report_training-data-set-70.fStopWords_False.fSymbols_False.txt
14.3 KB
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
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt
best params:{'c2': 0.07914565142816338, 'c1': 0.21725964976439643}
best CV score:0.8106074404273954
model size: 0.11M
Flat F1: 0.8356545961
precision recall f1-score support
GENE 0.915 0.769 0.836 390
avg / total 0.915 0.769 0.836 390
Top likely transitions:
O -> O 1.957922
O -> GENE 0.947353
GENE -> GENE -0.007648
GENE -> O -4.309323
Top unlikely transitions:
O -> O 1.957922
O -> GENE 0.947353
GENE -> GENE -0.007648
GENE -> O -4.309323
Top positive:
2.685072 GENE b'lemma:gremlin'
2.608752 GENE b'word:CTGF'
2.608752 GENE b'lemma:Ctgf'
2.419715 GENE b'lemma:transforming'
2.349081 GENE b'word:beta-galactosidase'
2.349081 GENE b'lemma:beta-galactosidase'
2.174001 O b'word[-2:]:ed'
2.168049 O b'lemma[-1:]:m'
2.120173 O b'word[:1]:o'
2.073788 GENE b'lemma[-3:]:gal'
2.073788 GENE b'word:beta-gal'
2.073788 GENE b'word[-3:]:gal'
2.073788 GENE b'lemma:beta-gal'
2.013105 GENE b'lemma:PTEN'
2.013105 GENE b'lemma[-2:]:EN'
2.013105 GENE b'lemma[-3:]:TEN'
1.933060 GENE b'word:receptors'
1.925691 O b'word[:1]:-'
1.904296 O b'word:TGF'
1.904296 O b'lemma:tgf'
1.883335 GENE b'word[-3:]:vin'
1.883335 GENE b'word:activin'
1.883335 GENE b'lemma:activin'
1.883335 GENE b'lemma[-3:]:vin'
1.879420 GENE b'word[:2]:CD'
1.814306 GENE b'word:TGF-beta1'
1.814306 GENE b'lemma:TGF-beta1'
1.768325 GENE b'word:alpha-smooth-muscle-actin'
1.768325 GENE b'lemma:alpha-smooth-muscle-actin'
1.753390 O b'word[:2]:Cy'
1.726440 GENE b'word:ligand'
1.720519 GENE b'word:HGF'
1.720519 GENE b'lemma:HGF'
1.688715 O b'word[:1]:,'
1.678661 GENE b'word:protease'
1.678661 GENE b'lemma:protease'
1.668226 GENE b'word[:1]:C'
1.667293 GENE b'word:factor'
1.602555 O b'word[-1:]:y'
1.589130 GENE b'lemma[-2:]:-8'
1.589130 GENE b'word[-2:]:-8'
1.573694 O b'word[-1:]:s'
1.568569 O b'lemma[-3:]:in'
1.568569 O b'lemma:in'
1.512324 GENE b'word[:2]:HA'
1.512324 GENE b'word[:3]:HAI'
1.504657 O b'word[:2]:th'
1.504231 GENE b'lemma:ligand'
1.503836 GENE b'lemma[-2:]:-A'
1.503836 GENE b'word[-2:]:-A'
1.487440 GENE b'lemma:Pigment-epithelium-derived-factor'
1.487440 GENE b'word:Pigment-epithelium-derived-factor'
1.487440 GENE b'word[:3]:Pig'
1.476848 O b'word[:1]:k'
1.475005 GENE b'word[:1]:E'
1.432543 GENE b'lemma[-3:]:SMA'
1.432543 GENE b'word[-3:]:SMA'
1.432543 GENE b'word:alpha-SMA'
1.432543 GENE b'lemma:alpha-SMA'
1.407013 GENE b'word[:2]:IL'
1.397260 O b'lemma[-1:]:o'
1.390507 O b'lemma[-1:]:y'
1.387690 GENE b'word:transforming'
1.383684 GENE b'word[:2]:IF'
1.383684 GENE b'word[:3]:IFN'
1.379408 O b'word[:1]:L'
1.375716 GENE b'word:bone'
1.368611 GENE b'word[:3]:bon'
1.363564 GENE b'word[:3]:che'
1.356982 GENE b'word:TNF-alpha'
1.356982 GENE b'lemma:TNF-alpha'
1.326882 O b'word[:3]:R-I'
1.326882 O b'word[:2]:R-'
1.324190 O b'word[:3]:cyt'
1.310759 GENE b'word[-3:]:yte'
1.305700 GENE b'lemma:fibronectin'
1.305700 GENE b'word:fibronectin'
1.305260 GENE b'lemma[-1:]:N'
1.304592 GENE b'word[:3]:ext'
1.300737 O b'word[-1:]:d'
1.278849 GENE b'word[-3:]:L-4'
1.278849 GENE b'lemma:IL-4'
1.278849 GENE b'lemma[-3:]:L-4'
1.278849 GENE b'word:IL-4'
1.277782 GENE b'word[:3]:ERK'
1.259804 GENE b'lemma[-3:]:yte'
1.248605 O b'lemma:CTGF/TGF-beta'
1.248605 O b'word:CTGF/TGF-beta'
1.238688 GENE b'word[:3]:lig'
1.228904 GENE b'lemma:b-FGF'
1.228904 GENE b'word:b-FGF'
1.228904 GENE b'lemma[-3:]:FGF'
1.228904 GENE b'word[:2]:b-'
1.228904 GENE b'word[:3]:b-F'
1.228904 GENE b'word[-3:]:FGF'
1.212553 GENE b'word[:1]:H'
1.180210 GENE b'lemma:vimentin'
1.180210 GENE b'word[:3]:vim'
1.180210 GENE b'word:vimentin'
1.179272 GENE b'word[-3:]:mor'
1.179272 GENE b'word:tumor'
1.179272 GENE b'lemma[-3:]:mor'
1.179272 GENE b'lemma:tumor'
1.179121 GENE b'lemma[-2:]:T2'
1.179121 GENE b'word[-2:]:T2'
1.173436 O b'word[:1]:w'
1.167407 O b'lemma[-2:]:12'
1.167407 O b'word[-2:]:12'
1.153127 GENE b'word[:2]:TG'
1.153127 GENE b'word[:3]:TGF'
1.150437 GENE b'lemma[-1:]:I'
1.139320 GENE b'word[:3]:TNF'
1.139320 GENE b'word[:2]:TN'
1.134561 GENE b'word:interleukin-1beta'
1.134561 GENE b'lemma:interleukin-1beta'
1.132836 O b'word[:3]:Cyc'
1.132836 O b'word:Cyclin'
1.132442 GENE b'word:cyclin'
1.127347 GENE b'word[:2]:en'
1.122117 GENE b'word[:3]:MT5'
1.122117 GENE b'lemma:MT5-MMP'
1.122117 GENE b'word:MT5-MMP'
1.116045 GENE b'word:serine'
1.111781 GENE b'lemma:serine'
1.109123 GENE b'word[:1]:M'
1.106625 GENE b'lemma[-3:]:Fas'
1.106625 GENE b'lemma:Fas'
1.093286 GENE b'word[-2:]:DF'
1.093286 GENE b'lemma[-3:]:EDF'
1.093286 GENE b'word:PEDF'
1.093286 GENE b'lemma[-2:]:DF'
1.093286 GENE b'lemma:PEDF'
1.093286 GENE b'word[-3:]:EDF'
1.093286 GENE b'word[:2]:PE'
1.093286 GENE b'word[:3]:PED'
1.090129 O b'word[:2]:MA'
1.089527 GENE b'word[:3]:BMP'
1.089527 GENE b'word[:2]:BM'
1.079711 GENE b'word[:3]:alp'
1.073819 O b'word[-1:]:o'
1.073379 GENE b'word[-2:]:in'
1.068255 GENE b'lemma:IFN-gamma'
1.068255 GENE b'word:IFN-gamma'
1.064494 GENE b'word:NOS'
1.064494 GENE b'lemma:nos'
1.064494 GENE b'word[:3]:NOS'
1.050682 GENE b'lemma[-3:]:emt'
1.050682 GENE b'lemma:emt'
1.050682 GENE b'word[-3:]:EMT'
1.050682 GENE b'word:EMT'
1.046833 GENE b'word[-2:]:10'
1.046833 GENE b'lemma[-2:]:10'
1.044023 GENE b'word:Angiotensin'
1.044023 GENE b'lemma:Angiotensin'
1.039755 O b'word[:3]:MAP'
1.035043 GENE b'lemma[-3:]:BMP'
1.035043 GENE b'word[-3:]:BMP'
1.035043 GENE b'lemma:BMP'
1.035043 GENE b'word:BMP'
1.024162 O b'word[:2]:an'
1.014152 O b'word[:3]:IPF'
1.012327 GENE b'lemma[-3:]:F-2'
1.008418 GENE b'word[:3]:ins'
1.000743 O b'lemma[-2:]:on'
0.994406 GENE b'lemma:Transforming'
0.993303 GENE b'word[:2]:NO'
0.989415 O b'lemma:simvastatin'
0.978677 O b'word[:1]:a'
0.977070 GENE b'word:VEGF'
0.977070 GENE b'lemma:vegf'
0.977070 GENE b'lemma[-3:]:egf'
0.977070 GENE b'word[:3]:VEG'
0.977070 GENE b'word[:2]:VE'
0.974536 GENE b'word[-1:]:8'
0.974536 GENE b'lemma[-1:]:8'
0.970620 GENE b'word[-3:]:F-2'
0.964584 GENE b'word[:2]:AC'
0.964584 GENE b'word[-2:]:CE'
0.964584 GENE b'word:ACE'
0.964584 GENE b'word[:3]:ACE'
0.964584 GENE b'word[-3:]:ACE'
0.964584 GENE b'lemma:ace'
0.957851 GENE b'lemma:RHOA'
0.957851 GENE b'lemma[-2:]:OA'
0.957851 GENE b'word:RhoA'
0.957851 GENE b'word[-3:]:hoA'
0.957851 GENE b'lemma[-3:]:HOA'
0.956459 GENE b'lemma[-3:]:ace'
0.930562 GENE b'word[:2]:p3'
0.930562 GENE b'lemma:p38'
0.930562 GENE b'word[:3]:p38'
0.930562 GENE b'lemma[-3:]:p38'
0.930562 GENE b'word:p38'
0.930562 GENE b'word[-3:]:p38'
0.917083 GENE b'word[-3:]:eta'
0.917083 GENE b'lemma[-3:]:eta'
0.913861 GENE b'word[:2]:MT'
0.913087 GENE b'word[:1]:V'
0.906233 GENE b'word:metalloproteinase'
0.904096 O b'word[-2:]:er'
Top negative:
-0.366794 O b'lemma[-2:]:21'
-0.366794 O b'word[-2:]:21'
-0.367406 O b'word[-2:]:rs'
-0.369970 GENE b'lemma[-1:]:e'
-0.370216 O b'word[-3:]:ors'
-0.379214 GENE b'word[-1:]:g'
-0.380560 O b'word[:2]:ly'
-0.381500 O b'lemma[-2:]:-1'
-0.381500 O b'word[-2:]:-1'
-0.382487 O b'lemma[-2:]:rs'
-0.388022 O b'word[-2:]:63'
-0.388022 O b'lemma[-2:]:63'
-0.391124 O b'word[-3:]:NOS'
-0.391124 O b'lemma[-3:]:nos'
-0.395261 O b'word[-3:]:P-1'
-0.395261 O b'lemma[-3:]:P-1'
-0.395327 O b'word[:3]:tis'
-0.396166 O b'word[:3]:lym'
-0.396953 O b'lemma[-1:]:s'
-0.397075 O b'word[-2:]:MP'
-0.409251 O b'word[:1]:c'
-0.411906 GENE b'lemma[-1:]:t'
-0.412786 O b'lemma:metalloproteinase'
-0.412913 O b'word:tissue'
-0.415718 O b'word[:2]:fi'
-0.418347 GENE b'word[-1:]:t'
-0.421337 O b'lemma[-2:]:in'
-0.422552 O b'word[:2]:HS'
-0.422552 O b'word[:3]:HSP'
-0.432876 O b'lemma[-2:]:MP'
-0.435752 O b'lemma[-2:]:-B'
-0.435752 O b'word[-2:]:-B'
-0.437611 O b'word[:3]:sup'
-0.438135 GENE b'lemma[-1:]:r'
-0.441082 O b'lemma[-2:]:-3'
-0.441082 O b'word[-2:]:-3'
-0.446614 O b'word[:3]:Gre'
-0.456106 GENE b'word[:3]:Ang'
-0.459372 O b'word[:2]:se'
-0.465484 O b'word[:3]:mor'
-0.465575 O b'lemma[-3:]:-10'
-0.465575 O b'word[-3:]:-10'
-0.467478 O b'word[:2]:li'
-0.467808 GENE b'word[:2]:An'
-0.469099 O b'lemma[-3:]:pha'
-0.469099 O b'word[-3:]:pha'
-0.469099 O b'word[-2:]:ha'
-0.469099 O b'lemma[-2:]:ha'
-0.482003 O b'word[:2]:va'
-0.525903 O b'word[:3]:int'
-0.531367 O b'word[-1:]:B'
-0.532490 O b'lemma[-2:]:-I'
-0.532490 O b'word[-2:]:-I'
-0.534037 O b'lemma[-1:]:A'
-0.535822 O b'word[:2]:AL'
-0.543042 O b'word[:3]:ALK'
-0.543132 O b'word:endothelial'
-0.543132 O b'lemma:endothelial'
-0.546994 O b'lemma[-3:]:ing'
-0.547612 O b'word[:2]:CC'
-0.553984 GENE b'lemma[-1:]:l'
-0.565518 O b'word[:2]:mo'
-0.568142 O b'lemma:factor'
-0.570032 O b'word[:2]:RA'
-0.580240 O b'word[-2:]:ta'
-0.582775 O b'word[:1]:I'
-0.584803 O b'word:fibroblast'
-0.590575 O b'lemma:superoxide'
-0.590575 O b'word:superoxide'
-0.598882 O b'word[-2:]:ES'
-0.599564 O b'word[:2]:FG'
-0.605306 O b'lemma[-2:]:ta'
-0.608000 O b'word[:3]:nec'
-0.608210 O b'word[:2]:EC'
-0.614308 O b'word:necrosis'
-0.614308 O b'lemma:necrosis'
-0.616327 O b'word[:3]:cas'
-0.624078 O b'lemma[-1:]:G'
-0.626598 O b'word[:3]:con'
-0.648962 O b'word[:1]:J'
-0.657170 O b'word[:2]:tu'
-0.663259 O b'word[:3]:SOC'
-0.663259 O b'word[:2]:SO'
-0.665217 O b'word[:3]:tum'
-0.673605 GENE b'word[:1]:i'
-0.674339 O b'word[:3]:fib'
-0.678405 O b'lemma:dismutase'
-0.678405 O b'word:dismutase'
-0.679035 O b'word[-1:]:T'
-0.685189 O b'word[-2:]:-6'
-0.685189 O b'lemma[-2:]:-6'
-0.687452 O b'word[:2]:AN'
-0.688504 O b'word[:1]:P'
-0.691511 O b'word[:3]:tra'
-0.693167 O b'word[:2]:JN'
-0.693167 O b'word[:3]:JNK'
-0.694641 O b'lemma[-2:]:MA'
-0.694641 O b'word[-2:]:MA'
-0.702467 O b'word[:3]:bet'
-0.706543 O b'lemma[-2:]:nk'
-0.708396 O b'lemma[-1:]:B'
-0.722924 O b'word[:3]:ET-'
-0.722924 O b'word[:2]:ET'
-0.726088 GENE b'lemma[-1:]:d'
-0.729231 O b'word[:2]:ER'
-0.734147 O b'word[:2]:IG'
-0.734147 O b'word[:3]:IGF'
-0.750532 O b'word[:3]:vas'
-0.752846 O b'word[:2]:E-'
-0.752846 O b'word[:3]:E-c'
-0.755338 O b'word[:2]:Sm'
-0.756963 O b'word[:2]:MM'
-0.756963 O b'word[:3]:MMP'
-0.759412 GENE b'lemma[-1:]:h'
-0.760020 GENE b'word[:1]:1'
-0.766542 O b'lemma[-3:]:tin'
-0.766744 O b'word[-3:]:tin'
-0.767515 O b'lemma:vascular'
-0.767515 O b'word:vascular'
-0.768256 O b'word[:2]:Tr'
-0.777292 O b'word:morphogenetic'
-0.777292 O b'lemma:morphogenetic'
-0.780433 O b'word[:3]:Sma'
-0.782127 O b'word[-1:]:7'
-0.782127 O b'lemma[-1:]:7'
-0.782575 O b'word[:2]:EM'
-0.782575 O b'word[:3]:EMT'
-0.796060 O b'word[-3:]:Fas'
-0.801875 O b'word[:3]:Rho'
-0.801875 O b'word[:2]:Rh'
-0.802815 O b'word[:3]:Tra'
-0.809954 O b'lemma:connective'
-0.809954 O b'word:connective'
-0.818483 O b'word[:3]:gre'
-0.818495 O b'word[-3:]:ase'
-0.823615 O b'word[:3]:ser'
-0.824815 O b'word[:2]:c-'
-0.832235 O b'word[:3]:Fas'
-0.838616 O b'word[:3]:ANG'
-0.841970 O b'word[:1]:A'
-0.846024 O b'word:Fas'
-0.860588 O b'word[:2]:Pi'
-0.868045 O b'word[:2]:gr'
-0.868310 O b'word[-1:]:3'
-0.868310 O b'lemma[-1:]:3'
-0.869209 O b'word[-1:]:2'
-0.869209 O b'lemma[-1:]:2'
-0.871073 O b'lemma:bone'
-0.880174 O b'word[-2:]:GF'
-0.887924 O b'word[:3]:cyc'
-0.893861 O b'lemma[-3:]:HGF'
-0.896107 GENE b'lemma:beta'
-0.896107 GENE b'word:beta'
-0.903338 O b'lemma[-1:]:1'
-0.903338 O b'word[-1:]:1'
-0.906233 O b'word:metalloproteinase'
-0.913087 O b'word[:1]:V'
-0.913861 O b'word[:2]:MT'
-0.917083 O b'lemma[-3:]:eta'
-0.917083 O b'word[-3:]:eta'
-0.956459 O b'lemma[-3:]:ace'
-0.970620 O b'word[-3:]:F-2'
-0.974536 O b'lemma[-1:]:8'
-0.974536 O b'word[-1:]:8'
-0.978677 GENE b'word[:1]:a'
-0.993303 O b'word[:2]:NO'
-1.008418 O b'word[:3]:ins'
-1.046833 O b'lemma[-2:]:10'
-1.046833 O b'word[-2:]:10'
-1.073379 O b'word[-2:]:in'
-1.079711 O b'word[:3]:alp'
-1.089527 O b'word[:2]:BM'
-1.089527 O b'word[:3]:BMP'
-1.109123 O b'word[:1]:M'
-1.111781 O b'lemma:serine'
-1.127347 O b'word[:2]:en'
-1.139320 O b'word[:3]:TNF'
-1.139320 O b'word[:2]:TN'
-1.150437 O b'lemma[-1:]:I'
-1.153127 O b'word[:3]:TGF'
-1.153127 O b'word[:2]:TG'
-1.212553 O b'word[:1]:H'
-1.238688 O b'word[:3]:lig'
-1.259804 O b'lemma[-3:]:yte'
-1.300737 GENE b'word[-1:]:d'
-1.304592 O b'word[:3]:ext'
-1.305260 O b'lemma[-1:]:N'
-1.310759 O b'word[-3:]:yte'
-1.363564 O b'word[:3]:che'
-1.368611 O b'word[:3]:bon'
-1.383684 O b'word[:3]:IFN'
-1.383684 O b'word[:2]:IF'
-1.387690 O b'word:transforming'
-1.407013 O b'word[:2]:IL'
-1.475005 O b'word[:1]:E'
-1.504231 O b'lemma:ligand'
-1.573694 GENE b'word[-1:]:s'
-1.667293 O b'word:factor'
-1.668226 O b'word[:1]:C'
-1.933060 O b'word:receptors'