rainbow_test): Use new file type split.c functions.  
	(rainbow_test_files): Remove commented out code for building a new
	model.

	* split.c (bow_set_all_files_untagged): New function.
	(bow_set_file_types_preprocess): New function.
	(bow_set_file_types_randomly_by_count_per_class): New function.
	(bow_set_file_types_randomly_by_count): New function.  Takes
	over from bow_test_split().
	(bow_set_file_types_randomly_by_fraction): New function.
	(bow_set_files_to_type): New function.  Takes over from
	bow_test_set_files().
	(bow_test_split, bow_test_split2, bow_test_split3): Functions
	removed.
	(bow_test_new_heap, bow_heap_next_wv_guts, bow_heap_next_wv,
	bow_cdoc_is_*): Functions moved to next.c.

	* next.c: New file.
	* Makefile.in (LIBBOW_C_FILES): Added next.c.

	* random.c (bow_random_set_seed): Moved to this file from split.c.

1998-08-17  Kamal Nigam  <knigam@zeno.jprc.com>

	* bow/libbow.h (bow_doc_type): Changed values and added an
	unlabeled doc type.

	* bow/em.h (bow_em_perturb_weights): New prototype.

	* em.c: Major overhaul to em.c.  Cleaned up code, removed obsolete
	functionality, and added some annealing functionality.
	
	(bow_em_stat_method): Removed all but two methods. 
	(ignored_model_are_false_unknown): removed.
	(use_leave_one_out): Removed.
	(use_train_for_stats): Removed.
	(use_priors_for_initial_class_probs): Removed.
	(bow_em_unlabeled_start_method): New type for how to start the
	starting point for EM using the unlabeled documents.
	(bow_em_multi_hump_init_method): new type for how to distribute the
	labeled documents among the multiple negative humps.
	(ignored_model_percent): Removed.
	(bow_em_pr_window_size): Removed.
	(bow_em_take_best_barrel): Removed.
	(bow_em_print_stat_summary): Removed.
	(em_score_normalize_log): Removed.
	(em_unlabeled_classname): Removed.
	(use_even_for_initial_class_probs): Removed.
	(em_anneal): New option variable.
	(em_temperature): new option variable.
	(em_temp_reduction): new option variable.
	(em_print_correct): New option variable.
	(em_unlabeled_start): New option variable.
	(em_multi_hump_init): new option variable.
	(em_options): Removed options em-unlabeled-class and
	em-even-unlabeled-priors em-score-normalize-log.  Added options
	em-anneal em-temperature em-temp-reduce em-print-progress
	em-unlabeled-start and em-multi-hump-init.
	(em_parse_opt): Likewise.  Also removed extra stat method types.
	(bow_em_new_vpc_with_weights): Removed code for all options removed
	from em_options.  Only handle stat methods for nb_score and
	simple.  A general clean-up and re-organization to put related
	pieces near each other, and de-spaghetti-ization.  Added code to
	do some deterministic annealing by a specified temperature
	reduction schedule.  Added code for option to print accuracy after
	each round of em (option em-print-progress).  Cleaned up code for
	specifying how to treat unlabeled docs when specifying starting
	point by adding option em-unlabeled-start.  Added option to
	initialize the multiple negative humps by either randomly putting
	a document in a hump, or spreading a document randomly across
	humps (option em-multi-hump-init).  Changed document types to be
	in accordance with new doc types (model -> bow_doc_train, ignore
	-> bow_doc_unlabeled, etc.).  Prune the vocab before doing
	multi-hump initialization based only on the two-class split.
	(bow_em_test_accuracy): New function.
	(bow_em_set_priors_using_class_probs): Changes for new doc types.
	(bow_em_score): Changes for new doc types.  Additions for
	deterministic annealing code to handle the temperature correctly.
	Remove code for em-score-normalize-log.

Tue Aug  4 14:54:55 1998  Andrew's Laptop Account  <mccallum@jprc.com>

	* mn.c (hac_em_one_mn_iteration): Re-written.

1998-08-04  Andrew McCallum  <mccallum@jprc.com>

	* mn.c: New file.

Tue Aug  4 14:35:32 1998  Andrew's Laptop Account  <mccallum@jprc.com>

	* hac.c (hac_split_kl_threshold): Change default value from 2000
 	to 0.4.
	(hac_hypothesize_grandchildren): Use treenode_children_kl_div()
	instead of treenode_children_weighted_kl_div().
	(MN): New macro, set to 0.  Include "mn.c" if true.
	(hac_generates_class): New global variable.
	(hac_em_one_iteration): Simply return hac_em_one_mn_interation if MN.
	(hac_cluster): If CROSSBOW_CLASSES_COUNT, print the class distribution.

	* crossbow.c (crossbow_index): Always set CROSSBOW_CLASSES_COUNT,
 	indepedent of BUILD_HIER_FROM_DIR.  Also set classes distribution
 	to uniform in the root, so that all children will get space
 	allocated for this distribution.

1998-07-30  Jason Rennie  <jrennie@cyclone.jprc.com>

	* lex-suffixing.c (suffixing_snarf_suffix): added hack so that
	arrow will (hopefully) work on Cora 23k+ document data set

1998-07-28  Jason Rennie  <jrennie@cyclone.jprc.com>

	* arrow.c (main): Don't load everything into memory at start.

1998-07-22  Jason Rennie  <jrennie@cyclone.jprc.com>

	* docnames.c (bow_map_filenames_from_dir): Try opening as file if
	directory doesn't work.

	* docnames.c (bow_map_filenames_from_dir): Give warning and return
	if no directory found.

1998-07-17  Andrew McCallum  <mccallum@jprc.com>

	* hac.c (hac_cluster): Print the iteration number.
	(hac_full_em): Don't assert HAC_LOO.  Print the word distribution
	immediately after depositing the data.  Add (commented out) code
	for initializing the lambdas to a skewed distribution.  Print the
	iteration number.

	* treenode.c (treenode_pr_wi_loo_local): Handle the case in which
	there is no data left after the LOO document is removed.
	(treenode_keywords_print): Use treenode_pair_kl_div() instead of
	treenode_pair_weighted_kl_div().

	* bow/treenode.h: Declare Kamal's new function.

1998-07-15  Kamal Nigam  <knigam@zeno.jprc.com>

	* hac.c (hac_shrinkage): New variable for shrinkage option.
	(hac_loo): New variable for loo option.
	(cluster_hac_options): Changes for loo and shrinkage options.
	(cluster_hac_parse_opt): Likewise.
	(hac_hypothesize_grandchildren): Move code to create children to new
	function.
	(hac_create_children_for_node): New function.
	(hac_perplexity): Changed shrinkage and loo compiler options to
	runtime optionns.
	(hac_em_one_iteration): Likewise.    Added loo-no shrinkage
	option.
	(hac_cluster): Also created children of root identically to how other
	children are created.
	(hac_full_em): check that loo and shrinkage are in use.

	* treenode.c (treenode_log_local_prob_of_wv_loo): New function.

1998-07-15  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (crossbow_filename2di): New global variable.
	(crossbow_classes_count): New global variable.
	(crossbow_archive): Write CROSSBOW_FILENAME2DI.
	(crossbow_unarchive): Read it, and initialize CROSSBOW_CLASSES_COUNT.
	(crossbow_index): Initialize CROSSBOW_FILENAME2DI.  Set
	CROSSBOW_CLASSES_COUNT and create space in the root for CLASSES
	distribution.
	(crossbow_classify_test_docs): In addition to calculating fraction
	correct, also calculate average inverse rank, and average score
	difference between top ranked class and correct class.
	* bow/crossbow.h: Declare new global variables.

	* hac.c (hac_cluster): Don't print newlines before TEMPERATURE.
	(hac_full_em): Use alpha=1 when setting leaf prior, instead of 0.
	Don't print leaf priors since they don't change.  Print top words
	if HAC_VERTICAL_WORD_MOVEMENT.

	* treenode.c (treenode_new): Set CLASSES_CAPACITY from PARENT if
	there is a parent, then also initialize CLASSES to uniform.
	(treenode_write): Write the CLASSES information to disk.  NOTE: This
	changes the file format for the model.
	(treenode_new_from_fp): Read in the CLASSES information.
	(treenode_set_classes_uniform): New function.
	(treenode_set_classes_from_new_classes): New function.
	* bow/treenode.h: Declare new functions.

1998-07-14  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (main): Tell the lexer to toss words longer than 20.

	* hac.c (hac_hypothesize_grandchildren): Instead of void, return
	non-zero int if a split was made.
	(hac_consider_splitting): Likewise.
	(hac_cluster): Write classification and keywords to separate files for
	different iterations.

	* treenode.c (treenode_set_words_from_new_words): Renormalize
	WORDS distribution after accelerated EM.
	(treenode_set_new_words_from_perturbed_words): Add NOISE_WEIGHT
	argument.
	(treenode_set_new_words_from_perturbed_words_all): Likewise.
	(treenode_set_lambdas_from_new_lambdas): Always avoid accelerated EM,
	even if USE_ACCELERATED_EM is non-zero.
	(treenode_keywords_print): New function.
	(treenode_keywords_print_all): New function.
	(treenode_pair_kl_div): New function.
	(treenode_pair_weighted_kl_div): New function.
	* bow/treenode.h: Declare new functions.

1998-07-13  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (crossbow_classify_test_docs): Add SHRINKAGE argument
	and use it instead of macro.
	(crossbow_classify): Use TEST_FRACTION when splitting.
	(crossbow_options): New option "test-percentage".
	(crossbow_parse_opt): Handle it.
	(main): Initialize it to .3.

	* hac.c (hac_em_one_iteration): If ANCESTOR_MEMBERSHIP is zero,
	continue.  Set the leaf prior before setting word distribution,
	not after.
	(hac_place_labeled_data): New function.
	(hac_full_em): Use it.  Move hac_em_one_iteration() to after the
	diagnostic printing, not before.

	* treenode.c (treenode_set_lambdas_uniform_all): New function.
	(treenode_set_words_from_new_words): Don't assert that
	TOTAL_WORD_COUNT is greater than zero.  If it is zero, set the
	distribution to uniform, with ALPHA equal to 1/N.
	(treenode_set_leaf_prior_from_new_prior_all): 
	(treenode_set_lambdas_from_new_lambdas): Likewise.
	(treenode_log_local_prob_of_wv): Use log()-prob, not prob!
	(treenode_word_probs_print_all): Only print the prior for leaf nodes. 
	(treenode_children_kl_div): Don't assert that KLDIV is less than 10.
	* bow/treenode.h: Declare new functions.

1998-07-09  Andrew McCallum  <mccallum@jprc.com>

	Let crossbow do classification.

	* crossbow.c (SHRINKAGE): New macro.
	(crossbow_arg_state): New element BUILD_HIER_FROM_DIR.
	(crossbow_docs_split): New function.
	(crossbow_doc_is_model): New function.
	(crossbow_doc_is_test): New function.
	(crossbow_doc_is_ignore): New function.
	(crossbow_new_root_from_dir): New function.
	(crossbow_index): Initialize DOC.TAG.  Obey BUILD_HIER_FROM_DIR.
	(crossbow_classify_test_docs): New function.
	(crossbow_classify): Filled out.
	(crossbow_options): New command-line options "build-hier-from-dir" and
	"classify".
	(main): Set default BUILD_HIER_FROM_DIR to 0.
	* bow/crossbow.h: Declare new functions.
	(crossbow_doc): New element CI.

	* hac.c (hac_deterministic_horizontal): New variable.
	(hac_vertical_word_movement): New variable.
	(cluster_hac_options): New command-line option
	"hac-no-vertical-word-movement".
	(cluster_hac_parse_opt): Handle it.
	(hac_perplexity): New function.
	(hac_em_one_iteration): Obey HAC_DETERMINISTIC_HORIZONTAL and
	HAC_VERTICAL_WORD_MOVEMENT.
	(hac_cluster): Don't initialize children of root if there already are
	some.  Add LOO counts in the initial random E-step.
	(hac_full_em): New function.

	* treenode.c (treenode_new): Add NAME argument.  All callers
	changed.  Initialize CLASSES to NULL.
	(treenode_new_from_fp): Initialize CLASSES to NULL.
	(treenode_children_weighted_kl_div): New function.
	* bow/treenode.h: Declare new functions.
	(treenode): Add new elements CLASSES_CAPACITY, CLASSES, NEW_CLASSES.

	* bow/libbow.h (bow_array_next_index): Declare function.

1998-07-09  Jason Rennie  <jrennie@cyclone.jprc.com>

	* rainbow-stats.pl (read_trial): try to sort class names

1998-07-06  Andrew McCallum  <mccallum@jprc.com>

	* hac.c (LOO): New macro.
	(cluster_hac_options): New command-line option "hac-maximum-depth".
	(cluster_hac_parse_opt): Handle it.
	(hac_hypothesize_grandchildren): Obey it.
	(hac_em_one_iteration): Implement LOO.

	* treenode.c (treenode_new): Initialize LOO treenode variables.
	(treenode_new_from_fp): Likewise.
	(treenode_add_new_loo_for_di_wvi): New function.
	(treenode_free_loo): New function.
	(treenode_set_loo_from_new_loo): New function.
	(treenode_set_words_from_new_words): Set NEW_WORDS_NORMALIZER.
	(treenode_pr_wi_loo_local): New function.
	(treenode_pr_wi_loo): New function.
	(treenode_word_likelihood_ratios): Use shrinkage estimates for word
	probabilities intead of the local estimates.
	* bow/treenode.h: Declare new functions.
	(treenode): Add elements DI_LOO, DI_WVI_LOO, NEW_DI_LOO and
	NEW_DI_WVI_LOO.

	* configure.in (CFLAGS): Change default to include -Wimplicit
	instead of -Wno-implicit.
	* bow/crossbow.h (crossbow_convert_log_probs_to_probs): Declare
	function.

1998-07-03  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (crossbow_arg_state): New member CLUSTER_OUTPUT_DIR.
	(crossbow_leaf_document_probs_print): Calculate cross entropy instead
	of probability.
	(crossbow_archive): Add DIRNAME argument.
	(crossbow_unarchive): Likewise.
	(crossbow_classify_all_docs): New function.
	(crossbow_options): New command-line option "cluster-output-dir".
	(main): Handle it.

	* hac.c: Add command-line options for many parameters.  Call
	crossbow_classify_all_docs().

	* treenode.c (USE_ACCELERATED_EM): New macro.
	(EM_ACCELERATION): New macro.
	(treenode_set_words_from_new_words): Use EM_ACCELERATION.
	(treenode_set_lambdas_from_new_lambdas): Likewise.
	(treenode_iterate_all_under_node): New function.
	(treenode_pr_wi): Make it work for interior nodes of the tree as well
	as the leaves.
	(treenode_prior): New function.
	(treenode_node_count): New function.
	(treenode_normalized_word_prob_all_print): New function.
	* bow/treenode.h: Declare new functions.

1998-06-27  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_fwrite_double): New function.
	(bow_fread_double): New function.

	* bow/treenode.h: Declare new functions.
	(treenode): Change all float's to double's.

	* crossbow.c (crossbow_unarchive): Use renamed function
	treenode_new_from_fp().

	* hac.c (SHRINKAGE): New macro.
	(hac_hypothesize_grandchildren): Change KLDIV threshold from 0.0001 to
	0.2.  Instead of setting new LAMBDAS to uniform, re-divide the
	distribution from the new leaf's parent.  Use shrinkage.
	(hac_em_one_iteration):  Use shrinkage. 
	(hac_consider_splitting): New function.
	(cluster_hac): Use it.  Initialize by dividing each document
	probabilistically among children, instead of by hard assignment.
	Print just the word prob distributions, not the likelihood ratios.

	* treenode.c (treenode_new): Initialize LAMBDAS and NEW_LAMBDAS to
	put all the weight on the new treenode.
	(treenode_write): Write the PRIOR and NEW_PRIOR.  Everything that was
	a float is now a double.
	(treenode_new_from_fp): Read them.  Likewise.
	(treenode_set_lambdas_uniform): New function.
	(treenode_set_lambdas_from_new_lambdas): New function.
	(treenode_log_local_prob_of_wv): New function.
	(treenode_complete_log_prob_of_wv): New function.
	(treenode_pr_wi): New function.
	(treenode_log_prob_of_wv): Changed to use shrunken pr_wi estimates.
	(treenode_word_leaf_likelihood_ratios): Deal with zero word probs.
	(treenode_children_kl_div): Likewise.

1998-06-24  Andrew McCallum  <mccallum@jprc.com>

	* hac.c (hac_branching_factor): Renamed from NUM_CLUSTERS.
	(hac_hypothesize_grandchildren): Renamed from
	hac_hypothesize_grandchidren, and implemented.
	(hac_em_one_iteration): Fix bug in perplexity calculation.
	(cluster_hac): Intead of clustering flatly, grow a tree.  Print more
	diagnostics.
	* bow/treenode.h: Declare more functions.

	* treenode.c (treenode_new): Fix parenthezation of strlen for
	NAME.  Set WORDS_CAPACITY from parent.
	(treenode_word_likelihood_ratios): Calculate weighted log likelihood
	ratio instead of straight log likelihood.
	(treenode_word_leaf_likelihood_ratios): New function.
	(treenode_word_leaf_odds_ratios): New function.
	(treenode_word_leaf_mean_ratios): New function.
	(treenode_word_leaf_likelihood_ratios_print): New function.
	(treenode_word_leaf_odds_ratios_print): New function.
	(treenode_children_kl_div): New function.
	(treenode_is_leaf_parent): New function.

	* random.c (bow_random_double): Add LOW value after the
	multiplication!

	* em.c (random_double): Add LOW value after the multiplication!

1998-06-23  Jason Rennie  <jrennie@cyclone.jprc.com>

	* barrel.c (bow_barrel_add_from_text_dir): when printing
	bow_num_words, allow 8 spaces

1998-06-22  Andrew McCallum  <mccallum@jprc.com>

	* Makefile.in (LIBBOW_C_FILES): Add random.c.
	(CROSSBOW_C_FILES, CROSSBOW_O_FILES): New variables.
	(crossbow): New target.

	* bow/crossbow.h: Remove treenode functions.  Declare new
	functions. 

	* bow/libbow.h (bow_sparray): Declaration for a sparse array, but
	it's not implemented yet.
	(bow_wv_word_count): Declare new function.
	(bow_random_double, bow_random_01): Declare new functions.

	* crossbow.c: Move all treenode functions to treenode.c.
	(crossbow_convert_log_probs_to_probs): New function.
	(crossbow_leaf_document_probs_print): New function.
	(crossbow_index): Create the root with space for 10 children.
	(crossbow_cluster): Call cluster_hac().

	* random.c: Fix typos.

1998-06-19  Andrew McCallum  <mccallum@jprc.com>

	* random.c: New file.

	* wv.c (bow_wv_word_count): New function.
	* array.c (bow_array_next_index): New function.

1998-06-18  Kamal Nigam  <knigam@kamal.jprc.com>

	* cluster-flat.c (cluster_flat): Initial check-in.

1998-06-18  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c (treenode_word_likelihood_ratio): New function.
	(treenode_word_likelihood_ratio_print_top): New function.

	* bow/crossbow.h: Declare many functions.

	* crossbow.c (treenode_new): Initialize the WORDS and NEW_WORDS to
	zero.
	(crossbow_wv_at_di): New function.
	(crossbow_load_doc_wvs): New function.
	(crossbow_unarchive): Call it.  Read wv's from file named "wvs".
	(crossbow_index): Get the WV_SEEK_POS from the correct FP!  Write wv's
	to file named "wvs".
	(crossbow_options): New option "cluster".
	(crossbow_parse_opt): Handle it.
	(main): Call crossbow_unarchive if WHAT_DOING isn't crossbow_index.

	* crossbow.c: Move definitions to crossbow.h.  Create read and
	write an array of crossbow_doc structures.
	(crossbow_index) Fix bug that was causing crash.
	* crossbow.h: New file.

1998-06-17  Andrew McCallum  <mccallum@jprc.com>

	* crossbow.c: Completely re-written in preparation for
	implementing hierarchical clustering.

	* array.c (bow_array_init): Use bow_malloc instead of malloc.

1998-06-09  Jason Rennie  <jrennie@cyclone.jprc.com>

	* tfidf.c: change 'extern int' to 'int' so that
	bow_tfidf_num_hit_documents is defined

1998-06-09  Andrew McCallum  <mccallum@jprc.com>

	* tfidf.c (bow_tfidf_set_weights): When DOING_LOG_COUNTS, use the
	count+1, not just count.  This avoids unwanted zeros when
	count==1!
	* wv.c (bow_wv_set_weights_to_log_count_times_idf): Likewise.

	* tfidf.c (bow_tfidf_num_hit_documents): New global variable.
	(bow_tfidf_score): Set it.
	* bow/tfidf.h: Declare new global variable.
	* arrow.c (arrow_query): Print BOW_TFIDF_NUM_HIT_DOCUMENTS.

1998-06-08  Andrew McCallum  <mccallum@jprc.com>

	* arrow.c (arrow_query): Cast argument to bow_free to avoid
	warning.

	* tfidf.c (DOING_LOG_COUNTS): New macro.
	(bow_tfidf_set_weights): Use it to (conditionally) set weights to the
	log(count)*idf, instead of count*idf.  This is an attempt to
	improve IR for Cora by more strongly insisting on having all query
	terms be present.
	(bow_tfidf_score): Likewise.  Calculate the total number of documents
	that had query terms present, and print this number to standard
	out as a directive to the Cora CGI script as ",HITCOUNT %d".

	* wv.c (bow_wv_set_weights_to_log_count_times_idf): New function.
	* libbow.h: Declare new function.

	* arrow.c (arrow_query): Use NUM_SUFFIXES an another place it
	should be, instead of the old constant 5.  Print the score on each
	line, in addition to the filename and hit words.

1998-06-05  Andrew McCallum  <mccallum@jprc.com>

	* tfidf.c (bow_tfidf_score): Fix bug in query word recording, and
	uncomment code.

	* tfidf.c (bow_tfidf_score): Only return documents that contain
	one or more query terms.  Add code for returning the query words
	that were found in each document, but comment it out since it
	isn't working yet.

	* arrow.c (NUM_SUFFIXES): New macro.
	(arrow_query): Use it.  Print not just the FILENAME, but also the
	HITS[I].NAME, which, in the case of TFIDF, should contain the
	query words that were found in this document.

1998-06-04  Andrew McCallum  <mccallum@jprc.com>

	* barrel.c (bow_barrel_new_from_printed_barrel_file): Read word
	count as a float, not an integer.  Initialize the barrel's wi2dvf
	WEIGHT as well as COUNT with the word count.

1998-06-03  Andrew McCallum  <mccallum@jprc.com>

	* lex-suffixing.c (suffixing_snarf_suffix): Change suffix boundary
	from '-' to "xxx".  Lowercase the suffix.
	* arrow.c (arrow_query): Likewise.

1998-06-01  Andrew McCallum  <mccallum@jprc.com>

	* STANDARDS: New file.

	* rainbow-h.c (hier_barrel): New element LOO_DOC_WI2DVF.
	(hier_barrel_new): Initialize it to NULL.
	(hier_barrel_init_all_new_class_wi2dvf): If it is NULL, initialize it
	to an empty wi2dvf.
	(hier_barrel_set_class_model_from_new_class_wi2dvf): Instead of
	making a new empty NEW_CLASS_WI2DVF for the next round, just set
	it to NULL; hier_barrel_init_all_new_class_wi2dvf() will create a
	new one for us, now that it is being called inside the
	while()-loop in the function hier_barrel_calc_lambdas_all_nodes().
	(hier_barrel_calc_lambda_one_iteration): Calculate the DI in the root
	of each document from heap.  Then use this to add
	E-step-probability-mass to the SOURCE_HBARREL->LOO_DOC_WI2DVF.
	(hier_barrel_calc_lambdas_all_nodes): Call
	hier_barrel_init_all_new_class_wi2dvf() inside the while loop, so
	that the LOO_DOC_WI2DVF gets properly re-initialized.
	(hier_barrel_word_probabilities_for_hbarrel): Comment out unused
	variable.
	(rainbowh_unarchive): Initialize the FILENAME -> DI mapping in the
	root's DOC_BARREL.  This is used in
	hier_barrel_calc_lambda_one_iteration() to calculate ROOT_DI.

1998-06-02  Kamal Nigam  <knigam@kamal.jprc.com>

	* active.c: active_select_stream_kl: New function.
	(active_selection_type): added skl as a method.
	(active_parse_opt): Likewise.
	(active_learn): Cleaner futzing and restoring of EM options when 
	calculating test stats.  Correctly rebuild barrel for testing
	stats.

	* em.c (bow_em_new_vpc_with_weights): Don't try to set priors if
	doing uniform class priors; this avoids potential badness.  If
	zero labeled docs, only create a random starting point if we're
	not doing 'em-no-splitting'; active learning needs specific
	starting points.  Create full word-class matrix for all words in
	vocabulary; this avoids problems when perturbing the barrel for
	zero-occurring words.

	* barrel.c (bow_barrel_copy): initialize classnames correctly

1998-06-01  Andrew McCallum  <mccallum@jprc.com>

	These changes from Sean Slattery <Sean.Slattery@cs.cmu.edu>
	* bow/libbow.h (bow_bitvec): Added element BITS_SET.
	* bitvec.c (bow_bitvec_set): Keep BITS_SET up to date.

1998-06-01  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c: First attempts at Full EM.  It doesn't do
	leave-one-document out properly because it doesn't keep track of
	how a document's data was distributed among the ancestors.
	
	(rainbowh_options): Added "emfull" as a shrinkage option.
	(rainbowh_parse_opt): Handle it.
	(struct rainbowh_arg_state): New element FULL_EM.
	(hier_barrel_prune_words_not_in_map_and_set_vpc): Remind myself to set
	the CDOC->NORMALIZER here.
	(hier_barrel_set_local_class_model): Likewise.
	(hier_barrel_init_all_new_class_wi2dvf): Create NEW_CLASS_WI2DVF with
	space enough for bow_num_words() + 2, not jus tbow_num_words().
	(hier_barrel_set_class_model_from_new_class_wi2dvf): Return
	immediately if HBARREL->CLASS_BARREL is NULL, and only do the
	replacement if HBARREL->NEW_CLASS_WI2DVF is non-NULL.
	(hier_barrel_prob_wi_in_ci_wittenbell): Function gutted.
	(old_hier_barrel_prob_wi_in_ci_shrink): Function removed.
	(hier_barrel_prob_wi_in_ci_local): Comment out assertion about WEIGHT
	equalling COUNT.  As a temporary measure, check for negative
	counts and make them zero.
	(hier_barrel_prob_wi_in_ci_local): As a temporary measure, check for
	negative counts and make them zero.
	(hier_barrel_prob_wi_local): Comment out assertion about WEIGHT
	equalling COUNT.  As a temporary measure, check for negative
	counts and make them zero.
	(hier_barrel_calc_lambda_one_iteration): Attend to
	RAINBOWH_ARG_STATE.FULL_EM.
	(hier_barrel_all_reset_cdoc_word_count_from_wi2dvf_weights): New
	function. 
	(hier_barrel_calc_lambdas_all_nodes): Print overall perplexity and do
	new necessary resets.
	(hier_barrel_word_probabilities_for_class): Don't bother trying entire
	CLASS_BARREL->WI2DVF->SIZE, because many will have null DV's.  Get
	local probabilities instead of shrunken ones.
	(hier_barrel_word_probabilities_for_hbarrel): New function.
	(hier_barrel_print_word_probabilities_for_hbarrel): Use new function.
	(hier_barrel_print_all_highest_prob_words): New function.
	(_hier_barrel_local_score): When printing scores, print count instead
	of weight.
	(hier_barrel_set_lambdas): Do full EM if requested by attending to
	RAINBOWH_ARG_STATE.FULL_EM.
	(main): Initialize RAINBOWH_ARG_STATE.FULL_EM.

	* Makefile.local (rainbow-h): Include argp/libargp.a in the
	dependencies.

	* naivebayes.c
	(bow_naivebayes_set_cdoc_word_count_from_wi2dvf_weights): New
	function.
	* bow/naivebayes.h
	(bow_naivebayes_set_cdoc_word_count_from_wi2dvf_weights): Declare
	function.

	* wa.c (bow_wa_append): Fix boundary condition for array growth.

1998-06-01  Jason Rennie  <jrennie@kamal.jprc.com>

	* arrow.c (arrow_query): return 0 if query words all have 0 IDF

1998-05-31  Jason Rennie  <jrennie@kamal.jprc.com>

	* libbow.h (BOW_MAX_WORD_LENGTH): increased to 4096

1998-05-29  Jason Rennie  <jrennie@kamal.jprc.com>

	* arrow.c (arrow_query): added a feedline to a verbosify statement

1998-05-29  Jason Rennie <jrennie@data.jprc.com>

	* arrow.c (arrow_serve): kill child after serving is done.
	(main): prevent zombie children in System V environment.

1998-05-22  Andrew McCallum  <mccallum@jprc.com>

	* arrow.c (arrow_index): Make default method tfidf instead of
	prind.
	(arrow_query): Add suffixes "-Title", "-Author", "-Institution",
	"-Abstract" to the query.

	* lex-suffixing.c: New file.
	* Makefile.in (LIBBOW_C_FILES): Added lex-suffixing.c.
	* bow/libbow.h (bow_suffixing_lexer, bow_default_lexer_suffixing):
	Declare variables.
	* bow/tfidf.h (bow_method_tfidf): Declare method.
	* deflexer.c (_bow_default_lexer_init): Add suffixing lexer.
	* opts.c (bow_options): New command-line option "lex-suffixing".
	(parse_bow_opt): Handle it.

	* error.c (_bow_error): fflush() before aborting.

	* rainbow-rank.pl: Calculate average inverse rank, instead of
	average rank.

1998-05-06  Andrew McCallum  <mccallum@jprc.com>

	* split.c (bow_basename): Don't include the `/' at the beginning
	of the NUM_COMPONENTS components.  This way Reuters experiments,
	with a --testing-files file containing only the document numbers
	will still work; before this function was returning strings like
	"/15232" for the filenames in the CDOCS.

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Avoid crashing
	when PRIOR_SUM is zero.

	* em.c (random01): Make sure the this doesn't return a number
	equal to 0 or 1, just as "Recipes in C" says it should for doing
	the Gamma distribution properly.  We were getting negative values
	somewhere later in the code and suspect this is the culprit.
	(bow_em_perturb_weights): Don't check the cdoc->type of the class
	CDOCS; they aren't set.  Assert that CDOC->WORD_COUNT is
	non-negative.

1998-05-05  Andrew McCallum  <mccallum@jprc.com>

	* Makefile.in (PERL_FILES): Added rainbow-rank.pl.  Written by
	Andrew Y. Ng <ayn@ai.mit.edu>.

1998-05-04  Andrew McCallum  <mccallum@jprc.com>

	* em.c (bow_em_perturb_weights): Properly perturb zero-valued
	WEIGHTS when doing dirichlet-based perturbation.

1998-04-30  Andrew McCallum  <mccallum@jprc.com>

	* kl.c (bow_kl_score): Don't insist on a non-empty QUERY_WV.  If
	the query is empty, just use the class priors.  Accomplish this by
	setting QUERY_WORD_COUNT equal to 1.

	* naivebayes.c (bow_naivebayes_set_weights): Avoid errors when the
	barrel is completely empty.

1998-04-28  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_prune_words_not_in_map_and_set_vpc):
	Return immediately if HBARREL is NULL.
	(hier_barrel_print_infogain_hier): Likewise.
	(hier_barrel_set_vpc_and_populate_lower_branches): After freeing the
	DOC_BARREL's, immediately re-create them, instead of relying on
	later code to create them on demand.
	(hier_barrel_is_leaf_parent): New function.
	(_hier_barrel_set_node_scores): Use it to determine when to avoid
	scoring an interior node.  The previous test only worked with
	uniform-depth trees, and would cause some classes never to win.
	(main): Likewise.

	* split.c (bow_basename): Fix handling of NUM_COMPONENTS.

	* active.c (active_learn): Fix typo:
	em_perturb_starting_point_by_variance ->
	bow_em_perturb_starting_point.

1998-04-25  Andrew McCallum  <mccallum@jprc.com>

	* em.c (bow_em_perturb_starting_point): Renamed from
	em_perturb_starting_point_by_variance.  Changed from int (treated
	as binary) to an bow_em_perturb_method (an enum), for none,
	gaussian and dirichlet.
	(em_options): Expand documentation for "em-perturb-starting-point".
	(em_parse_opt): Handle it.
	(random01): New function.
	(bow_gamma_distribution): New function.
	(bow_em_perturb_weights): Use it to implement dirichlet perturbation.
	* bow/em.h (bow_em_perturb_method): New typedef.
	(bow_em_perturb_starting_point): Renamed from
	em_perturb_starting_piont_by_variance.
	* active.c: Rename em_perturb_starting_point_by_variance to
	bow_em_perturb_starting_point.  Note that this variable is now an
	enum.

1998-04-24  Andrew McCallum  <mccallum@jprc.com>

	* arrow.c (arrow_arg_state): New element SERVE_WITH_FORKING.
	(arrow_query): New argument NUM_HITS_TO_SHOW.
	(arrow_socket_init): Add verbosity.
	(arrow_serve): Initial code thinking about a forking server.
	(main): In query_serving, touch all dv's if we are a forking server.

1998-04-24  Kamal Nigam  <knigam@hurricane.jprc.com>

	* bow/libbow.h: New prototypes for bow_barrel_copy and split.c
	changes.

	* active.c (active_selection_type): added stream vote entropy.
	(active_stream_epsilon): New option for stream vote entropy.
	(active_perturb_after_em): New option.
	(active_select_stream_ve): New function.
	(active_learn):  Only calculate density if needed for dkl.  Code for
	new option active_perturb_after_em.

	* barrel.c (bow_barrel_copy): New function.

	* split.c (bow_cdoc_is_nontest): New function.
	(bow_cdoc_is_ignore): New Function.
	(bow_cdoc_is_ignored_model): New function.
	(bow_test_next_wv): Converted to use bow_heap_next_wv so returns all
	docs.
	(bow_nontest_next_wv): Likewise.
	(bow_model_next_wv): Likewise.
	(bow_ignore_next_wv): Likewise.
	(bow_ignored_model_next_wv): Likewise.

1998-04-24  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_test): Make the format of the infogain
	filename conform to the new standard in the hier/Makefile.

	* rainbow-h.c (rainbowh_options): Add new command line argument
	"testing-files-use-basename" and have it take an optional numeric
	argument to indicate how many path components to take from the end
	of the path name.
	(rainbowh_parse_opt): Handle it.
	* rainbow.c (rainbow_options): Make "testing-files-use-basename"
	take an optional numeric argument to indicate how many path
	components to take from the end of the path name.
	(rainbow_parse_opt): Handle it.
	* split.c (bow_basename): Added new argument NUM_COMPONENTS, so we
	can grab a certain number of the directory names too.
	(bow_test_set_files): Use new argument.

1998-04-24  Jason Rennie  <jr6b@andrew.cmu.edu>

       * arrow.c (arrow_process_commands): New function.
       (arrow_serve): Added capability to fork off child servers
       (arrow_parse_opt): added option "--query-forking-server"

1998-04-23  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_calc_lambda_one_iteration):
	Temporarily turn off use of NEW_CLAS_WI2DVF.
	(hier_barrel_print_barrel): Use correct function name to print
	selected. 

1998-04-22  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_print_barrel): Avoid crashes, and print
	documents only from their leaves.

	* barrel.c (bow_barrel_printf_selective): Renamed from
	bow_barrel_printf, and added third argument.
	(bow_barrel_printf): Now a wrapper around bow_barrel_printf_selected.
	* bow/libbow.h: Declare new function.

	* rainbow-h.c: Removed calls to
	hier_barrel_check_weight_equals_count.

	* rainbow-h.c (hier_barrel_for_filename): Make sure
	LONGEST_MATCH_CI is initialized.
	(hier_barrel_wa_flat_infogain): Initialize MARGINAL_TOTAL to zero.

	* Makefile.local (rainbow-h): Depend on rainbow-h.o instead of
	rainbow-h.c, so rainbow-h.o gets built.

	* bow/libbow.h: Include <mcheck.h> if BOW_MCHECK is defined.
	(bow_malloc_hook, bow_free_hook): Global variables declared.
	(bow_malloc): Call the hook.  Do special things if MCHECK is defined.
	(bow_realloc): Call the hook.
	(bow_free): Likewise.
	(bow_test_split3, bow_ignore_split, bow_argp_add_child): Functions
	declared.
	* bmalloc.c (bow_malloc_check_all): New function.
	(_bow_malloc_hook): New function.
	(_bow_free_hook): New function.
	(bow_malloc_hook, bow_free_hook): Global variables defined.

	* arrow.c: Declare external wicoo functions.
	* bow/naivebayes.h: Declare some functions in naivebayes.c.
	* naivebayes.c: Declare external simple_good_turing function.
	* istext.c (NUM_TEST_CHARS): Change from "static const int" to a
	macro.

	* rainbow-h.c (hier_barrel): New element NEW_CLASS_WI2DVF.
	(hier_barrel_check_weight_equals_count): New function.
	(hier_barrel_init_all_new_class_wi2dvf): New function.
	(hier_barrel_set_class_model_from_new_class_wi2dvf): New function.
	(hier_barrel_set_all_class_model_from_new_class_wi2dvf): New function.
	(hier_barrel_add_stats): Add the doc_barrel COUNT to the class_barrel
	WEIGHT, instead of adding zero for the weight.
	(hier_barrel_ancestor): In third argument return the CI, which in the
	returned hbarrel points towards the HBARREL argument.
	(hier_barrel_is_ancestor): New function.
	(hier_barrel_prob_wi_in_ci_local): Use WEIGHT instead of COUNT to
	calculate probabilities.
	(hier_barrel_calc_lambda_one_iteration): Check that the weight equals
	the count, temporarity as debugging.  Prepare to do *full* EM, by
	accumulating probability mass of beta's in NEW_CLASS_WI2DVF.
	(hier_barrel_calc_lambdas_all_nodes): New function.
	(hier_barrel_print_word_probabilities_for_class): Now uses bow_wa, and
	takes new argument specifying now many to print.
	(hier_barrel_print_all_highest_prob_words): New function.
	(hier_barrel_word_probabilities_for_class): New function.
	(hier_barrel_print_infogain_flat): Free the WA at end!
	(main): Pass new argument to
	hier_barrel_print_word_probabilities_for_class.

1998-04-21  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hash_elt_t): typedef removed.
	(hier_barrel): Remove all elements having to do with Andrew Ng's old
	hash.
	(hier_barrel_new_from_file): Remove second, conditional fclose(fp).
	That is, don't close the fp twice!  On RedHat5.0 this crashes,
	although it didn't on RedHat4.x.
	(HIER_TEST): Preprocessor conditional removed.

	* rainbow-h.c (hier_dir_is_leaf): Remove "const" from type of
	argument to dir_leaf_select.  Avoids warning with new RedHat5.0.

	* rainbow-h.c (rainbowh_options): New command line option
	"use-vocab-size-hier", and old command line option,
	"use-vocab_size" is now an alias for it.  Functionality of this
	option unchanged.  New command line options "use-vocab-size-flat",
	"print-word-infogain-flat", "print-word-infogain-hier".
	(struct rainbowh_arg_state): New elements VOCAB_SIZE_METHOD and
	FORCE_TRIVIAL_HIER.
	(rainbowh_parse_opt): Handle new options.  Add new shrinkage method
	"emtriv", setting FORCE_TRIVIAL_HIER.
	(hier_barrel_calc_lambda_one_iteration): Don't print warning about
	zero lambda if FORCE_TRIVIAL_HIER.
	(hier_barrel_initialize_lambdas): If FORCE_TRIVIAL_HIER, set middle
	lambdas to zero, and local and root lambdas to .5.
	(hier_barrel_print_infogain_hier): Renamed from
	hier_barrel_print_infogain.
	(hier_barrel_wa_flat_infogain): New function.
	(hier_barrel_print_infogain_flat): New function.
	(hier_barrel_test): Change sprintf of filename in which to store the
	reduce vocabulary.  Now has pattern "infogain%d-%s-%05d", where
	string is the vocab size method.  Obey VOCAB_SIZE_METHOD.
	(main): Change defaults from populate_by_scoring=1 and
	hier_structure=neice to populate_by_scoring=0 and
	hier_structure=leaf.  Print the total number of words using
	bow_verbosify instead of fprintf.  Implement
	RAINBOWH_PRINTING_INFOGAIN_FLAT.

Tue Apr 21 11:17:46 1998  Andrew's Laptop Account  <mccallum@jprc.com>

	* bow/libbow.h (bow_entropy): Declare function.
	(bow_event_models): Document with comments.
	(bow_infogain_event_model): Declare global variable.

	* info_gain.c (bow_entropy): Change type of first argument from
 	count[] to count*.
	(bow_infogain_per_wi_new): Instead of using an infogain event
 	model that matches the word probability event model, use whichever
 	event model is specified by new global variable
 	BOW_INFOGAIN_EVENT_MODEL.  Default is "document event model".
  	Thus the default is the old behavior before the binomial paper was
 	written.  Before this change, naive Bayes by default used a "word
 	event model".

	* naivebayes.c (bow_naivebayes_set_weights): Fix the setting of
 	IDF to Pr(w).  Consolodate some code that no longer needs to be
 	separate because we no longer set the DV weights in this function.

	* opts.c (bow_infogain_event_model): New global variable.
	(bow_options): New option "infogain-event-model".
	(parse_bow_opt): Handle it.

	* wa.c (bow_wa_sort): Fix bug by which the wrong pointer was
 	passed to qsort.
	(bow_wa_sort_reverse): Likewise.
	(bow_wa_fprintf): If N is less than 0, print all entries.

Wed Apr 15 11:06:25 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_correct_cdoc_prior_recurse): Fix typo.
	(rainbowh_query): Add new filename argument to call to
	bow_wv_new_from_text_fp().

	* mix.c (mix_num_centroids_per_class): Change default from 4 to 2.
	(mix_num_iterations): New static variable.
	(mix_options): New command-line option "mixture-num-em-iterations".
	(mix_parse_opt): Handle it.
	(mix_perplexity): New function, (empty).
	(mix_new_vpc): Fix bugs.

	* rainbow-h.c (hier_barrel_correct_cdoc_prior_recurse): Change the
 	method of correction.  Instead of multiplying by a ratio of the
 	number of children, multiply by all the priors up the tree to the
 	root.
	(hier_barrel_total_of_cdoc_word_counts): New function (not used).

	* Makefile.in (STANDARD_METHOD_C_FILES): Renamed from
 	METHOD_C_FILES.
	(METHOD_C_FILES): Set from $(STANDARD_METHOD_C_FILES).
	(DIST_FILES): Use STANDARD_METHOD_C_FILES instead of
	METHOD_C_FILES.  Thus we exclude methods added in Makefile.preamble.

	* rainbow-stats.pl: Changes by Jason Rennie to make it more memory
 	efficient.

	This version in the snaphot for today's date.

	* rainbow.c (rainbow_query): Add new filename argument to
 	bow_wv_new_from_text_fp.
	(rainbow_lisp_query): Likewise.
	(rainbow_test_files): Likewise.
	* arrow.c (arrow_query): Likewise.
	(main): Likewise.
	* crossbow.c (main): Likewise.

	* active.c (active_selection_type): New method "dkl".
	(active_alpha): New static variable.
	(active_beta): New static variable.
	(active_options): New command-line option "active-beta".
	(active_parse_opt): Handle it.
	(active_parse_opt): Look for "dkl" method.
	(active_select_dkl): New function.
	(active_doc_barrel_set_entropy): Use active_alpha.
	(active_wv_density): Likewise.  Make it KL divergence instead of cross
	entropy.
	(active_learn): Turn on and off cross entropy not just for wkl, but
	also for dkl.

Mon Apr 13 14:08:56 1998  Andrew McCallum  <mccallum@jprc.com>

	* Makefile.in: Include file Makefile.preamble, if it is there.
	(%.o:%.c): Move rule down into the Rules section.

	* active.c (active_select_weighted_kl): Use new density
 	calculation to weight the scores by which we select documents for
 	labeling.
	(active_doc_barrel_set_entropy): New function.
	(active_doc_barrel_set_pr_w): New function.
	(active_wv_density): New function.
	(active_doc_barrel_set_density): New function.
	(active_learn): Call active_doc_barrel_set_density().

	* Makefile.preamble: New file.  Moved METHOD_C_FILES appending
	line here.
	* Makefile.local (METHOD_C_FILES): Remove.
	* Makefile.in (METHOD_C_FILES): Remove active.c, em.c and mix.c
 	from here.
	* Makefile.local: Add a line that appends active.c, em.c, and
 	mix.c to METHOD_C_FILES.

	* naivebayes.c (bow_naivebayes_new_odds_ratio_for_ci): Create the
 	RET with a little more space to avoid memory overrun and crash.
  	Set the ratio using a weighted likelihood ratio instead of
 	unweighted.
	(bow_naivebayes_print_odds_ratio_for_all_classes): Print the number of
	words in each class to stderr.

	* rainbow-stats.pl: Include the pruned suffix in the printed
 	message to STDERR when it is used.

	* rainbow.c (rainbow_test): Use BOW_BARREL_CLASSNAME_AT_INDEX on
 	the RAINBOW_DOC_BARREL, instead of using FILENAME_TO_CLASSNAME on
 	the CDOC->FILENAME.  This works better when there is not a
 	one-to-one correspondence between classes and documents.
	(rainbow_test_files): Count the number of classes with
	BOW_BARREL_NUM_CLASSES on the RAINBOW_DOC_BARREL, not the class
 	barrel.  Again this is necessary for methods in which there are
 	multiple mixtures per class, as in the "mixture method.  Set the
 	CURRENT_CLASS using BOW_BARREL_CLASSNAME_AT_INDEX instead of
 	FILENAME_TO_CLASSNAME.

	Now --lex-pipe-command's get the fully-qualified path name of the
	file being lexed in their environment variable RAINBOW_LEX_FILENAME.

	* lex-simple.c (bow_lexer_simple_open_text_fp): New argument
 	FILENAME.  Set the environment variable RAINBOW_LEX_FILENAME
 	before forking a lex pipe command, so the command can have access
 	to this filename.
	* bow/libbow.h (bow_lexer): Make OPEN_TEXT_FP function take a new
 	argument, the filename.  Add FILENAME as an argument to several
 	functions.
	* int4str.c (bow_int4str_new_from_text_file): Pass FILENAME to lex
 	creation function.
	* int4word.c (bow_words_add_occurrences_from_text_dir): Likewise.
	* lex-gram.c (bow_lexer_gram_open_text_fp): New argument FILENAME;
 	pass it on.
	* lex-indirect.c (bow_lexer_indirect_open_text_fp): Likewise.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): New argument FILENAME.
  	Pass to lex creation function.
	* wv.c (bow_wv_new_from_text_fp): Likewise.
	* robin.c (robin_index): Pass FILENAME to lex creation function.
	* barrel.c (bow_barrel_add_from_text_dir): Pass FILENAME to
 	bow_wi2dvf_add_di_text_fp().

Mon Mar 30 18:48:19 1998  Andrew McCallum  <mccallum@jprc.com>

	* wa.c (bow_wa_new): Malloc ENTRY.
	(bow_wa_free): Free it.
	(bow_wa_append): Expand ENTRY as necessary.
	* bow/libbow.h (bow_wa): Make ENTRY a separate malloc'ed pointer.

Tue Mar 24 11:19:46 1998  Andrew McCallum  <mccallum@jprc.com>

	Implement variable-depth hierarchies.
	
	* rainbow-h.c (hier_barrel): Remove element CHILDREN_RANKINGS.
  	Add elements DEPTH and LAMBDAS.
	(hier_barrel_new): Initialize LAMBDAS to NULL.
	(hier_barrel_set_depth_and_allocate_lambdas): New function.
	(hier_barrel_free): Free LAMBDAS.
	(EXTRA_CHECKS): Change from 0 to 1.
	(hier_barrel_ancestor): New function.
	(hier_barrel_prob_wi_in_ci_local): If CI == CI_IN_PARENT_ROOT, then
	take probability from root, even if HBARREL is NULL.  This
 	provides a way to use this function to query the root, which was
 	impossible before.
	(hier_barrel_prob_wi_in_ci_shrink): Replace individual calls to
	ancestor word distributions with a loop.
	(hier_barrel_calc_lambda_one_iteration): Likewise.  Return perplexity
	instead of log-probability of the data.
	(hier_barrel_prob_wi_shrink): Since the body only ever work on the
	root, only shrink local and uniform, instead of uniform three
 	times.
	(hier_barrel_initialize_lambdas): Set initial values with loop.
	(hier_barrel_calc_lambda): Keep doing EM iterations until perplexity
	change is less than 0.1, instead of going until all lambdas remain
 	constant.
	(hier_barrel_calc_lambdas): Don't print "Calculting lambda", just
	print the hbarrel name.
	(rainbowh_unarchive): Do some post-processing after unarchiving.  Set
	the depth and allocate lambdas.
	(main): Verbosify the total number of words instead of fprintf'ing it.

Mon Mar 23 19:59:33 1998  Andrew McCallum  <mccallum@jprc.com>

	* naivebayes.c (bow_naivebayes_new_odds_ratio_for_ci): New
 	function.
	(bow_naivebayes_print_odds_ratio_for_all_classes): New function.
	(bow_naivebayes_set_weights): Don't assert that we are using one of a
	limited number of methods.
	(bow_naivebayes_score): Initialize BSCORES[CI].NAME to NULL.
	* bow/naivebayes.h: Declare functions.

	* bow/libbow.h (bow_ws): New structure.
	(bow_wa): New structure.
	Declare new bow_wa_* functions.

	* Makefile.in (LIBBOW_C_FILES): Added mix.c and wa.c
	* wa.c: New file.
	* mix.c: New file.

1998-03-23  Kamal Nigam  <knigam@yawp.jprc.com>

	* em.c (em_no_reset_doc_types): New variable for resetting option.

	* split.c (bow_test_split_for_em_binary): Function removed.
	(bow_test_split3): New function.
	(bow_test_split_for_em_multihump): Function removed.

	* em.c (bow_em_binary_model_counts): Code for fancy counts.
	(bow_em_fancy_counts): Likewise.
	(em_options): Likewise, and for new option --em-no-reset-doc-types.
	(em_parse_opt): Likewise, and for specifying number of multiple
	negative humps.
	(bow_em_new_vpc_with_weights): Changed array lengths to static for
	debugging sanity.  Added code for fancy counts, multiple neg
	humps, and not resetting doc types.  Fixed initial assert to be
	more allowable.
	(bow_em_score): Conditional rescaling so binary scoring works
	correctly.

Mon Mar 23 09:57:11 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_test): Assert that only one trial was
 	requested, because there is no point in testing the training
 	documents twice, and also, otherwise the EM method will mess up.

	* rainbow.c (rainbow_options): New command-line option
 	"test-on-training".
	(rainbow_parse_opt): Handle it.
	(rainbow_test): Implement it.
	(struct rainbow_arg_state): New element TEST_ON_TRAINING.
	(main): Initialize it.

	In naivebayes, use the WEIGHT field of DV's instead of the COUNT
	field. 

	* naivebayes.c (bow_naivebayes_pr_wi_ci): Calculate this from the
 	DV's WEIGHT not from its COUNT.
	(bow_naivebayes_set_weights): Use WEIGHT instead of COUNT.
	(bow_naivebayes_score): Likewise.
	* vpc.c (bow_barrel_new_vpc): Add code to update the
 	CDOC->WORD_COUNT in the DOC_BARREL in order to match the
 	(potentially) pruned vocabulary.  When building the wi2dvf, add
 	WEIGHT correctly for the different event models.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): When incorporating the
 	word that has just been tokenized, add one to both the COUNT and
 	the WEIGHT, not just the COUNT.  Note that this will change the
 	way the barrel->wi2dvf is built from data, and barrels tokenized
 	before this change will now be different from barrels tokenized
 	afterwards.  This change is inkeeping with naivebayes' use of the
 	WEIGHT field instead of the COUNT field, although vpc.c has a fix
 	to make the old-style wi2dvf's work.
	* split.c (bow_tmp_word_struct): Add element WEIGHT.
	(bow_test_next_wv): Put WEIGHT into the WV to be returned.

Thu Mar 19 10:45:25 1998  Andrew McCallum  <mccallum@jprc.com>

	* info_gain.c (bow_infogain_per_wi_new_document_event): Renamed
 	from bow_infogain_per_wi_new.
	(bow_infogain_per_wi_new_word_event): New function.
	(bow_infogain_per_wi_new): New function.

Sat Mar  7 11:16:56 1998  Andrew McCallum  <mccallum@jprc.com>

	* dv.c (_bow_dv_index_for_di): In embedded function
 	grow_if_necessary(), grow if LENGTH is >= SIZE, not just ==.
  	Also, add 1 to SIZE before multiplying for growth, so that if SIZE
 	is 1, it will grow.  (Reported by Sean Slattery.)  These changes
	fix bugs that prevented adding to a barrel read from disk.

Fri Mar  6 11:07:32 1998  Andrew McCallum  <mccallum@jprc.com>

	* naivebayes.c (bow_naivebayes_pr_wi_ci): If using the document
 	event model, force special kind of smoothing.
	(bow_naivebayes_score): Change loop over words to be more readable.
	Fix bug in condition for when to use the word count in the query.
  	Properly handle zero-length documents.

Thu Mar  5 12:30:36 1998  Kamal Nigam  <knigam@hurricane.jprc.com>

	* int4str.c (bow_int4str_new_from_string_file): switched
 	reading_numbers back to regular.

Thu Mar  5 11:31:55 1998  Andrew McCallum  <mccallum@jprc.com>

	Implement the "document" event model, i.e. the multi-variate
	Bernoulli. 

	* naivebayes.c (bow_naivebayes_set_weights): If we are using the
 	document event model, don't check that the sum of P(w|c) over all
 	words in a single class equals one, because it isn't true.
	(bow_naivebayes_score): Change the inner loop over words.  If we're
	using the document event model, loop over all words in the
 	vocabulary instead of just the words in the query.  When
 	incorporating the probability of a word that does not occur in the
 	query document, make it 1-p.  Don't use the count of the word when
 	using the document event model.
	* vpc.c (bow_barrel_new_vpc): Assert that the word count is
 	non-zero before adding a count of 1 when using the document event
 	model.

Thu Mar  5 11:18:16 1998  Kamal Nigam  <knigam@hurricane.jprc.com>

	* .cvsignore: added kl-div

	* active.c (active_selection_type): added vote entropy.
	(active_parse_opt): Likewise.
	(active_no_final_em): New option for not finishing with an EM round.
	(active_options): Likewise.
	(active_parse_opt): Likewise.
	
	(active_document_entropy): New function.
	(active_select_weighted_kl): Correct weighting metric
	(active_select_vote_entropy): New function.
	(active_learn): prune vocab and set word counts at each round.  add
	code for active_no_final_em option.  turn off cross entropy for
 	final model building.

	* barrel.c (bow_barrel_printf): fixed array bounds bug.

	* em.c (bow_em_new_vpc_with_weights): set word counts after pruing
 	the vocab.  Remove buggy conditions when calculating normalizer.

Mon Mar  2 14:51:32 1998  Andrew McCallum  <mccallum@jprc.com>

	This version used for the ICML'98 hierarchical classification paper.

	* rainbow-h.c (hier_barrel_prob_wi_in_ci_local): Don't assert that
 	LOCAL_COUNT > 0, just return the uniform distribution if it is.
	(hier_barrel_calc_lambda_one_iteration): Don't assert that LAMBDA must
	be greater than 0, (because sometimes EM makes it go to zero);
 	just print a warning if it is.
	(_hier_barrel_set_node_scores): Goto DO_CHILDREN only if we are
	pruning, not always whenever SCORE is -FLT_MAX.  Remove
 	bow_error() call for HIER_STRUCTURE!=HIER_LEAF.
	(hier_barrel_score): Initialize the root HBARREL->SCORE to 1.
	(main): Print the number of words in each top-level branch, and the
	total number of words.

Fri Feb 20 13:04:45 1998  Andrew McCallum  <mccallum@jprc.com>

	* active.c (active_document_entropy): New function.
	(active_select_weighted_kl): Use it to weight document selection
	weights by e^(-KLdiv).

Thu Feb 19 11:46:14 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (rainbowh_options): new command-line option
 	"scoring-pruning".
	(struct rainbowh_arg_state): New element SCORING_PRUNING_NUM_CHILDREN.
	(rainbowh_parse_opt): Handle it.
	(hier_barrel_prob_wi_in_ci): Raise error if we try to use wittenbell
	smoothing.
	(_hier_barrel_set_node_scores): Pay attention to
	SCORING_PRUNING_NUM_CHILDREN.
	(main): Initialize SCORING_PRUNING_NUM_CHILDREN.

Fri Feb 20 12:45:30 1998  Kamal Nigam  <knigam@server7.jprc.com>

	* bow/em.h (em_cross_entropy): made extern

	* em.c (em_cross_entropy): made non-static

	* active.c (active_selection_type): added new type length.
	(active_parse_opt): added new length selection method.
	(active_select_qbc): reverted some changes lost from bad conflict
	resolution.
	(active_select_weighted_kl): fixed bugs to make run.
	(active_select_length): New function.
	(active_learn): create a dummy vpc barrel before trying to set word
	counts.  turn off crossentropy for generating test stats.

Wed Feb 18 20:36:38 1998  Andrew McCallum  <mccallum@jprc.com>

	* em.c (em_cross_entropy): Renamed from em_crossentropy.
	(bow_em_score): Make it do cross entropy if above var is non-zero.

Wed Feb 18 20:08:03 1998  Kamal Nigam  <knigam@server7.jprc.com>

	* active.c (active_parse_opt): new option for new selection method
 	wkl

	* em.c (em_parse_opt): new option for crossentropy scoring
	(em_crossentropy): Likewise.

Wed Feb 18 20:24:57 1998  Andrew McCallum  <mccallum@jprc.com>

	* naivebayes.c (naivebayes_cross_entropy): New static variable,
 	turned off by default.
	(bow_naivebayes_score): Obey it.

	* active.c (active_select_weighted_kl): New function.

Wed Feb 18 20:08:03 1998  Kamal Nigam  <knigam@server7.jprc.com>

	* bow/libbow.h (bow_smoothing): added goodturing.
	(bow_cdoc_yes): prototype for new function.
	(bow_smoothing_goodturing_k): new global for options.

	* bow/em.h (bow_em_pr_struct): New from em.c

	* em.c (bow_em_pr_struct): moved to header file.

	* naivebayes.c (bow_naivebayes_initialize_goodturing): new
 	function.
	(bow_naivebayes_goodturing_discounts): new variable.
	(bow_naivebayes_goodturing_barrel): new variable.
	(bow_naivebayes_pr_wi_ci): added option for goodturing smoothing
	(bow_naivebayes_set_weights): Likewise.

	* split.c (bow_cdoc_yes): new function.

	* opts.c (bow_options): added option smoothing-goodturing-k and
 	added to smoothing-method option.
	(parse_bow_opt): Likewise.

	* Makefile.in (LIBBOW_C_FILES): add goodturing.c
	* active.c (active_select_relevant): fixed so it picks most
 	relevant docs instead of least relevant.
	(active_remap_scores): New function.
	(active_parse_opt): New options for remapping scores to probabilities.
	(active_pr_print_stat_summary): Likewise.
	(active_pr_window_size): Likewise.
	(active_remap_scores_pr): Likewise.
	(active_learn): add word count calculation.  Call remap for new option.

Wed Feb 18 14:04:00 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_test): Handle case where
 	RAINBOWH_ARG_STATE.VOCAB_SIZE is zero.  Now we can do tests with
 	the full, unpruned vocabulary.

Tue Feb 17 17:05:54 1998  Andrew McCallum  <mccallum@jprc.com>

	* info_gain.c (bow_infogain_per_wi_new): Use correct type in RET
 	allocation.

Mon Feb 16 17:11:21 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_options): New command-line option
 	"testing-files-use-basename".
	(rainbow_parse_opt): Handle it.
	(rainbow_test): Remove old document iteration code.
	* split.c (bow_test_set_files): Obey
 	BOW_TEST_SET_FILES_USE_BASENAME.
	(BASENAME_ONLY): Macro removed.
	* opts.c (bow_test_set_files_use_basename): New global variable.
	* bow/libbow.h: Declare new global variable.

Sat Feb 14 09:54:33 1998  Andrew McCallum  <mccallum@jprc.com>

	This version used for most ICML results.
	* rainbow-h.c (hier_barrel): New element CLASS_WORD_COUNT.
	(str_match_len): Move it out of hier_barrel_filename_to_classname.
	(hier_barrel_for_filename): New function.
	(hier_barrel_set_class_word_count): New function.
	(hier_barrel_wi_count): New function.
	(EXTRA_CHECKS): New macro.
	(hier_barrel_prob_wi_in_ci_local): New argument LOO_G1CHILD_CI.  This
	allows you to leave out a grandchild from the stats.
	(hier_barrel_prob_wi_in_ci_shrink): Likewise.
	(hier_barrel_prob_wi_local): New argument LOO_CHILD_CI.  This allows
	you to leave out a child from the stats.
	(hier_barrel_prob_wi_shrink): Likewise.
	(LOO_CI_IN_PARENT): New macro.
	(LOO_PARENT_CI_IN_G1PARENT): New macro.
	(hier_barrel_calc_lambda_one_iteration): Use New arguments to prob
	functions.

Thu Feb 12 16:12:24 1998  Kamal Nigam  <knigam@server7.jprc.com>

	* bow/em.h (em_perturb_starting_point_by_variance): Made
 	externally viewable.
	(bow_em_num_em_runs): Likewise.

	* rainbow.c (rainbow_test): Added warning message if going into
 	buggy code.

	* em.c (em_perturb_starting_point_by_variance): Made non-static so
 	active.c can change its value.
	(bow_em_num_em_runs): Likewise.
	(bow_method_em): Added element for bow_barrel_free.

	* active.c (active_final_em): new global for new option.
	(active_print_committee_matrices): Likewise.
	(active_qbc_low_kl): Likewise.
	(active_options): added three new options.
	(active_parse_opt): Likewise.
	(active_select_qbc): Fixed for roundoff error.  Added code for new
	option.
	(active_learn): Print the names of initial docs.
	Code for new options.  Change all non-test docs back to model at
 	end.
	(active_test): Change to use new heap routine that gets all docs.

Wed Feb 11 10:05:34 1998  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_free_barrel): Remove check for NULL function,
 	so that the absence of this function will be noticed.  Previously
 	we had not noticed that em's barrel free function was NULL, and
 	where getting major memory leaks.

Tue Feb 10 18:26:53 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (main): Fix typos.

	Make --prune-vocab-by-occur-count and --prune-vocab-by-doc-count
	work in conjunction with --print-barrel.
	* rainbow.c (main): Obey options -O and -D before doing things
 	that don't update the vocab on their own.
	* wi2dvf.c (bow_wi2dvf_hide_words_by_occur_count): New function.
	* int4word.c (bow_words_occurrences_for_wi): Just return 0 when WI
 	is too large, instead of raising an assertion.

Mon Feb  9 18:00:40 1998  Andrew McCallum  <mccallum@jprc.com>

	* vpc.c (bow_barrel_new_vpc): Assert that the cdoc's from the
 	DOC_BARREL are at least as large as necessary.  This can fail when
 	reading from a disk archive that was created before CLASS_PROBS
 	was added to BOW_CDOC.

	* rainbow.c: Initialize DOC_CDOC, when using bow_test_next_wv()!

	* normalize.c (bow_wv_normalize_weights_by_vector_length): Handle
 	an empty WV.
	(bow_wv_normalize_weights_by_summing): Likewise.

	* naivebayes.c (naivebayes_normalize_log): New static variable.
	(naivebayes_rescale_scores): New static variable.
	(naivebayes_final_rescale_scores): New static variable.
	(naivebayes_options): New command-line option
	"naivebayes-normalize-log". 
	(naivebayes_parse_opt): Handle it.
	(bow_naivebayes_pr_wi_ci): Fix Witten-Bell.  It should now be working
	properly.
	(NO_SCALING): Macro removed, replaced by NAIVEBAYES_RESCALE_SCORES.
	(bow_naivebayes_score): Calculate the entropy of words in the
	document, H_W_D, although it is currently unused.  Do scaling or
 	not depending on new static variable.  Handle
 	NAIVEBAYES_NORMALIZE_LOG: when scoring, instead of using exp(),
 	return -1/(log(P(C|d)^3)) rescaled so highest is -2, normalized to
 	sum to one instead of P(C|d).  This results in values that are not
 	so close to zero and one.

	* em.c (em_options): New command-line option
 	"em-score-normalize-log".
	(em_parse_opt): Handle it.
	(bow_em_score): Obey it.  When scoring, return -1/(log(P(C|d)^3)
	(where the scores have been rescaled so that the highest value is -2),
	normalized to sum to one instead of P(C|d).  This results in
 	values that are not so close to zero and one

Mon Feb  9 17:52:18 1998  Kamal Nigam  <knigam@server7.jprc.com>

	* em.c (em_score_normalize_log): new option.
	(bow_em_perturb_weights): fixed bug for calculating perturbation.
	(bow_em_score): code for new normalization option

Sat Feb  7 12:41:39 1998  Andrew McCallum  <mccallum@jprc.com>

	* active.c (active_select_qbc): Set WEIGHT to average
 	KL-divergence-to-the-mean, not average entropy.

1998-02-07  Kamal Nigam  <knigam@tsunami.jprc.com>

	* active.c (active_options): added active-committee-size
	(active_select_qbc): checked for p(w_c) = 0

	* em.c (bow_em_perturb_weights): fix looping and calculation bugs
	(bow_em_new_vpc_with_weights): skip E-step on last iteration

	* active.c (active_selection_type): changes for committee learning
	(active_learn): made changes to support committee learning

Fri Feb  6 10:36:19 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_correct_cdoc_prior): Check prior
 	consistency more carefully.
	(HBARREL_LAMBDA_PARENT): New macro.
	(hier_barrel_calc_lambda_one_iteration): Increment with COUNT, not ++!
	When printing P(w|c) for Agriculture/Org, print the count.  Use
 	new macro; particularly when calculating LOG_PROB_OF_DATA where
 	the old version did not use the correct value for lambda parent.
  	Use COUNT in calculation of LOG_PROB_OF_DATA.
	(hier_barrel_calc_lambda): Print ">" when LOG_PROB_OF_DATA goes down
	in order to help debugging.
	(hier_barrel_calc_lambdas): Get NUM_WORDS in the class, then print it,
	so we can see it with the EM iteration numbers.

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Print warning if
 	class has zero prior.

	* em.c (em_options): New command-line option
 	"em-perturb-starting-point".
	(em_parse_opt): Handle it.
	(random_double): New static function.
	(bow_em_gaussian): New function.
	(bow_em_perturb_weights): New function.
	(bow_em_new_vpc_with_weights): Use it.

	* active.c (active_select_qbc): Added assertion.

1998-02-06  Kamal Nigam  <knigam@tsunami.jprc.com>

	* active.c: changes for compilation bugs

	* bow/libbow.h (bow_test_set_files): added prototype

	* split.c (bow_random_set_seed): new function.
	(bow_test_split): Uses bow_random_set_seed.
	(bow_test_split2): Likewise.
	(bow_test_split_for_em_binary): Likewise.
	(bow_test_split_for_em_multihump): Likewise.
	(bow_ignore_split): Likewise.

Fri Feb  6 10:36:19 1998  Andrew McCallum  <mccallum@jprc.com>

	* active.c (active_commitee_size): New static variable.
	(active_options): New command-line option "committee-size".
	(active_parse_opt): Handle it.
	(active_select_qbc): New function.
	(active_select_uncertain): Add new COMMITTEE_SIZE argument.
	(active_select_relevant): Likewise.
	(active_select_random): Likewise.

1998-02-06  Kamal Nigam  <knigam@tsunami.jprc.com>

	* em.c (em_parse_opt): added check for --em-num-iterations

	* bow/libbow.h (bow_test_split2): new prototype for removed option
	em_seed
	
	(bow_split_seed): new option.

	* split.c (already_seeded): new variable to ensure only one
	seeding
	(bow_test_split): code for already_seeded and new option --split-seed
	(bow_ignore_split): Likewise.
	(bow_test_split2): Likewise.
	(bow_test_split_for_em_binary): Likewise.
	(bow_test_split_for_em_multihump): Likewise.

	* rainbow.c (rainbow_test): moved print statement for run header
	for active learning

	* opts.c (bow_split_seed): new variable for new option
	(bow_options):  code for new option --split-seed
	(parse_bow_opt): likewise

	* em.c (em_parse_opt): added new option --em-no-splitting and
	removed option --em-split-seed
	(bow_em_new_vpc_with_weights): added code for active learning to be
	compatible.  removed em-split-seed option (superseeded by a bow
	option) and added --em-no-splitting option
	
	* Makefile.in (METHOD_C_FILES): added active.c

	* active.c: new file.

Wed Feb  4 21:18:54 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (rainbowh_options): New command-line option
 	"print-lambdas-to-file".
	(rainbowh_parse_opt): Handle it.
	(struct rainbowh_arg_state): New member LAMBDA_FP.
	(hier_barrel_calc_lambda_one_iteration): Change all floats to doubles.
	When running through word data in E-step, explicitely skip words
 	that are not in the vocabulary, even though it shouldn't be
 	necessary, since bow_model_next_wv() should not include them
 	anyway.  Add some assertions and debugging verbosity.  Handle new
 	command-line option.
	(hier_barrel_calc_lambda): Base stopping condition on the sum of
	diff's across all lambda's, not just the child lambda.
	(hier_barrel_calc_lambdas): Handle LAMBDA_FP.
	(main): Likewise.

	* naivebayes.c (naivebayes_parse_opt): Make command-line option
 	"naivebayes-m-est-m" work.
	(bow_naivebayes_pr_wi_ci): Likewise.  Try to fix Witten-Bell, but
	still not working.  Use doubles instead of floats.
	(bow_naivebayes_set_weights): Use bow_naivebayes_pr_wi_ci().

Mon Feb  2 18:49:02 1998  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h: Declare new functions and global variables.
	(bow_event_models): New type.
	(bow_dv_heap): New members HEAP_WV, HEAP_WV_DI and LAST_DI, for use
	with new function bow_heap_next_wv().

	* heap.c (bow_make_dv_heap_from_wi2dvf): Initialize new members of
 	bow_dv_heap structure.

	* naivebayes.c (NO_SCALING): New macro to turn off rescaling of
 	scores.  Currently set so that Scaling is used.
	(bow_naivebayes_score): Handle "document event model" BOW_EVENT_MODEL.

	* opts.c (bow_event_model): New global variable.
	(bow_options): New command-line option "event-model".
	(parse_bow_opt): Handle it.

	* rainbow-h.c (rainbowh_options): New option "print-doc-names".
	(hier_barrel_correct_cdoc_prior_recurse): New function.
	(hier_barrel_total_of_cdoc_priors): New function.
	(hier_barrel_correct_cdoc_prior): New function.
	(hier_barrel_prune_words_not_in_map_and_set_vpc): Call new function
	hier_barrel_correct_cdoc_prior() at end.
	(hier_barrel_set_local_class_model): Raise an error if
	BOW_PRUNE_VOCAB_BY_INFOGAIN_N.
	(hier_barrel_set_vpc_and_populate_lower_branches): Use new function
	bow_heap_next_wv().
	(hier_barrel_set_vpc_and_populate_lower_branches): Call new function
	hier_barrel_correct_cdoc_prior() at end.
	(IMPOSSIBLE_SCORE_FOR_ZERO_CLASS_PRIOR): New macro.
	(_hier_barrel_local_score): Use it.  Empty documents now allowed!
	Move the initialization of NUM_WORDS_IN_QUERY_WV down after
 	setting of priors, because sometimes the document is empty anyway.
	(_hier_barrel_set_node_scores): Declare PARENT_SCORE double instead of
	float.
	(hier_barrel_test): Use hacked-up for-loop to make sure we don't skip
	empty documents.  Print scores with precision based on
 	BOW_SCORE_PRINT_PRECISION.
	(main): Handle new command line option.

	* rainbow.c (rainbow_parse_opt) [USE_VOCAB_IN_FILE_KEY,
 	HIDE_VOCAB_IN_FILE_KEY]: Use bow_int4str_new_from_text_file(), not
 	bow_int4str_new_from_text_string().  This makes the rainbow-h
 	infogain files useable for in this context.
	(rainbow_test): When determining when to alloca() HITS, use a
	condition on HITS, not TN, because TN is set past 0 when
 	--testing-files is used!  Use new function bow_heap_next_wv() for
 	looping through all test documents.  Only free EMPTY_WV if it is
 	non-NULL.

	* split.c (BASENAME_ONLY): Changed from 1 to 0.  Now when using
 	--testing-files, we compare the entire filename path, not just the
 	basename.  Warning: The AAAI'98 Reuters experiments relied on the
 	old setting.
	(bow_heap_next_wv_guts): New function.
	(bow_heap_next_wv): New function.
	(bow_cdoc_is_model): New function.
	(bow_cdoc_is_test): New function.

	* vpc.c (bow_barrel_new_vpc): Count the number of documents
 	properly by running through list of documents, not be looking at
 	DV's!  Handle the event=document bow_event_model.  Verbosify the
 	number of documents in each class.
	(bow_barrel_set_vpc_priors_by_counting): Change PRIOR_SUM from float
	to double.

	* TODO: Append email from Doug.

	* evi.c (_register_method_evi): Add new argument to
 	bow_register_with_name().

Fri Jan 30 10:49:28 1998  Andrew McCallum  <mccallum@jprc.com>

	* methods.c (bow_method_register_with_name): New argument CHILD
 	allows the automatic setting of the GROUP index in the options, so
 	that the help message for options will get grouped together at the
 	bottom of the help message.

	* knn.c (_register_method_knn): Add new argument to
	bow_method_register_with_name(). 
	* kl.c (_register_method_kl): Likewise.
	* em.c (_register_method_em): Likewise.
	* tfidf.c (_register_method_tfidf_): Likewise.
	* prind.c (_register_method_prind): Likewise.
	* naivebayes.c (_register_method_naivebayes): Likewise.
	* bow/libbow.h: Add new argument to
 	bow_method_register_with_name().

	* configure.in: Check for alloca.h, needed on DEC alpha machines.
	Suggested by Jason Rennie.

Wed Jan 28 17:45:34 1998  Andrew McCallum  <mccallum@jprc.com>

	* wi2dvf.c (bow_wi2dvf_hide_words_by_doc_count): Return
 	immediately if COUNT is 0.

	* rainbow.c (rainbow_options): New command-line option
 	"hide-vocab-indices-in-file".
	(rainbow_parse_opt): Handle it.
	(struct rainbow_arg_state): New member HIDE_VOCAB_INDICES_FILENAME.
	(rainbow_test): Implement new option.  Print scores even for empty
	documents.  They were skipped before.
	(main): Implement new option.

	* opts.c (bow_prune_words_by_doc_count_n): New global variable.
	(bow_options): New command-line option "prune-vocab-by-doc-count".
	(parse_bow_opt): Handle it.
	* bow/libbow.h: Declare new command-line option global variable.

	* int4word.c (bow_words_keep_top_by_infogain): Use qsort() instead
 	of previous N^2 implementation.

	* int4str.c (bow_int4str_new_from_string_file): If the first word
 	is all numbers, read interpret the strings as word indices instead
 	of strings.

	* barrel.c (bow_barrel_printf): Implement new format indicator,
 	'I'.  Print in format used by Mehran Sahami's feat-sel program.

Wed Jan 21 17:39:12 1998  Andrew McCallum  <mccallum@jprc.com>

	This version used for AAAI-98 submission.  CVS tagged with
	`aaai98-submission'.

	* rainbow.c (main): Move rainbow_word_count_printing below "Do
 	things that require the vocabulary or class/word weights to have
 	been updated" so that the class barrel will be re-made and
 	up-to-date.  Temporarily, call
 	bow_naivebayes_print_odds_ratio_for_class() for implementing the
 	--weight-vector option.

	* naivebayes.c (bow_naivebayes_print_odds_ratio_for_class): New
 	function.
	(bow_naivebayes_set_weights): Set IDF to P(w).

Wed Jan 21 17:39:53 1998  Kamal Nigam  <knigam@hurricane.jprc.com>

	* rainbow.c (rainbow_test): changes to support --em-multi-hump-neg
	* em.c (bow_em_new_vpc_with_weights): added support for new options
        --em-multi-hump-neg and --em-even-unlabeled-priors
        (bow_em_score): Likewise.

	* split.c (bow_test_split_for_em_multihump): New function.

Thu Jan 22 16:08:13 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_prune_words_not_in_map_and_set_vpc): No
 	longer unhiding the vocabulary at the end of the function.  Yipes.
  	Is this OK?
	(hier_barrel_set_local_class_model): Likewise.
	(_hier_barrel_local_score): No longer zero NUM_WORDS_IN_QUERY_WV at
	declaration time; do it just before the loop that counts them.  In
 	the loop, before incrementing for a particular word, check agains
 	the RAINBOWH_ARG_STATE.VOCAB_MAP, not the
 	HBARREL->CLASS_BARREL->WI2DVF!
	(hier_barrel_test): Expand comment about the loop over test documents
	skipping document that don't have any words in the vocabulary.

	* wicoo.c (bow_barrel_shrink_wv): New function.  Currently empty.

Sat Jan 17 12:27:41 1998  Andrew McCallum  <mccallum@jprc.com>

	* em.c (bow_em_new_vpc_with_weights): Only free BEST_WI2DVF under
 	correct conditions.  This fixes bug whereby rainbow produces no
 	output.

Fri Jan 16 09:51:46 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_options): New command-line option
 	"hide-vocab-in-file".
	(rainbow_parse_opt): Handle it.
	(struct rainbow_arg_state): New element hide_vocab_map.
	(rainbow_query): Handle --hide-vocab-in-file, and, importantly, put
	bow_keep_top_words_by_infogain above the bow_barrel_prune_vocab_
 	functions so that they will actually have an effect!  Remember,
 	bow_keep_top_words_by_infogain begins by unhiding all words!
	(rainbow_lisp_setup): Initialize rainbow_arg_state.hide_vocab_map.
	(rainbow_test): Put the bow_barrel_prune_vocab_ function calls inside
	the trial for()-loop, after the bow_keep_top_words_by_infogain,
 	for the same reason as above!
	(main): Handle --hide-vocab-in-file, and, importantly, put
	bow_keep_top_words_by_infogain above the bow_barrel_prune_vocab_
 	functions so that they will actually have an effect!

	* naivebayes.c (bow_naivebayes_pr_wi_ci): In wittenbell, use
 	LOO-adjusted class word count instead of CDOC->NUM_WORDS.

	* barrel.c (bow_barrel_prune_words_in_map): New function.
	* bow/libbow.h: Declare new function.

	* split.c (bow_basename): Fix so it will strip the leading `/'.

	* opts.c (bow_smoothing_method): New global variable.
	(bow_options): New command line option "smoothing-method";
	currently takes "laplace", "mestimate" and "wittenbell".
	"mestimate" is not yet implemented.
	(parse_bow_opt): Handle it.
	* bow/libbow.h (bow_smoothing): New enum typedef.
	(bow_smoothing_method): Declare new global variable set by opts.c.
	* naivebayes.c (bow_naivebayes_pr_wi_ci): Use different smoothing
 	methods depending on BOW_SMOOTHING_METHOD; laplace and wittenbell
 	implemented.
	* kl.c (bow_kl_score): Previously used wittenbell smoothing all
 	the time.  Now use wittenbell only if indicated on command-line
 	with --smoothing-method, otherwise use laplace.

Thu Jan 15 11:47:00 1998  Andrew McCallum  <mccallum@jprc.com>

	* vpc.c (bow_barrel_new_vpc): Remove assertion that all classes
 	have some words in their training data after vocabulary pruning.
	(bow_barrel_set_vpc_priors_by_counting): When calculating class
	priors, don't count documents that are not in the MODEL set!

	* rainbow.c (rainbow_test): Fix typo.

	* naivebayes.c (bow_naivebayes_score): If a class has a zero class
 	prior, set the score to a special flagged value, and then when
 	returning scores in the array, make those scores be -DBL_MAX.
	Now, for the first time, naivebayes can handle classes that have no
	training documents in them.

Thu Jan 15 14:15:22 1998  Kamal Nigam  <knigam@hurricane.jprc.com>

	* em.c (bow_em_new_vpc_with_weights): Fixed two memory leaks.

Thu Jan 15 11:47:00 1998  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_score_print_precision): New variable extern
 	declaration.

	* kl.c (bow_kl_score): Assert QUERY_WORD_COUNT to make sure we're
 	not trying to classify an empty document.

	* em.c (bow_em_compare_to_nb): Use BOW_SCORE_PRINT_PRECISION when
 	printing scores.

	* bow/libbow.h (bow_stoplist_replace_with_file): New function
 	declaration.

Thu Jan 15 11:39:44 1998  Kamal Nigam  <knigam@hurricane.jprc.com>

	* opts.c (bow_score_print_precision): New option, defaults to 10.
	(parse_bow_opt): Support for new option.

	* rainbow.c (rainbow_query): Print precision obeys new option.
	(rainbow_test): Likewise.
	(rainbow_test_files): Likewise.

	* naivebayes.c (naivebayes_binary_scoring): New option.
	(naivebayes_parse_opt): Support for new option.
	(bow_naivebayes_score): Support for new option.  If binary scoring,
	don't move scores out of log space or normalize them.  This
 	alleviates the 0-1 problem, at the cost of losing probabilities.

	* bow/libbow.h (bow_score): Changed weight from float to double.
	(bow_test_split2): Added prototype.

	* split.c (bow_ignore_split): New function.
	(bow_test_split2): Allows there to be too few documents to grab, and
	just grabs all of them if that's its only choice.  Takes an
 	optional random seed for seeding the random number generator.
	(bow_test_split_for_em_binary): New function.

	* em.c (use_priors_for_initial_class_probs): flipped value from 0
 	to 1
	(unlabeled_normalizer): moved from predefined value to an option
	(bow_em_num_em_runs): Likewise
	(bow_em_print_word_vector): Likewise
	(bow_em_making_barrel): if doing binary scoring, still use
	probabilities for rounds of EM
	(EM_LABELED_NUM_BY_CLASS): changed name from EM_UNLABELED_NUM_BY_CLASS
	(em_binary_pos_classname): added option for binary case
	(em_binary_neg_classname): added option for binary case
	(bow_em_unlabeled_num): added option for specifying number of
	unlabeled docs
	(bow_em_print_probs): added option to print word probabilities for
	kl-div across runs
	(bow_em_binary_case): added option for binary classification
	(bow_em_split_seed): added random seed option to facilitate paired
	trials
	(em_parse_opt): added support for new options
	(bow_em_new_vpc_with_weights): Added support for binary
	classification, although it's commented out now.  Makes only
 	initial labeled docs be all positive ones and sets priors of
 	unlabeled docs to be all negative.  Added support for seeding the
 	random number generator for labeled docs so we can have paired
 	trials.  Added support for specifying the number of unlabeled
 	docs.  This requires a new doc type, so conditions on doc types
 	have changed slightly.  If pruning vocab by info gain, we need to
 	do this after the labeled docs are selected instead of before the
 	barrel is built, so this logic is added in here.  Allow number of
 	labeled docs to be zero.  In this case, we need to be careful
 	about calculating priors with no docs, and also need to initialize
 	the class vectors randomly.  Added condition around printing class
 	probabilities with new option.  Only score docs for score to prob
 	mapping if its needed by the method.  Make naive bayes scoring
 	respect the unlabeled_normalizer.
	(bow_em_set_priors_using_class_probs): made condition changes for new
	doc type.
	(bow_em_score): Change the scoring if doing binary classification.
	Don't convert back from log space and don't normalize.  We lose
 	probabilities, but it avoids the 0-1 problem, and we can still
 	rank the predictions.

Tue Jan 13 14:41:55 1998  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_query): Print scores with precision %.20g
 	instead of default 6.
	(rainbow_test): Likewise.
	(main): When printing top words by infogain with -I, if
	--testing-files was on the command line, then do this test/train
 	split before calculating the infogains.

Thu Jan  8 12:56:22 1998  Andrew McCallum  <mccallum@jprc.com>

	* opts.c (bow_options): New command-line option
 	"replace-stoplist-file".
	(parse_bow_opt): Handle it.
	* stoplist.c (bow_stoplist_replace_with_file): New function.

Wed Jan  7 17:14:59 1998  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h (bow_doc_type): Added types UNUSED_MODEL and
 	UNUSED_IGNORE.

Tue Jan  6 16:39:30 1998  Andrew McCallum  <mccallum@jprc.com>

	* em.c (bow_em_new_vpc_with_weights): When printing P(C|w)
 	distributions, initialize TOTAL_WORD_COUNT inside the loop over
 	words!

	* int4word.c (bow_int2word): If INDEX is larger than the number of
 	words in the underlying word map, return NULL.

	* em.c (bow_em_new_vpc_with_weights): After the M-step, before the
 	E-step, print out the P(C|w) distribution for all words to a file
 	named pcw01, where "01" is the EM-iteration number.

	* int4word.c (bow_word2int_no_add): New function.
	* bow/libbow.h: Declare new function.

Sun Dec 21 20:36:08 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_options): Document --print-barrel's FORMAT
 	better.

	* Makefile.in (DIST_FILES): Added $(METHOD_C_FILES).

	* rainbow.c (rainbow_options): New command-line option
 	"index-printed-barrel".
	(rainbow_parse_opt): Handle it.  Add a term to the conditions under
	which we complain about "Need data from more than one class"
 	because when doing --index-printed-barrel the filename is in the
 	place of a classname, and there is supposed to be only one.
	(rainbow_index_printed_barrel): New function.
	(main): Handle two different ways of what_doing == rainbow_indexing.
	* barrel.c (getline): New function.
	(bow_barrel_new_from_printed_barrel_file): New function.
	* bow/libbow.h: Declare new function.

Wed Dec 17 14:47:40 1997  Andrew McCallum  <mccallum@jprc.com>

	* lex-simple.c (bow_not_isspace): New function.
	(_bow_white_lexer): Instead of insisting on starting with a alphabetic
	character, downcasing and stoplisting, etc, instead just grab
 	tokens delimited by whitespace, making no changes to the contents.
	* bow/libbow.h: Change comment on BOW_WHITE_LEXER.
	(bow_default_lexer_white): New declaration.
	* opts.c (bow_options): New command-line option "lex-white".
	(parse_bow_opt): Implement it.
	* deflexer.c: Add a lexer structure for BOW_DEFAULT_LEXER_WHITE.

	* int4str.c (_str2id): Re-written to make sure it never returns 0,
 	which would cause an infinite loop in _str_hash_add().

Tue Dec 16 12:24:49 1997  Andrew McCallum  <mccallum@jprc.com>

	* kl-div.c: New file.
	* Makefile.in (kl-div): New target.
	(OTHER_C_FILES): New variable, includes kl-div.
	(DIST_FILES): Add it.
	(libbow.a): Include the $(METHOD_O_FILES) in there too, so that simple
	executables like kl-div can properly get the default_lexer.
	(all): Added kl-div.
	(default): Target now just depends on `all'.

Mon Dec 15 14:35:16 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (rainbow_unarchive): Use filename_to_classname() when
 	initializing CLASSNAMES.

	* wicoo.c: New file.  Builds a structure for calculating 
	word co-occurrence statistics.
	* Makefile.in (LIBBOW_C_FILES): Added wicoo.c.

	* arrow.c: Include headers for socket server implementation.
	(arrow_options): New command-line option "query-server" and "print-coo"
	(struct arrow_arg_state): New element SERVER_PORT_NUM.
	(arrow_parse_opt): Implement new options.
	(arrow_query): Take new arguments for in and out FILE*'s.  Print
	filenames instead of file contents.
	(arrow_socket_init): New function.
	(arrow_serve): New function.
	(arrow_coo): New function.
	(main): Call new functions.

	* rainbow-h.c (rainbowh_options): New command-line option
 	"print-word-probabilities".
	(rainbowh_parse_opt): For 't', be smarter about warning when this badly
	interacts with --use-vocab-in-file.  Likewise for
 	`--use-vocab-in-file'.  Implement new option.
	(hier_barrel_class_index_of_classname): New function.
	(hier_barrel_prob_wi_uniform): New function.
	(hier_barrel_prob_wi_in_ci_local): Use it.
	(hier_barrel_prob_wi_in_ci_shrink): Likewise.
	(hier_barrel_prob_wi_local): Likewise.
	(hier_barrel_prob_wi_shrink): Likewise.
	(hier_barrel_print_word_probabilities_for_class): New function.
	(_hier_barrel_local_score): Avoid counting out-of-vocabulary words
	when calculating NUM_WORDS_IN_QUERY_WV.
	(hier_barrel_set_lambdas): New function
	(hier_barrel_test): Call it.
	(main): No longer avoid handling BOW_PRUNE_VOCAB_BY_OCCUR_COUNT_N.
	Handle new options.

	* kl.c (bow_kl_score): When setting QUERY_WORD_COUNT be sure to
 	only count the words that are part of the barrel's vocabulary.
  	Use QUERY_WORD_COUNT properly for leave-one-out evaluation instead
 	of only the number of times the word in question occurs.

	* naivebayes.c (bow_naivebayes_pr_wi_ci): New function.
	(bow_naivebayes_print_word_probabilities_for_class): New function.
	(bow_naivebayes_score): Get the total number of words in the query for
	doing proper leave-one-out evaluation.  Use
 	bow_naivebayes_pr_wi_ci() instead of calculating it locally.

	* dv.c (bow_dv_add_di_count_weight): Verbosify about count
 	overflow at level BOW_PROGRESS instead of BOW_VERBOSE.

	* split.c (BASENAME_ONLY): New macro.
	(bow_basename): New function.
	(bow_test_set_files): Use it for comparing basename of file only.
	Useful for comparisons of hier vs non-hier file lists.

	* wi2dvf.c (bow_wi2dvf_remove_wi): Call bow_error() because this
 	function is currently broken.
	(bow_wi2dvf_hide_words_by_doc_count): New function.
	(bow_wi2dvf_dv): Use ABS() when examining SEEK_START, to interact
	properly with word hiding when words haven't yet been read in.

	* vpc.c (bow_barrel_new_vpc): Assert DOC_BARREL->CLASSNAMES.

	* rainbow.c (*_KEY): Replace #define's with enum.
	(rainbow_options): New option "print-word-probabilities".
	"print-barrel" now takes an optional argument.
	(struct rainbow_arg_state): New element BARREL_PRINTING_FORMAT.
	(rainbow_parse_opt): Handle new options.
	(rainbow_unarchive): If RAINBOW_DOC_BARREL->CLASSNAMES is NULL, create
	it and fill it.  This is necessary when reading old barrels that
 	didn't archive CLASSNAMES.
	(rainbow_socket_init): Reformat.
	(rainbow_serve): Likewise.
	(rainbow_test_files): In nested function test_file(), make sure the
	file passes the bow_fp_is_text() test.  Otherwise we the counts
 	are off when doing leave-one-out-evaluation.
	(main): Move the barrel printing after the vocabulary reduction, and
	call with new argument.

	* bow/libbow.h: Declare new function.
	(assert): New commented out macro that is useful when the builtin
	assert() doesn't allow the debugger to examine the error-full
 	frame.

	* lex-html.c (bow_lexer_html_get_raw_word): Decrement
 	LEX->DOCUMENT_POSITION before returning when HTML `<' was
 	unterminated.  Otherwise we get errors when we catch the inifite
 	loop.

	* barrel.c (bow_barrel_prune_words_not_in_map): Hide words instead
 	of removing them.
	(bow_barrel_keep_top_words_by_infogain): Set BOW_WORD2INT_DO_NOT_ADD
	so that lexing doesn't add more words to the vocabulary.  This
 	fixes a bug in which new words in queries were causing the total
 	count of the number of words in a query document to be too high
 	during leave-one-out evaluation.
	(bow_barrel_printf_old1): Renamed from bow_barrel_printf.
	(bow_barrel_printf): New function that can print in different
	formats.

Tue Nov 25 11:10:12 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel): New element LAMBDA_G1PARENT.
	(hier_barrel_new): Initialize it to zero.
	(hier_barrel_add_stats): Initialize CDOC->CLASS_PROBS to NULL.
	(hier_barrel_add_document): Likewise.
	(hier_barrel_set_lambda_from_delta): Initialize LAMBDA_G1PARENT to 0.
	(HIER_BARREL_PARENT): New macro.
	(HIER_BARREL_G1PARENT): New macro.
	(hier_barrel_prob_wi_in_ci_shrink): Use LAMBDA_G1PARENT, get only
	local probs from each of them, and mix them.
	(hier_barrel_prob_wi_shrink): Likewise.
	(hier_barrel_calc_lambda_one_iteration): Use LAMBDA_G1PARENT.  Get
	only local probs from each of them, and mix them.
	(rainbowh_options): New option "print-barrel".
	(rainbowh_parse_opt): Handle it.
	(hier_barrel_print_barrel): New function.
	(main) Call it.

Mon Nov 24 16:36:55 1997  Andrew McCallum  <mccallum@jprc.com>

	* lex-simple.c (bow_lexer_simple_get_raw_word): Decrement
 	LEX->DOCUMENT_POSITION before assert().  Otherwise files that end
	without a newline seem to cause crashes.

	* rainbow.c (BASENAME): Removed macro.
	(rainbow_index): Use filename_to_classname() instead of BASENAME.

Mon Nov 24 12:57:52 1997  Kamal Nigam  <knigam@cs.cmu.edu>

	* em.c, bow/em.h: New files!
	* Makefile.in (LIBBOW_H_FILES): Added em.h.
	(METHOD_C_FILES): Added em.c.
	* vpc.c (bow_barrel_new_vpc): Initialize CLASS_PROBS to NULL.
	* split.c (bow_test_split2): New function.
	(bow_ignore_next_wv): New function.
	(bow_ignored_model_next_wv): New function.
	* rainbow.c (rainbow_class_barrel): Initialize to NULL.
	* bow/libbow.h: #include <bow/em.h>.  Declare new functions.
	(bow_cdoc): Add element CLASS_PROBS.
	* barrel.c (_bow_barrel_cdoc_free): Free CLASS_PROBS if non-NULL.
	(bow_barrel_add_from_text_dir): Initialize CLASS_PROBS to NULL.
	(_bow_barrel_cdoc_read): Likewise.

Mon Nov 24 08:45:29 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (*_KEY): Changed from #define's to enum.
	(struct rainbowh_arg_state): New member shinkage_method.
	(rainbowh_options): New option "shrinkage-method".
	(rainbowh_parse_opt): Implement it.
	(hier_barrel): New elements LAMBDA and LAMBDA_UNIFORM.
	(CI_IN_PARENT_ROOT): Macro deleted.
	(hier_barrel_new): Initialize LAMBDA and LAMBDA_UNIFORM.
	(hier_barrel_prune_words_not_in_map_and_set_vpc): Initialize
	DOC_BARREL->CLASSNAMES.
	(hier_barrel_set_local_class_model): Likewise.
	(hier_dir_is_leaf): New code, but commented out with AUTO_LEAF_DETECT.
	(_hier_barrel_new_from_text_dir_recurse): Rather than exiting with
	error if the directory was found to be empty of subdirectories,
 	instead call _hier_barrel_new_from_text_dir_leaf().  This means
 	that you don't have to create "rainbow-hier-leaf" files in the
 	directories at the leaf of the data directory.
	(hier_barrel_prob_wi_in_ci_wittenbell): Change LOO_CLASS from int to
	char*.
	(hier_barrel_prob_wi_in_ci): Likewise.
	(hier_barrel_score): Likewise.
	(hier_barrel_set_lambda_from_delta): New function.
	(hier_barrel_set_children_lambda_from_delta): New function.
	(hier_barrel_calc_delta): Once DELTA is determined, set LAMBDA's to
	match.
	(hier_barrel_calc_delta_recurse): Set LAMBDA of HBARREL root here.
	(last_pr_w_c): Global variable removed.
	(old_hier_barrel_prob_wi_in_ci_shrink): Renamed from
	hier_barrel_prob_wi_in_ci_shrink().
	(LOO_CLASS_IN_PARENT): Macro deleted.
	(LOO_CLASS_MATCH): New macro.
	(hier_barrel_prob_wi_in_ci_local): New function.
	(hier_barrel_prob_wi_in_ci_shrink): New function.
	(hier_barrel_prob_wi_local): New function.
	(hier_barrel_prob_wi_shrink): New function.
	(hier_barrel_calc_lambda_one_iteration): New function.
	(hier_barrel_calc_lambda): New function.
	(hier_barrel_calc_lambdas): New function.
	(check_prob_wi_in_ci): Don't immediately return; actually do the check.
	(_hier_barrel_local_score): Some minor clean-ups, and make it do KL
	instead of log-naivebayes, by dividing by document length.
	(_hier_barrel_set_node_scores): Change condition for doing local
	scoring so that if HIER_LEAF, we don't bother evaluating interior
 	nodes of the tree.  Remove some OVERRIDE_LOG_PROBS-commented-out
 	code.  Only call self recursively on HBARREL's with children.
	(hier_barrel_print_loo_accuracy): Don't evaluate from root of tree.
	Perhaps this should be changed back?
	(hier_barrel_print_loo_accuracy_vary_delta): Start at delta/1024
	instead of delta/1000.  Save the best delta, and set lambda from
 	it.
	(hier_barrel_test): Deal with NULL TEST_FILES_FILENAME.  Attend to
	SHRINKAGE_METHOD and do whichever was indicated on command-line.
	(rainbowh_archive): Write format version to file.
	(rainbowh_unarchive): Read it.
	(main): Initialize shrinkage method to em.  Don't
	check_prob_wi_in_ci() here because the LAMBDA's aren't ready.

Sun Nov 23 18:47:50 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow.c (BASENAME): New macro.
	(rainbow_index): Use it to initialize BARREL->CLASSNAMES with correct
	classnames!

	* rainbow.c (rainbow_test): Don't free the heap.  It was already
 	done automatically.
	(main): Likewise.

	* heap.c (bow_dv_heap_free): Add comment.

	* bow/libbow.h (ABS) New macro.

Mon Nov 17 10:09:20 1997  Andrew McCallum  <mccallum@jprc.com>

	* bow/libbow.h: Include <bow/knn.h>.
	(bow_barrel_add_classname): New macro.

	* Makefile.in (LIBBOW_C_FILES): Remove deflexer.c.
	(METHOD_C_FILES): Add deflexer.c, because it also has a constructor
	function that may not get linked in otherwise.

	* Makefile.local (rainbow-h): Add METHOD_O_FILES.

	* rainbow-h.c (hier_barrel_prune_words_not_in_map_and_set_vpc):
 	Free and reinitialize HBARREL->DOC_BARREL->CLASSNAMES, instead of
 	building a local array to be passed to the VPC function.
	(hier_barrel_set_local_class_model): Likewise.
	(hier_barrel_select_test): Function deleted.
	(hier_barrel_free): Don't free the hash; it's been deleted.
	(hier_barrel_set_vpc_with_weights): Comment out unused function.

	* rainbow-h.c: Remove old functions by Andrew Ng that are no
	longer used.
	(fix_up_node): Function deleted.
	(classify_from_rankings_helper: Likewise.
	(classify_from_rankings): Likewise.
	(hier_recursive_reping_document): Likewise.
	(new_bow_di_to_wv): Likewise.
	(hier_recursive_set_rankings): Likewise.
	(classify_single_doc): Likewise.
	(set_true_class): Likewise.
	(hier_recursive_reping_all_documents): Likewise.
	(new_hash_ele_t): Likewise.
	(free_hash_ele_t): Likewise.
	(hashit): Likewise.
	(create_hash): Likewise.
	(find_di_from_fn): Likewise.
	(find_child_di): Likewise.
	(find_di): Likewise.
	(free_hash): Likewise.
	(hier_barrel_single_pass_set_vpc_with_weights): Likewise.
	(classify_document): Likewise.
	(is_descendant_of): Likewise.
	(set_niece_pointer): Likewise.
	(fix_up_is_niece_field): Likewise.
	(fix_up_niece_pointers): Likewise.
	(init_ignore_structure): Likewise.
	(set_all_model): Likewise.

	* rainbow.c (rainbow_classnames): Deleted global variable.
	(rainbow_unarchive): Remove code for initializing RAINBOW_CLASSNAMES.
	(main): New local variable RAINBOW_CLASSNAMES.

	* vpc.c (bow_barrel_new_vpc): Drop CLASSNAMES and NUM_CLASSES
 	arguments.  Get that information from DOC_BARREL->CLASSNAMES
 	instead.
	(bow_barrel_new_vpc_merge_then_weight): Drop last two args.
	(bow_barrel_new_vpc_weight_then_merge): Likewise.
	* rainbow.c (rainbow_index): Drop last two arguments to vpc
 	function.
	(rainbow_query): Likewise.
	(rainbow_lisp_setup): Likewise.
	(rainbow_test): Likewise.
	(rainbow_test_files): Likewise.
	(main): Likewise.
	* rainbow-h.c (hier_barrel_set_vpc_with_weights): Drop last two
 	arguments to vpc function.
	(hier_barrel_set_local_class_model): Likewise.
	(hier_barrel_set_vpc_with_weights): Likewise.
	* knn.c (bow_knn_classification_barrel): Drop last two arguments.
	* bow/libbow.h (bow_method): VPC_WITH_WEIGHTS no longer takes
 	CLASSNAMES and NUM_CLASSES arguments.
	(bow_barrel_new_vpc_with_weights): Likewise.
	(bow_barrel_new_vpc): Likewise.
	(bow_barrel_new_vpc_merge_then_weight): Likewise.
	(bow_barrel_new_vpc_weight_then_merge): Likewise.

	* Makefile.in (clean): Remove PERL_RUNNABLE_FILES.

	The following changes mostly added with Sean Slattery.
	Add KNN method.  Add CLASSNAMES element to barrel structure, and
	use it to get classnames and the number of classes, rather than
	using the BARREL->CDOCS->LENGTH from the class barrel.

	* knn.c, bow/knn.h: New files that implement k-NN classification
	based on TFIDF weights and cosine-similarity.
	
	* bow/libbow.h (bow_barrel): Add new element CLASSNAMES.  It's a
 	str4int map between classnames and their indices.
	(bow_method): Add new element FREE_BARREL.  A function to call to free
	the barrel.
	(bow_free_barrel): New macro.
	(bow_barrel_num_classes): New macro.
	(bow_barrel_classname_at_index): New macro.
	(bow_barrel_add_from_text_dir): Declare type-change in last argument.
	(BOW_DEFAULT_FILE_FORMAT_VERSION): Bumped from 5 to 6.  Barrel's now
	write out their new CLASSNAMES map.
	* kl.c (bow_method_kl): Add new element bow_barrel_free().

	* Makefile.in (LIBBOW_C_FILES): Remove the .c files that implement
 	methods.
	(METHOD_C_FILES): Put them in this new variable.
	(METHOD_O_FILES): New variable.
	($(DEMO_EXECUTABLES)): Depend on METHOD_O_FILES and explicitly link
	them in.  Previously we just depending on linking them from the
 	library, but the executables didn't require any symbols from the
 	method files, so they would get linked in unless we added a kludgy
 	function call that required them.

	* barrel.c (bow_barrel_new): Initialize CLASSNAMES to NULL.
	(bow_barrel_add_document): Assert that CLASSNAMES is NULL, as a check
	to make sure that bow_barrel_add_from_text_dir wasn't used on the
 	barrel's in rainbow-h.
	(bow_barrel_add_from_text_dir): Change type of class argument: instead
	of specifying which class by integer index, specify by char*
 	classname.  Initialize the CLASSNAMES map if it hasn't been
 	already.
	(bow_barrel_new_from_data_fp): Read CLASSNAMES.
	(bow_barrel_write): Write CLASSNAMES.
	(bow_barrel_free): Free CLASSNAMES.

	* vpc.c (bow_barrel_new_vpc): Create and initialize CLASSNAMES new
 	element in VPC_BARREL.  Use BARREL_NUM_CLASSES to determine size
 	of VPC_BARREL, not the number of documents in the DOC_BARREL!

	* wi2dvf.c (bow_wi2dvf_new_from_data_fp): Add comment about this
 	not reading all the data.

	* prind.c (bow_method_prind): Add new element bow_barrel_free().
	* tfidf.c (bow_method_tfidf): Likewise.
	* naivebayes.c (bow_method_naivebayes): Likewise.

	* rainbow.c: Use bow_free_barrel() instead of bow_barrel_free().
  	Use bow_barrel_num_classes() instead of looking at the length of
 	cdocs.
	(rainbow_options): Say what the default is for "test-percentage".
	(rainbow_index): Use new last arg to bow_barrel_add_from_text_dir().
	(rainbow_test): Use bow_barrel_classname_at_index() instead of
	filename_to_classname().
	(main): Don't manually register methods kl and evi.  The proper .o's
	now get explicitly linked in by the Makefile.

	* robin.c (robin_index): Use new last argument for
 	bow_barrel_add_from_text_dir().

	* arrow.c (arrow_index): Use new last arg to
 	bow_barrel_add_from_text_dir().

	* rainbow-h.c: Use the macro bow_free_barrel() instead of
 	bow_barrel_free().
	(hier_barrel_print_loo_accuracy): New function.
	(hier_barrel_print_loo_accuracy_vary_delta): New function.
	(hier_barrel_print_loo_accuracy_vary_delta_recurse): New function.
	(hier_barrel_test): As a temporary test, instead of printing test
	results, just print varying delta LOO results and return.
	(rainbowh_hbarrel): Global variable moved up.
	(hier_barrel_new_from_text_dir): Use new last argument to
	bow_barrel_add_from_text_dir().
	(hier_barrel_prob_wi_in_ci_wittenbell): Add new arguments for LOO.
	(hier_barrel_prob_wi_in_ci_shrink): Likewise.  Use new arguments to
	implement LOO classification.
	(hier_barrel_prob_wi_in_ci): Add new arguments for LOO.
	(check_prob_wi_in_ci): Call above function with new arguments for LOO.
	(_hier_barrel_local_score): Likewise.
	(PRINT_TREE_SCORES):  Change macro value from 1 to 0.
	(_hier_barrel_set_node_scores): Add new argument for LOO.  Call
	bow_barrel_score() with LOO argument.
	(hier_barrel_print_scores): Call above function with new args for LOO.
	(hier_barrel_score): Likewise, and add new args for LOO.
	(hier_barrel_test): Call hier_barrel_score() with LOO argument.

Wed Nov  5 13:47:44 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (rainbowh_options): Rename "test-files" to
 	"testing-files" to avoid naming conflict.
	* rainbow.c (rainbow_options): Likewise.

Thu Oct 30 11:04:54 1997  Andrew McCallum  <mccallum@jprc.com>

	* rainbow-h.c (hier_barrel_test): Write the infogain-chosen
 	vocabulary in the local directory, named something like
 	"infogain2-hV00200" according to the the random seed and the
 	vocabulary size.

	* rainbow-h.c (hier_barrel_prob_wi_in_ci_shrink): Change the #elif
 	to do the "Witten-Bell"-like weighting between parent and child
 	instead of the "Method of Moments"-style weighting.
	(hier_barrel_test): Put two newlines at the beginning of the file so
	that even if we are lexing with --skip-headers, we'll still get
 	the words in the file.

Tue Oct 28 13:50:35 1997  Andrew McCallum  <mccallum@jprc.com>

	* arrow.c (arrow_query): Complain with message if the query vector
 	is emtpy.

	* barrel.c (bow_barrel_add_from_text_dir): Fill in the WORD_COUNT
 	entry in the created CDOC's.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Make it return the number
 	of words in the document, instead of void.
	* bow/libbow.h (bow_wi2dvf_add_di_text_fp): Now returns int
 	instead of void.

Thu Oct 16 09:58:14 1997  Andrew McCallum  <mccallum@jprc.com>

	Following changes actually made in September:

	* rainbow-h.c (USE_VOCAB_SIZE_KEY): New macro.
	(TEST_FILES_KEY): Likewise.
	(rainbowh_options): New options "use-vocab-size" and "test-files".
	(struct rainbowh_arg_state): New members VOCAB_SIZE and
	TEST_FILES_FILENAME.
	(rainbowh_parse_opt): Handle new options.
	(hier_barrel): New member DELTA.
	(hier_barrel_prune_words_not_in_map_and_set_vpc): New function.
	(hier_barrel_set_local_class_model): Uncomment code to free the class
	barrel before re-creating it.
	(rainbowh_total_unique_words): New global variable.
	(hier_barrel_prob_wi_in_ci_wittenbell): New function.
	(hier_barrel_calc_delta): New function.
	(hier_barrel_calc_delta_recurse): New function.
	(hier_barrel_prob_wi_in_ci_shrink): New function taken from
	hier_barrel_prob_wi_in_ci().  Implement Wasserman's "Method of
 	Moments".
	(hier_barrel_prob_wi_in_ci): New function that calls one of above two.
	(_hier_barrel_local_score): Find the root and total number of words.
	Initialize SCORES[] to log of prior class prob.  Handle case where
 	there is not training data for a class.  If DV is NULL, deal with
 	skipping the word sometimes, but not always, depending on the
 	right case.  When incrementing score for each word, deal with
 	classes that have no training data.  Remove code for
 	!OVERRIDE_LOG_PROBS.  When putting scores into return array, deal
 	with classes that have no training data.
	(_hier_barrel_set_node_scores): Set the local score or not depending
	on HIER_LEAF mode.
	(hier_barrel_print_infogain): Function moved up in file.  New first
	argument FILE*.
	(hier_barrel_test): Deal with TEST_FILES_FILENAME and VOCAB_MAP, etc.
	(main): Initialize VOCAB_SIZE to zero.  Register the KL method.  Call
	hier_barrel_print_infogain() with new argument.  Remove
 	"compile-command" local emacs variable.

	* vpc.c (bow_barrel_new_vpc): Deal with situations where there is
 	no training data for a class.  Instead of asserting MAX_CI > 0,
 	print a warning instead.  Loop over NUM_CLASSES instead of relying
 	on MAX_CI.  Allow the class prior prob to be equal to 0.0 or 1.0.

	* split.c (bow_test_set_files): New function.

	* opts.c (bow_options): Rearrange some options.

	* kl.c (bow_kl_score): When setting class prior prob, handle case
 	in which there was no training data for this class.  Also handle
 	this case when adding contribution of a WI for each class, and
 	when doing WITTEN_BELL, and when normalizing score.

	* int4str.c (bow_int4str_new_from_string_file): New function.

	* bow/libbow.h: Declare new functions.

	* Makefile.local (rainbow-h): Use $(CC) instead of gcc.

	* rainbow.c (TEST_FILES_KEY): New macro.
	(PRINT_DOC_NAMES_KEY): Likewise.
	(rainbow_options): New options "test-files" and "print-doc-names".
	(rainbow_parse_opt): Handle them.
	(filename_to_classname): Comment out early return of filename.  That
	is, revert to old behavior.
	(rainbow_test): If TEST_FILES_FILENAME is non-NULL use it instead of
	randomly setting which documents are for training and which are
 	for testing.
	(main): Initialize TEST_FILES_FILENAME to NULL.  Handle
	RAINBOW_DOC_NAME_PRINTING.

Thu Sep 25 17:35:01 1997  Andrew McCallum  <mccallum@@jprc.com>

	This version given to Rob Shapire and others at AT&T Research.

	* Makefile.in (LIBBOW_H_FILES): Added bow/kl.h.

Wed Sep 17 14:51:33 1997  Karl Kleinpaste  <karl@@jprc.com>

	* rainbow-h.c (top): Add socket #includes.
	(rainbowh_options): Add --query-server and -n options.  Also,
 	remove #define of PRINT_TREE_SCORES, in favor of runtime -n.
  	(rainbowh_arg_state): Add rainbowh_query_serving to what_doing,
 	plus server_port_num, for --query-server, and print_tree_scores,
	for -n.
  	(rainbowh_parse_opt): Add --query-server and -n detection.
  	(_hier_barrel_set_node_scores): Properly conditionalize tree score
 	printing.
	(hier_barrel_print_scores_recurse): Add FILE *out.
  	(hier_barrel_print_scores): Add FILE *out.
	(rainbowh_query): New routine, stripped from the mainline `if'.
  	(rainbowh_socket_init): Add for --query-server capability.
  	(rainbowh_serve): Add for --query-server capability.
	(main): Init print_tree_scores; init lexer end pattern; insert
 	conditional call to service --query-server; slice out mainline for
 	rainbowh_query().

Wed Sep 17 14:22:18 1997  Andrew McCallum  <mccallum@@jprc.com>

	* split.c (bow_test_split): Remove the assertion that we use at
 	least 90% of the documents as training data.

Tue Sep  9 10:55:31 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Change default method from prind to naivebayes.
	(_hier_barrel_cdoc_write): Handle bow_file_format_version 5.
	(_hier_barrel_cdoc_read): Likewise.
	(hier_barrel_set_local_class_model): Call vpc function with new
	argument.
	(hier_barrel_set_vpc_with_weights): Likewise.
	(hier_barrel_add_document): Set HBARREL->DOC_BARREL->METHOD to
	HIER_DEFAULT_METHOD.
	(hier_barrel_set_vpc_and_populate_lower_branches): Only recursively
	set vpc in children branches if there are documents there.
	(hier_barrel_prob_wi_in_ci): Assert that the CDOC->NORMALIZER has been
	set.  Set M_EST_M according to CDOC->NORMALIZER, which is number
 	of unique words.
	(_hier_barrel_local_score): Clean up a little.
	(main): Call hier_set_method() if BOW_ARGP_METHOD.

Sat Aug 30 19:03:17 1997  Andrew McCallum  <mccallum@@jprc.com>

	* kl.c (bow_kl_score): Initialize scores to class prior divided by
 	query document length, not just class prior.  This way our
 	classifications match Naive Bayes, as they should.

Fri Aug 29 09:12:05 1997  Andrew McCallum  <mccallum@@jprc.com>

	* barrel.c (bow_barrel_add_from_text_dir): Add newline before
 	warning about a file being skipped because it is not text.

	Before the following change we were overflowing DV->ENTRY[i].DI in
 	document barrel's when there were more than 32767 documents.
  	Karl's Yahoo experiments were trying to build models with about
 	60000 documents.  We would get an error in vpc.c at the assertion
 	that "ci < num_classes".
	* dv.c (bow_dv_add_di_count_weight): Warn if we overflow int,
 	not short.
	(bow_dv_write_size): Adjust for change of COUNT and DI from
	short to int.
	(bow_dv_write): Likewise.
	(bow_dv_new_from_data_fp): Likewise.
	* bow/libbow.h (bow_cdoc): Change member CLASS from short to int.
	(bow_de): Change members DI and COUNT from short to int.
	* barrel.c (_bow_barrel_cdoc_write): If BOW_FILE_FORMAT_VERSION is
 	5 or greater, change CDOC->CLASS from short to int.
	(_bow_barrel_cdoc_read): Likewise.
	* bow/libbow.h (BOW_DEFAULT_FILE_FORMAT_VERSION): Changed from 4 to 5.
	* io.c: Add comment about bow_file_format_version history.

Thu Aug 28 22:36:55 1997  Andrew McCallum  <mccallum@@jprc.com>

	* kl.c (bow_kl_score): Add class prior probabilities.

	* lex-simple.c (bow_lexer_simple_get_raw_word): When we find the
 	NULL at the end of the document, and before we find the beginning
 	of a word, back up DOCUMENT_POSITION (even though will return 0
 	this time already).  Add some assertions about DOCUMENT_POSITION.

	* lex-html.c (bow_lexer_html_get_raw_word): When we find the NULL
 	at the end of the document, back up DOCUMENT_POSITION so we will
 	return 0 next time we are called.  Add some assertions about
 	DOCUMENT_LENGTH.

Wed Aug 27 11:23:34 1997  Andrew McCallum  <mccallum@@jprc.com>

	* bow/libbow.h: Include <unistd.h>.

	* rainbow.c (rainbow_parse_opt): Fix typo.

	* rainbow.c (rainbow_parse_opt) [SERVER_KEY]: Set
 	DOCUMENT_END_PATTERN to a single dot on a line.
	(main): Don't set DOCUMENT_END_PATTERN here for server mode.

	* lex-simple.c (bow_lexer_simple_open_text_fp): Explicitly seek
 	the PRE_PIPE_FP to the end of the file!  Otherwise, we can
 	sometimes read the same file over and over again in the many
 	`while(open_text_fp())' loops throughout the library.

	* rainbow.c (rainbow_print_weight_vector): Change the test for
 	deciding when we need to multiply by CDOC->NORMALIZER before
 	printing the weight. Instead of looking specifically for
 	"naivebayes", look for a METHOD->NORMALIZE_WEIGHTS function
 	pointer that is NULL.  Now this works properly for the "kl" method
 	too.

	* kl.c (bow_kl_set_weights): Calculate the total number of
 	occurrences of each word; store this in DV->IDF.  The the DV
 	weights to the weighted log odds ratio P(w|C)*log(P(w|C)/P(w|~C)).

	* rainbow.c (rainbow_lisp_setup): Update for new default
 	arguments.
	(rainbow_lisp_query): Add LOO_CV argument to bow_barrel_score().

	* kl.c (bow_kl_score): Move declaration of SCORES_SUM.

Tue Aug 26 11:12:00 1997  Andrew McCallum  <mccallum@@jprc.com>

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Add assertion
 	about the PRIOR.

Mon Aug 25 14:03:58 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-ac.pl: As a diagnostic, print the number of predictions
 	found in the file.

	* naivebayes.c (bow_naivebayes_set_weights): Set CDOC->NORMALIZER
 	to the number of unique terms in each class.  (This is now used by
 	rainbow-h.)

	* kl.c (bow_kl_set_weights): Add assertion about CDOC->NORMALIZER.

	* foilgain.c (bow_foilgain_ci_per_wi_new): New function.

	* bow/libbow.h (bow_default_method_name): New macro.
	* barrel.c (bow_barrel_new): Use new macro
 	`bow_default_method_name' instead of "naivebayes".

Tue Aug 19 09:50:16 1997  Andrew McCallum  <mccallum@@jprc.com>

	* int4word.c (bow_words_set_map): Be sure to initialize the
 	map/counts if they haven't been initialized yet.  Otherwise,
 	WORD_MAP_COUNTS will point nowhere an we can tromp on memory.  I
 	was getting malloc() errors before this was fixed.
	(bow_words_keep_top_by_infogain): Change so that word indices are
	ordered by information gain, even when NUM_WORDS_TO_KEEP is less
 	than the number of words returned by bow_infogain_per_wi_new().

	* wi2dvf.c (bow_wi2dvf_entry_at_wi_di): New function.
	* dv.c (bow_dv_entry_at_di): New function.
	* bow/libbow.h: Declare new functions.

	* barrel.c (bow_barrel_add_from_text_dir): Add verbosity when a
 	file is skipped because istext() fails.
	(bow_new_slow_barrel_printf): New function.

	* vpc.c (bow_barrel_new_vpc): New argument, NUM_CLASSES.  Use it
 	to initialize an array that is filled with counts of the number of
 	documents per class.  Initialize CDOC->NUM_WORDS to be the number
 	of documents per class.  This can then be used in "event=document"
 	models.
	(bow_barrel_new_vpc_merge_then_weight): New argument, NUM_CLASSES.
	(bow_barrel_new_vpc_weight_then_merge): Likewise.

	* rainbow.c (rainbow_index): Use macro
 	bow_barrel_new_vpc_with_weights(), with new `num_classes'
 	argument.
	(rainbow_query): Likewise.
	(rainbow_test): Likewise.
	(main): Likewise.
	(rainbow_test_files): Likewise.  If QUERY_WV is NULL, verbosify a
	warning.

	* bow/libbow.h (bow_method): Add NUM_CLASSES argument to
 	VPC_WITH_WEIGHTS.
	(bow_barrel_new_vpc_with_weights): Add NUM_CLASSES argument.
	(bow_barrel_new_vpc): Likewise.
	(bow_barrel_new_vpc_merge_then_weight): Likewise.
	(bow_barrel_new_vpc_weight_then_merge): Likewise.

	* bow/naivebayes.h (bow_params_naivebayes): Remove
 	SCORE_WITH_LOG_PROBABILITIES.

	* kl.c (bow_kl_score): Reformat error message.

	* naivebayes.c (bow_naivebayes_set_weights): Only set
 	CDOC->WORD_COUNT if not doing BOW_BINARY_WORD_COUNTS, otherwise
 	leave them as the "document counts" as they were initialized in
 	vpc.c.

Thu Aug 14 11:46:46 1997  Andrew McCallum  <mccallum@@jprc.com>

	* naivebayes.c: Remove all references and code for
 	SCORE_WITH_LOG_PROBABILITIES.  Use KL method instead.
	(bow_method_crossentropy): Removed, and all related structures and
	functions.
	* opts.c (bow_options): Remove "naivebayes-score-with-log-probs"
 	option.
	(parse_bow_opt): Don't handle it anymore.

	* naivebayes.c: Add a naivebayes-specific command-line option by
 	using "argp child".
	(naivebayes_argp_m_est_m): New static variable.
	(naivebayes_options): New argp structure.  New command-line option
	"naivebayes-m-est-m".
	(naivebayes_parse_opt): New function.
	(naivebayes_argp: New structure.
	(naivebayes_argp_child): New structure.
	(_register_method_naivebayes): Add the argp child.
	(bow_naivebayes_score): Comment out assertion that (loo_class == -1)
	because it trips up rainbow-h.

	These changes were made a while ago.
	* rainbow-h.c (hier_recursive_set_rankings): Pass new LOO argument
 	to bow_barrel_score.
	(classify_single_doc): Likewise.
	(hier_barrel_set_vpc_and_populate_lower_branches): Likewise.
	(hier_barrel_prob_wi_in_ci): Add two new pass-by-ref arguments that
	return certain counts.  Pass new arguments.
	(check_prob_wi_in_ci): Pass new arguments.
	(_hier_barrel_local_score): Call above function with new arguments,
	and print them out.
	(main): Switch back to using POPULATE_BY_SCORING and HIER_NIECE
	options by default.

Wed Aug 13 16:44:07 1997  Andrew McCallum  <mccallum@@jprc.com>

	* lex-simple.c (bow_lexer_simple_open_text_fp): Print error
 	message if popen() call failed.

	* opts.c (bow_argp_add_child): Change asssertion.  Add call to
 	memset(), which should be unnecessary.

	Before this code was added, some inlinks WebKB files were being
	declared as "nontext" and skipped because many lines had the same
	length.
	
	* istext.c (bow_fp_is_text): Pay attention to
 	BOW_ISTEXT_AVOID_UUENCODE.
	* opts.c (bow_istext_avoid_uuencode): Declare new global variable.
	(bow_options): New option "istext-avoid-uuencode".
	(parse_bow_opt): Handle it.
	* bow/libbow.h (bow_istext_avoid_uuencode): New global variable
 	set by command-line option.
	(bow_lex_pipe_command): Make it extern!

	* kl.c (bow_kl_score): Give more detailed error message for LOO
 	negative probabilities.

	Before this code was added, some WebKB files were being skipped
	because the non-MIME-header part was already buffered in STDIO.

	* lex-simple.c (bow_lexer_simple_open_text_fp): When using
 	BOW_LEX_PIPE_COMMAND, make sure that the file descriptor file
 	position matches the stdio FP position, otherwise we can get a
 	premature EOF because the stdio has already read much of the file
 	for buffering.

Mon Aug 11 11:51:11 1997  Andrew McCallum  <mccallum@@jprc.com>

	* info_gain.c (bow_infogain_per_wi_print): If NUM_TO_PRINT is 0,
 	then print infogain of all words, not zero words.

	* bow/libbow.h (bow_model_next_wv): Declare new split function.

Mon Jul 14 11:09:04 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-stats.pl (overall_accuracy): Shorten the label before
 	the numbers.

	* istext.c (bow_fp_is_text): Initialize
 	MAX_LINE_LENGTH_HISTOGRAM_LENGTH to avoid warning.

	* istext.c (bow_fp_is_text): Re-enable the uuencode-block
 	detection.  Now, in order to reject the file, insist that the
 	length of the lines with the most common length be greater than
 	or equal to 50.  Hopefully this will not falsely reject HTML files
	as it did before.

Tue Jul  1 08:39:25 1997  Andrew McCallum  <mccallum@@jprc.com>

	* kl.c (bow_kl_score): Remove assertion that SCORE_INCREMENT be
 	non-zero.  It can be zero when PR_W_C == PR_W_D, then
 	LOG(PR_W_C/PR_W_D) will be zero, and SCORE_INCREMENT will be zero.

Mon Jun 30 17:41:06 1997  Karl Kleinpaste  <karl@@jprc.com>

	* rainbow.c (rainbow_serve): Added.
	(rainbow_socket_init): Added.
  	(rainbow_parse_opt): Added SERVER_KEY case.
	(rainbow_query): Modified FILE * handling for use of other than
	stdin/stdout.
  	(main): Added query-server handling.

Sat Jun 28 12:22:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_test_files): Temporarilty comment out code
 	that removes some of the training documents from training until we
 	add a scheme that really makes the default test percentage 0.
	(main): Put the call of rainbow_test_files after doing things
	necessary to update the class/word weights for the command-line
 	options.  Temporarily, ALWAYS rebuild the VPC model, even if non
 	of the parameters change because the weights read from disk were
 	bad; find out why eventually!

	* prind.c (bow_prind_score): When BOW_PRINT_WORD_SCORES, also
 	print PR_W_C.

	* prind.c (bow_prind_score): When all pre-normalized scores are
 	zero, set normalized scores to -1.0/#classes, don't leave them as
 	zero.  [Perhaps we should set the scores to the class priors?
  	Althought this does not fall our of the PrInd derivation.]

	* kl.c (bow_kl_score): When all pre-normalized scores are zero,
 	set normalized scores to -1.0/#classes, not -9999.

	* arrow.c (arrow_query): Pass LOO_CV argument to score.

Thu Jun 26 14:48:28 1997  Andrew McCallum  <mccallum@@jprc.com>

	* lex-simple.c (bow_lexer_simple_open_text_fp): Attend to
 	BOW_LEX_PIPE_COMMAND and implement it.
	* opts.c (bow_lex_pipe_command): New global variable.
	(bow_options): New command-line option "lex-pipe-command".
	(parse_bow_opt): Handle it.
	* bow/libbow.h: Declare new global variable.

	* istext.c (bow_fp_is_text): Move local variables to avoid GCC
 	warning.

	--test-files-loo should now work.
	* prind.c: Convert scoring function to take LOO_CLASS arguement.
	* kl.c: Likewise.
	* naivebayes.c: Likewise.
	* tfidf.c: Likewise.
	* evi.c: Likewise.
	* rainbow.c: Call scoring function with LOO_CLASS argument.

	* bow/libbow.h (bow_barrel_score): Add extra LOO_CLASS argument.
	(bow_method): Likewise to (*score) member.

	* rainbow-ac.pl: Make sure last confidence number gets printed
 	properly.  Before it was always just zero.

	* rainbow.c (rainbow_options): Added "test-files-loo" for
 	Leave-One-Out testing.  Not implemented yet, however.
	(struct rainbow_arg_state): New member LOO_CV.
	(rainbow_query): Do proper checks before using lisp score truncation.
	(rainbow_test): Likewise.  Also, add (commented out) code to print
	more stats.
	(main): Call _register_method_evi() to make sure it gets linked in.

	* Makefile.in (LIBBOW_C_FILES): Added evi.c.
	* evi.c: New file.

	* naivebayes.c (bow_naivebayes_set_weights): Add checks that make
 	sure that Sum_w Pr(w|c) is 1 for all classes.

	* kl.c (bow_kl_score_loo): Implement normalized KL scores, with
 	Witten-Bell discounting.  (NOTE: NaiveBayes does not yet have
	Witten-Bell implemeted.  Thus the accuracy of Witten-Bell can be
	easily compared with Laplace by comparing "kl" with "naivebayes".)

	* rainbow-stats.pl (confusion): Initialize $MAX_CLASSNAME_LENGTH
 	to the length of "classname", so that we still get proper
 	formatting with very short classnames.

	* istext.c (bow_fp_is_text): Temporarily comment out the code that
 	tries to avoid files with uuencoded blocks, because the current
 	scheme also seems to avoid many HTML files.  (Reported by Sean
 	Slattery.)  Warning, trying to index the 20_newsgroups data in
 	this state will give bad results.

Mon Jun 23 11:59:50 1997  Andrew McCallum  <mccallum@@jprc.com>

	* prind.c (bow_prind_score): Comment fixes.  Describe the
 	smoothing situation accurately.

	* int4word.c (bow_words_keep_top_by_infogain): Don't try to "keep"
 	more words than are available in the BARREL!  (Bug reported by
 	Daniel A Dipasquo <greenface+@@CMU.EDU>.)  If NUM_WORDS_TO_KEEP is
 	greater than or equal to the number of words in the BARREL, put
 	all these words in the new vocabulary.

Wed Jun 11 16:40:14 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_test): Don't do CommonLisp score truncation
 	if the score is negative.  (This change should be made to other
 	score-printing functions too.)
	(main): Gratuitously call _register_method_kl(), so that kl.c gets
	linked in with the rainbow executable.

	* kl.c (_register_method_kl): Make sure we can't register the
 	method twice, even if this function is called twice.

	* naivebayes.c (bow_naivebayes_score_loo): When using uniform
 	class priors, set SCORES[CI] based on log of uniform distribution
 	of classes, not to 1.  When setting log_pr_tf, instead of using
 	pow() before taking the log(), just multiply after using log().

	* Makefile.in (LIBBOW_C_FILES): Added kl.c.

Fri Jun  6 09:48:06 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (NO_LISP_SCORE_TRUNCATION_KEY): New macro.
	(rainbow_options): New option "no-lisp-score-truncation".
	(rainbow_parse_opt): Handle it.
	(struct rainbow_arg_state): New member USE_LISP_SCORE_TRUNCATION.
	(rainbow_query): Obey it.
	(rainbow_test): Likewise.
	(main): Make its default value 1.

Tue Jun  3 10:31:10 1997  Andrew McCallum  <mccallum@@jprc.com>

	* readme.texi: Use BOWVERSION, not BOW_VERSION to match
 	version.texi.

Thu May 29 15:25:06 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Version (BOW_MINOR_VERSION): Version 0.8.
	* bow/libbow.h (BOW_MINOR_VERSION): Version 0.8.

	* docnames.c (bow_map_filenames_from_dir): Remove local variables
 	no longer used.

Mon May 26 12:59:50 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (main): New commented-out code for computing the
 	number of word co-occurrences.

Fri May 23 11:34:05 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (USE_VOCAB_IN_FILE_KEY): New macro.
	(rainbow_options): New option "use-vocab-in-file".
	(rainbow_parse_opt): Handle it.
	(struct rainbow_arg_state): New member VOCAB_MAP.
	(rainbow_query): Use it to remove words from the vocabulary.
	(rainbow_test): Likewise.
	(main): Likewise.

	* rainbow-stats.pl (prune_from_classname): New global variable.  A
 	regular expression to be removed from the end of classnames before
 	gathering stats on them.  This allows us to gather stats on
 	performance in the middle of class hierarchies.
	(read_trial): Use it.

	* int4str.c (bow_int4str_new_from_text_file): Return MAP instead
 	of NULL!

	* barrel.c (bow_barrel_prune_words_not_in_map): Define MAX_WI and
 	use it, so we don't ask for word indices larger than
 	bow_num_words().
	(bow_barrel_print_word_count): Also print word probability according
	to counts.

	* rainbow-h.c (main) [printing_word_counts]: Print word that is
 	being counted.

Wed May 21 15:01:51 1997  Andrew McCallum  <mccallum@@jprc.com>

	* barrel.c (bow_barrel_prune_words_not_in_map): Remove the words
 	instead of hiding them, so that future
 	bow_keep_top_words_by_infogain() calls won't unhide them.

	This version got 46% on hier/yahoo-science (dataset with a 10
	document-per-class threshold).

	* rainbow-h.c (rainbowh_options): Added --use-vocab-in-file
 	command-line option.
	(rainbowh_arg_state): Added PARENT and CI_IN_PARENT.  Added HIER_LEAF.
	Removed printing of leaf- and intermediate-results.
	(hier_barrel_prob_wi_in_ci): New function.
	(check_prob_wi_in_ci): New function.
	(_hier_barrel_local_score): New function.
	(_hier_barrel_set_node_scores): Use it.
	(hier_barrel_print_infogain): Print FULL_NAME with interspersed
	spaces, so it won't get lexed by bow_int4str_new_from_text_file().
	(main): Change defaults.  Before populate_by_scoring=1 and
	hier_structure=hier_niece.  Populate branches first thing, and
 	check prob_wi_ci consistency.

	* naivebayes.c (bow_naivebayes_score_loo): Comment change.

	* int4str.c (bow_int4str_new_from_text_file): New function.

	* bow/libbow.h: Declare new functions.

Tue May 20 16:02:24 1997  Andrew McCallum  <mccallum@@jprc.com>

	* barrel.c (bow_barrel_prune_words_not_in_map): New function.

Mon May 19 09:52:09 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-stats.pl (confusion): Calculate longest classname and
 	use it to fix indentation.

	* wi2dvf.c (bow_wi2dvf_add_di_wv): Set SEEK_START to special flag
 	2.
	(bow_wi2dvf_add_wi_di_count_weight): Likewise.
	(bow_wi2dvf_hide_wi): Decrement WI2DVF->NUM_WORDS in the right place.
	(bow_wi2dvf_unhide_all_wi): Increment WI2DVF->NUM_WORDS.
	(bow_wi2dvf_write): Unhide all words first.
	(bow_wi2dvf_dv): Change assertion to deal with special flag 2.

	* rainbow.c (main): Pass new argument to
 	bow_infogain_per_wi_print().

	* rainbow-h.c: Misc changes.  Print infogain during run.
	(hier_barrel_set_local_class_model): Add IS_ROOT argument.  Unhide
	vocabulary after pruning by infogain, so lower levels get all
 	words.

	* naivebayes.c (M_EST_M): New macro.
	(M_EST_P): New macro.
	(bow_naivebayes_score_loo): Use them to implement M-estimates, instead
	of old Laplace smoothing.

	* info_gain.c (bow_infogain_per_wi_print): Add FP argument.
	* bow/libbow.h: Add argument to infogain function.

	* barrel.c: Fix the math for assigning CDOC->PRIOR, and add
 	assertion checks.

Fri May 16 10:19:19 1997  Andrew McCallum  <mccallum@@jprc.com>

	This was state of code on Thursday night.

	* rainbow-h.c: Add options for changing population scheme and tree
 	structure.  Add ability to output intermediate and leaf results.

	* naivebayes.c (WORD_PRIOR_COUNT): New macro.  Current value 1.0.
	(bow_naivebayes_score_loo): Use it.

Thu May 15 16:22:27 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_test): Assert that the ACTUAL_NUM_HITS
 	returned by bow_barrel_score() is the same as the
 	NUM_HITS_TO_RETRIEVE requested.

	* split.c (bow_test_split): Use rand() properly so that the number
 	of test documents in each class are not so biased.  Add special
 	code that *ensures* that the test documents are evenly distributed
 	across classes.

	* rainbow.c (rainbow_print_weight_vector): Don't use
 	CDOC->NORMALIZER if the method is "naivebayes", because NaiveBayes
 	doesn't use it.  Previously the printed values were bogus.

Wed May 14 11:02:44 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: -q RAINBOWH_QUERYING now seems to work.

	* naivebayes.c (bow_naivebayes_score_loo): Add assertion that
 	CDOC->PRIOR is greater than zero.  This restriction should be
 	relaxed!

	* array.c (bow_array_free): Decrement length after testing for
 	non-zero-ness, not before.  Without this change, empty arrays
 	would call free() on un-malloc'ed() memory.

Tue May 13 18:16:31 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Add code for doing selective population of lower
 	branches.  This population seems to be working.  Querying/scoring
 	does not yet work.

	* wi2dvf.c (bow_wi2dvf_hide_wi): Change assertion to "if" so that
 	we won't crash if we try to hide words that are already hidden.

	* split.c (bow_tmp_word_struct2): New type.
	(bow_model_next_wv): New function.
	(bow_nontest_next_wv): New function.

	* rainbow.c (rainbow_options): Fix documentation for test-files.
	(rainbow_test): Choose vocabulary by info gain *after* the test/train
	split.  Add temporary code to test bow_naivebayes_score_loo().
  	Remove this later!

	* naivebayes.c (bow_naivebayes_score_loo): New function, copy of
 	bow_naivebayes_score_loo, with extra code to do leave-one-out
 	testing if argument LOO is non-negative.
	(bow_naivebayes_score): Call above function with -1 for LOO.
	(bow_method_naivebayes): Change NORMALIZE_WEIGHTS from
	bow_barrel_normalize_weights_by_summing() to NULL.  The
 	normalizing function was not taking account of the Laplace
 	smoothing numbers, and was giving incorrect weights.
	(bow_method_crossentropy): Likewise.

	* istext.c (bow_fp_is_text): Increase NUM_LINE_LENGTHS to
 	NUM_TEST_CHARS to avoid potential crash.

	* docnames.c (bow_map_filenames_from_dir): For directory names and
 	filenames, make it use names of soft links, not the directories
 	that the links point to.

	* barrel.c (bow_barrel_add_document): New function.
	* bow/libbow.h: Declare new function.

	* docnames.c (bow_map_filenames_from_dir): Change commented-out
 	code so that, if uncommented, this function will work if you pass
 	it a filename instead of a directory name.

Tue May  6 15:30:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.local (rainbow-h): Make it depend on libbow.a.

	* rainbow-h.c: May 5 changes from Andrew Ng.
	(rainbowh_unarchive): Switch order of unarchiving for vocabulary
	and hier_barrel.
	(hier_barrel_new_from_file): Use bow_barrel_new_from_data_file()
	instead of bow_barrel_new_from_fp(), so we close FILE*'s instead
	of keeping them open.  Otherwise we run out of UNIX's available
	open file descriptor's.

	* wi2dvf.c (FREE_WHEN_HIDING_WI): New macro.
	(bow_wi2dvf_hide_wi): Heed it.
	(bow_wi2dvf_dv): Don't check to make sure that WI is less than
	bow_num_words().  Check SEEK_START before returning a non-NULL DV,
 	because if SEEK_START is less than -1, the DV should be considered
 	`hidden'.

	* opts.c (bow_exclude_filename): New global variable.
	(bow_options): New option "exclude-filename".
	(parse_bow_opt): Handle it.

	* docnames.c (bow_map_filenames_from_dir): Make sure
 	BOW_EXCLUDE_FILENAME is non-NULL before passing it to strcmp().

	* bow/libbow.h (bow_exclude_filename): Declare new global
 	variable.

	* barrel.c (bow_barrel_set_cdoc_priors_to_class_uniform): Use
 	bow_malloc() instead of alloca(), so that bow_realloc() will work.
  	free() it at the end.
	(bow_barrel_new_from_data_file): New function.

Mon May  5 21:08:34 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Changes by Andrew Ng, before Andrew McCallum's
 	changes to close barrel FP's.

Fri May  2 09:53:12 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Additions by Andrew Ng to implement cousin scheme.

Wed Apr 30 10:48:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in: Include Makefile.local, avoiding error if it isn't
 	present.

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Unhide and
 	hide the DVF's instead of removing them, so that we can call this
 	function mulitple times with increasing NUM_WORDS_TO_KEEP.

	* wi2dvf.c (bow_wi2dvf_hide_wi): New function.
	(bow_wi2dvf_unhide_all_wi): New function.
	(bow_wi2dvf_dv): Handle new negative values of SEEK_START set by
	BOW_WI2DVF_HIDE_WI().
	* bow/libbow.h: Declare new functions.
	(bow_doc_type): Add ignored_model, for rainbow-h.c.

Thu Apr 24 09:03:10 1997  Andrew McCallum  <mccallum@@jprc.com>

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Fix crash that
 	occurs if limited vocabulary causes all files in a class to be
 	empty.

	* stoplist.c (bow_stoplist_add_word): New function.

	* rainbow-stats.pl (confusion): Print percentage correct for each
 	category.

	* istext.c (bow_fp_is_text): Also return 0 for files that have
 	more than 30% of their lines of the same length.  This way we
 	avoid files containing uuencoded blocks.

	* bow/libbow.h: Declare new function.

Tue Apr 22 11:19:03 1997  Andrew McCallum  <mccallum@@jprc.com>

	* deflexer.c (bow_default_lexer): Add cast to initialization to
 	avoid warning.

	Add a uniform, global way of keeping track of binary file format
	versions.
	* io.c (bow_file_format_version): New global variable.
	(bow_write_format_version_to_file): New function.
	(bow_read_format_version_from_file): New function.
	* bow/libbow.h (bow_file_format_version): Declare new global
 	variable.
	(BOW_DEFAULT_FILE_FORMAT_VERSION): New macro.
	(bow_write_format_version_to_file): New function declaration.
	(bow_read_format_version_from_file): New function declaration.
	* rainbow.c (FORMAT_VERSION_FILENAME): New macro.
	(rainbow_archive): Write format version to disk.
	(rainbow_unarchive): Read it from disk if the file exists, otherwise
	set it to 3, which is the format version number of data before
 	BOW_FILE_FORMAT_VERSION was added to the library.

	* rainbow.c (rainbow_options): New option "print-word-counts",
 	alias for "print-counts-for-words".  Hide the later option from
 	the --help text.

	* rainbow-stats.pl (confusion): Print confusion matrix in a more
 	readable format.

	Add new command-line option to rainbow for using only 0 or 1 word
	counts. 
	* opts.c (bow_binary_word_counts): New global variable.
	(bow_options): New option "binary-word-counts".
	(parse_bow_opt): Handle it.
	* bow/libbow.h: Declare new global variable.
	* dv.c (bow_dv_add_di_count_weight): When BOW_BINARY_WORD_COUNTS
 	is true, insist on keeping DV's entry count below 2, i.e. 0 or 1.
	
Fri Apr 18 16:09:06 1997  Andrew McCallum  <mccallum@@jprc.com>

	* configure.in: Add -Wno-implicit to default CFLAGS.

	* rainbow.c (rainbow_lisp_query): Return if QUERY_WV is emtpy.
  	(Previously would have crashed.)

	* tfidf.c (TFIDF_METHOD): Fix typo that defined
 	_register_method_tfidf_.. functions without the last underscore.
	(Reported by Kamal Nigam.)
	
	* split.c (bow_test_split): When selecting documents for test set,
 	and randomly pick a document that was already in the test set,
 	don't just scan sequentially for the next non-test document, pick
 	a new random number.  This will avoid long contiguous stretches of
 	test documents.

	* naivebayes.c (bow_naivebayes_score): Move the handling of
 	SCORE_WITH_LOG_PROBABILITIES.

	* barrel.c (bow_barrel_set_cdoc_priors_to_class_uniform): Assert
 	that CDOC->PRIOR must be greater or equal, not just greater.

Thu Apr 10 14:54:08 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Fix the `compile-command'.
	(PRINT_TREE_SCORES): New macro.
	(hier_set_method): New function.
	(main): Call it if BOW_ARGP_METHOD is non-NULL.

	* deflexer.c (bow_default_lexer): Initialize it to -1, so that
 	deflexer.o will get linked in under SunOS.  Ug.  See comment.

	* bow/libbow.h (bow_methods): Declare extern!

Wed Apr  9 11:14:13 1997  Andrew McCallum  <mccallum@@jprc.com>

	* lex-html.c (bow_lexer_html_get_raw_word): Return last word in
 	document, even if it is not followed by a non-word character!
	* lex-simple.c (bow_lexer_simple_get_raw_word): Likewise.

	* rainbow.c (rainbow_lisp_setup): Call all
 	__attribute__((constructor)) functions here since this will be
 	dynamically loaded and the contructor functions won't be called
 	then.
	* opts.c (parse_bow_opt): Remove call to
 	_bow_default_lexer_init(); moved to rainbow.c.

	Fix a bug whereby --skip-html was a no-op.
	* deflexer.c (bow_default_lexer_simple,
 	bow_default_lexer_indirect, bow_default_lexer_gram,
 	bow_default_lexer_html, bow_default_lexer_email): Change global
 	variable from struct's to pointers to structs.
	(_bow_default_lexer_simple, _bow_default_lexer_gram,
	_bow_default_lexer_html, _bow_default_lexer_email): New static
 	variables.
	(_bow_default_lexer_init): Set BOW_DEFAULT_LEXER_INDIRECT to point
	inside of BOW_DEFAULT_LEXER_GRAM, which is the BOW_DEFAULT_LEXER.
	* opts.c: Now use all default lexers as pointers to struct's
 	instead of struct's.
	* bow/libbow.h (bow_default_lexer_simple,
 	bow_default_lexer_indirect, bow_default_lexer_gram,
 	bow_default_lexer_html, bow_default_lexer_email): Change global
 	variable from struct's to pointers to structs.

	* vpc.c (bow_barrel_new_vpc_merge_then_weight): Assert the method
 	name.

	* Makefile.in (dist-cmu, bow-$(BOW_VERSION).tar.gz): New targets.

Tue Apr  8 08:00:00 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Version (BOW_MINOR_VERSION): Version 0.7.
	* bow/libbow.h (BOW_MINOR_VERSION): Likewise.
	* rainbow.c (RAINBOW_MINOR_VERSION): Version 0.2.
	* arrow.c (ARROW_MINOR_VERSION): Version 0.2.
	* NEWS: Update for new version of library and rainbow.
	* readme.texi: Likewise.
	* Makefile.in (DIST_FILES): Add NEWS.

	* Makefile.in (dist): Fix invocation of `tr' for cvs rtag.

	* split.c (bow_test_next_wv): Initialize CURRENT_DI to avoid
 	warning.
	* split.c (bow_test_split): Initialize DOC to avoid warning.
	* int4word.c (bow_words_keep_top_by_infogain): Initialize
 	MAX_IG_WI to avoid warning.

	* dv.c (bow_dv_add_di_count_weight): Only give "overflowed short"
 	message at BOW_VERBOSE level, not BOW_PROGRESS level.

	* crossbow.c (main): Initialize NORMALIZER to zero.

	* Makefile.in (dist): Create ./bow directory.  Fix invocation of
 	argp.
	(snapshot): Likewise.

	* configure.in: Add -O to the default CFLAGS.

	* rainbow.c (rainbow_options): Improve some option help text.
	(rainbow_parse_opt) [INFOGAIN_PAIR_VECTOR_KEY]: Handle it.
	* opts.c (bow_options): Improve some option help text.

	* Makefile.in (version.texi): Define BOWVERSION instead of
 	BOW_VERSION, so makeinfo can get the value.
	(%.dvi, %.info): Fix typo.
	* libbow.texi: Fix typos and begin preliminary documentation.

	* rainbow.c (rainbow_options): New option "repeat"/'r'.
	(rainbow_parse_opt): Handle it.
	(rainbow_arg_state): New member REPEAT_QUERY.
	(rainbow_query): Attend to REPEAT_QUERY.

	* naivebayes.c (bow_naivebayes_set_weights): Fix assertion so it
 	works for both naivebayes and crossentropy.

Mon Apr  7 11:00:06 1997  Andrew McCallum  <mccallum@@jprc.com>

	* sarray.c (bow_sarray_entry_at_keystr): If there is no index for
 	that KEYSTR, print an error message.  This way if user mistypes a
 	method name to rainbow's -m option, they get a message that makes
 	some sense.

	* opts.c (_help_filter): New function to add the names of the
 	available methods to the help text.
	(bow_argp): Put it in.

	Use strings to identify methods instead of integers.  Separate
	method declarations instead separate .h files.
	* bow/tfidf.h, bow/naivebayes.h, bow/prind.h: New files.
	* Makefile.in (LIBBOW_H_FILES): Add files bow/naivebayes.h,
 	bow/tfidf.h, bow/prind.h.
	* naivebayes.c (bow_method_naivebayes, bow_method_crossentropy):
 	Use string method identifier instead of integer.
	* prind.c (bow_method_prind): Likewise.
	* tfidf.c (TFIDF_METHOD): Likewise.
	* rainbow.c (rainbow_parse_opt) [G]: Step through methods
 	according to new BOW_METHODS bow_sarray, instead of old static
 	array.
	* methods.c (bow_methods): Static array removed.
	(bow_methods): Renamed from _bow_str4method, and made non-static.
	* barrel.c (bow_method_id, _old_bow_methods): Put copies of what
 	used to be in libbow.h here, so we can unarchive old-format
 	barrel's.
	(BOW_DEFAULT_BARREL_VERSION): Changed from 2 to 3.
	(bow_barrel_new_from_data_fp): If VERSION_TAG is less than 3, read the
	method id integer and use _OLD_BOW_METHOD, otherwise, read a
 	string and use new BOW_METHOD_AT_NAME().
	(bow_barrel_write): Write the method as a string instead of as an
	integer.

	* Makefile.in (ALL_CPPFLAGS): -I$(srcdir) instead of
 	-I$(srcdir)/bow.
	* All files: Include <bow/libbow.h> instead of "libbow.h".

	* bow/libbow.h: Include <bow/tfidf.h>, <bow/naivebayes.h>,
	<bow/prind.h>.
	(bow_method_register_with_name,	bow_method_at_name): Declare functions.
	(bow_method_id): Typedef removed.
	(bow_str_to_method_id): Macro removed.
	(bow_methods): Global variable removed.
	(bow_method_tfidf_words, bow_method_tfidf_log_words,
	bow_method_tfidf_log_occur, bow_params_tfidf): Removed.
	(bow_method_prind, bow_params_prind): Removed.
	(bow_method_naivebayes, bow_params_naivebayes): Removed.

	* methods.c (bow_method_at_name): Comment function.
	(bow_method_register_with_name): Likewise.

	* opts.c (parse_bow_opt) [m]: Use bow_method_at_name().

	* naivebayes.c: Use bow_method_register_with_name().  Add new
 	method "crossentropy".
	(bow_naivebayes_score): Pay attention to SCORE_WITH_LOG_PROBABILITIES
	when setting class priors.  When it is true, use inverse of
 	cross-entropy instead of negative!

	* prind.c: Use bow_method_register_with_name().

	* tfidf.c: Use bow_method_register_with_name().

	* rainbow.c (main): Strip any trailing `/'s from classnames, so
 	FILENAME_TO_CLASSNAME() will find the classnames.  (Reported by
 	Jason Rennie <jr6b@@syrinx.res.cmu.edu>.)

	* rainbow-h.c (PRINT_COUNTS_FOR_WORD_KEY): New macro.
	(rainbowh_options): New option "print-counts-for-words".
	(rainbowh_parse_opt): Handle it.
	(struct rainbowh_arg_state): New member PRINTING_WORD.
	(hier_barrel_print_word_counts): New function.
	(main): Handle new option.  Do the right think for `-O' if 
	BOW_PRUNE_VOCAB_BY_OCCUR_COUNT_N.

	* info_gain.c (LEAVE_OUT_LAST_CLASS): Macro defined once at top.
  	Changed from 0 to 1.

	* install.texi: Explain the results of --prefix.  Remove old
 	references to Objective C installation.

Thu Apr  3 12:50:23 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_test_files): Use macros for setting QUERY_WV
 	weights, so we can handle case in which the wv normalizer is NULL!
	(main): Replace code for implementing word-count-printing with
	call to new function.

	* barrel.c (bow_barrel_set_cdoc_priors_to_class_uniform):
 	Initialize ci2dc entries to zero!
	(bow_barrel_print_word_count): New function.

	* opts.c (bow_options): Add new option
 	"naivebayes-score-with-log-probs".
	(parse_bow_opt): Handle it.
	* naivebayes.c (bow_naivebayes_score): Begin adding code to
 	support SCORE_WITH_LOG_PROBABILITIES parameter; not yet finished.
	(bow_naivebayes_params): Add initializer for
	SCORE_WITH_LOG_PROBABILITIES, initialize it BOW_NO.

	* bow/libbow.h: Declare new function.
	(bow_params_naivebayes): New entry SCORE_WITH_LOG_PROBABILITIES.

Wed Apr  2 10:07:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* configure.in: Add a check to see if __attribute__((constructor))
 	works.  If it does not, define CONSTRUCTOR_FAILS.

	* rainbow.c (rainbow_lisp_setup): Fix typo.

	* Makefile.in ($(PERL_RUNNABLE_FILES)): Use % in pattern and $< in
 	rule so that we get the .pl file from the $(srcdir).

	* rainbow-h.c (rainbowh_options): New option
 	"print-infogain-vector", 'I'.
	(struct rainbowh_arg_state): Add state for it.
	(rainbowh_parse_opt): Handle it.
	(hier_barrel_write_to_file): Close the FP after writing a barrel.
	(hier_barrel_set_vpc_with_weights): Construct and pass a CLASSNAMES
	array.
	(hier_barrel_set_cdoc_priors_to_class_uniform): New function.
	(_hier_barrel_set_node_scores): Print a little header/separator if
	BOW_PRINT_WORD_SCORES.
	(hier_barrel_test): Initialize the QUERY_WV to NULL, so
	BOW_TEST_NEXT_WV doesn't try to free unallocated memory.
	(hier_barrel_print_infogain): New function.
	(rainbowh_archive): New function.
	(rainbowh_unarchive): New function.
	(main): Use above two functions.  Deal with printing infogain.

	* rainbow.c: Re-written for using libargp.  This should make it
	work with the WebKB lisp crawler again.

	* prind.c (bow_prind_score): Make sure CDOC->FILENAME is non-NULL
 	before trying to print it when BOW_PRINT_WORD_SCORES is true.

	* opts.c (parse_bow_opt) [ARGP_KEY_INIT]: Call
 	_bow_default_lexer_init().

	* deflexer.c (_bow_default_lexer_init): Don't make it static.  Use
 	static local variable to make sure we don't run through it twice.
  	This is because we will call is explicitly in
 	opts.c:parse_bow_opt(), because __attribute__ ((constructor))
 	doesn't seem to work on SunOS.

	* Makefile.in (PERL_FILES): Added rainbow-ac.pl and rainbow-pr.pl.
	* (rainbow-ac.pl, rainbow-pr.pl): New files from
	Dayne Freitag <dayne@@cs.cmu.edu>.

Tue Apr  1 10:11:03 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c (rainbowh_parse_opt): Implement option 'M' for
 	use_maximum_likelihood_path.
	(hier_default_method): Renamed from METHOD; all uses changed.
	(hier_barrel): New member NUM_NON_REST_CDOCS, to keep track of
	DOC_BARREL->CDOCS->LENGTH *before* the `rest' documents start
 	getting added, so that we can implement
 	HIER_PARENT_DI_TO_CHILD_INDEX_AND_DI properly.
	(hier_barrel_new): Initialize it to -1.
	(hier_barrel_add_child): Set it.
	(hier_barrel_new_from_text_dir_leaf): Set it.
	(hier_barrel_write_to_file): Write it.
	(hier_barrel_new_from_file): Read it.
	(hier_parent_di_to_child_index_and_di): Use it.
	(hier_barrel_print): Print it instead of DOC_BARREL->CDOCS->LENGTH.
	(hier_barrel_add_stats): New function split out from
	HIER_BARREL_ADD_CHILD.
	(hier_barrel_add_child): Use it.
	(hier_barrel_add_rest): New function.
	(hier_barrel_new_from_text_dir): Call it to add `rest' documents.
	(hier_barrel_test): Allocate space for 3 as many SCORES, to make room
	for the `rest' classes.
	(main): Set HIER_DEFAULT_METHOD from BOW_ARGP_METHOD, if non-NULL.

	* scale.c (bow_barrel_scale_weights_by_given_infogain): Only
 	verbosify every 100 words.
	(bow_barrel_scale_weights_by_given_foilgain): Likewise.

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Fix indentation.

	* rainbow-h.c: Converted to do command-line argument processing
 	with libargp.

	* opts.c (bow_options): Remove "version" 'V' option.  libargp can
 	handle that automatically.
	(_print_version): New function to print both program version and
	library version.
	(argp_program_version_hook): Set it to _PRINT_VERSION().

	* rainbow.c (rainbow_print_usage): Function removed.  Libargp does
 	that now.

Mon Mar 31 11:07:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* barrel.c (bow_barrel_set_cdoc_priors_to_class_uniform): Use
 	ALLOCA() instead of BOW_MALLOC() to avoid memory leak.

	* Makefile.in (configure, config.status): Sprinkle with $(srcdir).

	* configure.in: Move the setting of CFLAGS above AC_PROC_CC, so
 	that it will have an effect.

	* install.texi: Mention how to set CPPFLAGS in the ./configure
 	line.

	* vpc.c (bow_barrel_set_vpc_priors_by_counting): Properly set the
 	CDOC->PRIOR's.

	* rainbow.c (INFOGAIN_PAIR_VECTOR_KEY): New macro.
	(rainbow_options): New option "infogain-pair-vector".
	(rainbow_parse_opt): Handle it.
	(main): Likewise.  When RAINBOW_WORD_COUNT_PRINTING, also print the
	total number of words in each class.

	* prind.c (bow_prind_set_weights): Get MAX_WI from MIN of
 	WI2DVF->SIZE and BOW_NUM_WORDS(), not just BOW_NUM_WORDS().

	* opts.c (bow_uniform_class_priors): New global variable.
	(bow_options): New option "uniform-class-priors".
	(parse_bow_opt): Handle it.

	* naivebayes.c (bow_naivebayes_set_weights): Get MAX_WI from MIN
 	of WI2DVF->SIZE and BOW_NUM_WORDS(), not just BOW_NUM_WORDS().
	(bow_naivebayes_score): Pay attention to BOW_UNIFORM_CLASS_PRIORS.
	Don't sum in score of words that don't have a DV entry!
  	Previously we were allowing words that `aren't in the vocabulary'
 	of the BARREL to contribute!  This was wrong.  They were
 	contributing according to the Laplace Estimators, and classes with
 	larger numbers of words were getting penalized.

	* info_gain.c (bow_infogain_per_wi_new): Sum floating point
 	CDOC->PRIOR's instead of increment integer count of documents, so
 	that infogain can be calculated from documents with different
 	`weights'.
	(bow_infogain_per_wi_new_using_pairs): New function.  For now it
	prints its results instead of returning them.

	* barrel.c (bow_barrel_set_cdoc_priors_to_class_uniform): New
 	function.

	* bow/libbow.h: Declare new functions.

Mon Mar 31 11:56:48 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* Makefile.in (CFLAGS, CPPFLAGS): Get values from configure.
	* configure.in: Do AC_SUBST() for CPPFLAGS and CFLAGS.

Fri Mar 28 10:28:26 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: Fix spelling: "heir" -> "hier".  How embarrassing!

	* dv.c (bow_dv_new_from_data_fp): Fix typo in feof() assertion.
  	(Reported by Doreen Cheng <dcheng@@PRPA.Philips.COM>.)

	* rainbow.c (PRINT_COUNTS_FOR_WORD_KEY): New macro.
	(rainbow_options): New option "print-counts-for-word".
	(rainbow_parse_opt): Handle it.
	(main): Implement it.

	* bow/libbow.h: (bow_wi2dvf): Add new element to structure:
	`num_words'.
	(bow_barrel): Put `is_vpc' at end of structure instead of the
	beginning. 

	* wi2dvf.c (bow_wi2dvf_new): Initialize NUM_WORDS.
	(bow_wi2dvf_add_di_wv): Increment it.
	(bow_wi2dvf_add_wi_di_count_weight): Likewise.
	(bow_wi2dvf_new_from_data_fp): Likewise.
	(bow_wi2dvf_remove_wi): Decrement it.
	(bow_wi2dvf_print_stats): Print it.

	* prind.c (bow_prind_set_weights): Use BARREL->WI2DVF->SIZE and
 	BARREL->WI2DVF->NUM_WORDS instead of BOW_NUM_WORDS().  In
 	particular, this will allow us to set the Laplace estimators using
 	the correct number of words in the barrel, not the arbitrary
 	libbow-wide vocabulary size.  Properly use CDOC->WORD_COUNT
 	instead of overloading CDOC->NORMALIZER.
	(bow_prind_score): Likewise use BARREL->WI2DVF->SIZE and
	BARREL->WI2DVF->NUM_WORDS instead of BOW_NUM_WORDS().
	(bow_print_word_scores): Removed to opts.c.

	* opts.c (bow_print_word_scores): Global variable moved here from
 	prind.c.
	(bow_options): New option "print-word-scores".
	(parse_bow_opt): Handle it.

	* naivebayes.c (bow_naivebayes_set_weights): Use
 	BARREL->WI2DVF->SIZE and BARREL->WI2DVF->NUM_WORDS instead of
 	BOW_NUM_WORDS().  In particular, this will allow us to set the
 	Laplace estimators using the correct number of words in the
 	barrel, not the arbitrary libbow-wide vocabulary size.
	(bow_naivebayes_score): Likewise, and add code to print scores
	contributions of each word with BOW_PRINT_WORD_SCORES is non-NULL.
	(SCORE_WITH_LOG_PROBABILITIES): New macro.

	* barrel.c (bow_barrel_printf): Comment out the code that would
 	skip over documents that are not of type `model'.

Thu Mar 27 11:29:34 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-stats.pl: Make output labels more descriptive.  Say
 	`average percentage accuracy'.

	* split.c (bow_test_split): Use the micro-seconds field from
 	gettimeofday() instead of time() to set the random number
 	generator seed.  Otherwise, if we re-call this function too
 	quickly we'll get exactly the same seed!  ...because time()
 	returns a number of seconds.

	* demos/script: New shell script file that will demo rainbow,
	with running commentary.
	* demos/data: New directory containing 20 articles 2 newsgroups.
	This is for use with demos/script.

	* install.texi: Remove mention of `checks' and `examples'
 	directory; they don't exist.  (Reported by Doreen Cheng
	<dcheng@@PRPA.Philips.COM>.)

Mon Mar 24 12:07:53 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in (rainbow-lisp.o): Use $(ALL_CPPFLAGS) and
 	$(ALL_CLFAGS) instead of non-ALL versions.

	* rainbow.c (rainbow_lisp_setup): Rewrite for use with libargp.

	* methods.c (bow_method_at_name): Fix typo.
	(bow_method_at_index): Likewise.

	* opts.c (parse_bow_opt): Use 'g' instead of 'N' for setting gram
 	size.

	* rainbow.c (rainbow_lisp_query): Free the QUERY_WV before
 	returning!

	* methods.c (bow_method_register_with_name): New function.
	(bow_method_at_name): New function.

	* arrow.c (PRINT_IDF_KEY): New macro.
	(arrow_options): Add new option "print-idf".
	(struct arrow_arg_state): New enum ARROW_PRINTING_IDF.
	(arrow_index): Prune the vocabulary if
	BOW_PRUNE_VOCAB_BY_OCCUR_COUNT_N is non-zero.
	(main): Add code to print idf values.

	* lex-simple.c (bow_alpha_lexer, bow_alpha_only_lexer,
 	bow_white_lexer): Initialize STEM_FUNC to 0 instead of
 	BOW_STEM_PORTER.

	* tfidf.c (bow_tfidf_set_weights): Comment out code that sets
 	total_word_count.  Do the DF_TRANSFORM on DF, not on IDF!
  	Otherwise we get negative IDF's.

	* rainbow-h.c (use_maximum_likelihood_path): New global variable.
	(_heir_barrel_set_node_scores): Use it.
	(main): Set it when -M passed on command line.
	(num_top_words): Moved from main-local variable to global.
	(heir_barrel_test): Reduce vocab by infogain.

Fri Mar 21 14:02:39 1997  Andrew McCallum  <mccallum@@jprc.com>

	* bow/libbow.h (bow_lexer_simple): Add entry
 	TOSS_WORDS_LONGER_THAN.
	(bow_wv_set_weights_to_count_times_idf): Declare new function.

	* wv.c (bow_wv_set_weights_to_count_times_idf): New function.

	* tfidf.c (bow_tfidf_set_weights): Comment out code saying that
 	TFIDF is broken.  Rewrite the way IDF is calculated.
	(bow_tfidf_score): Set and normalize the QUERY_WV weights here (even
	though it is redundant) so that we can properly use the IDF from
 	the BARREL when normalizing weights.  Normalize the QUERY_WV
 	weight when incrementing CURRENT_SCORE.

	* prind.c (bow_prind_set_weights): Skip a document if it does not
 	of type model, both when setting NORMALIZER and TOTAL_TERM_COUNT,
 	and when setting weights.
	(bow_prind_score): Skip a document if it does not of type model.

	* lex-simple.c (bow_lexer_simple_postprocess_word): Add code to
 	toss words longer than SELF->TOSS_WORDS_LONGER_THAN.  Set WORDLEN
 	at beginning.  It appeared that it was getting used uninitialized
 	before!
	(bow_alpha_lexer, bow_alpha_only_lexer, bow_white_lexer): Add value
	for new field TOSS_WORDS_LONGER_THAN.

	* opts.c (APPEND_STOPLIST_FILE_KEY): New macro.
	(bow_options): Added "append-stoplist-file"
	(parse_bow_opt): Handle new option.

	* int4str.c (_str2id): Return the absolute value of the old return
 	value.  Sometimes with really long strings, the return value was
 	going negative.
	(_str_hash_lookup): Assert that ID is non-negative.

Thu Mar 20 11:47:49 1997  Andrew McCallum  <mccallum@@jprc.com>

	These changes by Karl Kleinpaste <karl@@jprc.com>
	* int4word.c (bow_words_reread_from_file): Use fopen() instead of
 	bow_fopen(), so we are sure not to call abort().
	* wv.c (bow_wv_sprintf): Fix function to account for length
 	troubles properly.
	(bow_wv_sprintf_words): New function, prints the words themselves,
	rather than the word indices.
	* bow/libbow.h: Declare new function.

	* naivebayes.c (bow_naivebayes_set_weights): Add commented-out
 	code that forces all counts to either 0 or 1.  This was used on
 	some experiments with Shumeet.

	* lex-html.c (bow_lexer_html_get_raw_word): Add a ! to the
 	FALSE_TO_END condition test, so we don't end the tokenization too
 	early.

Tue Mar 18 14:47:35 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_parse_opt) [ARGP_KEY_END]: Print a useful
 	error when only one classname is given.
	(main): Check for rainbow_infogain_printing properly.

	* opts.c (parse_bow_opt) [ARGP_KEY_END]: Check for the existance
 	of BOW_DATA_DIRNAME in a way that works even when the directory is
 	owned by someone else.

	* bow/libbow.h (bow_fread_string): Assert that the string length
 	is non-negative.

	* barrel.c (_bow_barrel_version): New variable.
	(BOW_DEFAULT_BARREL_VERSION): New macro.
	(bow_barrel_new_from_data_fp): Read the version number instead of a
	null_tag.
	(bow_barrel_write): Likewise, for writing.

	* arrow.c (main): Remove redundant code that is now in opts.c.

Mon Mar 17 12:09:32 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in (%.o:%.c): Fix the order on this pattern rule.
	($(DEMO_EXECUTABLES):%:%.o): Put $(DEMO_EXECUTABLES) at the beginning
	of this pattern, so it matches only those files.

	* arrow.c: Don't include getopt.h; we're using argp.h instead.
	(arrow_index): Fix typo.

	* configure.in: Don't look for getopt.h anymore.  We don't need it
 	now that we are using libargp.

	* configure.in: AC_INIT looking for int4str.c instead of libbow.h.

	* Makefile.in (%): Use this pattern to make DEMO_EXECUTABLES
 	instead of listing them all.  This avoids making all the .o's for
 	one of the DEMO_EXECUTABLES.

	* rainbow.c: Converted to use argp command-line argument
 	processing.

	* opts.c (bow_argp_method): Renamed from bow_default_method.
	(parse_bow_opt) [ARGP_KEY_INIT]: Add words to stoplist.

	* deflexer.c (_bow_default_lexer_init): Initialize
 	bow_default_lexer to BOW_DEFAULT_LEXER_GRAM, not BOW_LEXER_GRAM!

	* bow/libbow.h (bow_argp_method): Renamed from bow_default_method.

	* arrow.c (arrow_parse_opt) [q]: Set query.filename.
	(arrow_index): BOW_DEFAULT_METHOD renamed to BOW_ARGP_METHOD.

	* arrow.c (arrow_index): Set the method according to
 	BOW_DEFAULT_METHOD.

	* opts.c: Fleshed out into first working version.

	* error.c: Comment fix.  Include libbow.h and stdio.h.

	* deflexer.c (_bow_default_lexer_init): New constructor function.
	(bow_default_lexer_simple, bow_default_lexer_indirect,
	bow_default_lexer_gram, bow_default_lexer_html,
 	bow_default_lexer_email): New variables, default instantiations of
 	lexers.

	* bow/libbow.h: Add argp declarations.
	(bow_argp_children): New variable.
	(bow_prune_vocab_by_infogain_n): New variable.
	(bow_prune_vocab_by_occur_count_n): New variable.
	(bow_default_method): New variable.
	(bow_data_dirname): New variable.

	* arrow.c: Convert to using argp for command-line processing.

	* Makefile.in: Change all instances of `libbow.h' to `bow/libbow'.
	(includedir): Add `/bow' to end.
	(LIBBOW_C_FILES): Add opts.c.
	(ALL_CPPFLAGS): add -I$(srcdir)/bow and -I$(srcdir)/argp.
	(rainbow-lisp.o): Use $< instead of rainbow.c, so VPATH will find it
	when compiling in a different directory than the source.

	* bow/libbow.h (STRINGIFY): New macro.
	(bow_default_lexer_simple, bow_default_lexer_indirect,
	bow_default_lexer_gram, bow_default_lexer_html,
 	bow_default_lexer_email): Declare default instantiations of
 	lexers.

Fri Mar 14 11:01:14 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in (LIBBOW_C_FILES): Renamed defparser.c to deflexer.c.
	* deflexer.c: Renamed from defparser.c.

	Add the `argp' subdirectory, and incorporate it into the Makefile.
	* HACKING: Add argp autoconf instruction.
	* configure.in: Call AC_CONFIG_SUBDIRS to configure argp also.
	* Makefile.in (ALL_LIBS): Move it closer to $(DEMO_EXECUTABLES)
 	target.  $(DEMO_EXECUTABLES): Make this target depend on
 	argp/libargp.a.
	(install): Call make install in argp directory also.
	(dist, snapshot): Call make in argp directory to include its files too.
	
Wed Mar 12 20:00:27 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in (CPPFLAGS): Don't include $(DEFS) here, it's now in
 	ALL_CPPFLAGS.

	* Makefile.in (ALL_CPPFLAGS): New variable.
	(ALL_CFLAGS): New variable.
	(.c.o): New pattern rule that uses above new variables.  Now Kamal can
	safely type `make CPPFLAGS=-DNDEBUG'.

	* rainbow-h.c (_heir_barrel_set_node_scores): Don't threshhold the
 	scores to 0/1.
	(strdup): New function.  Implement this local version to help with
	debugging.  Consider removing it later.

	* libbow.h (bow_params_prind): Remove variable SCALE_BY_FOILGAIN.
	It isn't needed since we have a function pointer for it in BOW_METHOD.
	* prind.c (bow_prind_params): Remove BOW_NO for scaling.
	* rainbow.c (rainbow_lisp_setup): Remove setting of
 	BOW_PRIND_SCALE_BY_INFOGAIN; it now defaults to on.
	(rainbow_print_usage): Change the sense of -G.  It now turns off
	foilgain scaling, instead of turning on.  (Actually, it was the
 	default before this anyway.)
	(main): Given -G, zero-out the SCALE_WEIGHTS entries in all the
	methods. 

Tue Mar 11 11:58:03 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Version (BOW_MINOR_VERSION): Version 0.6.
	* libbow.h: Likewise.

	* Makefile.in (DIST_FILES): Add TODO.  Remove p.inc.
	(p-alpha.o, p-alonly.o, p-white.o): Targets removed.

	* rainbow.c (rainbow_query): Use bow_barrel_ macros instead of
 	indexing into the methods structure manually.

	* crossbow.c: Add copyright info.

	* readme.texi: Fill out.
	* libbow-desc.texi: Add description.
	* install.texi: Add pointer to the README.  Say that it requires GCC. 
	* HACKING: Update CVS repository machine name.

	* tfidf.c (bow_tfidf_set_weights): Insert dislaimer explaining
 	that TFIDF is broken.

Tue Mar 11 11:31:39 1997  Rahul Sukthankar  <rahuls@@syzygy.jprc.com>

	* Makefile.in (DEMO_C_FILE): Added crossbow.c.
	* crossbow.c: New file.

Mon Mar 10 18:52:03 1997  Andrew McCallum  <mccallum@@jprc.com>

	* int4str.c (_str2id): Keep return value smaller using modulus.
	This fixes bug Rosie Jones encountered with negative hash values.
	(_str_hash_lookup): Assert that H is non-negative.

	* Makefile.in (LIBBOW_C_FILES): Added lex-email.c.

Fri Mar  7 10:54:09 1997  Andrew McCallum  <mccallum@@jprc.com>

	* int4word.c (bow_words_reread_from_file): Make sure LAST_FILE is
 	non-NULL.

Tue, 18 Feb 1997 20:15:42 -0500  Jason Rennie <jr6b@@andrew.cmu.edu>

        * lex-email.c: New file.  Created lexer for e-mail/newsgroup messages

	* lex-html.c: Changed code to allow words separated by HTML tags
 	to be tokenized as single words.  <FONT SIZE=+2>B</FONT>ig is now
 	tokenized as "Big".  Nested brackets are now ignored.  This should
 	more closely model the way HTML is interpreted.

	* rainbow.c: Added rainbow_email_lexer as a bow_lexer_indirect.
  	Added '-M' option to allow user to make use of
 	rainbow_email_lexer.  rainbow_email_lexer will remove
 	"Newsgroups:" and "Path:" headers from message.

	* libbow.h (bow_email_headers_to_remove): Declare new global variable. 
	(bow_email_lexer): Likewise.

Tue Mar  4 11:51:53 1997  Andrew McCallum  <mccallum@@jprc.com>

	* libbow.h (bow_barrel_scale_weights): Don't call underlying
	function if it's NULL.
	(bow_barrel_normalize_weights): Likewise.
	(bow_wv_set_weights): Likewise.
	(bow_wv_normalize_weights): Likewise.
	* vpc.c (bow_barrel_new_vpc_merge_then_weight): Use macros for
 	weight setting.
	(bow_barrel_new_vpc_weight_then_merge): Likewise.

	* rainbow-h.c (_heir_barrel_cdoc_write): Write WORD_COUNT.
	(_heir_barrel_cdoc_read): Read it.
	(heir_dir_is_leaf): Check the return status from CHDIR(), and print
	appropriate error message.
	(heir_barrel_keep_top_words_by_infogain): Return immediately if
	num_words_to_keep is 0 or the children count is 0.
	(heir_barrel_set_vpc_with_weights): Return immediately if the children
	count is 0.
	(_heir_barrel_set_node_scores): Add temporary #if'ed code to make
	score either 1 or 0, so winner takes all.
	(heir_barrel_score_recurse): New argument DEPTH.  All callers changed.
	(main): Change default NUM_TOP_WORDS from 3000 to 0.  Add new command
	line argument -m and -N.

	Changes made with Sean Slattery.
	* naivebayes.c (bow_naivebayes_set_weights): Store class-wide word
 	count in CDOC->WORD_COUNT instead of overloading CDOC->NORMALIZER.
	(bow_naivebayes_score): Use CDOC->WORD_COUNT instead of
	CDOC_NORMALIZER.  Use it to fix PR_W_C in case where that word
	doesn't appear in the class.  Instead of (1.0 / MAX_WI) use (1.0 /
	(MAX_WI + CDOC->WORD_COUNT)).  Don't normalize the weight by
 	CDOC->NORMALIZER because it it set to already by normalized
 	correctly, including the words that don't appear in the in class.
	(bow_method_naivebayes): Change the weight normalizing function from
	BOW_NORMALIZE_WEIGHTS_BY_SUMMING to NULL, because we don't use
 	CDOC->NORMALIZER anymore.
	* libbow.h (bow_cdoc): Add WORD_COUNT.
	* barrel.c (_bow_barrel_cdoc_write): Write WORD_COUNT.
	(_bow_barrel_cdoc_read): Read it.

	* vpc.c (bow_barrel_new_vpc): Assert MAX_CI is positive, otherwise
 	this means we didn't find any classes.

Wed Feb 26 11:08:50 1997  Andrew McCallum  <mccallum@@jprc.com>

	* HACKING: Fix sandbox's name.

Wed Feb 19 11:27:55 1997  Andrew McCallum  <mccallum@@jprc.com>

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Return
 	immediately if NUM_WORDS_TO_KEEP is 0.

Tue Feb 18 13:39:34 1997  Andrew McCallum  <mccallum@@jprc.com>

	* libbow.h (bow_str_to_method_id): Use a temporary variable, to we
 	use statements like ARGI++ as an argument.

	* info_gain.c (bow_infogain_per_wi_new): Change assertion to
 	handle round-off error.

	* rainbow-h.c: Include <math.h>, <time.h>.
	(heir_barrel): Add components INDEX_IN_PARENT, NUM_LEAVES, FULL_NAME.
	(heir_barrel_new): Set them.
	(heir_dir_is_leaf): Use chdir() so that symlinks are dealt with
	properly. Free() the results of scandir().
	(heir_barrel_new_from_text_dir_leaf): Set FULL_NAME and add assertions.
	(_heir_barrel_new_from_text_dir_recurse): New parameter PARENT_NAME.
	Move the chdir() to handle symlinks properly.  Don't make a
 	SUBDIRNAME.
	(heir_barrel_new_from_text_dir): New function.
	(heir_barrel_write_to_file): Write new heir_barrel components.
	(heir_barrel_new_from_file): Read them.
	(heir_barrel_free): Free FULL_NAME.
	(heir_barrel_keep_top_words_by_infogain): New function.
	(heir_parent_di_to_child_index_and_di): New function.
	(heir_di_to_classname): New function.
	(heir_barrel_test_split): New function.
	(_heir_barrel_set_node_scores): Use bow_barrel_score() instead to
	bow_get_best_matches().
	(heir_barrel_print_scores_recurse): Return void not int.  Print all on
	same line.
	(heir_barrel_score_recurse): New function.
	(heir_barrel_score): New function.
	(heir_barrel_test): New function.
	(heir_barrel_print_weight_vectors): Change formatting.
	(set_vocabulary_from_file): New function (unused).
	(main): Allow user to set DATADIR (-d) and NUM_TOP_WORDS (-T), 
	test (-t).
	Compile with -Wall.

Mon Feb 17 10:36:32 1997  Andrew McCallum  <mccallum@@jprc.com>

	* configure.in: Remove check for <float.h>, all ANSI compilers
 	should have it.

	* split.c: Remove SunOS declarations of rand() and srand().
	(RAND_MAX): Define macro, if not already defined.  These two
	changes needed to compile on SunOS.

	* naivebayes.c (bow_naivebayes_set_weights): Uncomment assertion
 	about METHOD->ID.

	* rainbow.c (rainbow_lisp_setup): Add `-N' to effective arguments.
	(rainbow_lisp_query): Fix typo in BOW_FOPEN() call.

	* rainbow.c (rainbow_query): Check for QUERY_WV being NULL, and
 	output more useful messages in that case.

	* naivebayes.c (bow_naivebayes_score): Rearrange the code for
 	stepping through a DV so we always get the CDOC.  This change
 	should have no effect on the outcome.

	* lex-simple.c (bow_lexer_simple_open_text_fp): Fix test for
 	matching END_PATTERN_PTR.  Don't push the DOCUMENT_END_PATTERN
 	back on the input stream after we find it; this is a stylistic
 	choice.

	* docnames.c (bow_map_filenames_from_dir): Pass relative instead
 	of absolute directory names to recursive calls.  Before I was
 	having trouble with symbolic links.  This seems to fix it.

	* int4word.c (bow_words_keep_top_by_infogain): Fix assertions; its
 	OK to have infogain equal to 0.

	* prind.c: Comment fixes.

	* foilgain.c (bow_foilgain_per_wi_ci_new): Use malloc() for
 	POS_PER_WI_CI and NEG_PER_WI_CI, instead of using stack.  We were
 	overflowing the stack before.

Tue Feb 11 12:15:30 1997  Andrew McCallum  <mccallum@@jprc.com>

	* naivebayes.c (bow_naivebayes_score): When word doesn't appear in
 	the class vector, make Pr(w|C) include CDOC->NORMALIZER.
  	(Suggested by Sean Slattery).

	* naivebayes.c (bow_naivebayes_score): Fix constant in assertion.

	* configure.in: When perl5 isn't found, PERL will be "", not ":".
  	Deal with it properly.

	* libbow.h: Don't bother with HAVE_FLOAT, just always include
 	<float.h>.
	(bow_get_best_matches): Remove declaration.  The function no longer
	exists.

	* rainbow.c (rainbow_test): Use macros for accessing method
 	functions.

	* split.c: Fix author comment.

	* info_gain.c (bow_infogain_per_wi_new): Use double instead of
 	float, because before we were loosing resolution and getting
 	negative IG's.
	(bow_entropy): Likewise.

Mon Feb 10 16:25:04 1997  Andrew McCallum  <mccallum@@jprc.com>

	* docnames.c (bow_map_filenames_from_dir): Use perror() when can't
 	open directory.

Fri Feb  7 11:00:50 1997  Andrew McCallum  <mccallum@@jprc.com>

	* int4word.c (bow_words_read_from_file): Fix typo.

	* rainbow.c (rainbow_lisp_query): Use bow_barrel_score instead of
 	bow_get_best_matches.

	These changes by Tony Brusseau <brusseau@@jprc.com>, with
	modifications by <mccallum@@jprc.com>.
	* wv.c (bow_wv_new_from_text_string): New function.
	(bow_wv_sprintf): New function.
	* int4word.c (bow_words_set_map): Add new argument indicating if
 	old map should be freed.  All callers changed.
	(bow_words_reread_from_file): New function.
	* docnames.c: Include <stdio.h>.
	(bow_map_filenames_from_dir): Add WindowsNT backslashes to first
	assertion.
	* libbow.h: Declare new functions.

Thu Feb  6 18:33:21 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c: Updated for below library changes.
	* arrow.c: Likewise.

	* libbow.h: Declare many new functions, variables and types,
 	including:
	(bow_boolean): New type.
	(bow_wv_set_weights_to_count): New function declaration.
	(bow_wv_normalize_weights_by_vector_length): Likewise.
	(bow_wv_normalize_weights_by_summing): Likewise.
	(bow_str_to_method_id): Macro renamed from bow_str2method.
	(bow_method_id): New enum, replacing bow_method.
	(bow_method): Now a struct.
	(bow_barrel_set_weights, bow_barrel_scale_weights,
	bow_barrel_normalize_weights, bow_new_vpc_with_weights,
 	bow_barrel_score, bow_wv_set_weights, bow_wv_normalize_weights):
 	New macros.
	(bow_methods): New global variable declaration.
	(bow_params_*): New types.
	(bow_score): Renamed from bow_doc_score.

	* wv.c (bow_wv_set_weights_to_count): New function.

	* weight.c: File removed.

	* vpc.c (bow_barrel_new_vpc_merge_then_weight): New function.
	(bow_barrel_new_vpc_weight_then_merge): New function.
	(bow_barrel_set_vpc_priors_by_counting): Renamed from
	_bow_barrels_set_naivebayes_vpc_priors.

	* tfidf.c: File contents totally replaced to implement TFIDF.
  	Functions removed from weight.c and other places.
	(bow_tfidf_set_weights): Function renamed.
	(bow_tfidf_score): Function renamed from bow_get_best_matches().
	(bow_tfidf_params_{words,log_words,log_occur}): New variables.
	(bow_method_tfidf_{words,log_words,log_occur}): New global variables.

	* prind.c (bow_prind_uniform_priors): Global variable removed.
	(bow_prind_scale_by_infogain): Likewise.
	(bow_prind_normalize_scores): Likewise.
	(bow_prind_set_weights): Renamed from _bow_barrel_set_prind_weights.
	(bow_prind_score): Renamed from _bow_score_prind_from_wv, and updated
	for library changes.
	(bow_prind_params): New variable.
	(bow_method_prind): New global variable.

	* score.c: File removed.

	* naivebayes.c (_bow_barrels_set_naivebayes_vpc_priors): Function
 	removed.  Replacement in vpc.c.
	(bow_naivebayes_set_weights): Minor updates for library changes.
	(bow_naivebayes_params): New variable.
	(bow_method_naivebayes): New global variable.

	* info_gain.c (bow_barrel_scale_weights_by_info_gain): Function
 	removed.  Replacement is now in scale.c.
	(bow_barrel_scale_weights_by_foilgain): Likewise.
	(bow_foilgain_per_wi_ci_new): Likewise.  Replacement now in foilgain.c.
	(bow_foilgain_free): Likewise.

	* barrel.c (bow_barrel_new): Make the default method naivebayes,
 	instead of tfidf_log_occur.
	(bow_barrel_new_from_data_fp): Get the METHOD pointer from
	BOW_METHODS.
	(bow_barrel_write): Write the ID.

	* Makefile.in (CPPFLAGS): Add $(DEFS).
	(ALL_INCLUDE_FLAGS, ALL_CPPFLAGS, ALL_CFLAGS, ALL_LDFLAGS): Variables
	removed.
	(LIBBOW_C_FILES): Added foilgain.c, methods.c, normalize.c, scale.c,
	tfidf.c.  Removed score.c, weight.c.
	(DEMO_EXECUTABLES): Don't use ALL_LDFLAGS.

Tue Feb  4 14:21:08 1997  Andrew McCallum  <mccallum@@jprc.com>

	* split.c (bow_test_split): Properly deal with the fact the rand()
 	returns an int between 0 and RAND_MAX, and the previously-use
 	drand48() returned a double between 0 and 1.

Mon Feb  3 12:44:18 1997  Andrew McCallum  <mccallum@@jprc.com>

	Following changes made by Tony Brusseau for WindowsNT compatibility.
	* configure.in: Check for <float.h>.
	* libbow.h: Include float.h if we have it; otherwise include
 	values.h and redefine its macros.
	(htonl, htons, ntohl, ntohs): Temporarily define as identity for
	WindowsNT.
	(bow_fwrite_string): Cast sizeof() to int.
	* split.c: Use rand() and srand() instead of drand48() and
 	srand48().
	* rainbow.c (rainbow_test_files): Make DIRLEN unsigned, to avoid
 	warning under WindowsNT.
	* primes.c: Use unsigned int's instead of int's in several places,
 	to avoid warnings under WindowsNT.
	* dv.c: Don't include <netinet/in.h>.  Use <limits.h>-style
 	MAX'es.
	* naivebayes.c: Use <limits.h>-style MAX'es.
	* int4word.c: Likewise.
	* configure.in: Look for the wsock32 library.

	* prind.c (_bow_score_prind_from_wv): Don't die if SCORES_SUM is
 	zero; just leave zero scores on all classes.

	* rainbow.c (main): Add `s' to getopt call.
	(rainbow_index): Add newline to end of "No text files" message.

Fri Jan 31 11:28:54 1997  Andrew McCallum  <mccallum@@jprc.com>

	* Makefile.in (rainbow-lisp.o): New target.

	* rainbow.c (rainbow_lisp_setup): New function.  (From Kamal.)
  	Surround this and rainbow_lisp_query by #if RAINBOW_LISP.
	(main): Surround by #if !RAINBOW_LISP.

	* HACKING: Change the cvsroot in directions for networked
 	`pserver' use.

	* libbow.h: If under WinNT, include <winnt.h>, otherwise include
 	<values.h>.
	* bitvec.c (BITSPERBYTE): Surround it with an #ifndef.
	* prind.c: Don't include <values.h>.
	* naivebayes.c: Likewise.
	* int4word.c: Likewise.
	* dv.c: Likewise.
	* bitvec.c: Likewise.
	(BITSPERBYTE): New macro.

Wed Jan 29 10:10:11 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow.c (rainbow_lisp_query): New function.

	* Makefile.in (maintainer-clean): Add config.* files.

	* configure.in: Add quotes around $PERL so test will still work if
 	$PERL is empty.

	* rainbow-h.c (_heir_barrel_set_node_scores): Add some temporary
 	progress printing.
	(heir_barrel_print_scores_recurse): Renamed.
	(heir_barrel_print_scores): New function.
	(heir_barrel_print_foilgain): New function.
	(heir_barrel_print_weight_vectors): New function.
	(main): Add new options for calling new functions.

	* prind.c (_bow_score_prind_from_wv): Add three checks for NaN.

	* int4word.c (bow_words_write_to_file): New function.
	(bow_words_read_from_file): New function.
	* libbow.h: Declare new word functions.

	* rainbow-h.c (method): New global variable.
	(heir_barrel): Added component SCORE.
	(heir_barrel_new_from_text_dir_leaf): Set doc_barrel method.
	(heir_barrel_new_from_text_dir): Likewise.
	(main): Take -i and -q arguments.

	* libbow.h (bow_fwrite_string): Change type of LEN from int to
 	short.

	* vpc.c (bow_barrel_new_vpc): Don't abort if CLASSNAMES is NULL.

Tue Jan 28 15:49:46 1997  Andrew McCallum  <mccallum@@jprc.com>

	* rainbow-h.c: New file.

	* barrel.c (bow_barrel_write): Handle case in which BARREL is NULL.
	(bow_barrel_new_from_data_fp): Likewise.  (xxx Although there is some
	strangeness with FGETC returning -1, which I am currently
 	ignoring.  I should look at this again...)

	* defparser.c (bow_default_lexer): Temporary fix to confusion
 	about constant initializers and pointers.

	* Makefile.in: Fix copyright.

	* barrel.c: Fix header comment.
	(bow_barrel_printf): Print the word as well as the word index.

	* docnames.c (bow_map_filenames_from_dir): Remove commented-out
 	code for checking whether the file contains text.

Thu Jan 23 13:47:01 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* barrel.c (bow_barrel_printf): Don't print with paren's, so it
 	will be easier to process with AWK.

	* rainbow.c (main): Add new option -B for printing barrel word
 	vectors in ASCII.
	(rainbow_print_usage): Document it.

	* barrel.c (bow_barrel_printf): New function.
	* libbow.h: Declare new barrel function.

Sat Jan 18 08:14:59 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow.c (main): Add -N option for turning off normalization of
 	PrInd scores by setting BOW_PRIND_NORMALIZE_SCORES.
	(rainbow_print_usage): Document it.

	* vpc.c (FOILGAIN): New macro, defined to be 1.  Switching back to
 	doing foilgain by default.

	* prind.c (bow_prind_normalize_scores): Change to 1.  Now
 	normalizing scores by default.
	* libbow.h: Declare prind normalization global variable.

	* vpc.c (bow_barrel_new_vpc_with_weights): Condition choice of
 	weight-scaling on FOILGAIN.  Now default is to do scaling by
 	information gain (again).

	* prind.c (bow_prind_normalize_scores): New global variable.
  	Default: 0, don't normalize.  Note, this is different than what we
 	were doing before, and the default should be changed back to 1.
	(_bow_score_prind_from_wv): Use it.

	* rainbow.c (rainbow_index): Don't exit with error when a class
 	directory is empty, just print a message.
	(rainbow_usage): Fix description of -G to Foil-gain, not info-gain.

	* prind.c:  Improve formating of score printing.

	* rainbow.c (main): New command-line argument `-P' sets
 	BOW_PRINT_WORD_SCORES.
	(rainbow_print_usage): Document it.

	* prind.c (bow_print_word_scores): Define new global variable.
	(_bow_score_prind_from_wv): Use it to decide when to print
	per-word/class score information.
	* libbow.h (bow_print_word_scores): Declare new global variable.

Fri Jan 17 09:39:30 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow.c (printing_class): Global variable renamed from
 	weight_vector_printing_class.
	(rainbow_print_foilgain): New function.
	(main): Call it, and add -F option for doing so.
	(rainbow_print_usage): Document it.

	* vpc.c (bow_barrel_new_vpc_with_weights): Use new foilgain
 	function for PrInd, instead of infogain function.

	* info_gain.c (bow_barrel_scale_weights_by_info_gain): Set max_wi!
  	Previously it was uninitialized.
	(bow_foilgain_per_wi_ci_new): New function.
	(bow_foilgain_free): New function.
	(bow_barrel_scale_weights_by_foilgain): New function.
	* libbow.h: Declare new foilgain functions.

	* docnames.c (bow_map_filenames_from_dir): Add assertion that
 	checks for conditions under which directory-vs-file detection is
 	unreliable.  I should figure out why this isn't working as
 	expected.

	* prind.c (bow_prind_scale_by_infogain): New global variable.
	* libbow.h (bow_prind_scale_by_infogain): New declared global
 	varible.
	* rainbow.c (main): Add -G for setting
 	bow_prind_scale_by_infogain.
	* vpc.c (bow_barrel_new_vpc_with_weights): Use
 	BOW_PRIND_SCALE_BY_INFOGAIN.

	* rainbow.c (rainbow_query): Only re-build the
 	RAINBOW_CLASS_BARREL if -m or -T arguments require its change.

Thu Jan 16 13:35:31 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* vpc.c (bow_barrel_new_vpc_with_weights): For PrInd, scale
 	weights by information gain.  (Oooh, this may not be kosher;
 	perhaps remove it later.)

	* rainbow.c (rainbow_print_weight_vector): Multiply the weight by
 	its normalizer.

	* info_gain.c (bow_barrel_scale_weights_by_info_gain): Leave more
 	space for verbosifying progress, because the numbers are big.

	* prind.c (_bow_barrel_set_prind_weights): Remove the information
 	gain scaling, i.e. undo previous change.

	* info_gain.c (bow_barrel_scale_weights_by_info_gain): Change the
 	arguments so that the information gain array is passed in, not
 	calculated inside the function.
	* libbow.h: Change arguments to weight info gain scaling function.

	* naivebayes.c (_bow_score_naivebayes_from_wv): Scale DV WEIGHT by
 	CDOC NORMALIZER!

	* prind.c (_bow_score_prind_from_wv): Scale DV WEIGHT by CDOC
 	NORMALIZER!

	* rainbow.c (rainbow_query): If score is less than 1e-35, then
 	just print zero.  Do this for the sake of CommonLisp, which can't
 	read numbers smaller than 1e-35.
	(rainbow_test): Likewise.
	(rainbow_test_files): Likewise.

Wed Jan 15 10:52:13 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* scan.c (bow_scan_fp_for_string): Change the for() to a while()
 	to clean up the handling of STRING_PTR incrementation.

	* rainbow.c (method): Fix its handling from last change.
	(rainbow_print_weight_vector): New function.
	(main): Call it.
	(rainbow_print_usage): Add -W.

	* prind.c (_bow_barrel_set_prind_weights): Added comment.

	* lex-simple.c (bow_lexer_simple_get_raw_word): Back up
 	DOCUMENT_POSITION to point at terminating character.  Add more
 	comments.

	* int4str.c (_str_hash_lookup): Add assertion.
	(_str_hash_add): Add assertions.
	(bow_str2int): Increment MAP->STR_ARRAY_LENGTH++ first, then return -1
	the value, instead of returning the value++.  This makes the
 	intermediate calls more clear and safe.

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Improve
 	verbosity and reduce number of times printed.

	* lex-simple.c (bow_lexer_simple_open_text_fp): When checking to
 	see if we should realloc to increase the DOCUMENT buffer size,
 	make sure we leave room for the terminating '\0' that we'll add
 	later in the function!  (Wow!  This was a wild bug that's been
 	around for a while, but only recently caused occasional crashes.
  	The crashes were in totally unrelated functions in int4str.c.  The
 	GDB `watch' command came to the rescue!)

	* scan.c (bow_scan_fp_for_string): Make it ignore Carriage-Return
 	'\r' characters, so we can reliably scan for MIME header
 	separators.

	* barrel.c (bow_barrel_keep_top_words_by_infogain): Make it more
 	efficient by using qsort().

	* rainbow.c (method): Initialize to -1.
	(DEFAULT_METHOD): New macro, equal to bow_method_naivebayes.
	(rainbow_index): Use new macro.
	(rainbow_query): Cause `-m' to have an effect here.
	(rainbow_test): Likewise.
	(rainbow_test_files): Likewise.
	(rainbow_print_usage): Rearrange flags to reflect new contexts in
	which -T, -m, and -U are valid.
	(main): Don't use the length of argv[0] to determine value of
	BOW_VERBOSITY_USE_BACKSPACE.

Tue Jan 14 09:35:20 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* prind.m: Comment fixes.

	* rainbow.c (test_percentage): Initialize it to 0, not 30.
	(DEFAULT_TEST_PERCENTAGE): New macro, equal to 30.
	(rainbow_test): Set TEST_PERCENTAGE to DEFAULT_TEST_PERCENTAGE if its
	zero.  Set RAINBOW_CLASS_BARREL->METHOD to METHOD so we can give
 	the -m option when using -t.
	(rainbow_test_files): Use TEST_PERCENTAGE and NUM_TEST_DOCS to
	determine how many training examples to ignore.  Set
 	RAINBOW_CLASS_BARREL->METHOD to METHOD so we can give the -m
 	option when using -t.

	* dv.c (bow_dv_add_di_count_weight): Add parens around MAXSHORT,
 	which seems to be needed on SunOS.

	* dv.c (_bow_dv_index_for_di): Reverse direction of for()-loop
 	that scoots document entries up to make room!  (Reported by Kamal
	Nigam.)

	* wi2dvf.c (bow_wi2dvf_dv): Gracefully handle arithmetic overflow
 	of in COUNT.  Print a warning the first time it happens.

	* rainbow.c (rainbow_test_files): Close the FP in the nested
 	function TEST_FILE!  Append "/" to the DIR.  Use
 	FILENAME_TO_CLASSNAME when setting CURRENT_CLASS.
	(main): Add 'x' to the getopt call.

	* configure.in: Look for perl5 before looking for perl.

Mon Jan 13 09:51:32 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow.c (rainbow_test_files): New function.
	(main): Added local variable WHAT_DOING; use it.  Add command-line
	option -x; call rainbow_test_files.  Add command-line option -b.

	* lex-html.c: Use bow_verbose, instead of bow_quiet to print
	message about unterminated `<'.

	* docnames.c (bow_map_filenames_from_dir): Make it work even when
 	DIRNAME is actually a filename.

Sun Jan 12 12:37:32 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow.c (filename_to_classname): Make it work even when there
 	isn't a `/' in the FILENAME.
	(rainbow_index): Use filename_to_classname().

	* install.texi: Mention the need for GNU make.
	Add missing @@end enumerate.

	* Makefile.in (default): Make it depend on all the
 	DEMO_EXECUTABLES and the PERL_RUNNABLE_FILES, instead of just
 	rainbow.

	* libbow.h: Update copyright.

	* primes.c (_bow_nextprime): Replace bzero by memset, for SunOS.

	* prind.c (_bow_barrel_set_prind_weights): Remove warning about
 	old do-nothing loop.  Remove the loop.

	* rainbow.c (rainbow_query): Set NUM_HITS_TO_SHOW equal to the
 	number of classes, instead of just 2.  Simplify output so it is
 	more machine readable.
	(main): Require a length of 39, not 10, for argv[0] in order to turn
	off BOW_VERBOSITY_USE_BACKSPACE.  (This was a hack so we don't get
 	a lot of \b's inside gdb inside emacs.)  Fix the getopt string to
 	include a `:' after `v'.

	* Makefile.in (snapshot): cvs tag the repository.

	* rainbow.c: Deal with systems that don't have getopt.h.

	* weight.c (_bow_add_to_normalizer_total): Add case for
 	BOW_METHOD_PRIND.
	(_bow_total_to_normalizer): Likewise.

Sat Jan 11 17:57:16 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* arrow.c: Fix typo in last change.

Fri Jan 10 11:03:51 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* configure.in: Look for getopt.h.

	* arrow.c: Deal with systems that don't have getopt.h.

	* rainbow-stats.pl (overall_accuracy): Print stderr for both
 	verbosity levels!

Thu Jan  9 11:46:41 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow-stats.pl (overall_accuracy): Print standard error, not
 	standard deviation.

Wed Jan  8 11:19:13 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* info_gain.c (bow_infogain_per_wi_new): Assert info gain is >= 0,
 	not > 0.
	* barrel.c (bow_barrel_keep_top_words_by_infogain): Likewise.

	* rainbow.c (rainbow_index): Rearrange
 	REUSE_ARCHIVED_BARREL_COUNTS logic so it works now.

	* vpc.c (bow_barrel_new_vpc): Don't assert DV, just continue if
 	it's NULL.

Tue Jan  7 09:45:54 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h: Declare new barrel info gain function.

Mon Jan  6 10:28:17 1997  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* barrel.c (bow_barrel_keep_top_words_by_infogain): New function. 

	* lex-gram.c (bow_lexer_gram_open_text_fp): Return NULL if LEX is
	NULL. 

	* wi2dvf.c (bow_wi2dvf_remove_wi): New function.
	(bow_wi2dvf_write): Use new SEEK_START convention, in which it is
	-1 when DV is NULL; previously, when DV was NULL, it was equal to
	the previous SEEK_START.
	(bow_wi2dvf_new_from_data_fp): Likewise.
	* libbow.h:  Declare new wi2dvf function.

	* rainbow.c, weight.c, vpc.c, score.c, libbow.h: Separate
	PrTFIDF from PrInd (Fuhr's Probabilistic Indexing).
	* prind.c: New file, for Fuhr's Probabilistic Indexing method.

	* rainbow.c (rainbow_index): Prune words by info gain in barrel,
 	not in the word vocabulary, so that `-L' can work properly.

Fri Jan  3 12:56:53 1997  Andrew McCallum  <mccallum@@pad>

	* rainbow.c (main): Add the -L option, for turning off lexing the
 	text files, and instead using the word counts in the archived
 	barrel.
	(rainbow_print_usage): Likewise.
	(reuse_archived_barrel_counts): New global variable, controlling this.

	* lex-html.c (bow_lexer_html_get_word): Change type of argument
 	SELF to match BOW_LEXER.

	* rainbow.c (main): Add the -s option, for turning off use of the
 	stoplist.
	(rainbow_print_usage): Likewise.

	* rainbow.c (main): Add the -U option, for turning off uniform
 	priors in PrTFIDF.
	(rainbow_print_usage): Likewise.

	* rainbow-stats.pl: Add test of $#ARGV to the `-s' test, so it
 	actually works the way it's supposed to.

Wed Jan  1 16:54:28 1997  Andrew McCallum  <mccallum@@pad>

	* lex-html.c (bow_lexer_html_get_raw_word): Print warning when we
 	find an unterminated open bracket `<'.  Verbosify about close
 	bracket warning with priority of BOW_VERBOSE, not BOW_PROGRESS.

	`rainbow -i -H -S' now seems to be working.

	* rainbow.c (rainbow_underlying_lexer): New global variable.
	(rainbow_html_lexer): New global variable.
	(rainbow_print_usage): Overhauled to accurately describe the valid
	arguments.
	(main): Rearrange and clean up argument handling.

	* libbow.h: Change type of argument SELF in BOW_LEXER_SIMPLE
 	word-getting subfunctions.

	* lex-simple.c (bow_lexer_simple_open_text_fp): Deal with EOF in
 	FP.  Deal with zero-length documents.  After we find END_PATTERN,
 	move the DOCUMENT_POINTER back to the beginning of of the
 	END_PATTERN.
	(bow_lexer_simple_postprocess_word): Change type of SELF from
	BOW_LEXER to BOW_LEXER_SIMPLE.
	(old_bow_lexer_simple_get_word): Old, unused function removed.

	* lex-html.c (bow_lexer_html_get_raw_word): Keep a count of the
 	HTML bracket nestings, instead of keeping track as a boolean.
	(bow_lexer_html_get_word): Postprocess word using the underlying
	lexer from SELF, not SELF itself.

Tue Dec 31 12:36:21 1996  Andrew McCallum  <mccallum@@pad>

	* int4word.c (bow_num_words): If WORD_MAP has not yet been
 	created, return 0, instead of raising an error.

	* lex-html.c (bow_lexer_html_get_raw_word): Look for end by
 	comparing to 0, not EOF.  Fix termination condition of
 	true-to-start loop.  Change type of SELF to BOW_LEXER_SIMPLE from
 	BOW_LEXER.
	(bow_lexer_html_get_word): Change type of SELF to BOW_LEXER_INDIRECT
	from BOW_LEXER.

	* lex-simple.c (bow_lexer_simple_get_raw_word): Look for end by
 	comparing to 0, not EOF!

	* libbow.h (bow_str2method): Add "tfidf" as a synonym for
 	tfidf_log_occur.

	* rainbow-stats.pl: Now the `-s' argument causes it to print only
 	accuracy average and standard deviation.
	(verbosity): New variable.

Mon Dec 30 15:34:25 1996  Andrew McCallum  <mccallum@@pad>

	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Loop over all documents
 	(LEX's) in the file.
	* int4word.c (bow_words_add_occurrences_from_text_dir): Likewise.

	* wv.c (bow_wv_new_from_lex): New function.
	(bow_wv_new_from_text_fp): Use it.  Handle NULL lex.
	* libbow.h: Declare new WV function.

	* lex-simple.c: Remove the N-gram lexer.
	* lex-gram.c: lex-indirect.c, lex-html.c: New files.
	* Makefile.in (LIBBOW_C_FILES): Added lex-gram.c, lex-html.c,
 	lex-indirect.c.
	* libbow.h: Declare new lexer functions, types and variables.

Sun Dec 29 13:04:17 1996  Andrew McCallum  <mccallum@@pad>

	* lex-simple.c: Make all the instances of BOW_LEXER use a NULL
 	DOCUMENT_END_PATTERN.
	(bow_lexer_simple_open_text_fp): Instead of scanning the FP twice,
	have it fill and grow the document buffer as it reads the FP for
 	the first time.  (This now seems to work on STDIN, although I
 	haven't tried non-NULL DOCUMENT_END_PATTERN's with it; I'm not
 	sure if FSEEK works on STDIN.)

	* libbow.h (bow_lexer): Comment the start and end patterns.

	* scan.c (bow_scan_fp_for_string): If STRING is the empty string,
 	return immediately instead of scanning to EOF.  The NULL string
 	still scans to EOF.

Fri Dec 27 20:00:30 1996  Andrew McCallum  <mccallum@@pad>

	The changes for the new lexer.  It now seems to be working.

	* libbow.h (bow_lex): New type, replacing BOW_PARSE.
	(bow_lexer): New type, replacing BOW_PARSER.
	(bow_lexer_simple): New type.  New lexers based on this.
	(bow_lex_gram): New type.
	(bow_lexer_gram): New type.
	(bow_default_lexer): Renamed from BOW_DEFAULT_PARSER.
	(bow_stem_porter): Renamed from BOW_STEM.
	(bow_isalpha): New function declaration.
	(bow_isgraph): Likewise.

	* Makefile.in (LIBBOW_C_FILES): Remove p-alpha.c, p-alonly.c,
 	p-gram.c, p-white.c.  Add lex-simple.c.
	(DEMO_C_FILES): Remove robin.c.

	* defparser.c (bow_default_lexer): Renamed from
 	BOW_DEFAULT_PARSER.

	* int4word.c (bow_words_add_occurrences_from_text_dir): Use new 
	lexer instead of old parser.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Likewise.
	* wv.c (bow_wv_new_from_text_fp): Likewise.

	* rainbow.c (rainbow_lexer): New global variable.
	(main): Use new lexer instead of old parser.  Using BOW_ALPHA_LEXER
	as the underlying lexer instead of the old BOW_ALPHA_ONLY_PARSER.

	* stem.c (bow_stem_porter): Renamed from BOW_STEM.

	* lex-simple.c: New file.

	* scan.c (bow_scan_fp_for_string): If STRING is NULL or
 	zero-length, then instead of immediately returning zero, scan
 	through the FP until EOF.

Thu Dec 26 12:20:44 1996  Andrew McCallum  <mccallum@@pad>

	The last version before the many `lexer' changes.

	* int4word.c (bow_words_write): Write the WORD_MAP_COUNTS also.
	(bow_words_read_from_fp): Read and create them.

	* dv.c (bow_dv_add_di_count_weight): Assert that the new count is
 	greater than zero.
	* prtfidf.c (_bow_barrel_set_prtfidf_weights): Assert that DV->IDF
 	is greater than zero.

Tue Dec 24 17:36:09 1996  Andrew McCallum  <mccallum@@pad>

	* rainbow-stats.pl (calculate_accuracy): Use printf and %g instead
 	of print.
	(overall_accuracy): Calculate and print standard deviation also.

	* rainbow.c (main): Use BOW_GRAM_PARSER_PARSER.

	* p-gram.c (bow_gram_parser_parser): New global variable.
	(bow_gram_parser_open_text_fp): Set it to BOW_DEFAULT_PARSER if it's
	NULL.  Use it.
	(bow_gram_parser_close): Use it.
	(bow_gram_parser_get_word): Likewise.
	* libbow.h: Declare BOW_GRAM_PARSER_PARSER.

	* prtfidf.c (bow_prtfidf_uniform_priors): New global variable.
	Default is to use *uniform* class prior probabilities.
	(_bow_barrel_set_prtfidf_weights): Don't set the DV->IDF here, we'll
	use its current value later.
	(_bow_score_prtfidf_from_wv): Move the test for !DV.  Pay attention to
	BOW_PRTFIDF_UNIFORM_PRIORS, and do the right thing.

Sun Dec 22 13:35:03 1996  Andrew McCallum  <mccallum@@pad>

	* .cvsignore: Added executables arrow, robin, rainbow-stats.

	* Makefile.in (INSTALL_FILES): New variable.
	(install): Use it.  Fix removing of old executables.  Install Perl
	files. 

	* libbow.h (bow_str2method): New macro.
	(bow_words_keep_top_by_infogain): Declare function.
	* int4word.c: Add comment.

	* rainbow.c (rainbow_index): Remove words with occurrences less
 	than X even if NUM_TOP_WORDS_TO_KEEP is non-zero.
	(main): New command-line argument `-R'.  Use new bow_str2method().

	* stoplist.c: Turn back on the builtin stoplist.

Fri Dec 20 15:53:50 1996  Andrew McCallum  <mccallum@@pad>

	* prtfidf.c: New file.

Tue Dec 17 18:19:55 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow.c (main): Added prtfidf for `-m'.

	* score.c (bow_get_best_matches): Do the right thing for prtfidf,
 	call _bow_score_prtfidf_from_wv.

	* stoplist.c (init_stopwords): Temporarily turn off the builtin
 	stoplist, for use with the demo data.  Yipes, this needs to
 	be turned back on!

	* vpc.c (bow_barrel_new_vpc): Do the right thing for prtfidf;
 	treat it like naivebayes.
	(bow_barrel_new_vpc_with_weights): Likewise.

	* weight.c (bow_barrel_set_weights): Call
 	_bow_barrel_set_prtfidf_weights when appropriate.

	* Makefile.in (LIBBOW_C_FILES): Added prtfidf.c.

Mon Dec 16 13:11:59 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* arrow.c (arrow_unarchive): Add verbosification.
	* info_gain.c (bow_infogain_per_wi_new): Fix verbosification.
	* info_gain.c (bow_infogain_per_wi_new): Add verbosifying.

	* rainbow.c (num_top_words_to_keep): Set to zero as a default.
	(rainbow_index): Make it possible to call both occurrence pruning and
	infogain pruning.
	(main): New command-line argument `-m'.

	* vpc.c (bow_barrel_new_vpc_with_weights): Create the VPC barrel,
 	and then normalize the weights, otherwise we get -1 normalizers!
	* score.c (bow_get_best_matches): Delete more leftover naivebayes
 	code.  Assert that the normalizer is greater than 1.

	* rainbow.c (num_top_words_to_keep): New global variable set from
 	command line.
	(rainbow_index): New nest function DO_INDEXING.  Use it.  Add term
	pruning according to information gain.
	(main): New command line argument `-T' to set num top words.

	* robin.c (robin_index): Do the right thing when WI is -1.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Likewise.
	* wv.c (bow_wv_new_from_text_fp): Likewise.

	* int4word.c (bow_words_keep_top_by_infogain): Implemented.
	(bow_words_add_occurrences_from_text_dir): Do the right thing when WI
	is -1.

	* info_gain.c (bow_infogain_per_wi_new): Set info gain to 0 when
 	the DV for that word NULL.

	* barrel.c (bow_barrel_new): Add new argument.  Separate
 	capacities for the cdocs array and the wi2dvf.
	* libbow.h: Declare new argument in bow_barrel_new.
	* arrow.c (arrow_index): Use new extra argument to barrel_new.
	* vpc.c (bow_barrel_new_vpc): Use new extra argument to
 	barrel_new.

	* naivebayes.c (_bow_score_naivebayes_from_wv): Removed ununsed
 	local variable.

Wed Dec 11 15:19:44 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* Makefile.in (diff): Ignore the non-zero exit status from `diff'.

	* Makefile.in (dist): Call cvs rtag.
	(diff): New target.
	(clean): Delete *.info and *.dvi.
	(maintainer-clean): Delete $(PERL_RUNNABLE_FILES), configure, README,
	and INSTALL.

	* int4word.c (bow_words_keep_top_by_infogain): New function; not
 	yet implemented.

	* naivebayes.c (_bow_score_naivebayes_from_wv): Incoporate P(w|C)
 	for all words in query document, not just those in the DV.

	* rainbow.c: Added more comments.
	(rainbow_wi2dvf_sum_classes): Function removed.

	* Version (BOW_MINOR_VERSION): Version 0.5.
	* libbow.h (BOW_MINOR_VERSION): Likewise.
	This version given to Kamal.

Tue Dec 10 20:22:29 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* rainbow-stats.pl: New file.  Changed from Sean's version to
	include scientific notation in number regular expression.

	Naive-Bayes code runs without crashing, but it provides horrible
	results on the CIA type data.  Average accuracy of 7%.  It almost
	always chooses Defense_Forces.

	* naivebayes.c (_bow_barrel_set_naivebayes_weights): Rewrite from
 	scratch, avoiding the use of heaps.

	* libbow.h: Include <limits.h>, so we get PATH_MAX.

	* naivebayes.c: New file.
	* Makefile.in (LIBBOW_C_FILES): Added naivebayes.c.
	* weight.c: Remove the NaiveBayes code to naivebayes.c.
	* score.c (bow_get_best_matches): Likewise.
	* vpc.c (bow_barrel_new_vpc): Remove the NaiveBayes prior-setting
 	to naivebayes.c.

	* rainbow.c: Remove the commented-out pre-vpc code.  Change the
 	default method to naivebayes.

Mon Dec  9 10:11:05 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	CIA type data shows performance improvement from 1-grams to
	1/2-grams: 79% to 68% accuracy.
	
	* wi2dvf.c (bow_wi2dvf_dv): Fix assertion for when doing the last WI.

	* vpc.c (bow_barrel_new_vpc): Verbosify and fix off-by-one error
 	in class index handling.

	* rainbow.c (rainbow_classnames): New global variable.
	(rainbow_unarchive): Set it.
	(rainbow_index): Verbosify while we read files for word pruning.

	* libbow.h (PATH_MAX): Avoid warning in surrounding #if.
	(bow_fopen): Use perror() as well as bow_error.

	* int4word.c (bow_words_add_occurrences_from_text_dir): Keep track
 	of the text file count, and verbosify.

	* barrel.c (bow_barrel_new): Create the new wi2dvf with
 	bow_num_words(), not CAPACITY.
	(_bow_barrel_cdoc_free): Only free FILENAME if it's non-NULL.

	* array.c (bow_array_entry_at_index): Fix off-by-one error in
 	assertion.

	* rainbow.c: Make it work with new vpc function, but old code is
 	still there commented-out.

	* libbow.h: Declare new vpc and infogain functions.

	* info_gain.c: Comment new functions.

	* score.c (bow_get_best_matches): Add code to do NaiveBayes;
 	thanks to Dunja, who helped.

	* vpc.c (bow_barrel_new_vpc): Totally rewritten.  Now simpler and
 	faster.  Don't create a dv_heap, just go through the wi2dvf by
 	words.
	(bow_barrel_new_vpc_with_weights): New function.

	* weight.c (_bow_barrel_set_weights_naivebayes): Renamed from
 	_bow_barrel_set_weights_sans_idf.  Verify that the class priors
 	are set.
	(bow_barrel_set_weights): Use new function name.

	* split.c (drand48, srand48) [__sun__]: Add prototypes.

Fri Dec  6 17:57:46 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* wi2dvf.c (bow_wi2dvf_print_stats): Don't use //-style comments.
	* weight.c (bow_barrel_set_weight_normalizers): Likewise.

	* libbow.h: Add inclusions and declarations needed for SunOS;
 	thanks to Sean.

	* rainbow.c (prune_words_with_occurrences_less_than): New global
 	variable.
	(rainbow_index): Use it.
	(rainbow_query): Set and normalize the QUERY_WV weights!
	(rainbow_test): Likewise.

	* dv.c (bow_dv_default_capacity): Value changed from 4 to 2, in an
 	effort to reduce memory use.

	* email.c (bow_email_get_replyid): Don't insist that the opening
 	`<' is on the same line as "In-Reply-To:".

	* int4word.c (word_map_counts, word_map_counts_size): New static
 	variables.
	(bow_word2int_do_not_add): New static variable.
	(_bow_int4word_initialize): New function.
	(bow_word2int): Use it.  Pay attention to bow_word2int_do_not_add.
	(bow_words_set_map): New function.
	(bow_word2int_add_occurrence): New function.
	(bow_words_occurrences_for_wi): New function.
	(bow_words_remove_occurrences_less_than): New function.
	(bow_words_add_occurrences_from_text_dir): New function.

	* libbow.h: Declare new bow_words_ functions.

	* robin.c (robin_index): Use new function
 	bow_word2int_add_occurrence().

	* weight.c (bow_barrel_set_weight_normalizers): Free the heap
 	before returning!

	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Use new function
 	bow_word2int_add_occurrence().

	* wv.c (bow_wv_new): Initialze normalizer to 1.
	(bow_wv_new_from_text_fp): Likewise.
	(bow_wv_new_from_text_fp): Use new bow_word2int_add_occurrence().

Thu Dec  5 09:49:46 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* score.c (bow_get_best_matches): Make sure QUERY_WV->NORMALIZER
 	is non-zero.
	* weight.c (bow_wv_set_weight_normalizer): Make sure TOTAL is
 	non-zero.

	* rainbow.c: Include <errno.h> for DEC Alpha's.
	* arrow.c: Likewise.

Wed Dec  4 10:44:52 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* Makefile.in (PERL): New variable.
	(LIBBOW_C_FILES): Added p-gram.c.
	(PERL_FILES): New variable.
	(PERL_RUNNABLE_FILES): New variable.
	(DIST_FILES): Added PERL_FILES.
	(all): Add dependancy on PERL_RUNNABLE_FILES.
	(PERL_RUNNABLE_FILES): New rule.
	* configure.in: Look for perl in path.

	* rainbow.c (infogain_words_to_print): New global variable, set by
 	command-line arguments.
	(main): Set BOW_DEFAULT_PARSER to BOW_GRAM_PARSER; set
	BOW_GRAM_PARSER_GRAM_SIZE to 1.  New command line options, -g, -I,
 	-h.  Call BOW_INFOGAIN_PER_WI_PRINT.

	* info_gain.c (bow_infogain_per_wi_new): New function.
	(bow_infogain_per_wi_print): New function.
	(bow_barrel_scale_by_info_gain): Use new function above.

	* p-gram.c: New file.
	* libbow.h (bow_parser_skip_net_header): Declare new global
 	variable.
	(bow_gram_parser): Declare new parser struct.
	(bow_gram_parser_gram_size): Declare new global variable.
	* defparser.c (bow_parser_skip_net_header): Define and initialize
 	to 0.
	* p.inc (BOW_P_OPEN_NAME): If BOW_PARSER_SKIP_NET_HEADER is
 	non-zero, scan into the FP past the first "\n\n", in order to skip
 	over the email/news header.

Tue Dec  3 10:20:11 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* wv.c (bow_wv_count_for_wi): Use bow_wv_entry_for_wi() instead of
 	duplicating code.

	* wi2dvf.c (bow_wi2dvf_new): Initialize the FP to NULL!
	(bow_wi2dvf_dv): Assert that WI isn't larger than the WI2DVF->SIZE.
	Assert that IDF isn't NaN; twice.

	* split.c (bow_test_new_heap): Drastically simplify.
	(bow_test_next_wv): Free the old *WV if isn't non-NULL.  Use
	bow_wv_new() instead of creating it with malloc by hand.  When
 	we've reached the end of the heap, free the *WV.

	* score.c (bow_get_best_matches): Make CURRENT_SCORE a double
 	instead of a float.  Assert that IDF isn't NaN.  Don't normalize
 	the query WV.  Most important: avoid a memory leak by freeing the
 	HEAP when we are done with it!

	* rainbow.c (rainbow_wi2dvf_sum_classes): Set the class IDF from
 	the doc IDF.  Still add in the count and weight, even if the
 	weight is zero.  This means the wi2dvf will expand to the proper
 	size so we can meaningfully get DV's from it.
	(rainbow_set_weights): Don't scale by info gain.
	(rainbow_test): Initialize the QUERY_WV to NULL so bow_test_next_wv()
	will know not to free an uninitialized value.

	* heap.c (bow_dv_heap_free): New function.
	(bow_make_dv_heap_from_wv): Add assertion checking for IDF NaN.

	* dv.c (bow_dv_new_from_data_fp): Add comment about FP assertion.

	* weight.c: Assert that IDF is not NaN.  Don't print progress
 	verbosity every time through the loop---it's slowing us
 	down---only print it every 10 times through the loop.

	* dv.c (bow_dv_new): Initialize the IDF to zero!
	(bow_dv_write_size): Include the IDF size in the return value.
	(bow_dv_write): Write the IDF.
	(bow_dv_new_from_data_fp): Read the IDF.

	* rainbow.c: Keep two barrels: one for classes, one for documents.
	(num_trials, test_percentage, method): New global variables set by
	command-line switches.
	(rainbow_archive): Deal with both barrels.
	(rainbow_unarchive): Likewise.
	(rainbow_set_weights): New function...
	(rainbow_wi2dvf_sum_classes): ...using code pulled from here.
	(filename_to_classname): New function.
	(rainbow_test): New function.
	(main): Add new command line switches -t, -p.  Call rainbow_test().

	* arrow.c: Use new weight normalization functions.

	* split.c: Renamed functions to all begin with `bow_test_'.  Use
 	argument `barrel' instead of `cdoc' and `wi2dvf'.

	* weight.c: Use bow_method instead of bow_idf_type and
 	bow_normalize_type.  All functions changed.

	* score.c (bow_get_best_matches): Rename some variables.  Add
 	mechanics of NaiveBayes.  Normalize query vector.  Normalize
 	non-NaiveBayes outside the loop.

	* barrel.c (bow_barrel_new): Fix initialization of METHOD.
	(bow_barrel_add_from_text_dir): Initialize the PRIOR.
	(_bow_barrel_cdoc_write): Write the PRIOR.
	(_bow_barrel_cdoc_read): Read the PRIOR.
	(bow_barrel_new_from_data_fp): Read the METHOD properly.

	* libbow.h: Remove types as arguments to some weight functions.
  	Rename the test/train split functions.
	(bow_cdoc): Added member PRIOR.
	(bow_barrel): Added member METHOD.
	(bow_method): New enum.
	(bow_idf_type): Removed.
	(bow_normalize_type): Removed.

	* Makefile.in (LIBBOW_C_FILES): Added split.c.

	* barrel.c (bow_barrel_new): Set RET->METHOD to default of
 	BOW_METHOD_TFIDF.
	(bow_barrel_new_from_data_fp): Read METHOD.
	(bow_barrel_write): Write METHOD.

	* weight.c (_bow_add_to_normalizer_total): New function.
	(_bow_total_to_normalizer): New function.
	(bow_barrel_set_weight_normalizers): Use them.  
	(bow_wv_set_weights): Function moved here from wv.c.
	(bow_wv_set_weight_normalizer): Likewise.
	* wv.c: Weight and normalizer functions moved to weight.c.

	* libbow.h: Move the WV weight-setting functions next to the
 	barrel weight-setting functions.
	(bow_cdoc): Rename memeber LENGTH to NORMALIZER, for clarity.
	(bow_barrel_set_weight_normalizers): Renamed from
	bow_barrel_normalize_weights, since it doesn't actually change the
 	weight values.

	* wv.c: Include <math.h>
	(sqrtf): New macro.
	(bow_wv_set_normalizer): Renamed from bow_wv_set_norm().  New argument
	TYPE.  Obey new argument.
	(bow_wv_set_weights): New argument TYPE. Obey it.  Don't call the
	normalizer function.
	(bow_wv_write): Use new name WV->NORMALIZER.
	(bow_wv_new_from_data_fp): Likewise.
	* score.c (bow_get_best_matches): Use renamed NORMALIZER member.
	* barrel.c (_bow_barrel_cdoc_write): Likewise.
	(_bow_barrel_cdoc_read): Likewise.

	* libbow.h: Rename and add new arguments to WV functions.

Mon Dec  2 13:14:10 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* arrow.c (arrow_unarchive): Don't close the barrel FP, because we
 	still have yet to read the DV's from it!

	* barrel.c (bow_barrel_add_from_text_dir): Print warning if we end
 	up finding more binary files than text files.

	* score.c: Some formatting and comment changes.

	* weight.c: Some comment and variable name changes.
	(_bow_add_to_idf): Renamed from bow_add_to_total.
	(_bow_barrel_set_weights_nb): New function for doing Naive Bayes.
	(bow_barrel_set_weights): Call it if necessary.

	* libbow.h: Declare new vpc function.
	(bow_idf_nb): New idf type.
	* Makefile.in (LIBBOW_C_FILES): Added vpc.c.
	* vpc.c (bow_barrel_new_vpc): Renamed from bow_barrel2vpc_barrel.
  	Replace use of printf() with bow_verbosify().  Minor formatting
 	changes.

Mon Dec  2 13:09:10 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* vpc.c: New file - implements vector per class models. Basically,
 	take a barrel and produce a vector per class barrel from it.

Tue Nov 26 15:56:07 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* weight.c (_bow_add_to_total): Renamed to include a prefixing
 	`_'.  Declared `static inline'.
	(bow_barrel_set_weights): Overhauled and simplified.  I'm not sure
 	I haven't broken it, though.  Previously some of the `if()else'
 	clauses seemed contradictory to me.

	* score.c (bow_get_best_matches): Add comment about my perceived
 	pending need for normalization of the query vector.

	* dv.c (_bow_dv_index_for_di): Add 1 to the DV length when it was
 	zero!
	(bow_dv_add_di_count_weight): New function, replacing
	bow_dv_add_di_count.
	(bow_dv_add_di_weight): Function removed.
	* libbow.h: Declare new wi2dvf function, and remove old ones.
	* rainbow.c (rainbow_wi2dvf_sum_classes): Use new dv function.
	* wi2dvf.c (bow_wi2dvf_add_wi_di_count_weight): New function,
 	replacing bow_wi2dvf_add_wi_di_count.  Use new dv function.
	(bow_wi2dvf_add_di_wv): Use new dv function.
	(bow_wi2dvf_add_di_text_fp): Likewise.

	* Makefile.in (LIBBOW_C_FILES): Added scan.c; although this will
 	be taken away once I change parsing to use strings and librx.
	* scan.c: New file.

	* heap.c (bow_make_dv_heap_from_wi2dvf): Add silly assert()ion.

	* email.c (bow_email_get_date): Don't cause error when Date isn't
 	found, just return 0.

	* dv.c (_bow_dv_index_for_di): New function that captures the guts
 	of preparing a spot to add a count or weight.
	(bow_dv_add_di_count): Use it.
	(bow_dv_add_di_weight): Use it.

	* info_gain.c (bow_entropy): Ensure COUNTS[i] isn't zero before
 	calculating entropy.

Mon Nov 25 11:51:35 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* weight.c: Added support of bow_prtfidf weighting which gives an
 	idf = sqrt(total occurances/occurances).
	(bow_barrel_set_weights): added code to calculate the total number
 	of occurances and changed idf calculations that had those pesky
 	1.0's with the real totals intended. Doing things this way ensures
 	the weights don't go below 0.

	* score.c (bow_get_best_matches_euclidian): New function.  Gets
 	best matches badet on the euclidean distance between vectors
 	instead of the cosine of the angel between them.

	* dv.c (bow_dv_add_di_weight): Made this function capable of
 	updating weights that occur before the last element entered. It
 	assumes the documents are in the list in ascending order of their
 	indices. Should make this change to the bow_dv_add_di_count
 	function as well, but this was the minimum I needed to get vector
 	per class stuff done.

Mon Nov 18 14:17:55 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* wv.c (bow_wv_set_norm): Initialize TOTAL to zero!  It was
 	uninitialized.
	(bow_wv_write): Write the NORM!
	(bow_wv_new_from_data_fp): Read it.
	(bow_wv_write_size): Adjusted for writing NORM.

	* stoplist.c (bow_stoplist_add_from_file): Screaming verbosify
 	each word that's added.

	* heap.c (bow_make_dv_heap_from_wv): Get the DV using
 	bow_wi2dvf_dv(), not by accessing the structure directly.
  	Otherwise, we will no properly properly read in the DVF from disk.
	* weight.c (bow_barrel_set_weights): Likewise.

	* p.inc (BOW_P_GET_WORD_NAME): Also check if word is on the
 	stoplist *after* stemming.

Tue Nov  5 12:15:37 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* weight.c (bow_barrel_set_weights): Use the total number of
 	documents instead of 1.0.

Fri Nov  1 11:27:23 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* p.inc: Fix the handling of BOW_P_STOPLIST_CHECKER.

	* int4str.c (bow_int4str_new_from_fp): Make it work even for
 	strings that contain spaces, (but not newlines).
	(bow_int4str_write): Make sure the strings don't contain newlines.

	Add generalizable parsing facilities.
	* libbow.h (bow_parse, bow_parser): New types.  Add new parsing	funcs.
	(bow_get_word): Function removed.  Use new parsing facilities instead.
	* Makefile.in (DIST_FILES): Added p.inc.
	* Makefile.in (LIBBOW_C_FILES): Added p-alpha.c, p-alonly.c, p-white.c.
	* p.inc, p-alpha.c, p-alonly.c, p-white.c: New files.
	* Makefile.in (LIBBOW_C_FILES): Added defparser.c.  Removed
 	getword.c.
	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): Use new parser.
	* wv.c (bow_wv_new_from_text_fp): Use new parser.

	* arrow.c (arrow_index): Use new bow_barrel_add_from_text_dir
 	function.

Thu Oct 31 15:18:49 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* Version (BOW_MINOR_VERSION): Version 0.4.
	* libbow.h (BOW_MINOR_VERSION): Version 0.4.

	* rainbow.c: Add output filename feature.  Use bow_idf_words,
 	which unlike bow_idf_log_words, seems to work.
	(rainbow_index): Scale by information gain.

	* barrel.c (bow_barrel_add_from_text_dir): Add new EXCEPT_NAME
 	argument.  Deal with NULL EXCEPT_NAME.
	* libbow.h: Add new argument to barrel function.

	* weight.c (bow_barrel_set_weights): Add prefix and postfix
 	verbosity strings.
	(bow_barrel_normalize_weights): Add verbosifying.
	* info_gain.c (bow_barrel_scale_by_info_gain): Add verbosifying.
	* barrel.c (bow_barrel_add_from_text_dir): Don't print the number
 	of "binary files".
	* rainbow.c: Added some verbosifying.

	* rainbow.c: Don't close the rainbow_barrel fp.  Set the weights
 	in the right place.  Put the indexing code in main().  Now running
	to completion.

	* dv.c (bow_dv_new_from_data_fp): Add new assertion that should
 	help us catch closed FP's.

	* docnames.c (bow_map_verbosity_level): New global variable.
	(bow_map_filenames_from_dir): Use it.

	* barrel.c (bow_barrel_add_from_text_dir): Renamed from
 	bow_barrel_new_from_text_dir.  Don't create a new barrel, just add
 	to a pre-existing one.
	* libbow.h: Declare renamed function.

	* libbow.h (bow_fwrite_string): Handle the NULL string for
 	argument S.
	(bow_fread_string): Match bow_fwrite_string handling of NULL.

Mon Oct 28 12:03:11 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* info_gain.c (bow_barrel_scale_by_info_gain): Renamed from
 	bow_wi2dvf_scale_by_info_gain.
	* libbow.h: Rename info gain function to use `barrel'.

	* rainbow.c: Totally rewritten to be a document classifier.

	* wi2dvf.c (bow_wi2dvf_add_di_wv): Increase wi2dvf size with a
 	MAX(), so we are guaranteed to be big enough.
	(bow_wi2dvf_add_wi_di_count): Likewise.
	(bow_wi2dvf_add_wi_di_weight): Likewise.
	(bow_wi2dvf_write): Incorporate initial seek position into
	calculations, in case we are writing to a file that already has
 	other stuff at the beginning.

	* barrel.c (bow_barrel_free): New function.
	(bow_barrel_new_from_text_dir): Print shorter verbosity.
	* libbow.h: Declare bow_barrel_free().

	* arrow.c (arrow_index): Set the weights.
	(main): Raise error if no text documents found.

	* libbow.h: Declare bow_barrel_new(), and fix typo.

	* wi2dvf.c (bow_wi2dvf_add_wi_di_weight): New function.
	* libbow.h: Declare new wi2dvf function.

	* dv.c (bow_dv_add_di_weight): New function.
	* libbow.h: Declare new dv function.

	* weight.c (bow_barrel_set_weights): Renamed from
 	bow_wi2dvf_set_weights.
	(bow_barrel_normalize_weights): Renamed from
	bow_wi2dvf_normalize_weights.
	* libbow.h: Rename weight functions to use `barrel'.

	* barrel.c (bow_barrel_new_from_text_dir): Take new CLASS
 	argument.  Set the `class' of the new cdoc's accordingly.
	* libbow.h: Add new argument to barrel function.

Fri Oct 25 13:05:16 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* arrow.c (main): Create the data directory if it doesn't exist
 	already.

	* Version (BOW_MINOR_VERSION): Version 0.3.

	* sarray.c (bow_sarray_new_from_data_fp): Renamed from
 	bow_sarray_new_from_fp.
	* libbow.h: Rename sarray function.

	* Makefile.in (version.texi): Use renamed BOW_ variables.
	(libbow.h): New target with rules that keep it up to date with
	./Version.
	* libbow.h (BOW_MAJOR_VERSION): New macro.
	(BOW_MINOR_VERSION): New macro.
	(BOW_VERSION): New macro.
	* Version (BOW_MAJOR_VERSION): New variable.
	(BOW_MINOR_VERSION): New variable.
	(BOW_VERSION): Use them; renamed from LIBBOW_VERSION.

	* arrow.c: New file.
	* Makefile.in (DEMO_C_FILES): Added arrow.c.

	* barrel.c: New file.
	* libbow.h: Declare barrel archiving functions.

	* stoplist.c (bow_stoplist_add_from_file): Add a verbosify
 	message.

Wed Oct 23 16:45:46 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h (bow_barrel): New type.  Use it in all places where a
 	WI2DVF and CDOCS were used together; several function arguments
 	changed.
	* wi2dvf.c (bow_wi2dvf_new_from_text_dir): Function removed.
  	Similar function is now in barrel.c.
	* weight.c (bow_wi2dvf_set_weights): Use bow_barrel.
	(bow_wi2dvf_normalize_weights): Likewise.
	* score.c (bow_get_best_matches): Use bow_barrel.
	* info_gain.c (bow_wi2dvf_scale_by_info_gain): Use new bow_barrel
 	type.
	* Makefile.in (LIBBOW_C_FILES): Add barrel.c.

	* array.c (bow_array_new_from_data_fp): Renamed from
 	bow_array_new_from_fp.
	* sarray.c (bow_sarray_new_from_fp): Use renamed function
 	bow_array_new_from_data_fp.

Tue Oct 22 14:03:38 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* email.c (_scan_fp_for_string): Make `\n' at the beginning of the
 	search string match the beginning of the file.

	* error.c (_bow_error) [__linux__]: Call abort() instead of exit()
 	because it lets us find ourselves in GDB.  Still don't do it for
 	non-Linux systems, because apparently on other systems there was a
 	problem with flushing stderr when calling abort().

	* docnames.c (bow_map_filenames_from_dir): Don't verbosify the
 	directory names if we're not BOW_VERBOSITY_USE_BACKSPACE.

	* email.c: To several functions add new argument that negates
 	test, or that insists on a search all on one line.
	(_bow_email_get_email_address): New function.
	(bow_email_get_sender): New function.
	(bow_email_get_recipient): New function.
	(bow_email_get_date): New function.
	* libbow.h: Declare new email functions.

Mon Oct 21 12:08:45 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h (bow_parse_news_headers): Add missing semi-colon to
 	declaration.

	* info_gain.c (bow_entropy): Get the "document vector" with
 	bow_wi2dvf_dv(), not by following the pointer directly.
  	Otherwise, we won't properly read the DV in from the file, and may
 	get inappropriate NULLs.

	* Makefile.in (LIBBOW_C_FILES): Add info_gain.c.

	* HACKING: Correct directions for checking out bow from CVS.

Sat Oct 19 00:49:08 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* news.c: Function for parsing news article headers. Useful for looking
	for crosspostings for multiple classifications.
	(bow_parse_news_headers): Added a getc to dump the first whitespace
	character after the : proceeding the header
	(bow_headers2newsgroups): New function to grok the bow_sarray returned
	by bow_parse_new_headers and return a bow_array of strings 
	corresponding to every newsgroup mentioned in the newsgroup line.
	* libbow.h: Added def'n for new function

	* libbow.h: Added bow_parse_news_headers

Fri Oct 18 10:50:23 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* info_gain.c (log2f): #define it if ./configure determined that
 	we don't have it.
	(bow_entropy): Use log2f instead of log2.
	(MIN): Macro removed.  It's now in libbow.h.

Fri Oct 18 21:32:42 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* array.c (bow_array_append): Changed test from array->length > 
	array->size to array->length >= array->size. When array->length = 
	array->size, we're run out of space.
	(bow_array_init): Assigned array->free_func to free_func. Otherwise
	free_func is not initialised and the bow_array_free function will
	sometimes crash.

Fri Oct 18 10:50:23 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h: Declare new functions.
	(bow_wv): LENGTH entry renamed to NORM.

	* wv.c (bow_wv_set_norm): New function.
	(bow_wv_set_weights): New function.

	* error.c (_bow_error): Call exit(-1) instead of abort().  It
	makes a prettier error message on the console.

	* heap.c (bow_make_dv_heap_from_wi2dvf): Separate the index into
 	words and index into the heap so that we can handle wi2dvf's that
 	have some NULL "document vectors".

	* libbow.h (MIN): New macro.
	(MAX): New macro.
	(bow_verbosity_use_backspace): New global variable declaration.
	* error.c (bow_verbosity_use_backspace): New global variable.
	(bow_verbosify): Use it.
	* weight.c (MIN): Remove definition. It's now in libbow.h.

	* libbow.h (bow_wi2dvf_normalize_weights): Change from `normalise'
 	to American spelling.  The *.c file had already been changed.

Fri Oct 18 01:15:57 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* info_gain.c (bow_wi2dvf_scale_by_info_gain): New file,
	information gain routine.
	(bow_entropy): Cast some of the arithmitic to floats - dividing one 
	integer by another tends to go to 0 here.
	* libbow.h: added definition for above.
 
	* split.c: (bow_next_test_wv) Free heap when we've exhausted the
 	test set (for tidyness)

	* heap.c (bow_make_dv_heap_from_wi2dvf): Changed malloc to
 	bow_malloc
	(bow_make_dv_heap_from_wv): Changed malloc to bow_malloc

Thu Oct 17 11:08:42 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* score.c (bow_get_best_matches): Add an assert()'ion that WI
 	match the word index of our current location in the word vector.

	* libbow.h: Rename local variables from num_written to num_read
 	where appropriate.

	* heap.c (bow_make_dv_heap_from_wv): Fix typo: continue when DV is
 	NULL, not the other way around.

	* wi2dvf.c (bow_wi2dvf_write): Don't close the FP at the end!  We
 	didn't open it.
	(bow_wi2dvf_new_from_data_file): Don't close the FP, it will still be
	needed to read the DV's.

	* libbow.h (bow_wi2dvf_write_data_file,
 	bow_wi2dvf_new_from_data_file): Re-add declarations for these
 	functions.

	* heap.c (bow_make_dv_heap_from_wv): WV->LENGTH is not the number
 	of entries in the word vector, it is the Euclidean length!  Change
 	all uses of WV->LENGTH to WV->NUM_ENTRIES.
	* libbow.h (bow_wv): Renamed element `length' to `total' in an
 	attempt to choose a less confusing name.  Other naming suggestions
 	welcome.

	* array.c (bow_array_new_from_fp): Set the LENGTH of the new
 	array; before it was uninitialized!

	* libbow.h (bow_fwrite_string): Properly calculate the number of
 	characters written.
	(bow_fread_string): Likewise, and parenthesis indexing of S for proper
	termination.
	(bow_idf_type): Added `bow_idf' as prefix to enum members, and removed
	`total' from end.
	* weight.c: Use new bow_idf enum names.
	(bow_wi2dvf_set_weights): Handle the case in which a document vector
	in the WI2DVF is NULL.

	* libbow.h: Include <assert.h>

	* heap.c (bow_make_dv_heap_from_wv): Make it work even when not
 	all the words in WV have document vectors in WI2DVF.  Keep
 	separate indices into the word vector and into the heap.

	* int4str.c (HEADER_STRING): New macro.
	(bow_int4str_write): Write it to the FP.
	(bow_int4str_new_from_fp): Expected it from the FP.

	* array.c (HEADER_STRING): New macro.
	(bow_array_write): Write it to the FP.
	(bow_array_new_from_fp): Expected it from the FP.

	* bmalloc.c: Remove previous contents.  Now get the functions
 	directly from libbow.h.
	* io.c: Likewise.
	* Makefile.in (io.o bmalloc.o): Indicate that they now depend
 	(completely) on libbow.h.
	* libbow.h (_BOW_MALLOC_INLINE_EXTERN): New macro for compiling
 	these extern inline functions in library .o files.
	(_BOW_IO_INLINE_EXTERN): Likewise.
	(bow_fwrite*, bow_fread): Assert the return values.

	* int4docn.c (bow_docnames_write): Take FILE* argument instead of
 	const char *.
	(bow_docnames_read_from_fp): Renamed frombow_docnames_read(), likewise
	as above.
	* libbow.h: Change argument types and function name for
 	bow_docnames archiving.
	* docnames.c (bow_map_filenames_from_dir): Use renamed
 	bow_verbosity_level enum.

	* libbow.h (bow_error): Don't print anything if
 	bow_verbosity_level indicates bow_silent.

Thu Oct 17 14:36:44 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* split.c (bow_next_test_wv): Function now takes a pointer to a pointer
	to a bow_wv. It sets this to point to a pointer to the wv it creates
	and returns the integer document index to the test document 
	described by this word vector. 
	(bow_test_split): Fixed bug in counting that meant we sometimes ended
	up with fewer test docs than asked for.
	(bow_test_split): Random number generator is now seeded with time.

	* libbow.h: (bow_next_test_wv) Argument change as above.

Wed Oct 16 08:35:45 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h (bow_screaming): Renamed from bow_shutup_already.
  	Commented all bow_verbosity_levels.

	* wi2dvf.c (bow_wi2dvf_write_data_file): Close the FP at the end!
	(bow_wi2dvf_new_from_data_file): Likewise.
	(bow_wi2dvf_new_from_data_fp): Don't assert feof(), because there may
	be multiple things written to one file.

	* io.c (bow_fread_string): Add parenthesis in order to dereference
 	string pointer properly.

	* libbow.h: Comment changes to #include lines.
	(bow_fopen): New macro.

	* wi2dvf.c (bow_wi2dvf_new_from_data_fp): Renamed from
 	bow_wi2dvf_new_from_fp.  All callers changed.
	* libbow.h: Renamed function.

	* Makefile.in (LIBBOW_C_FILES): Added heap.c.

	* io.c (bow_fwrite_string): New function from libbow.h.
	(bow_fread_string): Likewise.

Wed Oct 16 14:03:07 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* weight.c: Checked for case total == 0 which can occur if no 
	documents in the model had this word. Without this check, we get
	a floating point error when trying to divide by total

	* score.c: (bow_get_best_matches) Added support for a bow_array of
	cdocs.

	* weight.c: Messed up loop test on outer loop - Reset it to the max_wi
	which Andrew changed it to before.

	* libbow.h: Added defs for functions in split.c

	* split.c: New file with functions for dealing with test sets.

	* weight.c: Added bow_array *cdoc arguments to
 	bow_wi2dvf_set_weights
	(so we can only do docs in the model), and to
 	bow_wi2dvf_normalize_weights where we only calculate the length of
 	docs in the model and we store the length in the corresponding
 	cdoc structure.

	* libbow.h: Added include of string.h to stop compiler complaint
	on alpha

Wed Oct 16 08:35:45 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* int4word.c (bow_words_write): Now takes FILE* argument instead
 	of filename.
	(bow_words_read_from_fp): Renamed from bow_words_read_from_file, and
	likewise as above.
	* libbow.h (bow_words_read_from_fp): Renamed from bow_words_read.

	* libbow.h: Change argument types of bow_words_write function.
	(bow_error): Enclose expansion in parenthesis, so that it parses
	properly when put inside an `else' statement without brackets.

	* wi2dvf.c (bow_wi2dvf_write): New function.
	(bow_wi2dvf_write_data_file): Use it.  This function is now deprecated.
	(bow_wi2dvf_new_from_fp): New function.
	(bow_wi2dvf_new_from_data_file): Use it.  This function deprecated.
	(bow_wi2dvf_free): New function.
	* libbow.h: Declare new functions.  Remove deprecated functions.

	* sarray.c (bow_sarray_write): New function.
	(bow_sarray_new_from_fp): New function.
	* libbow.h: Declare new functions.

	* wv.c (bow_wv_new): New function.
	(bow_wv_write_size): New function.
	(bow_wv_write): New function.
	(bow_wv_new_from_data_fp): New function.
	* libbow.h: Declare new functions.

	* weight.c (bow_wi2dvf_normalize_weights): Use renamed variable
 	wv_length.

	* array.c (bow_array_write): New function.
	(bow_array_new_from_fp): New function.
	* libbow.h: Declare new functions.

	* int4str.c (bow_int4str_write): Make second argument a FILE*
 	instead of a filename.
	(bow_int4str_new_from_fp): New function.
	* libbow.h: Declare new function.  Update argument type.

Tue Oct 15 10:07:42 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* wv.c (bow_wv_entry_for_wi): New function.
	* libbow.h: Declare new function.

	* libbow.h: Update for function name changes.
	(bow_class): New structure.

	* weight.c (bow_wi2dvf_normalize_weights): Renamed from
 	bow_normalize_word_vectors.  Minor format, comments and variable
 	name changes.

	* configure.in: Check for existance of log2f() and sqrtf()
 	functions.

	* weight.c (bow_wi2dvf_set_weights): Renamed from
 	bow_assign_tfidf_weights because it is specific to wi2dvf
 	structures, and we could imagine having a di2wvf structure in the
 	future, and because we could imagine non-TFIDF weight-setting
 	schemes.  Don't loop over all word indices up to bow_num_words(),
 	only loop up to the min of that and size of WI2DVF.  Raise an
 	error if there is an unrecognized TYPE.  Fix bow_verbosify() call.

Mon Oct 14 16:17:26 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h: Indentation and comment fixes.

	* rainbow.c (main): Don't exit() prematurely.  Actually write the
 	data file and read it back in again.

	* wi2dvf.c (bow_wi2dvf_write_data_file): Use sizeof(int) instead
 	of sizeof(long) since it better matches reality.

	* dv.c (bow_dv_write_size): Sum short's, not int's, or else we'll
 	lie about the results of bow_dv_write.

	* getword.c (bow_get_word) [NON_ALPHA_IN_WORD]: New macro
 	selecting new code that will reject a word if it contains any
 	non-alphabetic characters.  Current default is to include this
 	code.

	* bitvec.c (bow_bitvec_new): Properly initialize all values to 0,
 	not to 1.

Fri Oct 11 17:37:28 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* bitvec.c: Finish and debug implementation.
	* libbow.h: Add bow_bitvec declarations.

	* Makefile.in (LIBBOW_C_FILES): Added bitvec.c.
	* bitvec.c: New file.

Fri Oct 11 17:14:12 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* libbow.h: Resolved a conflict in bow_cdoc / bow_doc definition.

Thu Oct 10 09:44:55 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* stoplist.c (bow_stoplist_add_from_file): Don't raise an error if
 	we can't open the file.  This way, we can simply call the function
 	with several "guessed" filenames.
	* libbow.h: Update comment for stoplist function.

	* getword.c (bow_get_word): Delineate words by space characters
 	and non-printable characters, not by non-alphabetic characters,
 	(but still reject words with "too many" digits).  This is an
 	effort to return entire email addresses and URL's as single words.

	* stoplist.c: Totally re-written using a bow_int4str.
	(bow_stoplist_present): Renamed from bow_on_stoplist.
	(bow_stoplist_add_from_file): New function.
	* libbow.h: Declare new stoplist functions.
	* Makefile.in (LIBBOW_C_FILES): Added stopwords.c.
	* getword.c (bow_get_word): Use renamed stoplist function.

	* email.c (bow_email_get_receivedid): New function.
	* libbow.h: Declare new email functions.

	* rainbow.c (main): Use new function name
 	bow_wi2dvf_write_data_file().

	* Makefile.in ($(DEMO_EXECUTABLES):): Depend on all the
 	$(DEMO_O_FILES).

	* int4word.c (bow_num_words): Print error if WORD_MAP has not yet
 	been initialized.

	* docnames.c (bow_map_filenames_from_dir): Don't forget to copy
 	the CWD and the D_NAME into the FILENAME!

	* wv.c (bow_wv_count_for_wi): Return 0 if WV is NULL.

	* Makefile.in (LIBBOW_C_FILES): Added email.c.
	(DEMO_EXECUTABLES:): Changed rule to make $*.o separately.
	* email.c: New file.
	* libbow.h: Declared new email functions.

	* wi2dvf.c (bow_wi2dvf_write_data_file): Renamed from
 	bow_wi2dvf_write().
	* libbow.h: Rename function declaration.

	* wv.c (bow_wv_count_for_wi): New function.
	* libbow.h: Declare new function.

	* sarray.c (bow_sarray_index_at_keystr): New function.
	* libbow.h (bow_sarray_index_at_keystr): Declare new function.

	* sarray.c: New file.
	* docs.c: Old file, no longer used.

	* Makefile.in (LIBBOW_C_FILES): Add sarray.c.  Remove docs.c.
  	Temporarily remove heap.c because it hasn't been checked into the
 	CVS, and I don't have access to it.

	* libbow.h (bow_sarray): New typedef, and new function
 	declarations.
	(bow_cdoc): Renamed from bow_doc.  SEEK_START and SEEK_LENGTH elements
	removed.  Many users will need to define their own "document
 	entries" with different elements; this is just one example
 	typically used for classification.
	(bow_docs): Typedef removed.
	(bow_cdocs): New macro, a bow_array of cdoc's.  Also add macro's for
	functions.
	(bow_wi2dvf_add_di_text_fp): Declare new function.

	* int4str.c (bow_int4str_init): New function.
	(bow_int4str_new): Use it.

	* array.c (bow_array_default_capacity): Renamed from
 	bow_array_default_size.
	(bow_array_init): Use new name.
	(bow_array_append): Renamed from bow_array_add_at_index, since the
	user really doesn't have a choice of index anyway.  No INDEX
 	argument now.

	* wi2dvf.c (bow_wi2dvf_add_di_text_fp): New function.
	(bow_wi2dvf_new_from_text_dir): Use it.

Wed Oct  9 15:53:52 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* array.c (bow_array_add_at_index): Include ENTRY_SIZE in
 	calculation of realloc() size.

Tue Oct  8 14:38:59 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h (bow_array): New structure and suite of functions.
	(bow_docs): Use it.

	* Makefile.in (LIBBOW_C_FILES): Added array.c.  Renamed doc.c to
 	docs.c.

	* array.c: New file.
	* docs.c: New file.

	* Makefile.in (LIBBOW_C_FILES): Added doc.c.

Tue Oct  8 15:27:45 1996  Sean Slattery  <jslttery@@anther.learning.cs.cmu.edu>

	* libbow.h: Added definitions for heap functions, weight functions
	and scoring functions. Also added length field to bow_doc
	structure.

	* Makefile.in (LIBBOW_C_FILES): Added score.c, weight.c and
	heap.c.
	* heap.c: New file.
	* weight.c: New file.
	* score.c: New file.

Mon Oct  7 12:14:50 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* docnames.c (bow_map_filenames_from_dir): New function.
	(bow_doc_list_append): Use it to do most of the work.
	* libbow.h: Declare new function.

	* Makefile.in (snapshot): New target.

	* getword.c (bow_get_word): Avoid returning a post-stemmed word of
 	length 1.

	* libbow.h (bow_wv): Renamed member "length" to "num_entries".
  	Added member "length", meaning Euclidean length of the vector.
	(bow_doc): Added member "class".  Removed member "wv".
	* wv.c: Use new member name "num_entries".
	* wi2dvf.c: Likewise.

	* Makefile.in (DIST_FILES): Added HACKING.

Sat Oct  5 18:26:47 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* Version (LIBBOW_VERSION): Version 0.2.

	* libbow.texi: Cleaned up and added some sections.

	* dv.c (bow_dv_add_di_count): Fix bugs in calculation of DV_INDEX.
  	In an effort to reduce wasted memory, don't reallocate double the
 	previous SIZE, but 3/2 the previous size; this almost cuts in half
 	the amount of wasited "document vector" memory; (perhaps
 	multiplying 4/3 would help even more?).

	* wi2dvf.c (bow_wi2dvf_dv): Use new function name
 	bow_dv_new_from_data_fp().
	(bow_wi2dvf_print_stats): Fix typo.  Also print average number of
	unused document vector entries.
	(bow_wi2dvf_new_from_text_dir): Don't use "word vectors".  Instead
	grab each word individually from a text file, and add it to the
	map using bow_wi2dvf_add_wi_di_count().
	(bow_wi2dvf_add_wi_di_count): Newly implemented.
	* libbow.h (bow_dv_new_from_data_fp): Renamed from
 	bow_dv_new_from_fp.

	* dv.c (bow_dv_add_di_count): Don't use a new "document entry" if
 	the "document vector" already has an entry for the given DI.

	* wi2dvf.c (bow_wi2dvf_print_stats): Print stats about number of
 	used and unused "document entries" to get a better idea of memory
 	usage.

	* rainbow.c (main): Use getopt() to enable setting of
 	bow_verbosity_level.

Wed Oct  2 11:20:58 1996  Andrew McCallum  <mccallum@@cs.cmu.edu>

	* libbow.h (bow_wi2dvf_add_wi_di_count): New function declaration;
 	not yet implemented.

	* rainbow.c (main): Don't set bow_verbosity_level to bow_quiet.

	* docnames.c: Change many FL variable names to DL.
	(bow_doc_list_append): Don't set *DL to NULL at the beginning, because
	it won't work recursively.
	* wi2dvf.c (bow_wi2dvf_new_from_text_dir): Add assertion that
 	verifies length of the document list.

	* Version 0.0.  CVS rtag with `release-0-0'.

	* wi2dvf.c (bow_wi2dvf_new_from_text_dir): Clean up and count text
 	files and binary files differently.

	* rainbow.c (main): Comment out setting to bow_quiet.

	* Makefile.in: Include Version.
	(version.texi): Fix dependancy.
	(dist): Fix it.

	* docnames.c (bow_doc_list_append): Don't print extra newline.
	(bow_doc_list_length): New function.

	* libbow.h (bow_de): Define di and count as short int's, not
 	int's.
	(bow_fwrite_short): New function.
	(bow_fread_short): New function.
	(bow_doc_list_length): Declare new function.
	* dv.c (bow_dv_write): Write di and count as short ints.
	(bow_dv_new_from_fp): Read them as short ints.
	* io.c (bow_fwrite_short): New function.
	(bow_fread_short): New function.

	* Version: New file.
	* libbow-desc.texi: New file.

	* Makefile.in (clean): Fix name of libbow.a; also remove the
 	$(DEMO_EXECUTABLES).

	* rainbow.c (main): Print messages during stages of wi2dvf map
 	testing.  Clean up the other test code.

	* wi2dvf.c: (bow_wi2dvf_print_stats): New function.

	* dv.c: (bow_dv_default_capacity): Decreased from 512 to 4 in an
	attempt to avoid exhausted memory.
	(bow_dv_count): New global variable.
	(bow_dv_new): Increment it.
	(bow_dv_free): Decrement it.

	* libbow.h (bow_malloc): New function.
	(bow_realloc): New function.
	(bow_free): New function.
	* wv.c: Use bow_malloc() instead of malloc().
	* stoplist.c: Likewise.
	* primes.c: Likewise.
	* int4str.c: Likewise.
	* docnames.c: Likewise.
	* dv.c: Likewise.
	* wi2dvf.c: Likewise.

	* Makefile.in (LIBBOW_C_FILES): Added bmalloc.c.

	* Placed under CVS with release-tag `first'.