Carlos-Francisco Méndez-Cruz / automatic-extraction-growth-conditions

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report_S1_True_S2_False_v1.txt 17.1 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70_v4.txt

best params:{'c1': 0.3717925853055416, 'c2': 0.017924580629424793}
best CV score:0.8125475599052483
model size: 0.07M

Flat F1: 0.8015576085711513
             precision    recall  f1-score   support

         OD      0.789     0.405     0.536        37
         pH      1.000     1.000     1.000        12
  Technique      1.000     0.909     0.952        22
        Med      0.891     0.860     0.875        57
       Temp      0.818     1.000     0.900        18
       Vess      0.000     0.000     0.000         0
       Agit      0.000     0.000     0.000         0
      Phase      1.000     0.895     0.944        19
        Air      0.783     0.758     0.770        62
       Anti      0.857     0.667     0.750         9
     Strain      1.000     1.000     1.000         1
      Gtype      0.897     0.821     0.857       106
  Substrain      0.000     0.000     0.000         1
       Supp      0.857     0.662     0.747       136
   Gversion      0.000     0.000     0.000         0

avg / total      0.868     0.754     0.802       480


Top likely transitions:
Agit   -> Agit    6.913143
OD     -> OD      6.546357
Temp   -> Temp    5.712726
Med    -> Med     5.305596
Anti   -> Anti    5.023718
Supp   -> Supp    4.631165
Phase  -> Phase   4.500208
Gtype  -> Gtype   4.293158
Air    -> Air     4.246276
Gversion -> Gversion 4.168987
O      -> O       3.925497
Technique -> Technique 3.566379
pH     -> pH      2.052884
O      -> Supp    1.936178
Gtype  -> Supp    1.326152
Air    -> O       1.051292
O      -> Technique 0.918460
O      -> Gtype   0.855955
O      -> Anti    0.549728
Med    -> O       0.455808
Phase  -> O       0.391302
O      -> Temp    0.389367
OD     -> Phase   0.349412
Supp   -> O       0.327410
Substrain -> Gtype   0.326440
Temp   -> O       0.267368
O      -> Med     0.077179
O      -> Phase   0.028994
O      -> Gversion 0.026775
Technique -> pH      -0.006596
Air    -> Temp    -0.006647
Phase  -> OD      -0.020087
Gtype  -> Anti    -0.153729
Supp   -> Gtype   -0.163416
Gtype  -> OD      -0.192090
Supp   -> Med     -0.235685
OD     -> O       -0.243341
Med    -> Supp    -0.274565
Agit   -> O       -0.322550
Gtype  -> O       -0.369110
OD     -> Air     -0.568717
O      -> Air     -0.731642
Technique -> O       -0.757868
Substrain -> O       -0.822866


Top unlikely transitions:
Agit   -> Agit    6.913143
OD     -> OD      6.546357
Temp   -> Temp    5.712726
Med    -> Med     5.305596
Anti   -> Anti    5.023718
Supp   -> Supp    4.631165
Phase  -> Phase   4.500208
Gtype  -> Gtype   4.293158
Air    -> Air     4.246276
Gversion -> Gversion 4.168987
O      -> O       3.925497
Technique -> Technique 3.566379
pH     -> pH      2.052884
O      -> Supp    1.936178
Gtype  -> Supp    1.326152
Air    -> O       1.051292
O      -> Technique 0.918460
O      -> Gtype   0.855955
O      -> Anti    0.549728
Med    -> O       0.455808
Phase  -> O       0.391302
O      -> Temp    0.389367
OD     -> Phase   0.349412
Supp   -> O       0.327410
Substrain -> Gtype   0.326440
Temp   -> O       0.267368
O      -> Med     0.077179
O      -> Phase   0.028994
O      -> Gversion 0.026775
Technique -> pH      -0.006596
Air    -> Temp    -0.006647
Phase  -> OD      -0.020087
Gtype  -> Anti    -0.153729
Supp   -> Gtype   -0.163416
Gtype  -> OD      -0.192090
Supp   -> Med     -0.235685
OD     -> O       -0.243341
Med    -> Supp    -0.274565
Agit   -> O       -0.322550
Gtype  -> O       -0.369110
OD     -> Air     -0.568717
O      -> Air     -0.731642
Technique -> O       -0.757868
Substrain -> O       -0.822866


Top positive:
7.111444 Technique b'lemma[:2]:Ch'
4.825937 O        b'lemma[:2]:re'
4.279457 Air      b'lemma:anaerobic'
3.725935 O        b'lemma[:2]:ge'
3.543228 O        b'lemma:1'
3.543228 O        b'lemma[:2]:1'
3.524472 OD       b'lemma[:2]:od'
3.478950 Phase    b'lemma:stationary'
3.469718 Gtype    b'-1:lemma:\xe2\x88\x86'
3.448630 Gtype    b'lemma:arca8myc'
3.428352 Air      b'-1:lemma:ChIP-Seq'
3.363763 Air      b'lemma:aerobic'
3.207046 O        b'lemma:rpob'
3.019693 Supp     b'lemma:Iron'
3.019693 Supp     b'lemma[:2]:Ir'
3.010875 O        b'-1:lemma:ChIP-exo'
2.921711 Supp     b'+1:lemma:\xc2\xb5m'
2.911305 Gtype    b'lemma[:1]:\xce\xb4'
2.889155 O        b'-1:lemma:tag'
2.855933 O        b'lemma:with'
2.855646 Med      b'lemma[:1]:L'
2.846749 Technique b'lemma:chipseq'
2.827870 O        b'lemma:2'
2.827870 O        b'lemma[:2]:2'
2.817912 Air      b'lemma[:2]:ae'
2.797895 Substrain b'lemma:mg1655'
2.792078 Phase    b'lemma:mid-log'
2.745493 Supp     b'+1:lemma:1'
2.729132 Technique b'lemma[:2]:rn'
2.682269 O        b'lemma:3'
2.682269 O        b'lemma[:2]:3'
2.657675 Gtype    b'lemma:type'
2.657675 Gtype    b'lemma[:2]:ty'
2.623761 Med      b'+1:lemma:0.4'
2.580684 Gtype    b'lemma[:2]:cr'
2.579976 O        b'lemma:_'
2.579976 O        b'lemma[:1]:_'
2.579976 O        b'lemma[:2]:_'
2.569904 O        b'+1:lemma:od600'
2.544048 Gtype    b'lemma[:2]:de'
2.507607 Temp     b'-1:lemma:sample'
2.491621 Supp     b'lemma:nitrate'
2.491621 Supp     b'lemma[:2]:ni'
2.487340 Gtype    b'lemma:flag-tag'
2.487340 Gtype    b'-1:lemma:c-terminal'
2.476917 Supp     b'lemma:arginine'
2.470339 Anti     b'+1:lemma:antibody'
2.468809 Gtype    b'lemma[:2]:fl'
2.457061 Air      b'lemma[:2]:an'
2.401035 Gversion b'lemma:nc'
2.401035 Gversion b'lemma[:2]:nc'
2.380072 O        b'-1:lemma:0.3-0.35'
2.346761 O        b'+1:lemma:pq'
2.337210 Supp     b'+1:lemma:2'
2.311094 Gversion b'-1:lemma:nc'
2.292513 Gtype    b'+1:lemma::'
2.281017 Med      b'lemma:MOPS'
2.281017 Med      b'lemma[:1]:M'
2.281017 Med      b'lemma[:2]:MO'
2.204715 Substrain b'lemma[:2]:mg'
2.199859 O        b'lemma:0.4'
2.194544 Gversion b'lemma[:2]:00'
2.169851 Temp     b'-1:lemma:\xcf\x8332'
2.168672 Gtype    b'lemma:fnr8myc'
2.159299 Air      b'-1:lemma:co2'
2.156668 Strain   b'lemma:k-12'
2.156668 Strain   b'lemma[:2]:k-'
2.155314 O        b'-1:lemma:Aerobic'
2.138255 Supp     b'-1:lemma:Cra'
2.135365 Anti     b'lemma[:2]:an'
2.117472 pH       b'lemma:ph5'
2.117472 pH       b'+1:lemma:.5'
2.108610 Temp     b'lemma[:1]:3'
2.107391 Air      b'lemma[:1]:A'
2.102650 Supp     b'lemma:pq'
2.102650 Supp     b'lemma[:2]:pq'
2.096866 Air      b'-1:lemma:-'
2.086323 Supp     b'lemma[:2]:gl'
2.074272 O        b'-1:lemma:anaerobic'
2.064241 Gtype    b'lemma:nsrr'
2.064241 Gtype    b'lemma[:2]:ns'
2.029654 O        b'lemma:b'
2.029654 O        b'lemma[:2]:b'
2.016572 Gtype    b'lemma[:1]:W'
1.998951 Technique b'lemma[:2]:ch'
1.998131 O        b'lemma:a'
1.998131 O        b'lemma[:2]:a'
1.968766 Gtype    b'-1:lemma:rpob'
1.962195 Gtype    b'hGreek'
1.961034 Med      b'lemma:lb'
1.961034 Med      b'lemma[:2]:lb'
1.938806 Gtype    b'lemma[:2]:ar'
1.930507 OD       b'+1:lemma:stationary'
1.923810 Gversion b'lemma:chip-seq'
1.891990 O        b'-1:lemma:0.3'
1.889150 Strain   b'+1:lemma:substr'
1.888844 Technique b'lemma[:1]:C'
1.884878 Gtype    b'+1:lemma:flagtag'
1.882512 O        b'postag::'
1.882512 O        b'postag[:1]::'
1.882512 O        b'postag[:2]::'
1.856991 O        b'+1:postag:RB'
1.851608 O        b'postag:IN'
1.851608 O        b'postag[:1]:I'
1.851608 O        b'postag[:2]:IN'
1.840138 Supp     b'-1:lemma:with'
1.839774 Supp     b'lemma[:1]:\xc2\xb5'
1.822500 Gtype    b'+1:lemma:type'
1.816568 O        b'lemma[:1]:C'
1.815184 Gversion b'lemma:asm584v2'
1.805652 Gversion b'lemma[:2]:as'
1.792629 O        b'+1:postag:NNP'
1.791305 Supp     b'lemma:fructose'
1.786544 O        b'-1:lemma:type'
1.762437 Supp     b'+1:lemma:_'
1.759820 O        b'-1:lemma:lb'
1.756744 O        b'-1:lemma:glucose'
1.754105 Vess     b'lemma:flask'
1.754105 Vess     b'-1:lemma:warm'
1.750186 O        b'lemma:Custom'
1.750186 O        b'lemma[:2]:Cu'
1.745341 Strain   b'lemma[:1]:k'
1.739577 Vess     b'lemma[:2]:fl'
1.726669 Supp     b'lemma:rifampicin'
1.707436 Supp     b'lemma[:2]:ri'
1.707207 Gtype    b'+1:lemma:with'
1.696113 O        b'lemma[:1]:-'
1.692259 Air      b'lemma[:1]:a'
1.639949 Air      b'lemma:Aerobic'
1.639949 Air      b'lemma[:2]:Ae'
1.635409 O        b'postag:CC'
1.635409 O        b'postag[:2]:CC'
1.628056 Med      b'+1:lemma:g/l'
1.615358 Technique b'symb'
1.610565 Supp     b'lemma[:1]:1'
1.597091 pH       b'+1:postag:CD'
1.589795 O        b'lemma:\xcf\x8332'
1.589795 O        b'lemma[:1]:\xcf\x83'
1.589795 O        b'lemma[:2]:\xcf\x833'
1.563036 O        b'-1:lemma:l1'
1.532125 Supp     b'lemma:acetate'
1.523450 Supp     b'lemma[:1]:I'
1.498488 O        b'+1:lemma:nacl'
1.484546 Supp     b'lemma:no3'
1.474134 Gtype    b'-1:lemma:_'
1.462775 Technique b'-1:lemma:input'
1.457922 O        b'+1:lemma:ph5'
1.445969 Gtype    b'-1:postag:VBG'
1.435822 Gtype    b'+1:lemma:_'
1.434655 Supp     b'lemma:Fe'
1.434655 Supp     b'lemma[:2]:Fe'
1.433511 Gtype    b'-1:lemma:vector'
1.429069 Supp     b'-1:postag:CD'
1.428528 Gtype    b'lemma[:1]:w'
1.424222 pH       b'lemma:.5'
1.424222 pH       b'-1:lemma:ph5'
1.424222 pH       b'lemma[:2]:.5'
1.422747 Med      b'+1:lemma:2.0'
1.408132 Supp     b'+1:lemma:hour'
1.397778 O        b'lemma:.'
1.397778 O        b'postag:.'
1.397778 O        b'postag[:1]:.'
1.397778 O        b'postag[:2]:.'
1.397778 O        b'lemma[:2]:.'
1.381316 Gtype    b'lemma:wt'
1.381316 Gtype    b'lemma[:2]:wt'
1.377815 Temp     b'lemma:43'
1.377815 Temp     b'lemma[:2]:43'
1.377716 Air      b'+1:postag:IN'
1.372036 Med      b'+1:postag:-LRB-'
1.371743 Med      b'+1:lemma:-lrb-'
1.357313 Anti     b'lemma:none'
1.356053 Temp     b'-1:lemma:43'
1.355054 Supp     b'lemma[:2]:fr'
1.352442 Gversion b'+1:lemma:000913'
1.348258 O        b'-1:lemma:\xc2\xb0c'
1.339531 Supp     b'-1:postag:SYM'
1.337456 O        b'lemma:delta'
1.335121 Supp     b'lemma[:2]:ac'
1.330202 O        b'+1:lemma:mid-log'
1.317551 Supp     b'-1:postag:CC'
1.312876 OD       b'lemma:od600'
1.304321 O        b'lemma[:1]:s'
1.301244 Technique b'+1:lemma:chip-exo'
1.288165 Supp     b'lemma[:1]:2'
1.287921 Phase    b'+1:lemma:-lrb-'
1.287384 Temp     b'-1:lemma:37'
1.287206 Supp     b'lemma:nh4cl'
1.287206 Supp     b'lemma[:2]:nh'
1.285698 Supp     b'lemma[:2]:0.'
1.283844 Supp     b'lemma[:2]:fe'
1.280443 Med      b'+1:lemma:supplement'
1.280143 Gtype    b'lemma[:1]:t'
1.278668 Phase    b'+1:postag:-LRB-'
1.258754 Technique b'-1:lemma:1'
1.258397 Med      b'+1:lemma:minimal'
1.256238 Med      b'lemma[:1]:m'
1.247668 OD       b'lemma[:1]:o'
1.247204 Gversion b'lemma:u00096'
1.247204 Gversion b'+1:lemma:.2'


Top negative:
-0.000006 O        b'lemma[:1]:f'
-0.000014 Temp     b'postag:NN'
-0.000014 O        b'lemma[:1]:4'
-0.000077 O        b'-1:postag:JJ'
-0.000104 O        b'lemma:\xe2\x88\x86'
-0.000104 O        b'lemma[:1]:\xe2\x88\x86'
-0.000104 O        b'lemma[:2]:\xe2\x88\x86'
-0.000117 O        b'-1:lemma:to'
-0.000117 O        b'-1:postag:TO'
-0.000139 Gtype    b'lemma[:1]:-'
-0.000165 O        b'-1:lemma:rifampicin'
-0.000244 Air      b'postag:-RRB-'
-0.000244 Air      b'postag[:2]:-R'
-0.000244 Air      b'lemma[:2]:-r'
-0.000251 O        b'+1:lemma:n2'
-0.000490 O        b'-1:lemma:\xe2\x88\x86'
-0.000570 OD       b'+1:postag:NNS'
-0.001255 Supp     b'postag[:1]:N'
-0.001255 Supp     b'postag[:2]:NN'
-0.001277 O        b'lemma[:2]:an'
-0.001620 Supp     b'+1:postag:IN'
-0.001834 O        b'-1:lemma:mid-log'
-0.004139 Air      b'lemma[:2]:25'
-0.004380 O        b'postag:VBP'
-0.004418 O        b'+1:lemma:phase'
-0.004475 Gtype    b'+1:lemma:-rrb-'
-0.004892 O        b'lemma:phase'
-0.005013 Anti     b'postag[:1]:N'
-0.005013 Anti     b'postag[:2]:NN'
-0.005037 O        b'lemma[:2]:ph'
-0.005405 Air      b'lemma:-lrb-'
-0.005662 O        b'-1:lemma:of'
-0.006882 O        b'lemma:media'
-0.007168 Gtype    b'lemma[:1]:g'
-0.007303 Air      b'postag:-LRB-'
-0.007303 Air      b'postag[:2]:-L'
-0.007303 Air      b'lemma[:2]:-l'
-0.007834 Air      b'+1:lemma:and'
-0.008160 Air      b'lemma:25'
-0.008761 OD       b'postag[:1]:C'
-0.010588 OD       b'postag:CD'
-0.010588 OD       b'postag[:2]:CD'
-0.012329 Phase    b'-1:lemma:at'
-0.013171 Med      b'postag[:1]:C'
-0.013817 Air      b'+1:lemma:until'
-0.016734 OD       b'postag[:1]:N'
-0.016734 OD       b'postag[:2]:NN'
-0.018208 Air      b'lemma[:1]:n'
-0.022588 Supp     b'hUpper'
-0.022588 Supp     b'hLower'
-0.023822 Air      b'postag[:1]:C'
-0.024287 O        b'symb'
-0.025967 Med      b'lemma[:1]:c'
-0.026538 Air      b'-1:postag:-LRB-'
-0.031765 Technique b'postag[:1]:N'
-0.031765 Technique b'postag[:2]:NN'
-0.032068 Supp     b'lemma[:2]:mi'
-0.037401 Air      b'lemma[:1]:o'
-0.040028 Med      b'postag:NN'
-0.043803 Air      b'+1:lemma:-lrb-'
-0.044062 OD       b'+1:postag:CD'
-0.044602 Supp     b'-1:lemma:%'
-0.044731 Air      b'+1:postag:-LRB-'
-0.046035 OD       b'postag:JJ'
-0.046795 Air      b'-1:lemma:-lrb-'
-0.048808 OD       b'postag[:1]:J'
-0.048808 OD       b'postag[:2]:JJ'
-0.049349 O        b'+1:lemma:rep1'
-0.050801 Supp     b'postag:CD'
-0.050801 Supp     b'postag[:2]:CD'
-0.056455 O        b'+1:lemma:0.3'
-0.057472 O        b'-1:lemma:from'
-0.066677 O        b'lemma:dissolve'
-0.071601 Supp     b'lemma[:1]:o'
-0.072755 O        b'lemma[:1]:k'
-0.073873 O        b'lemma:150'
-0.073873 O        b'+1:lemma:mg/ml'
-0.073873 O        b'lemma[:2]:15'
-0.076685 O        b'-1:lemma:ml'
-0.076846 O        b'lemma[:2]:gl'
-0.077209 O        b'-1:lemma:od600'
-0.083778 O        b'+1:lemma:300'
-0.087471 Air      b'symb'
-0.091928 Supp     b'+1:postag:VBN'
-0.092333 Air      b'postag:CC'
-0.092333 Air      b'postag[:2]:CC'
-0.092993 O        b'+1:lemma:%'
-0.100219 Supp     b'+1:lemma:rifampicin'
-0.100582 O        b'lemma:0.1'
-0.102695 O        b'-1:lemma:-lrb-'
-0.109000 Air      b'-1:lemma:or'
-0.111199 Supp     b'lemma[:2]:an'
-0.112020 Air      b'-1:postag:CC'
-0.113367 O        b'+1:lemma:shake'
-0.119111 Anti     b'+1:lemma:anti-fur'
-0.124927 O        b'+1:lemma:+'
-0.125975 O        b'-1:postag:VBN'
-0.128619 O        b'-1:lemma:ompr'
-0.137106 Gtype    b'-1:lemma:,'
-0.137106 Gtype    b'-1:postag:,'
-0.145475 Gtype    b'lemma[:1]:n'
-0.150071 O        b'lemma[:1]:d'
-0.151088 Anti     b'symb'
-0.158504 Air      b'+1:postag:JJ'
-0.162749 O        b'-1:lemma:37'
-0.168152 O        b'-1:lemma:grow'
-0.177645 Technique b'-1:lemma::'
-0.186245 O        b'-1:lemma:IP'
-0.188141 Temp     b'+1:lemma:to'
-0.188141 Temp     b'+1:postag:TO'
-0.189069 O        b'-1:lemma:rna'
-0.190006 O        b'+1:lemma:-rrb-'
-0.192143 O        b'lemma[:2]:30'
-0.219680 O        b'lemma:co2'
-0.231361 Agit     b'symb'
-0.256617 O        b'lemma:of'
-0.256617 O        b'lemma[:2]:of'
-0.259140 O        b'lemma:37'
-0.259140 O        b'lemma[:2]:37'
-0.267489 O        b'lemma[:2]:od'
-0.270561 Med      b'+1:postag:NN'
-0.273391 O        b'+1:lemma:fecl2'
-0.274839 O        b'+1:postag:IN'
-0.277041 Technique b'postag:NN'
-0.281854 O        b'+1:lemma:\xc2\xb0c'
-0.292441 O        b'lemma:20'
-0.295792 Med      b'-1:postag:CD'
-0.308709 Supp     b'postag[:1]:C'
-0.308783 O        b'lemma[:1]:p'
-0.311181 O        b'lemma:wt'
-0.311181 O        b'lemma[:2]:wt'
-0.318567 Med      b'+1:postag:IN'
-0.318793 O        b'lemma:2h'
-0.318793 O        b'-1:lemma:additional'
-0.318793 O        b'lemma[:2]:2h'
-0.330370 O        b'+1:postag:-RRB-'
-0.332499 Air      b'postag[:1]:N'
-0.332499 Air      b'postag[:2]:NN'
-0.334391 Med      b'-1:postag:NN'
-0.338586 Temp     b'hGreek'
-0.351814 O        b'lemma[:2]:me'
-0.363828 O        b'lemma[:1]:L'
-0.365790 Gtype    b'lemma:delta'
-0.396021 O        b'+1:lemma:.'
-0.396021 O        b'+1:postag:.'
-0.405253 OD       b'+1:postag:NN'
-0.409588 O        b'lemma[:2]:ri'
-0.436123 O        b'lemma[:2]:0.'
-0.437523 O        b'-1:postag:IN'
-0.461538 O        b'-1:postag:-LRB-'
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-0.603309 Supp     b'postag[:2]:JJ'
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