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

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report_Run_2_v12.txt 16.8 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt

best params:{'c1': 0.1779311060486324, 'c2': 0.0005619148999585256}
best CV score:0.8815860410516979
model size: 0.07M

Flat F1: 0.7874835473429163
             precision    recall  f1-score   support

         OD      1.000     0.818     0.900        22
         pH      1.000     1.000     1.000         8
  Technique      1.000     0.913     0.955        23
        Med      1.000     0.962     0.981        53
       Temp      1.000     0.931     0.964        29
       Vess      1.000     1.000     1.000         1
       Agit      0.000     0.000     0.000         0
      Phase      0.882     1.000     0.938        15
        Air      0.543     0.362     0.435        69
       Anti      1.000     1.000     1.000        11
     Strain      0.000     0.000     0.000         1
      Gtype      0.893     0.788     0.837        85
  Substrain      0.000     0.000     0.000         0
       Supp      0.677     0.799     0.733       134
   Gversion      0.000     0.000     0.000         0

avg / total      0.808     0.778     0.787       451


Top likely transitions:
Agit   -> Agit    7.599672
Temp   -> Temp    6.866268
OD     -> OD      6.223914
Med    -> Med     6.223896
Anti   -> Anti    5.733249
Supp   -> Supp    5.501969
Phase  -> Phase   5.255937
Air    -> Air     5.242444
Gversion -> Gversion 4.759517
Technique -> Technique 4.572796
Gtype  -> Gtype   4.408618
pH     -> pH      4.148766
O      -> O       3.770155
O      -> Technique 1.394833
Air    -> O       0.934701
O      -> Supp    0.603143
Gtype  -> Supp    0.602203
O      -> Temp    0.531294
O      -> Gtype   0.244043
Substrain -> Gtype   0.178777
Temp   -> O       0.116666
O      -> Anti    0.073374
Technique -> Air     0.057205
O      -> Phase   0.016593
Med    -> O       0.014656
O      -> OD      0.003771
O      -> pH      0.001976
Anti   -> O       -0.000356
Phase  -> O       -0.013827
Supp   -> O       -0.037801
Gversion -> O       -0.118955
OD     -> O       -0.146201
Air    -> Temp    -0.162047
O      -> Med     -0.221356
Gtype  -> Anti    -0.235366
OD     -> Air     -0.430187
Technique -> O       -0.658505
Supp   -> Med     -0.680587
O      -> Air     -1.100972
Gtype  -> O       -1.334900
Med    -> Supp    -1.533125
Substrain -> O       -2.088700


Top unlikely transitions:
Agit   -> Agit    7.599672
Temp   -> Temp    6.866268
OD     -> OD      6.223914
Med    -> Med     6.223896
Anti   -> Anti    5.733249
Supp   -> Supp    5.501969
Phase  -> Phase   5.255937
Air    -> Air     5.242444
Gversion -> Gversion 4.759517
Technique -> Technique 4.572796
Gtype  -> Gtype   4.408618
pH     -> pH      4.148766
O      -> O       3.770155
O      -> Technique 1.394833
Air    -> O       0.934701
O      -> Supp    0.603143
Gtype  -> Supp    0.602203
O      -> Temp    0.531294
O      -> Gtype   0.244043
Substrain -> Gtype   0.178777
Temp   -> O       0.116666
O      -> Anti    0.073374
Technique -> Air     0.057205
O      -> Phase   0.016593
Med    -> O       0.014656
O      -> OD      0.003771
O      -> pH      0.001976
Anti   -> O       -0.000356
Phase  -> O       -0.013827
Supp   -> O       -0.037801
Gversion -> O       -0.118955
OD     -> O       -0.146201
Air    -> Temp    -0.162047
O      -> Med     -0.221356
Gtype  -> Anti    -0.235366
OD     -> Air     -0.430187
Technique -> O       -0.658505
Supp   -> Med     -0.680587
O      -> Air     -1.100972
Gtype  -> O       -1.334900
Med    -> Supp    -1.533125
Substrain -> O       -2.088700


Top positive:
10.204453 Air      b'word[:2]:Ae'
7.959700 Strain   b'+1:lemma:substr'
7.931315 Gtype    b'word[:1]:\xce\x94'
7.211296 O        b'lemma:2'
6.951384 Technique b'word[:2]:Ch'
6.897705 Air      b'word[:2]:An'
6.430948 O        b'word[:2]:re'
6.304459 Supp     b'+1:lemma:\xc2\xb5m'
6.277176 O        b'lemma:3'
6.259509 O        b'-1:lemma:tag'
5.784951 Phase    b'lemma:stationary'
5.680889 O        b'lemma:1'
5.565991 Air      b'lemma:anaerobic'
5.496150 O        b'lemma:-'
5.307683 Phase    b'lemma:mid-log'
5.051659 O        b'lemma:a'
4.964154 O        b'+1:lemma:pq'
4.949696 O        b'lemma:with'
4.849415 Gversion b'-1:lemma:nc'
4.834323 Substrain b'word[:2]:MG'
4.807181 O        b'lemma:_'
4.807181 O        b'word[:1]:_'
4.804254 Supp     b'-1:lemma:Cra'
4.759024 Gtype    b'lemma:wt'
4.715524 Supp     b'lemma:Iron'
4.715524 Supp     b'word[:2]:Ir'
4.706542 Supp     b'lemma:arginine'
4.646874 Supp     b'-1:lemma:vol'
4.197413 O        b'word[:2]:Cr'
4.195753 O        b'-1:lemma:lb'
4.181423 Gtype    b'word[:2]:Fl'
4.134022 OD       b'word[:1]:O'
4.052226 Med      b'lemma:MOPS'
4.052226 Med      b'word[:2]:MO'
4.022958 pH       b'word[:2]:pH'
3.975313 Temp     b'-1:lemma:sample'
3.962014 Gversion b'lemma:chip-seq'
3.951951 Phase    b'word[:2]:ex'
3.931899 Supp     b'-1:lemma:with'
3.883643 Gtype    b'lemma:arca8myc'
3.879479 Supp     b'word[:2]:ni'
3.856134 Temp     b'+1:lemma:in'
3.810759 Gtype    b'-1:lemma:\xe2\x88\x86'
3.789132 Supp     b'-1:lemma:+'
3.786509 O        b'word[:2]:ha'
3.757509 Gtype    b'word[:1]:d'
3.684952 Supp     b'lemma:nacl'
3.663349 O        b'word[:2]:Cu'
3.647265 O        b'word[:2]:ge'
3.618268 Technique b'word[:2]:RN'
3.420924 Med      b'-1:lemma:ml'
3.399171 O        b'lemma:.'
3.399171 O        b'postag:.'
3.399171 O        b'postag[:1]:.'
3.295302 O        b'-1:lemma:0.3'
3.233537 O        b'-1:lemma:glucose'
3.232228 Anti     b'+1:lemma:antibody'
3.166537 O        b'word[:1]:B'
3.151800 Gtype    b'lemma:type'
3.151800 Gtype    b'word[:2]:ty'
3.074513 Supp     b'word[:1]:I'
3.066493 O        b'word[:1]:G'
3.049541 O        b'-1:lemma:into'
2.995715 O        b'word[:2]:Rp'
2.974033 Temp     b'-1:lemma:\xcf\x8332'
2.939937 O        b'lemma:delta'
2.929545 O        b'word[:1]:E'
2.889138 Supp     b'lemma:acetate'
2.884567 O        b'word[:1]:S'
2.849582 Supp     b'lemma:pq'
2.849582 Supp     b'word[:2]:PQ'
2.796468 Med      b'+1:lemma:0.4'
2.748041 Gtype    b'word[:2]:cr'
2.715155 O        b'postag::'
2.715155 O        b'postag[:1]::'
2.711740 Gtype    b'word[:1]:w'
2.648443 O        b'-1:lemma:0.3-0.35'
2.642979 Temp     b'-1:lemma:43'
2.605602 Supp     b'+1:lemma:1'
2.584485 Med      b'word[:1]:M'
2.543511 Gtype    b'lemma:nsrr'
2.543511 Gtype    b'word[:2]:Ns'
2.528316 Supp     b'+1:lemma:mm'
2.526101 Gtype    b'word[:1]:W'
2.518551 Supp     b'+1:lemma:2'
2.493071 Technique b'lemma:ChIP-exo'
2.492470 Gtype    b'word[:2]:PK'
2.417633 O        b'lemma:ompr'
2.417633 O        b'word[:2]:Om'
2.403384 O        b'lemma:purr'
2.399480 Air      b'-1:lemma:ChIP-Seq'
2.385701 Phase    b'-1:lemma:until'
2.383512 Gtype    b'word[:1]:t'
2.374150 Gtype    b'-1:lemma:rpob'
2.368626 O        b'word[:1]:R'
2.336211 Supp     b'-1:lemma:final'
2.331497 Gversion b'word[:2]:00'
2.322056 O        b'+1:lemma:od600'
2.317008 O        b'lemma:Custom'
2.307666 Gversion b'lemma:asm584v2'
2.307666 Gversion b'word[:2]:AS'
2.305354 Med      b'lemma:L'
2.305354 Med      b'+1:lemma:broth'
2.285067 Supp     b'lemma:sodium'
2.270312 O        b'postag:CC'
2.270312 O        b'postag[:2]:CC'
2.257396 Air      b'word[:1]:a'
2.233372 Med      b'+1:lemma:g/l'
2.223950 Supp     b'+1:lemma:phosphate'
2.222780 O        b'+1:lemma:mid-log'
2.221972 O        b'-1:lemma:type'
2.203153 O        b'word[:1]:C'
2.199367 Med      b'+1:lemma:2.0'
2.195464 Gversion b'lemma:nc'
2.195464 Gversion b'word[:2]:NC'
2.192101 O        b'+1:postag:RB'
2.162744 O        b'lemma:b'
2.159358 Air      b'-1:lemma:co2'
2.157857 Supp     b'+1:lemma:1m'
2.150708 O        b'-1:lemma:Aerobic'
2.149348 Air      b'+1:postag:IN'
2.138880 Anti     b'hGreek'
2.137978 O        b'+1:lemma:43'
2.122867 O        b'postag:IN'
2.122867 O        b'postag[:1]:I'
2.122867 O        b'postag[:2]:IN'
2.118447 Supp     b'word[:2]:Fe'
2.105815 Anti     b'word[:2]:an'
2.075029 Supp     b'+1:lemma:and'
2.072990 Gtype    b'symb'
2.065880 O        b'+1:postag:NNP'
2.062690 O        b'+1:lemma:250'
2.020409 Gtype    b'-1:postag:VBG'
2.013701 Gtype    b'lemma:flag-tag'
2.013701 Gtype    b'-1:lemma:c-terminal'
1.989019 Substrain b'word[:1]:M'
1.972823 Agit     b'+1:lemma:rpm'
1.953612 Supp     b'lemma:Fe'
1.940845 O        b'lemma:chip'
1.936105 Med      b'word[:1]:L'
1.928291 Supp     b'lemma:rifampicin'
1.926687 Supp     b'word[:2]:gl'
1.915939 Supp     b'word[:2]:ri'
1.913797 Gversion b'lemma:.2'
1.913797 Gversion b'-1:lemma:u00096'
1.913797 Gversion b'word[:2]:.2'
1.910063 Supp     b'lemma:fructose'
1.909338 Supp     b'word[:2]:30'
1.896702 O        b'lemma:growth'
1.895943 Supp     b'postag:VBP'
1.892910 Gtype    b'+1:lemma:type'
1.889532 O        b'lemma:0.4'
1.871889 Gtype    b'lemma:\xe2\x88\x86'
1.871889 Gtype    b'word[:1]:\xe2\x88\x86'
1.871050 O        b'lemma:at'
1.869248 O        b'word[:2]:In'
1.859503 Gtype    b'word[:1]:F'
1.851083 Supp     b'word[:2]:ac'
1.849424 O        b'-1:lemma:anaerobic'
1.842373 O        b'-1:lemma:media'
1.841449 Supp     b'-1:postag:CC'
1.836269 O        b'lemma:ml'
1.836269 O        b'word[:2]:ml'
1.828600 O        b'word[:1]:i'
1.828258 Gtype    b'word[:1]:f'
1.827189 Technique b'word[:1]:R'
1.813413 O        b'-1:lemma:mg1655'
1.805298 Temp     b'lemma:43'
1.805298 Temp     b'word[:2]:43'
1.800703 Med      b'lemma:broth'
1.800703 Med      b'-1:lemma:L'
1.800703 Med      b'word[:2]:br'
1.795613 O        b'word[:1]:u'
1.759212 O        b'postag[:1]:V'
1.759212 O        b'postag[:2]:VB'
1.754974 Gtype    b'-1:lemma:_'
1.745663 Supp     b'word[:1]:1'
1.723877 Supp     b'lemma:Leu'
1.723877 Supp     b'word[:2]:Le'
1.721581 Technique b'lemma:chipseq'
1.707824 Phase    b'+1:postag:NNS'
1.696873 Gtype    b'-1:lemma:vector'
1.690920 Air      b'word[:2]:an'
1.681189 Gtype    b'word[:2]:Ar'
1.652222 O        b'+1:postag:VBZ'
1.635512 O        b'+1:lemma:30'
1.623155 Med      b'+1:lemma:-lrb-'
1.621988 O        b'-1:lemma:stpa'
1.619973 Substrain b'+1:lemma:phtpg'
1.619895 Vess     b'lemma:flask'
1.619895 Vess     b'-1:lemma:warm'
1.613546 Supp     b'+1:lemma:min'
1.611072 Vess     b'word[:2]:fl'
1.610373 O        b'+1:postag:VBN'
1.603394 Air      b'+1:lemma:until'
1.591021 Temp     b'-1:lemma:degree'
1.586003 O        b'word[:1]:-'
1.583870 O        b'-1:lemma:phase'
1.582561 Supp     b'lemma:2h'
1.582561 Supp     b'-1:lemma:additional'


Top negative:
-0.059848 OD       b'postag[:1]:N'
-0.059848 OD       b'postag[:2]:NN'
-0.059922 O        b'-1:lemma:phosphate'
-0.060173 Technique b'-1:lemma::'
-0.060454 O        b'word[:1]:2'
-0.061725 OD       b'+1:lemma:0.4'
-0.062364 Technique b'postag[:1]:N'
-0.062364 Technique b'postag[:2]:NN'
-0.063877 Gtype    b'word[:1]:-'
-0.063940 O        b'-1:lemma:-lrb-'
-0.065863 Supp     b'-1:postag:NN'
-0.066673 OD       b'lemma:0.4'
-0.067069 O        b'word[:2]:fi'
-0.068494 O        b'word[:1]:.'
-0.070950 Air      b'postag:CC'
-0.070950 Air      b'postag[:2]:CC'
-0.078141 O        b'word[:1]:g'
-0.079781 Supp     b'word[:2]:10'
-0.085611 O        b'-1:postag:-LRB-'
-0.085744 O        b'lemma:minimal'
-0.086337 O        b'word[:1]:d'
-0.087082 Supp     b'word[:2]:vo'
-0.091121 Gtype    b'+1:postag:NN'
-0.094589 Supp     b'postag:CD'
-0.094589 Supp     b'postag[:2]:CD'
-0.098403 Temp     b'-1:lemma:\xc2\xb0c'
-0.099548 O        b'+1:postag:-LRB-'
-0.099870 O        b'+1:lemma:rep2'
-0.103006 O        b'+1:lemma:1/100'
-0.107449 Gversion b'+1:postag:NN'
-0.108265 Temp     b'postag[:1]:N'
-0.108265 Temp     b'postag[:2]:NN'
-0.108397 Supp     b'-1:lemma:.'
-0.108397 Supp     b'-1:postag:.'
-0.109037 Gtype    b'postag[:1]:V'
-0.109037 Gtype    b'postag[:2]:VB'
-0.109312 Supp     b'lemma:10'
-0.113057 O        b'+1:lemma:%'
-0.120224 Phase    b'-1:lemma:at'
-0.130743 O        b'+1:postag:CD'
-0.133476 Supp     b'lemma:,'
-0.133476 Supp     b'postag:,'
-0.133476 Supp     b'word[:1]:,'
-0.133476 Supp     b'postag[:1]:,'
-0.136463 Air      b'hUpper'
-0.136463 Air      b'hLower'
-0.150682 O        b'word[:2]:OD'
-0.151965 O        b'-1:lemma:rpob'
-0.154235 O        b'+1:lemma:-rrb-'
-0.158600 Gtype    b'-1:lemma:mg1655'
-0.164950 O        b'word[:1]:M'
-0.174920 Air      b'+1:postag:-LRB-'
-0.176710 Med      b'lemma:m9'
-0.176710 Med      b'word[:2]:M9'
-0.178022 Med      b'postag[:1]:C'
-0.180125 O        b'-1:lemma:of'
-0.181701 Phase    b'+1:postag:NN'
-0.183270 Supp     b'postag[:1]:C'
-0.184142 Med      b'-1:lemma:m9'
-0.185330 OD       b'lemma:od600'
-0.194943 O        b'word[:2]:ae'
-0.196910 Technique b'-1:postag::'
-0.198688 Supp     b'word[:1]:C'
-0.198890 Gtype    b'-1:lemma:-lrb-'
-0.199882 pH       b'postag[:1]:N'
-0.199882 pH       b'postag[:2]:NN'
-0.200375 Air      b'-1:lemma:grow'
-0.201809 O        b'lemma:2h'
-0.201809 O        b'-1:lemma:additional'
-0.201809 O        b'word[:2]:2h'
-0.205749 Supp     b'+1:lemma:10'
-0.216714 Gtype    b'+1:postag:CD'
-0.224065 O        b'+1:postag:-RRB-'
-0.226472 O        b'lemma:co2'
-0.226472 O        b'word[:2]:CO'
-0.232140 Air      b'-1:postag:VBN'
-0.241573 Air      b'-1:postag:CC'
-0.242963 Air      b'symb'
-0.250464 Phase    b'postag[:1]:J'
-0.250464 Phase    b'postag[:2]:JJ'
-0.270255 O        b'lemma:aerobically'
-0.270737 O        b'lemma:media'
-0.271988 O        b'word[:2]:gl'
-0.275321 O        b'+1:lemma:supplement'
-0.276089 O        b'-1:postag:IN'
-0.281202 O        b'word[:2]:ce'
-0.282921 O        b'-1:lemma:250'
-0.284342 Air      b'+1:postag:JJ'
-0.285982 O        b'lemma:of'
-0.285982 O        b'word[:2]:of'
-0.299888 Supp     b'word[:2]:an'
-0.300445 O        b'word[:1]:F'
-0.311626 O        b'+1:lemma:for'
-0.312645 Phase    b'postag:JJ'
-0.314439 Temp     b'postag:NN'
-0.318498 O        b'+1:lemma:mm'
-0.321300 Supp     b'-1:lemma:-lrb-'
-0.328758 O        b'lemma:1m'
-0.328758 O        b'word[:2]:1M'
-0.333791 O        b'-1:lemma:sodium'
-0.336871 Med      b'+1:postag:NN'
-0.348304 Gtype    b'+1:lemma:-lrb-'
-0.350520 Med      b'-1:postag:CD'
-0.352516 O        b'lemma:37'
-0.352516 O        b'word[:2]:37'
-0.362946 O        b'+1:lemma:.'
-0.362946 O        b'+1:postag:.'
-0.363307 Med      b'-1:postag:NN'
-0.370538 Air      b'postag:NN'
-0.375679 Supp     b'-1:postag:-LRB-'
-0.378467 O        b'+1:postag:VBG'
-0.380556 O        b'-1:lemma:ml'
-0.380799 O        b'-1:lemma:final'
-0.381345 O        b'+1:lemma:ph'
-0.383546 O        b'-1:lemma:n2'
-0.385967 O        b'lemma:mid-log'
-0.387867 Air      b'postag[:1]:N'
-0.387867 Air      b'postag[:2]:NN'
-0.397798 Supp     b'postag:JJ'
-0.400326 Supp     b'postag[:1]:J'
-0.400326 Supp     b'postag[:2]:JJ'
-0.407602 O        b'-1:lemma:mm'
-0.431970 Med      b'-1:postag:IN'
-0.434055 O        b'-1:lemma:1m'
-0.445787 Temp     b'hGreek'
-0.452175 Med      b'symb'
-0.460332 O        b'-1:lemma:IP'
-0.467068 O        b'-1:lemma:37'
-0.478293 O        b'+1:lemma:phosphate'
-0.537372 O        b'word[:2]:ni'
-0.545269 O        b'-1:lemma:until'
-0.548531 O        b'word[:2]:0.'
-0.623964 O        b'word[:1]:0'
-0.624246 Supp     b'-1:postag:NNP'
-0.632176 O        b'lemma:c'
-0.637617 O        b'+1:postag:IN'
-0.640663 OD       b'hUpper'
-0.640663 OD       b'hLower'
-0.643238 O        b'lemma:sodium'
-0.678960 O        b'word[:2]:pH'
-0.686405 O        b'word[:2]:ri'
-0.690472 Air      b'-1:lemma:or'
-0.706445 O        b'-1:lemma:delta'
-0.723520 O        b'+1:lemma:g/l'
-0.736143 Supp     b'hGreek'
-0.746481 O        b'lemma:methanol'
-0.769671 O        b'-1:lemma:nsrr'
-0.784252 Air      b'-1:postag:JJ'
-0.788281 Med      b'+1:postag:IN'
-0.822122 Supp     b'+1:lemma:rifampicin'
-0.838923 Supp     b'symb'
-0.852449 Agit     b'symb'
-0.867354 O        b'-1:lemma:co2'
-0.874419 O        b'-1:lemma:30'
-0.894271 O        b'word[:2]:me'
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-1.005990 O        b'-1:postag::'
-1.027364 O        b'+1:lemma:1m'
-1.029400 O        b'-1:lemma:dissolve'
-1.029400 O        b'+1:lemma:methanol'
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-1.052334 O        b'+1:lemma:until'
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-1.076834 O        b'word[:2]:fl'
-1.106973 O        b'word[:2]:30'
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-1.184488 Gtype    b'+1:lemma:-rrb-'
-1.190874 Agit     b'hUpper'
-1.190874 Agit     b'hLower'
-1.198537 Anti     b'postag:NNP'
-1.237479 Technique b'postag:NN'
-1.254724 Gtype    b'word[:1]:C'
-1.285720 O        b'+1:lemma:2.0'
-1.319520 O        b'-1:lemma:cra'
-1.367368 O        b'-1:lemma:sample'
-1.499105 O        b'-1:postag:VBG'
-1.499318 O        b'+1:lemma:in'
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-1.738083 O        b'word[:2]:Ch'
-1.860176 O        b'+1:lemma:1'
-1.912082 O        b'lemma:rifampicin'
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-2.120131 O        b'+1:lemma:2'
-2.321555 Supp     b'+1:lemma:,'
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-2.461859 O        b'word[:1]:P'
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-2.561836 O        b'-1:lemma:2'
-3.242599 O        b'postag:VBP'
-3.584101 O        b'-1:lemma:vol'
-5.325671 O        b'-1:lemma:_'
-5.823992 O        b'-1:lemma::'