1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
|
from __future__ import (division)
from pomegranate import *
from .assert_tools import assert_almost_equal
import pickle
import pytest
@pytest.fixture
def setup():
data = [ list('AAACBDAA'), list('DBBCBABD'), list('CBDCCDCBC'), list('DDDDC'),
list('DADBBCBBBACBC'), list('CBDBAC'), list('CACDDDBCAABA'), list('BBABDAADCABCCAD'),
list('DCBBBADBBCBC'), list('DCADDAAA'), list('AABBBCC'), list('CABBADACDBBDCC'),
list('AADDCDDDB'), list('CCDBDCDDDABDAC'), list('DDADB'), list('BCDACDBBBBAC'),
list('ADCBCCCB'), list('BDDBCA'), list('ACCDCBADCBBBB'), list('ACCBABCBA'),
list('DAABCCBBD'), list('CCAADACBDCDBABC'), list('BCDCACBBAD'), list('CBBBCDCA'),
list('CBDADACAADBCC'), list('DCDABCC'), list('AAAABCBC'), list('BDDDDACBBCABA'),
list('CCBDCBDCBADBBDB'), list('CBDAA'), list('CCDAAAB'), list('ABDBAC'),
list('DBCCDCC'), list('CCDCBB'), list('ACDBCDD'), list('CACCACCDBBDABB'),
list('DCDDAB'), list('ADDDCDACACA'), list('AAACACADB'), list('BDBBDDBACDCCAAA') ]
weights = [ 8, 7, 1, 2, 8, 1, 9, 2, 6, 2, 5, 6, 10, 10, 8, 4, 10, 10, 2, 9,
6, 2, 9, 9, 3, 1, 10, 6, 9, 1, 2, 9, 2, 1, 4, 1, 2, 7, 9, 4]
zeroth_dist = DiscreteDistribution( { 'A': 0.1, 'B': 0.2, 'C': 0.3, 'D': 0.4 } )
first_dist = ConditionalProbabilityTable(
[[ 'A', 'A', 0.8 ], [ 'A', 'B', 0.05 ], [ 'A', 'C', 0.05 ], [ 'A', 'D', 0.1 ],
[ 'B', 'A', 0.1 ], [ 'B', 'B', 0.2 ], [ 'B', 'C', 0.6 ], [ 'B', 'D', 0.1 ],
[ 'C', 'A', 0.15 ], [ 'C', 'B', 0.1 ], [ 'C', 'C', 0.25 ], [ 'C', 'D', 0.5 ],
[ 'D', 'A', 0.25 ], [ 'D', 'B', 0.25 ], [ 'D', 'C', 0.4 ], [ 'D', 'D', 0.1 ]],
[ zeroth_dist ] )
second_dist = ConditionalProbabilityTable(
[[ 'A', 'A', 'A', 0.05 ], [ 'A', 'A', 'B', 0.25 ], [ 'A', 'A', 'C', 0.15 ], [ 'A', 'A', 'D', 0.55 ],
[ 'A', 'B', 'A', 0.05 ], [ 'A', 'B', 'B', 0.05 ], [ 'A', 'B', 'C', 0.85 ], [ 'A', 'B', 'D', 0.05 ],
[ 'A', 'C', 'A', 0.7 ], [ 'A', 'C', 'B', 0.1 ], [ 'A', 'C', 'C', 0.1 ], [ 'A', 'C', 'D', 0.1 ],
[ 'A', 'D', 'A', 0.2 ], [ 'A', 'D', 'B', 0.4 ], [ 'A', 'D', 'C', 0.35 ], [ 'A', 'D', 'D', 0.05 ],
[ 'B', 'A', 'A', 0.3 ], [ 'B', 'A', 'B', 0.05 ], [ 'B', 'A', 'C', 0.15 ], [ 'B', 'A', 'D', 0.5 ],
[ 'B', 'B', 'A', 0.8 ], [ 'B', 'B', 'B', 0.1 ], [ 'B', 'B', 'C', 0.1 ], [ 'B', 'B', 'D', 0.0 ],
[ 'B', 'C', 'A', 0.1 ], [ 'B', 'C', 'B', 0.35 ], [ 'B', 'C', 'C', 0.3 ], [ 'B', 'C', 'D', 0.25 ],
[ 'B', 'D', 'A', 0.3 ], [ 'B', 'D', 'B', 0.1 ], [ 'B', 'D', 'C', 0.2 ], [ 'B', 'D', 'D', 0.4 ],
[ 'C', 'A', 'A', 0.2 ], [ 'C', 'A', 'B', 0.3 ], [ 'C', 'A', 'C', 0.3 ], [ 'C', 'A', 'D', 0.2 ],
[ 'C', 'B', 'A', 0.35 ], [ 'C', 'B', 'B', 0.45 ], [ 'C', 'B', 'C', 0.0 ], [ 'C', 'B', 'D', 0.2 ],
[ 'C', 'C', 'A', 0.25 ], [ 'C', 'C', 'B', 0.0 ], [ 'C', 'C', 'C', 0.6 ], [ 'C', 'C', 'D', 0.15 ],
[ 'C', 'D', 'A', 0.8 ], [ 'C', 'D', 'B', 0.1 ], [ 'C', 'D', 'C', 0.05 ], [ 'C', 'D', 'D', 0.05 ],
[ 'D', 'A', 'A', 0.5 ], [ 'D', 'A', 'B', 0.0 ], [ 'D', 'A', 'C', 0.5 ], [ 'D', 'A', 'D', 0.0 ],
[ 'D', 'B', 'A', 0.35 ], [ 'D', 'B', 'B', 0.5 ], [ 'D', 'B', 'C', 0.1 ], [ 'D', 'B', 'D', 0.05 ],
[ 'D', 'C', 'A', 0.1 ], [ 'D', 'C', 'B', 0.45 ], [ 'D', 'C', 'C', 0.0 ], [ 'D', 'C', 'D', 0.45 ],
[ 'D', 'D', 'A', 0.2 ], [ 'D', 'D', 'B', 0.1 ], [ 'D', 'D', 'C', 0.1 ], [ 'D', 'D', 'D', 0.6 ]],
[ zeroth_dist, first_dist ] )
return data, weights, zeroth_dist, first_dist, second_dist
def test_zeroth_dist(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
assert_almost_equal( zeroth_dist.log_probability( 'A' ), -2.3025850929940455 )
assert_almost_equal( zeroth_dist.log_probability( 'B' ), -1.6094379124341003 )
assert_almost_equal( zeroth_dist.log_probability( 'C' ), -1.2039728043259361 )
assert_almost_equal( zeroth_dist.log_probability( 'D' ), -0.916290731874155 )
assert zeroth_dist.log_probability( 'E' ) == -float('inf')
def test_first_dist(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
assert_almost_equal( first_dist.log_probability( ('A', 'A') ), -0.22314355131420971 )
assert_almost_equal( first_dist.log_probability( ('A', 'B') ), -2.9957322735539909 )
assert_almost_equal( first_dist.log_probability( ('B', 'B') ), -1.6094379124341003 )
assert_almost_equal( first_dist.log_probability( ('B', 'C') ), -0.51082562376599072 )
assert_almost_equal( first_dist.log_probability( ('C', 'C') ), -1.3862943611198906 )
assert_almost_equal( first_dist.log_probability( ('C', 'D') ), -0.69314718055994529 )
assert_almost_equal( first_dist.log_probability( ('D', 'D') ), -2.3025850929940455 )
assert_almost_equal( first_dist.log_probability( ('D', 'A') ), -1.3862943611198906 )
def test_second_dist(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
assert_almost_equal( second_dist.log_probability( ('A', 'A', 'C') ), -1.89711998489 )
assert_almost_equal( second_dist.log_probability( ('A', 'A', 'A') ), -2.99573227355 )
assert_almost_equal( second_dist.log_probability( ('A', 'B', 'A') ), -2.99573227355 )
assert_almost_equal( second_dist.log_probability( ('A', 'B', 'C') ), -0.162518929498 )
assert_almost_equal( second_dist.log_probability( ('A', 'C', 'C') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('A', 'C', 'D') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('A', 'D', 'B') ), -0.916290731874 )
assert_almost_equal( second_dist.log_probability( ('A', 'D', 'D') ), -2.99573227355 )
assert_almost_equal( second_dist.log_probability( ('B', 'A', 'B') ), -2.99573227355 )
assert_almost_equal( second_dist.log_probability( ('B', 'A', 'D') ), -0.69314718056 )
assert_almost_equal( second_dist.log_probability( ('B', 'B', 'B') ), -2.30258509299 )
assert second_dist.log_probability( ('B', 'B', 'D') ) == -float('inf')
assert_almost_equal( second_dist.log_probability( ('B', 'C', 'A') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('B', 'C', 'B') ), -1.0498221245 )
assert_almost_equal( second_dist.log_probability( ('B', 'D', 'D') ), -0.916290731874 )
assert_almost_equal( second_dist.log_probability( ('B', 'D', 'B') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('C', 'A', 'A') ), -1.60943791243 )
assert_almost_equal( second_dist.log_probability( ('C', 'A', 'B') ), -1.20397280433 )
assert second_dist.log_probability( ('C', 'B', 'C') ) == -float('inf')
assert_almost_equal( second_dist.log_probability( ('C', 'B', 'A') ), -1.0498221245 )
assert_almost_equal( second_dist.log_probability( ('C', 'C', 'D') ), -1.89711998489 )
assert second_dist.log_probability( ('C', 'C', 'B') ) == -float('inf')
assert_almost_equal( second_dist.log_probability( ('C', 'D', 'A') ), -0.223143551314 )
assert_almost_equal( second_dist.log_probability( ('C', 'D', 'C') ), -2.99573227355 )
assert second_dist.log_probability( ('D', 'A', 'D') ) == -float('inf')
assert_almost_equal( second_dist.log_probability( ('D', 'A', 'A') ), -0.69314718056 )
assert_almost_equal( second_dist.log_probability( ('D', 'B', 'D') ), -2.99573227355 )
assert_almost_equal( second_dist.log_probability( ('D', 'B', 'C') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('D', 'C', 'A') ), -2.30258509299 )
assert_almost_equal( second_dist.log_probability( ('D', 'C', 'D') ), -0.798507696218 )
assert_almost_equal( second_dist.log_probability( ('D', 'D', 'D') ), -0.510825623766 )
assert_almost_equal( second_dist.log_probability( ('D', 'D', 'A') ), -1.60943791243 )
def test_constructors(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
# raises no errors
first_chain = MarkovChain([ zeroth_dist, first_dist ])
second_chain = MarkovChain([ zeroth_dist, first_dist, second_dist ])
def test_first_log_probability(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
# test going one state back
first_chain = MarkovChain([ zeroth_dist, first_dist ])
assert_almost_equal( first_chain.log_probability( list('A') ), -2.3025850929940455 )
assert_almost_equal( first_chain.log_probability( list('B') ), -1.6094379124341003 )
assert_almost_equal( first_chain.log_probability( list('AC') ), -5.2983173665480363 )
assert_almost_equal( first_chain.log_probability( list('AD') ), -4.6051701859880909 )
assert_almost_equal( first_chain.log_probability( list('BD') ), -3.9120230054281455 )
assert_almost_equal( first_chain.log_probability( list('BA') ), -3.9120230054281455 )
assert_almost_equal( first_chain.log_probability( list('CA') ), -3.1010927892118172 )
assert_almost_equal( first_chain.log_probability( list('CB') ), -3.5065578973199818 )
assert_almost_equal( first_chain.log_probability( list('DB') ), -2.3025850929940455 )
assert_almost_equal( first_chain.log_probability( list('DC') ), -1.83258146374831 )
assert_almost_equal( first_chain.log_probability( list('ABDD') ), -9.9034875525361272 )
assert_almost_equal( first_chain.log_probability( list('CCCB') ), -6.2791466195597625 )
assert_almost_equal( first_chain.log_probability( list('CCBD') ), -7.1954373514339167 )
assert_almost_equal( first_chain.log_probability( list('ACAC') ), -10.191169624987909 )
assert_almost_equal( first_chain.log_probability( list('ABDBCCDC') ), -12.493754717981954 )
assert_almost_equal( first_chain.log_probability( list('DACCBDCB') ), -14.508657738524217 )
assert_almost_equal( first_chain.log_probability( list('BCCCACBDBDBABACD') ), -30.75583043175768 )
assert_almost_equal( first_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ), -53.616465272807112 )
# test going two states back
second_chain = MarkovChain([ zeroth_dist, first_dist, second_dist ])
assert_almost_equal( second_chain.log_probability( list('A') ), -2.30258509299 )
assert_almost_equal( second_chain.log_probability( list('B') ), -1.60943791243 )
assert_almost_equal( second_chain.log_probability( list('AC') ), -5.29831736655 )
assert_almost_equal( second_chain.log_probability( list('AD') ), -4.60517018599 )
assert_almost_equal( second_chain.log_probability( list('BD') ), -3.91202300543 )
assert_almost_equal( second_chain.log_probability( list('BA') ), -3.91202300543 )
assert_almost_equal( second_chain.log_probability( list('CA') ), -3.10109278921 )
assert_almost_equal( second_chain.log_probability( list('CB') ), -3.50655789732 )
assert_almost_equal( second_chain.log_probability( list('DB') ), -2.30258509299 )
assert_almost_equal( second_chain.log_probability( list('DC') ), -1.83258146375 )
assert_almost_equal( second_chain.log_probability( list('ABDD') ), -9.21034037198 )
assert_almost_equal( second_chain.log_probability( list('CCCD') ), -4.9982127741 )
assert second_chain.log_probability( list('CCBD') ) == -float('inf')
assert_almost_equal( second_chain.log_probability( list('ACAC') ), -6.85896511481 )
assert_almost_equal( second_chain.log_probability( list('ABDBCCDC') ), -18.9960448889 )
assert second_chain.log_probability( list('DACCBDCB') ) == -float('inf')
assert_almost_equal( second_chain.log_probability( list('BCCCACBDBDBABACD') ), -29.1792463442 )
assert second_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ) == -float('inf')
# if summarize and from summaries work, so does fit
def test_summarize_no_weights_no_inertia(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
first_chain = MarkovChain([ zeroth_dist, first_dist ])
# split in four
first_chain.summarize( data[:10] )
first_chain.summarize( data[10:20] )
first_chain.summarize( data[20:30] )
first_chain.summarize( data[30:] )
first_chain.from_summaries()
# check if probabilities are correct
assert_almost_equal( first_chain.log_probability( list('A') ), -1.29098418132 )
assert_almost_equal( first_chain.log_probability( list('B') ), -1.89711998489 )
assert_almost_equal( first_chain.log_probability( list('AC') ), -2.52493781785 )
assert_almost_equal( first_chain.log_probability( list('AD') ), -2.82721868973 )
assert_almost_equal( first_chain.log_probability( list('BD') ), -3.35240721749 )
assert_almost_equal( first_chain.log_probability( list('BA') ), -3.56371631116 )
assert_almost_equal( first_chain.log_probability( list('CA') ), -2.66812748722 )
assert_almost_equal( first_chain.log_probability( list('CB') ), -2.31672960038 )
assert_almost_equal( first_chain.log_probability( list('DB') ), -2.74959920402 )
assert_almost_equal( first_chain.log_probability( list('DC') ), -2.70514744144 )
assert_almost_equal( first_chain.log_probability( list('ABDD') ), -5.69233078086 )
assert_almost_equal( first_chain.log_probability( list('CCCB') ), -5.2049574644 )
assert_almost_equal( first_chain.log_probability( list('CCBD') ), -5.216130765 )
assert_almost_equal( first_chain.log_probability( list('ACAC') ), -5.30308884496 )
assert_almost_equal( first_chain.log_probability( list('ABDBCCDC') ), -11.1281275339 )
assert_almost_equal( first_chain.log_probability( list('DACCBDCB') ), -10.6827162728 )
assert_almost_equal( first_chain.log_probability( list('BCCCACBDBDBABACD') ), -23.2162130846 )
assert_almost_equal( first_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ), -43.7174844781 )
second_chain = MarkovChain([ zeroth_dist, first_dist, second_dist ])
# split into four
second_chain.summarize( data[:10] )
second_chain.summarize( data[10:20] )
second_chain.summarize( data[20:30] )
second_chain.summarize( data[30:] )
second_chain.from_summaries()
def test_summarize_no_weights_with_inertia(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
first_chain = MarkovChain([ zeroth_dist, first_dist ])
first_chain.summarize( data[:10] )
first_chain.summarize( data[10:20] )
first_chain.summarize( data[20:30] )
first_chain.summarize( data[30:] )
first_chain.from_summaries( inertia=0.4 )
assert_almost_equal( first_chain.log_probability( list('A') ), -1.58474529984 )
assert_almost_equal( first_chain.log_probability( list('B') ), -1.77195684193 )
assert_almost_equal( first_chain.log_probability( list('AC') ), -3.22112518823 )
assert_almost_equal( first_chain.log_probability( list('AD') ), -3.3619279842 )
assert_almost_equal( first_chain.log_probability( list('BD') ), -3.48675527002 )
assert_almost_equal( first_chain.log_probability( list('BA') ), -3.6470979201 )
assert_almost_equal( first_chain.log_probability( list('CA') ), -2.82601794483 )
assert_almost_equal( first_chain.log_probability( list('CB') ), -2.66015931757 )
assert_almost_equal( first_chain.log_probability( list('DB') ), -2.54362030796 )
assert_almost_equal( first_chain.log_probability( list('DC') ), -2.30916483161 )
assert_almost_equal( first_chain.log_probability( list('ABDD') ), -6.88185009599 )
assert_almost_equal( first_chain.log_probability( list('CCCB') ), -5.50132618677 )
assert_almost_equal( first_chain.log_probability( list('CCBD') ), -5.79554118026 )
assert_almost_equal( first_chain.log_probability( list('ACAC') ), -6.52834038129 )
assert_almost_equal( first_chain.log_probability( list('ABDBCCDC') ), -11.1045309105 )
assert_almost_equal( first_chain.log_probability( list('DACCBDCB') ), -11.519936158 )
assert_almost_equal( first_chain.log_probability( list('BCCCACBDBDBABACD') ), -24.8604337068 )
assert_almost_equal( first_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ), -44.8853484278 )
def test_summarize_with_weights_no_inertia(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
first_chain = MarkovChain([ zeroth_dist, first_dist ])
# split in four
first_chain.summarize( data[:10], weights=weights[:10] )
first_chain.summarize( data[10:20], weights=weights[10:20] )
first_chain.summarize( data[20:30], weights=weights[20:30] )
first_chain.summarize( data[30:], weights=weights[30:] )
first_chain.from_summaries()
assert_almost_equal( first_chain.log_probability( list('A') ), -0.961056745744 )
assert_almost_equal( first_chain.log_probability( list('B') ), -1.82454929205 )
assert_almost_equal( first_chain.log_probability( list('AC') ), -2.13478966488 )
assert_almost_equal( first_chain.log_probability( list('AD') ), -2.47837936927 )
assert_almost_equal( first_chain.log_probability( list('BD') ), -3.41892100613 )
assert_almost_equal( first_chain.log_probability( list('BA') ), -3.45702085236 )
assert_almost_equal( first_chain.log_probability( list('CA') ), -2.84952832968 )
assert_almost_equal( first_chain.log_probability( list('CB') ), -2.43790935599 )
assert_almost_equal( first_chain.log_probability( list('DB') ), -2.88910833385 )
assert_almost_equal( first_chain.log_probability( list('DC') ), -2.98200208074 )
assert_almost_equal( first_chain.log_probability( list('ABDD') ), -5.56874179664 )
assert_almost_equal( first_chain.log_probability( list('CCCB') ), -5.71252297888 )
assert_almost_equal( first_chain.log_probability( list('CCBD') ), -5.66958788152 )
assert_almost_equal( first_chain.log_probability( list('ACAC') ), -4.78548674538 )
assert_almost_equal( first_chain.log_probability( list('ABDBCCDC') ), -11.3892431338 )
assert_almost_equal( first_chain.log_probability( list('DACCBDCB') ), -11.0991865874 )
assert_almost_equal( first_chain.log_probability( list('BCCCACBDBDBABACD') ), -23.5462387667 )
assert_almost_equal( first_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ), -44.3127858762 )
def test_summarize_with_weights_with_inertia(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
first_chain = MarkovChain([ zeroth_dist, first_dist ])
# split in four
first_chain.summarize( data[:10], weights=weights[:10] )
first_chain.summarize( data[10:20], weights=weights[10:20] )
first_chain.summarize( data[20:30], weights=weights[20:30] )
first_chain.summarize( data[30:], weights=weights[30:] )
first_chain.from_summaries( inertia=0.4 )
assert_almost_equal( first_chain.log_probability( list('A') ), -1.3112125381 )
assert_almost_equal( first_chain.log_probability( list('B') ), -1.73288210353 )
assert_almost_equal( first_chain.log_probability( list('AC') ), -2.89339373397 )
assert_almost_equal( first_chain.log_probability( list('AD') ), -3.07392432189 )
assert_almost_equal( first_chain.log_probability( list('BD') ), -3.55414269165 )
assert_almost_equal( first_chain.log_probability( list('BA') ), -3.58268887356 )
assert_almost_equal( first_chain.log_probability( list('CA') ), -2.92624445535 )
assert_almost_equal( first_chain.log_probability( list('CB') ), -2.70099965753 )
assert_almost_equal( first_chain.log_probability( list('DB') ), -2.596587547 )
assert_almost_equal( first_chain.log_probability( list('DC') ), -2.43824119019 )
assert_almost_equal( first_chain.log_probability( list('ABDD') ), -6.77853581842 )
assert_almost_equal( first_chain.log_probability( list('CCCB') ), -5.75946483735 )
assert_almost_equal( first_chain.log_probability( list('CCBD') ), -6.05149283556 )
assert_almost_equal( first_chain.log_probability( list('ACAC') ), -6.10013721195 )
assert_almost_equal( first_chain.log_probability( list('ABDBCCDC') ), -11.2181867683 )
assert_almost_equal( first_chain.log_probability( list('DACCBDCB') ), -11.6681121956 )
assert_almost_equal( first_chain.log_probability( list('BCCCACBDBDBABACD') ), -25.0365515667 )
assert_almost_equal( first_chain.log_probability( list('DABBCBDACAAADCBDCDBCBDCACBDABBAA') ), -45.1660985662 )
def test_raise_errors(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
pass
def test_pickling(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
chain1 = MarkovChain([ zeroth_dist, first_dist ])
chain2 = pickle.loads( pickle.dumps( chain1 ) )
assert_almost_equal( chain1.log_probability( list('BCCCACBDBDBABACD') ),
chain2.log_probability( list('BCCCACBDBDBABACD') ) )
def test_json(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
chain1 = MarkovChain([ zeroth_dist, first_dist ])
chain2 = MarkovChain.from_json(chain1.to_json())
assert_almost_equal( chain1.log_probability( list('BCCCACBDBDBABACD') ),
chain2.log_probability( list('BCCCACBDBDBABACD') ) )
def test_robust_from_json(setup):
data, weights, zeroth_dist, first_dist, second_dist = setup
chain1 = MarkovChain([ zeroth_dist, first_dist ])
chain2 = from_json(chain1.to_json())
assert_almost_equal( chain1.log_probability( list('BCCCACBDBDBABACD') ),
chain2.log_probability( list('BCCCACBDBDBABACD') ) )
|
