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#!/usr/bin/env python2.7
# ----------------------------------
#
# Module pylib_ml_examples.py
#
# Functions and classes for handling sets of examples form machine
# learning, where each example contains an identifier, a set of
# features of different types, and a desired class.
#
# Copyright 2003 Stephan Schulz, schulz@informatik.tu-muenchen.de
#
# This code is part of the support structure for the equational
# theorem prover E. Visit
#
# http://www4.informatik.tu-muenchen.de/~schulz/WORK/eprover.html
#
# for more information.
#
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program ; if not, write to the Free Software
# Foundation, Inc., 59 Temple Place, Suite 330, Boston,
# MA 02111-1307 USA
#
# The original copyright holder can be contacted as
#
# Stephan Schulz (I4)
# Technische Universitaet Muenchen
# Institut fuer Informatik
# Boltzmannstrasse 3
# Garching bei Muenchen
# Germany
#
# or via email (address above).
from __future__ import generators
from types import *
import string
import random
from UserList import UserList
import pylib_basics
import pylib_io
import pylib_probabilities
def atofeatureval(str):
"""Try to convert a string to an integer or a float,
and return the converted value"""
try:
res=string.atoi(str)
return res
except ValueError:
pass
try:
res=string.atof(str)
return res
except ValueError:
pass
return str
def typemax(t1,t2):
"""Given two types (string, int, float), return
the more general one"""
if t1 == StringType:
return t1
if t2 == StringType:
return t2
if t1 == FloatType:
return t1
if t2 == FloatType:
return t2
assert(t1==IntType and t2==IntType)
return t1
def typemax_l(l):
"""
Reduce a list of types to the most specific one compatible with
all elements.
"""
return reduce(typemax, l, int)
class ml_example:
"""
Representing an example for machine learning, with am identifier
(id), a list of features values (features), and (optionally) a
class (tclass).
"""
def __init__(self,
rep,
classadmin = pylib_basics.name_number_hash()):
self.classadmin = classadmin
if type(rep) == StringType:
tmp = rep.split(":");
tmp = map(string.strip, tmp)
tmp[1] = tmp[1].split(",")
tmp[1] = map(string.strip, tmp[1])
else:
assert type(rep) == TupleType
assert len(rep) == 3 or len(rep)==4
tmp = rep
assert type(tmp[1]) == ListType
self.id = tmp[0]
self.features = map(atofeatureval,tmp[1])
if len(tmp)==3:
self.tclass = self.classadmin.insert(tmp[2])
else:
self.tclass = None
def feature_no(self):
"""
Return number of different features of example.
"""
return len(self.features)
def __repr__(self):
features = string.join(map(str, self.features),",")
res = self.id + " : " +features;
if self.tclass!=None:
res+= " : "+self.classadmin.get_name(self.tclass)
return res
def feature_val(self, f_no):
"""
Return value of a given feature.
"""
return self.features[f_no]
def tclass_val(self):
"""
Return target class of feature.
"""
return self.tclass
class ml_exampleset(UserList):
"""
Representing a set of examples for machine learning.
"""
def __init__(self, data=[]):
UserList.__init__(self)
self.feature_no = None
self.name = None
self.class_omega = None
self.init_precomputed()
self.classadmin = pylib_basics.name_number_hash()
for i in data:
self.append(i)
def set_name(self, name):
self.name = name
def append(self, element):
if self.feature_no:
assert self.feature_no == element.feature_no()
else:
self.feature_no = element.feature_no()
UserList.append(self, element)
self.init_precomputed()
def extend(self, l):
for i in l:
self.append(i)
def init_precomputed(self):
"""
Initialize/reset precomputed values that potentially change
with each new inertion.
"""
self.feature_types = None
self.feature_values = None
self.feature_dvalues = None
self.feature_range = None
self.class_values = None
self.class_dvalues = None
def get_feature_type(self, feature):
"""
Give the type of the requested feature.
"""
return self.get_feature_types()[feature]
def get_feature_types(self):
"""
Return a list of types of features used in examples,
recomputing it if necessary.
"""
if not self.feature_no:
return None
if self.feature_types:
return self.feature_types
self.feature_types = []
for i in range(0, self.feature_no):
self.feature_types.append(typemax_l(map(lambda element, f=i:
type(element.feature_val(f)),
self.data)))
return self.feature_types
def get_feature_values(self, feature):
"""
Return (sorted) list of all values for a given feature.
"""
if not self.feature_no:
return None
if not self.feature_values:
self.feature_values = [None] * self.feature_no
if not self.feature_values[feature]:
self.feature_values[feature] =\
map(lambda x, f=feature:x.feature_val(f), self)
self.feature_values[feature].sort()
return self.feature_values[feature]
def get_feature_range(self, feature):
"""
Return tuple with largest and smallest feature value (using
natural order of the type).
"""
if not self.feature_no:
return None
if not self.feature_range:
self.feature_range = [None] * self.feature_no
if not self.feature_range[feature]:
tmp = self.get_feature_values(feature)
self.feature_range[feature] = (tmp[0], tmp[-1])
return self.feature_range[feature]
def get_distinct_feature_values(self, feature):
"""
Return (sorted) list of all distinct values for a given
feature.
"""
if not self.feature_no:
return None
if not self.feature_dvalues:
self.feature_dvalues = [None] * self.feature_no
if not self.feature_dvalues[feature]:
self.feature_dvalues[feature] =\
pylib_basics.uniq(self.get_feature_values(feature))
return self.feature_dvalues[feature]
def get_class_values(self):
"""
Return (sorted) list of all classes of examples.
"""
if self.class_values == None:
self.class_values = map(lambda x:x.tclass_val(), self)
self.class_values.sort()
return self.class_values
def get_distinct_class_values(self):
"""
Return (sorted) list of all occuring classes.
"""
if self.class_dvalues == None:
self.class_dvalues = pylib_basics.uniq(self.get_class_values())
return self.class_dvalues
def get_class_number(self):
"""
Return the number of distinct classes.
"""
return self.classadmin.get_entry_no()
def parse(self, file):
f = pylib_io.flexopen(file,'r')
l = f.readlines()
pylib_io.flexclose(f)
for line in l:
if line[0] == "#":
continue
ex = ml_example(line, self.classadmin)
self.append(ex)
def __repr__(self):
if self.name:
res = "# "+self.name +"\n"
else:
res = ""
for i in self:
res+=repr(i)+"\n"
return res
def abs_freq_vector(self, abstracter):
tmppart = partition()
tmppart.abstracter = abstracter
tmppart.insert_set(self)
return tmppart.abs_freq_vector()
def most_frequent_class(self):
"""
Find the most frequent class of examples in the set and return
it (and its relative frequency).
"""
classes = self.get_distinct_class_values()
class_occ = self.get_class_values()
class_freq = [(class_occ.count(cl),cl) for cl in classes]
class_freq.sort()
abs_freq, mf_class = class_freq[-1]
rel_freq = float(abs_freq)/len(class_occ)
return (mf_class, rel_freq)
def class_freq_vector(self):
"""
Return an in-order vector of absolute class frequencies.
"""
res = [0] * self.get_class_number()
class_occ = self.get_class_values()
for i in class_occ:
res[i]+=1
# print res, len(res)
return res
def get_class_entropy(self):
return pylib_probabilities.compute_entropy_absdistrib(self.class_freq_vector())
def plain_rel_inf_gain(self):
apriori_entropy = pylib_probabilities.compute_entropy_absdistrib([1]
* self.get_class_number())
real_entropy = self.get_class_entropy()
return pylib_probabilities.rel_info_gain(apriori_entropy,
real_entropy,
real_entropy)
def random_split(self,n):
"""
Randomly split the example set into n neary equal-sized subsets.
"""
tmp = list(self)
random.shuffle(tmp)
res = []
for i in range(n):
res.append([])
count = 0
for i in tmp:
res[count].append(i)
count+=1
count = count % n
return res
def stratified_split(self,n):
"""
Randomly split the example set into n neary equal-sized
subsets stratified for class.
"""
def weird_cmp(ex1, ex2):
tmp = cmp(ex1.tclass_val(), ex2.tclass_val)
if tmp:
return tmp
return cmp(ex1.tmp, ex2.tmp)
tmp = list(self)
random.shuffle(tmp)
count = 0
for i in tmp:
i.tmp = count
count += 1
tmp.sort(weird_cmp)
res = []
for i in range(n):
res.append([])
count = 0
for i in tmp:
res[count].append(i)
count+=1
count = count % n
return res
def crossval_sets(self,n, stratified=True):
"""
Return a list of n tuples (training_set, test_set), so that
the union of both is the full set, the 10 test sets are
disjoint, and the union of the 10 test sets is the full set.
"""
res = []
if stratified:
tmp = self.stratified_split(n)
else:
tmp = self.random_split(n)
for i in range(len(tmp)):
train = ml_exampleset()
train.classadmin = self.classadmin
for j in range(len(tmp)):
if j!=i:
train.extend(tmp[j])
test = ml_exampleset()
test.classadmin = self.classadmin
test.extend(tmp[i])
res.append((train, test))
return res
def class_partitioner(example):
return example.tclass_val()
class partition:
"""
Represent a partition of examples with named parts. Partition
type is defined by the abstracter() function that should return a
partition label for each subset.
"""
def __init__(self, examples=[]):
self.parts = {}
self.insert_set(examples)
self.entropy = None
self.class_entropy = None
self.remainder_entropy = None
def empty(self):
return len(self.parts)==0
def trivial(self):
return len(self.parts)<=1
def insert(self, example, class_admin=None):
"""
Insert a single example.
"""
self.entropy = None
self.class_entropy = None
self.remainder_entropy = None
part = self.abstracter(example)
try:
self.parts[part].append(example)
except KeyError:
tmp = ml_exampleset()
tmp.classadmin = class_admin
tmp.set_name(part)
tmp.append(example)
self.parts[part] = tmp
def insert_set(self, examples):
"""
Insert a whole set of examples.
"""
if isinstance(examples, ml_exampleset):
class_admin = examples.classadmin
for i in examples:
self.insert(i, class_admin)
else:
for i in examples:
self.insert(i)
def get_size(self):
return len(self.parts)
def abstracter(self, example):
"""
Return a label. This is only defined for concrete instances.
"""
assert false, "Virtual function only!"
def __repr__(self):
res = "# Partition:\n"
tmp = self.parts.keys()
tmp.sort()
for i in tmp:
res = res+repr(i)+"\n"+repr(self.parts[i])
return res
def get_class_distributions(self):
res = [i.class_freq_vector() for i in self.parts.values()]
return res
def compute_entropies(self):
if self.entropy != None:
return
if len(self.parts)==1: # Avoid rounding errors
tmp = self.parts.values()[0].get_class_entropy()
(self.entropy, self.class_entropy, self.remainder_entropy) =\
(0,tmp,tmp)
else:
tmp = self.get_class_distributions()
(self.entropy, self.class_entropy, self.remainder_entropy) =\
pylib_probabilities.compute_entropies(tmp)
def get_class_entropy(self):
"""
Return the a-priory entropy of the class distribution.
"""
self.compute_entropies()
return self.class_entropy
def get_entropy(self):
"""
Return the entropy of the partion.
"""
self.compute_entropies()
return self.entropy
def get_remainder_entropy(self):
"""
Return the remainder entropy of the class test after
performing the paritioning.
"""
self.compute_entropies()
return self.remainder_entropy
class scalar_feature_test:
"""
Callable object representing a single interval constraint on a
scalar variable. It returns True for values with lb <= val < ub.
"""
def __init__(self, feature, lower_bound, upper_bound):
assert not lower_bound or not upper_bound or lower_bound <= upper_bound
self.lower_bound = lower_bound
self.upper_bound = upper_bound
self.feature = feature
self.name = "feature["+repr(feature)+"]"
def __call__(self, example):
value = example.feature_val(self.feature)
if self.lower_bound==None:
lb = True
else:
lb = (value >= self.lower_bound)
if self.upper_bound==None:
ub = True
else:
ub = (value < self.upper_bound)
return lb and ub
def __repr__(self):
if self.lower_bound==None and self.upper_bound==None:
return "always_true"
elif self.lower_bound==None:
return self.name+"<"+repr(self.upper_bound)
elif self.upper_bound==None:
return self.name+">="+repr(self.lower_bound)
return self.name+">="+repr(self.lower_bound)+\
" and "+self.name+"<"+repr(self.upper_bound)
class scalar_feature_partitioner(partition):
def __init__(self, feature, limits=[]):
assert(pylib_basics.is_sorted(limits))
self.feature_no = feature
tmpname = "feature["+repr(self.feature_no)+"]"
if len(limits)==0:
tmp = scalar_feature_test(None, None)
self.features = [tmp]
else:
lb = None
self.features = []
for i in limits:
tmp = scalar_feature_test(feature,lb,i)
self.features.append(tmp)
lb = i
tmp = scalar_feature_test(feature,lb, None)
self.features.append(tmp)
def __call__(self, example):
for i in self.features:
if i(example):
return i
assert False, "Not a partition!"
def __repr__(self):
res = "["
sep = ""
for i in self.features:
res = res+sep+repr(i)
sep = " ; "
res = res + "]"
return res
class class_partition(partition):
"""
Generate a partion of a set of examples based on the target class
if the examples.
"""
def __init__(self, examples):
self.abstracter = class_partitioner
partition.__init__(self, examples)
class scalar_feature_partition(partition):
"""
Generate a partion of a set of examples based on a scalar
feature test.
"""
def __init__(self, examples, feature, limits):
self.abstracter = scalar_feature_partitioner(feature, limits)
partition.__init__(self, examples)
def weird_filter(values, boundaries):
"""
Reduce a boundaries= [n0....nn] as follows:
For all i from 0 to n-1:If there is no element e in values with
ni<e<=ni+1, drop ni.
"""
tmpvals = list(values)
res = []
for i in boundaries:
found = False
while tmpvals!=[] and tmpvals[0]<i:
found = True
tmpvals.pop(0)
if found:
res.append(i)
return res
def equisplit_feature_space(feature_values, n):
"""
Return a set of boundaries that split the space of (distinct)
feature values into n approximately equal-sized parts. Works for
both distinct values and real values, as it will discard
boundaries occuring more than once.
"""
if n<=1:
return []
tmp = len(feature_values)
if n>tmp:
n = tmp
step = tmp/float(n)
res = [feature_values[int(i*step)] for i in range(1, n)]
res = weird_filter(feature_values,res)
return res
def equisplit_feature_range(dfeature_values, n):
"""
Return a set of boundaries that split the range of
feature values into n equal-sized parts.
"""
if n<=1:
return []
tmp = dfeature_values[-1]-dfeature_values[0]
step = tmp/float(n)
res = [(i*step) for i in range(1, n)]
return weird_filter(dfeature_values,res)
def prop_n_nary_split(feature_values, proportions):
"""
Return a set of boundaries located at the proporional values
given.
"""
tmp = len(feature_values)
res = [feature_values[int(p*tmp)] for p in proportions]
return weird_filter(feature_values,res)
def prop_n_nary_rangesplit(feature_values, proportions):
"""
Return a set of boundaries located at the proporional values
within the feature value range.
"""
tmp = feature_values[-1]-feature_values[0]
res = [((p*tmp)+feature_values[0]) for p in proportions]
return weird_filter(feature_values,res)
def first_n_and_rest_split(dfeature_values, n):
"""
Return a set of boundaries so that the first n values have their
own class, and all the other ones are lumped into one.
"""
return dfeature_values[1:(n+1)]
class discrete_feature_test:
def __init__(self, feature, set=[]):
self.set = set
self.feature = feature
self.name = "feature["+repr(feature)+"]"
self.positive = True
def __call__(self, example):
value = example.feature_val(self.feature)
return value in self.set
def __repr__(self):
res = self.name+" in "+repr(self.set)
return res
class discrete_feature_else_test(discrete_feature_test):
def __init__(self, feature, set=[]):
discrete_feature_test.__init__(self,feature,set)
self.positive = False
def __call__(self, example):
value = example.feature_val(self.feature)
return not(value in self.set)
def __repr__(self):
res = self.name+" notin "+repr(self.set)
return res
class discrete_feature_partitioner:
"""
Generate a functional object that will sort examples into feature
classes based on the possible values of a discrete feature.
"""
def __init__(self, feature, values, value_distrib):
assert len(values)!=0
self.feature_no = feature
most_freq = None
most_freq_count = 0
for i in values:
tmp_count = value_distrib.count(i)
if tmp_count>most_freq_count:
most_freq_count = tmp_count
most_freq = i
assert(most_freq)
else_set = list(values)
else_set.remove(most_freq)
self.ctests = []
for i in values:
if i==most_freq:
tmp = discrete_feature_else_test(feature,else_set)
self.ctests.append(tmp)
else:
tmp = discrete_feature_test(feature,[i])
self.ctests.append(tmp)
def __call__(self, example):
for i in self.ctests:
if i(example):
return i
assert False, "Not a partition!"
def __repr__(self):
res = "["
sep = ""
for i in self.ctests:
res = res+sep+repr(i)
sep = " ; "
res = res + "]"
return res
class discrete_feature_partition(partition):
"""
Generate a partion of a set of examples based on a discrete
feature test.
"""
def __init__(self, examples, feature, subsetlimit=0):
self.abstracter = \
discrete_feature_partitioner(feature,\
examples.get_distinct_feature_values(feature),\
examples.get_feature_values(feature))
partition.__init__(self, examples)
class one_and_rest_partitioner(discrete_feature_partitioner):
"""
Generate a functional object that will sort examples into two
classes based on wether a certain feature has a given value or
not.
"""
def __init__(self, feature, value):
self.feature_no = feature
self.ctests = []
tmp = discrete_feature_else_test(feature, [value])
self.ctests.append(tmp)
tmp = discrete_feature_test(feature, [value])
self.ctests.append(tmp)
class one_and_rest_partition(partition):
"""
Generate a partion of a set of examples based on a binary outcome
feature test (feature = value or feature != value)
"""
def __init__(self, examples, feature, value):
self.abstracter = one_and_rest_partitioner(feature, value)
partition.__init__(self, examples)
def partition_generator_feature(examples, feature, max_splits):
"""
Generate sequence of partitions for the given feature. Tries to
intelligently guess what to do and where to stop.
"""
type = examples.get_feature_type(feature)
if type == StringType:
tmp = discrete_feature_partition(examples, feature)
if not tmp.trivial():
yield tmp
dvalues = examples.get_distinct_feature_values(feature)
if len(dvalues) > max_splits:
return
for i in dvalues:
yield one_and_rest_partition(examples, feature, i)
return
values = examples.get_feature_values(feature)
dvalues = examples.get_distinct_feature_values(feature)
max_split = min(max_splits, len(dvalues))
#print values
#print dvalues
# Generate splits by evenly splitting sequence of all values
for i in range(2,max_split):
boundaries = equisplit_feature_space(values,i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
# Generate splits by evenly splitting sequence of all distinct values
for i in range(2,max_split):
boundaries = equisplit_feature_space(dvalues,i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
# Generate splits by evenly splitting the range of values
for i in range(2,max_split):
boundaries = equisplit_feature_range(dvalues,i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
# Generate some uneven binary splits
for i in range(1,9):
boundaries = prop_n_nary_split(dvalues, [0.1*i])
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
boundaries = prop_n_nary_rangesplit(dvalues, [0.1*i])
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
# Generate some weird splits:
ws = [[0.1,0.9], [0.2,0.8], [0.1,0.5,0.1]]
if max_splits >= 3:
for i in ws:
boundaries = prop_n_nary_split(dvalues, i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
boundaries = prop_n_nary_split(values, i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
boundaries = prop_n_nary_rangesplit(dvalues, i)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
# Generate some even weirder splits ;-)
limit = min(6,max_splits)
for i in range(1,limit):
boundaries = first_n_and_rest_split(dvalues,1)
if len(boundaries)>0:
part = scalar_feature_partition(examples, feature, boundaries)
yield part
return
def partition_generator(examples, max_split):
"""
Enumerate all possible feature partions for examples.
"""
for i in range(0,examples.feature_no):
pg = partition_generator_feature(examples, i, max_split)
while 1:
try:
part = pg.next()
yield part
except StopIteration:
break
return
def find_best_feature_partition(examples,
compare_fun,
feature,
max_splits):
assert isinstance(examples, ml_exampleset)
assert type(feature) == IntType
assert type(max_splits) == IntType
best_relinfgain = -1
best_absinfgain = -1
best_part = None
part_gen = partition_generator_feature(examples, feature, max_splits)
while 1:
try:
part = part_gen.next()
apriori = part.get_class_entropy()
cost = part.get_entropy()
remainder = part.get_remainder_entropy()
# print "# A-priori, cost, remainder = (%2.6f, %2.6f, %2.6f)" %\
# (apriori,cost,remainder)
absinfgain = apriori-remainder
relinfgain = pylib_probabilities.rel_info_gain(apriori,
remainder,
cost)
#print relinfgain, absinfgain
if compare_fun((relinfgain, absinfgain),
(best_relinfgain,best_absinfgain)) > 0:
best_relinfgain = relinfgain
best_absinfgain = absinfgain
best_part = part
except StopIteration:
break
return (best_relinfgain, best_absinfgain, best_part)
def find_best_partition(examples,
compare_fun,
max_splits):
assert type(max_splits == IntType)
best_relinfgain = -1
best_absinfgain = -1
best_part = None
if len(examples) > 1:
for i in range(0,examples.feature_no):
(relinfgain, absinfgain, part) = \
find_best_feature_partition(examples,
compare_fun,
i,
max_splits)
if pylib_basics.verbose():
print "# Evaluating feature %d: %1.6f, %1.6f "\
%(i,relinfgain, absinfgain),
if part:
if pylib_basics.verbose():
print part.abstracter
else:
if pylib_basics.verbose():
print "# No split possible, feature is homogenous:",
print examples.get_distinct_feature_values(i)
if compare_fun((relinfgain, absinfgain),
(best_relinfgain,best_absinfgain)) > 0:
best_relinfgain = relinfgain
best_absinfgain = absinfgain
best_part = part
return (best_relinfgain, best_absinfgain, best_part)
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