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report_training-data-set-70.fStopWords_False.fSymbols_False.txt 16.6 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt

best params:{'c1': 0.12296384618516742, 'c2': 0.001984598547992556}
best CV score:0.7223961938319273
model size: 0.07M

Flat F1: 0.6328175528971997
             precision    recall  f1-score   support

         OD      1.000     0.211     0.348        57
     Sample      0.000     0.000     0.000         0
  Technique      0.000     0.000     0.000         1
        Med      1.000     0.933     0.966        30
       Temp      1.000     0.615     0.762        13
      Serie      0.000     0.000     0.000         0
       Vess      0.000     0.000     0.000         0
       Agit      0.000     0.000     0.000         7
      Phase      0.750     0.923     0.828        13
        Air      0.000     0.000     0.000         0
       Anti      1.000     0.778     0.875        18
     Strain      0.000     0.000     0.000         0
      Gtype      0.884     0.551     0.679        69
       Supp      0.582     0.629     0.605        62
   Gversion      0.750     1.000     0.857         6

avg / total      0.831     0.569     0.633       276


Top likely transitions:
OD     -> OD      6.108207
Supp   -> Supp    5.784131
Gtype  -> Gtype   5.685374
Med    -> Med     5.675327
Temp   -> Temp    5.658789
Anti   -> Anti    5.031069
Gversion -> Gversion 4.774936
O      -> O       4.746806
Phase  -> Phase   3.575687
O      -> Gtype   1.949659
OD     -> Phase   1.047851
O      -> Gversion 0.297969
O      -> Supp    0.232142
O      -> OD      0.059228
O      -> Anti    0.035022
O      -> Med     0.022142
Supp   -> Phase   -0.082451
Supp   -> Med     -0.113938
Gtype  -> Anti    -0.177348
Vess   -> O       -0.195425
Phase  -> O       -0.308432
Anti   -> O       -0.319054
Phase  -> Supp    -0.418345
O      -> Technique -0.434100
Temp   -> O       -0.447292
Gtype  -> O       -0.546043
Supp   -> O       -0.756881
OD     -> O       -0.842201
Technique -> O       -0.857966
Med    -> O       -0.892055
Substrain -> O       -0.970661
O      -> Phase   -1.142533
Temp   -> Med     -1.246193
O      -> Temp    -1.298927
Phase  -> OD      -1.766899
Med    -> Supp    -2.805768


Top unlikely transitions:
OD     -> OD      6.108207
Supp   -> Supp    5.784131
Gtype  -> Gtype   5.685374
Med    -> Med     5.675327
Temp   -> Temp    5.658789
Anti   -> Anti    5.031069
Gversion -> Gversion 4.774936
O      -> O       4.746806
Phase  -> Phase   3.575687
O      -> Gtype   1.949659
OD     -> Phase   1.047851
O      -> Gversion 0.297969
O      -> Supp    0.232142
O      -> OD      0.059228
O      -> Anti    0.035022
O      -> Med     0.022142
Supp   -> Phase   -0.082451
Supp   -> Med     -0.113938
Gtype  -> Anti    -0.177348
Vess   -> O       -0.195425
Phase  -> O       -0.308432
Anti   -> O       -0.319054
Phase  -> Supp    -0.418345
O      -> Technique -0.434100
Temp   -> O       -0.447292
Gtype  -> O       -0.546043
Supp   -> O       -0.756881
OD     -> O       -0.842201
Technique -> O       -0.857966
Med    -> O       -0.892055
Substrain -> O       -0.970661
O      -> Phase   -1.142533
Temp   -> Med     -1.246193
O      -> Temp    -1.298927
Phase  -> OD      -1.766899
Med    -> Supp    -2.805768


Top positive:
9.769521 OD       b'+1:lemma:stationary'
6.573116 Gtype    b'-1:lemma:express'
6.473813 O        b'lemma:at'
6.401320 Gtype    b'+1:lemma:chip'
5.580269 Med      b'word:MOPS'
5.580269 Med      b'lemma:MOPS'
5.309599 Med      b'-1:lemma:ml'
5.105098 Gtype    b'+1:lemma:knock-out'
5.053371 Anti     b'+1:lemma:antibody'
4.833626 O        b'+1:lemma:until'
4.685736 Supp     b'word:nitrate'
4.685736 Supp     b'lemma:nitrate'
4.578724 Temp     b'-1:lemma:sample'
4.338845 O        b'+1:postag:VBP'
4.326050 Gversion b'word:NC'
4.326050 Gversion b'lemma:nc'
4.207716 O        b'word:.'
4.207716 O        b'lemma:.'
3.987856 O        b'lemma:chip'
3.914979 Phase    b'-1:lemma:mid-log'
3.836351 O        b'+1:postag:NNP'
3.819222 O        b'word:-'
3.819222 O        b'lemma:-'
3.774330 Gtype    b'-1:lemma:wild'
3.733417 Supp     b'word:2h'
3.733417 Supp     b'lemma:2h'
3.733417 Supp     b'-1:lemma:additional'
3.729860 O        b'word::'
3.729860 O        b'lemma::'
3.704485 O        b'-1:lemma:glucose'
3.673897 O        b'-1:lemma:-'
3.584033 Phase    b'word:mid-log'
3.584033 Phase    b'lemma:mid-log'
3.580641 Gtype    b'-1:lemma:k-12'
3.329333 Gtype    b'word:Flag-tag'
3.329333 Gtype    b'lemma:flag-tag'
3.329333 Gtype    b'-1:lemma:c-terminal'
3.313956 O        b'+1:lemma:coli'
3.198151 Supp     b'-1:lemma:vol'
3.190691 O        b'-1:lemma:lb'
3.168840 Supp     b'-1:lemma:with'
3.134166 Gtype    b'word:wild'
3.134166 Gtype    b'lemma:wild'
3.092894 O        b'word:K-12'
3.092894 O        b'lemma:k-12'
3.060219 O        b'word:MG1655'
3.060219 O        b'lemma:mg1655'
3.020191 Supp     b'+1:lemma:\xc2\xb5m'
2.959207 Gversion b'word:ASM584v2'
2.959207 Gversion b'lemma:asm584v2'
2.895464 Gversion b'word:000913'
2.895464 Gversion b'lemma:000913'
2.892382 Vess     b'word:flask'
2.892382 Vess     b'lemma:flask'
2.892382 Vess     b'-1:lemma:warm'
2.889484 Temp     b'+1:lemma:and'
2.864457 OD       b'word:OD450'
2.864457 OD       b'lemma:od450'
2.844361 O        b'+1:lemma:od600'
2.760592 O        b'word:Custom'
2.760592 O        b'lemma:Custom'
2.760592 O        b'+1:lemma:anti-fur'
2.749995 Supp     b'-1:lemma:without'
2.744252 Phase    b'word:exponential'
2.744252 Phase    b'lemma:exponential'
2.724404 Phase    b'word:stationary'
2.724404 Phase    b'lemma:stationary'
2.704170 Supp     b'word:glucose'
2.704170 Supp     b'lemma:glucose'
2.702637 Med      b'-1:lemma:LB'
2.698915 Med      b'word:LB'
2.648788 O        b'+1:lemma:fructose'
2.522068 Supp     b'word:arginine'
2.522068 Supp     b'lemma:arginine'
2.521702 O        b'+1:lemma:0.2'
2.510135 Gtype    b'-1:postag:VBG'
2.500086 Med      b'word:L'
2.500086 Med      b'lemma:L'
2.500086 Med      b'+1:lemma:broth'
2.438147 Gversion b'-1:lemma:nc'
2.435933 O        b'word:with'
2.435933 O        b'lemma:with'
2.424051 OD       b'word:OD600'
2.424051 OD       b'lemma:od600'
2.397049 Gversion b'word:U00096'
2.397049 Gversion b'lemma:u00096'
2.397049 Gversion b'+1:lemma:.2'
2.393316 Temp     b'-1:lemma:37'
2.384921 Med      b'+1:lemma:g/l'
2.343273 O        b'lemma:for'
2.287420 O        b'-1:lemma:\xc2\xb0c'
2.277217 Supp     b'word:acetate'
2.277217 Supp     b'lemma:acetate'
2.240391 Gtype    b'word:WT'
2.227767 O        b'word:Cells'
2.223138 Temp     b'+1:lemma:\xc2\xb0c'
2.207530 Gtype    b'word:PK4854'
2.207530 Gtype    b'lemma:pk4854'
2.204777 Technique b'word:RNA-Seq'
2.200781 Anti     b'-1:lemma:polymerase'
2.180743 O        b'-1:lemma:phase'
2.168855 Supp     b'+1:lemma:at'
2.168107 Supp     b'+1:lemma:arginine'
2.152384 O        b'word:Crosslink'
2.152384 O        b'lemma:Crosslink'
2.151825 O        b'word:for'
2.146611 Supp     b'+1:lemma:hour'
2.145369 Phase    b'+1:lemma:for'
2.130614 Supp     b'+1:lemma:and'
2.127595 Temp     b'word:\xc2\xb0C'
2.127595 Temp     b'lemma:\xc2\xb0c'
2.118493 Med      b'word:broth'
2.118493 Med      b'lemma:broth'
2.118493 Med      b'-1:lemma:L'
2.100174 Supp     b'word:Adenine'
2.100174 Supp     b'lemma:Adenine'
2.099073 Supp     b'word:hours'
2.099073 Supp     b'lemma:hour'
2.091461 Technique b'lemma:rna-seq'
2.081270 O        b'+1:lemma:0.4'
2.069166 OD       b'word:0.3'
2.069166 OD       b'lemma:0.3'
2.025934 O        b'-1:lemma:tag'
2.016740 Med      b'word:M63'
2.016740 Med      b'lemma:m63'
1.951269 Supp     b'-1:lemma:final'
1.951255 Anti     b'+1:lemma:polyclonal'
1.940092 O        b'+1:postag:CD'
1.937643 O        b'word:supplemented'
1.937643 O        b'lemma:supplement'
1.928437 Gtype    b'word:oxyR-8myc'
1.928437 Gtype    b'lemma:oxyr-8myc'
1.925371 Gtype    b'word:soxR-8myc'
1.925371 Gtype    b'lemma:soxr-8myc'
1.905981 Supp     b'-1:lemma:+'
1.904247 Gversion b'word:.2'
1.904247 Gversion b'lemma:.2'
1.904247 Gversion b'-1:lemma:u00096'
1.895301 Supp     b'-1:lemma::'
1.888517 Med      b'+1:lemma:minimal'
1.888285 O        b'+1:lemma:nitrate'
1.887992 O        b'+1:lemma:anaerobic'
1.887095 Phase    b'word:phase'
1.887095 Phase    b'lemma:phase'
1.873844 Anti     b'word:\xcf\x8332'
1.873844 Anti     b'lemma:\xcf\x8332'
1.858813 Med      b'lemma:LB'
1.856133 O        b'-1:lemma:-80'
1.850543 Supp     b'+1:lemma:be'
1.822229 Supp     b'word:leucine'
1.822229 Supp     b'lemma:leucine'
1.818630 O        b'-1:lemma:flag-tag'
1.810937 O        b'-1:lemma:_'
1.808829 Supp     b'word:fructose'
1.808829 Supp     b'lemma:fructose'
1.805654 OD       b'word:A'
1.799136 Gversion b'lemma:chip-seq'
1.792100 Phase    b'-1:lemma:until'
1.787880 Anti     b'-1:lemma:monoclonal'
1.786790 Anti     b'word:anti-myc'
1.786790 Anti     b'lemma:anti-myc'
1.784685 Substrain b'word:MG1655star'
1.784685 Substrain b'lemma:mg1655star'
1.778678 Technique b'lemma:chip-seq'
1.778353 O        b'word:<Air>'
1.751251 Supp     b'-1:lemma:1mm'
1.746035 Supp     b'+1:lemma:1/100'
1.733606 Anti     b'+1:lemma:from'
1.729502 Technique b'word:ChIP-Seq'
1.725373 O        b'+1:lemma:mid-log'
1.712485 Gversion b'word:ChIP-Seq'
1.709357 O        b'-1:postag:NNS'
1.693666 O        b'word:-RRB-'
1.693666 O        b'lemma:-rrb-'
1.656579 Supp     b'word:rifampicin'
1.656579 Supp     b'lemma:rifampicin'
1.654463 O        b'lemma:to'
1.646916 Anti     b'word:anti-RpoB'
1.646916 Anti     b'lemma:anti-rpob'
1.641270 Vess     b'-1:postag:VBN'
1.634955 Anti     b'word:SeqA'
1.634955 Anti     b'lemma:seqa'
1.626876 Med      b'+1:lemma:-lrb-'
1.621826 O        b'lemma:<air>'
1.616807 Supp     b'word:tryptophan'
1.616807 Supp     b'lemma:tryptophan'
1.616807 Supp     b'-1:lemma:mg/l'
1.584459 O        b'lemma:anaerobic'
1.571612 Med      b'word:medium'
1.571612 Med      b'lemma:medium'
1.550300 Vess     b'+1:lemma:at'
1.549343 O        b'word:B'
1.547972 Gtype    b'-1:lemma:\xe2\x88\x86'
1.546575 OD       b'+1:lemma:oxyr-8myc'
1.546406 O        b'+1:lemma:aerobic'
1.528557 Supp     b'+1:lemma:300'
1.505854 Temp     b'-1:lemma:at'
1.482950 Supp     b'-1:postag:IN'
1.477298 Med      b'-1:lemma:glucose'
1.476212 O        b'-1:lemma:media'


Top negative:
-0.033522 O        b'lemma:20'
-0.038038 Anti     b'isupper()'
-0.038347 OD       b'isupper()'
-0.045438 O        b'word:phosphate'
-0.045438 O        b'lemma:phosphate'
-0.046287 O        b'word:LB'
-0.047486 Gtype    b'-1:lemma:,'
-0.047486 Gtype    b'-1:postag:,'
-0.047973 O        b'+1:lemma:culture'
-0.048635 Med      b'-1:postag:NN'
-0.048786 Supp     b'-1:lemma:,'
-0.048786 Supp     b'-1:postag:,'
-0.049214 Temp     b'-1:postag:NN'
-0.055607 Supp     b'word:vol'
-0.055607 Supp     b'lemma:vol'
-0.055607 Supp     b'-1:lemma:1/100'
-0.057967 O        b'word:150'
-0.057967 O        b'lemma:150'
-0.057967 O        b'+1:lemma:mg/ml'
-0.065780 Med      b'+1:lemma:media'
-0.067419 O        b'-1:lemma:rifampicin'
-0.068390 O        b'+1:lemma:medium'
-0.069566 Gtype    b'+1:postag:JJ'
-0.069740 Supp     b'word:10'
-0.069740 Supp     b'lemma:10'
-0.072097 Supp     b'-1:lemma:;'
-0.074848 Supp     b'-1:lemma:.'
-0.074848 Supp     b'-1:postag:.'
-0.075753 O        b'word:min'
-0.075753 O        b'lemma:min'
-0.076584 Supp     b'-1:lemma:-lrb-'
-0.079109 Supp     b'word:uM'
-0.079109 Supp     b'lemma:um'
-0.079109 Supp     b'-1:lemma:250'
-0.083627 O        b'-1:lemma:m9'
-0.084086 Anti     b'-1:postag:NN'
-0.084792 Supp     b'-1:postag:-LRB-'
-0.085223 Med      b'-1:postag:IN'
-0.090978 O        b'-1:postag:VBN'
-0.091287 Supp     b'-1:lemma:10'
-0.093086 Gtype    b'isupper()'
-0.097632 O        b'word:1M'
-0.097632 O        b'lemma:1m'
-0.098995 O        b'-1:lemma:-lrb-'
-0.102411 O        b'-1:lemma:Fur'
-0.109527 Gtype    b'+1:postag:IN'
-0.110624 O        b'word:7.6'
-0.110624 O        b'lemma:7.6'
-0.110624 O        b'-1:lemma:ph'
-0.110624 O        b'+1:lemma:;'
-0.115984 O        b'-1:lemma:and'
-0.116488 O        b'-1:lemma:soxr-8myc'
-0.125176 O        b'+1:lemma:min'
-0.130318 Phase    b'-1:lemma:at'
-0.132219 O        b'word:crp'
-0.132219 O        b'lemma:crp'
-0.135378 Supp     b'word:,'
-0.135378 Supp     b'lemma:,'
-0.135758 Supp     b'word:250'
-0.135758 Supp     b'lemma:250'
-0.135758 Supp     b'+1:lemma:um'
-0.145733 Supp     b'word:and'
-0.145733 Supp     b'lemma:and'
-0.148126 O        b'-1:lemma:.'
-0.148126 O        b'-1:postag:.'
-0.149156 O        b'-1:lemma:until'
-0.157548 O        b'+1:lemma:\xc2\xb5m'
-0.160930 O        b'+1:lemma:tag'
-0.162355 O        b'+1:lemma:phase'
-0.193262 O        b'-1:lemma:2'
-0.194523 O        b'-1:lemma:43'
-0.194585 OD       b'+1:lemma:~'
-0.205225 O        b'-1:postag:CC'
-0.217098 Temp     b'+1:postag:IN'
-0.217465 O        b'word:%'
-0.217465 O        b'lemma:%'
-0.221369 Supp     b'+1:lemma:acetate'
-0.229086 O        b'word:43'
-0.229086 O        b'lemma:43'
-0.230011 O        b'-1:lemma:delta'
-0.230917 O        b'+1:postag:NNS'
-0.233042 Supp     b'+1:postag:VBN'
-0.234678 Med      b'+1:postag:CC'
-0.239379 O        b'word:pH'
-0.239379 O        b'lemma:ph'
-0.239379 O        b'+1:lemma:7.6'
-0.240087 O        b'+1:lemma:mg1655'
-0.243533 O        b'word:0.1'
-0.243533 O        b'lemma:0.1'
-0.247022 Anti     b'+1:postag:JJ'
-0.254824 O        b'-1:lemma:sodium'
-0.257080 O        b'+1:lemma:dissolve'
-0.258767 Supp     b'-1:postag:NN'
-0.262289 O        b'+1:postag:IN'
-0.268651 O        b'-1:lemma:od600'
-0.269420 O        b'-1:postag:-LRB-'
-0.278544 O        b'-1:lemma:0.2'
-0.280204 O        b'word:of'
-0.280204 O        b'lemma:of'
-0.289904 Gtype    b'word:,'
-0.289904 Gtype    b'lemma:,'
-0.293848 O        b'+1:lemma:sample'
-0.302903 O        b'-1:lemma:mid-log'
-0.308508 O        b'+1:lemma:1m'
-0.316766 O        b'lemma:sample'
-0.317700 O        b'-1:lemma:1m'
-0.317700 O        b'+1:lemma:ph'
-0.325320 O        b'-1:postag:IN'
-0.347306 O        b'-1:lemma:contain'
-0.353650 O        b'word:media'
-0.353650 O        b'lemma:media'
-0.361308 O        b'+1:lemma:-rrb-'
-0.363822 O        b'-1:lemma:mm'
-0.370286 O        b'-1:lemma:analyze'
-0.371370 O        b'word:medium'
-0.371370 O        b'lemma:medium'
-0.371526 O        b'word:0.2'
-0.371526 O        b'lemma:0.2'
-0.388795 Med      b'+1:lemma:m9'
-0.389065 O        b'-1:lemma:fresh'
-0.396824 Phase    b'isupper()'
-0.407829 O        b'word:methanol'
-0.407829 O        b'lemma:methanol'
-0.409652 O        b'word:dissolved'
-0.409652 O        b'lemma:dissolve'
-0.420228 Supp     b'word:.'
-0.420228 Supp     b'lemma:.'
-0.420585 O        b'-1:lemma:final'
-0.435371 O        b'word:mid-log'
-0.435371 O        b'lemma:mid-log'
-0.449869 Med      b'+1:postag:CD'
-0.453920 O        b'-1:lemma:or'
-0.462008 O        b'+1:lemma:in'
-0.464988 O        b'word:rifampicin'
-0.464988 O        b'lemma:rifampicin'
-0.468866 O        b'word:30'
-0.468866 O        b'lemma:30'
-0.490303 O        b'+1:lemma:-lrb-'
-0.521128 O        b'-1:lemma:of'
-0.549971 O        b'+1:postag:-RRB-'
-0.552220 O        b'-1:lemma:minimal'
-0.554112 Supp     b'+1:postag:CD'
-0.554855 Gtype    b'islower()'
-0.556777 O        b'word:OD600'
-0.556777 O        b'lemma:od600'
-0.558779 O        b'+1:lemma:antibody'
-0.581083 Med      b'islower()'
-0.588156 Supp     b'+1:postag:JJ'
-0.596135 O        b'+1:lemma:.'
-0.596135 O        b'+1:postag:.'
-0.603800 O        b'word:glucose'
-0.603800 O        b'lemma:glucose'
-0.604194 Temp     b'-1:postag:CD'
-0.610067 O        b'word:minimal'
-0.610067 O        b'lemma:minimal'
-0.613419 Supp     b'isupper()'
-0.618968 O        b'word:phase'
-0.618968 O        b'lemma:phase'
-0.635118 O        b'-1:lemma:ml'
-0.635236 O        b'-1:lemma:dissolve'
-0.635236 O        b'+1:lemma:methanol'
-0.649664 O        b'word:37'
-0.649664 O        b'lemma:37'
-0.653888 Med      b'+1:postag:NN'
-0.672366 Temp     b'islower()'
-0.679024 O        b'word:cra'
-0.697555 OD       b'+1:postag:NN'
-0.726875 Supp     b'islower()'
-0.736892 O        b'-1:lemma:growth'
-0.744187 O        b'-1:lemma:phosphate'
-0.779776 O        b'+1:lemma:minimal'
-0.789382 O        b'-1:lemma:rna'
-0.925215 O        b'+1:lemma:supplement'
-0.938635 O        b'+1:lemma:contain'
-0.959966 O        b'+1:lemma:1/100'
-1.005759 Gtype    b'isNumber()'
-1.020571 O        b'+1:postag:-LRB-'
-1.023100 O        b'+1:lemma:g/l'
-1.034129 O        b'+1:lemma:chip'
-1.057527 O        b'+1:lemma:0.3'
-1.097957 O        b'-1:lemma:37'
-1.274500 O        b'lemma:tag'
-1.286152 O        b'-1:postag::'
-1.303774 O        b'-1:lemma:the'
-1.380700 O        b'+1:lemma:oxyr-8myc'
-1.396643 O        b'-1:lemma:k-12'
-1.508771 O        b'+1:lemma:at'
-1.634199 Supp     b'+1:lemma:,'
-1.634199 Supp     b'+1:postag:,'
-1.651060 O        b'+1:lemma:for'
-1.669291 O        b'-1:lemma:30'
-1.845334 Gversion b'islower()'
-1.912631 Supp     b'+1:postag:-LRB-'
-1.916490 Supp     b'+1:lemma:-lrb-'
-2.376915 O        b'+1:lemma:<air>'
-2.666827 O        b'-1:lemma:vol'
-2.728484 OD       b'-1:postag:CD'
-3.072458 O        b'-1:lemma:sample'
-3.939533 O        b'-1:lemma::'
-4.411137 Phase    b'-1:postag:JJ'