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

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report_Run8_v10.txt 16.8 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt

best params:{'c1': 0.2336502013872894, 'c2': 0.09318602763483955}
best CV score:0.8712658288218513
model size: 0.12M

Flat F1: 0.8031511247172385
             precision    recall  f1-score   support

         OD      1.000     0.818     0.900        22
         pH      1.000     1.000     1.000         8
  Technique      1.000     1.000     1.000        23
        Med      1.000     0.962     0.981        53
       Temp      1.000     0.759     0.863        29
       Vess      1.000     1.000     1.000         1
       Agit      0.000     0.000     0.000         0
      Phase      0.875     0.933     0.903        15
        Air      0.556     0.362     0.439        69
       Anti      0.917     1.000     0.957        11
     Strain      0.000     0.000     0.000         1
      Gtype      0.864     0.824     0.843        85
  Substrain      0.000     0.000     0.000         0
       Supp      0.805     0.799     0.801       134
   Gversion      0.000     0.000     0.000         0

avg / total      0.840     0.776     0.803       451


Top likely transitions:
Supp   -> Supp    5.153612
Agit   -> Agit    4.790521
Temp   -> Temp    4.687582
OD     -> OD      4.667439
Med    -> Med     4.449149
Air    -> Air     4.119367
Anti   -> Anti    3.666040
Gversion -> Gversion 3.630622
Gtype  -> Gtype   3.343835
Phase  -> Phase   3.256517
O      -> O       3.120205
Technique -> Technique 2.701020
pH     -> pH      2.114033
O      -> Supp    1.047850
Gtype  -> Supp    0.792223
Air    -> O       0.728052
Supp   -> O       0.623465
O      -> Technique 0.585886
Substrain -> Gtype   0.536486
O      -> Gtype   0.295211
Med    -> O       0.290467
Gtype  -> Air     0.240427
Technique -> Air     0.102724
Temp   -> O       0.077445
Supp   -> Technique -0.001389
Phase  -> O       -0.001768
O      -> Agit    -0.009169
Anti   -> Gtype   -0.025365
Agit   -> O       -0.119785
Supp   -> Med     -0.148138
OD     -> Air     -0.152372
Anti   -> O       -0.184882
O      -> Med     -0.194559
Gtype  -> Anti    -0.207364
Gversion -> O       -0.213638
Technique -> Gtype   -0.242293
Technique -> pH      -0.279479
Gtype  -> Med     -0.396453
Gtype  -> Technique -0.457466
O      -> Air     -0.478572
Med    -> Supp    -0.652970
Technique -> O       -0.741574
Gtype  -> O       -0.868400
Substrain -> O       -0.904616


Top unlikely transitions:
Supp   -> Supp    5.153612
Agit   -> Agit    4.790521
Temp   -> Temp    4.687582
OD     -> OD      4.667439
Med    -> Med     4.449149
Air    -> Air     4.119367
Anti   -> Anti    3.666040
Gversion -> Gversion 3.630622
Gtype  -> Gtype   3.343835
Phase  -> Phase   3.256517
O      -> O       3.120205
Technique -> Technique 2.701020
pH     -> pH      2.114033
O      -> Supp    1.047850
Gtype  -> Supp    0.792223
Air    -> O       0.728052
Supp   -> O       0.623465
O      -> Technique 0.585886
Substrain -> Gtype   0.536486
O      -> Gtype   0.295211
Med    -> O       0.290467
Gtype  -> Air     0.240427
Technique -> Air     0.102724
Temp   -> O       0.077445
Supp   -> Technique -0.001389
Phase  -> O       -0.001768
O      -> Agit    -0.009169
Anti   -> Gtype   -0.025365
Agit   -> O       -0.119785
Supp   -> Med     -0.148138
OD     -> Air     -0.152372
Anti   -> O       -0.184882
O      -> Med     -0.194559
Gtype  -> Anti    -0.207364
Gversion -> O       -0.213638
Technique -> Gtype   -0.242293
Technique -> pH      -0.279479
Gtype  -> Med     -0.396453
Gtype  -> Technique -0.457466
O      -> Air     -0.478572
Med    -> Supp    -0.652970
Technique -> O       -0.741574
Gtype  -> O       -0.868400
Substrain -> O       -0.904616


Top positive:
3.844745 Anti     b'-2:lemma:antibody'
3.075298 O        b'-2:lemma:_'
3.031119 O        b'postag:IN'
2.910731 Gtype    b'word[:1]:\xce\x94'
2.767129 Technique b'word[:2]:Ch'
2.687293 O        b'word[:2]:re'
2.397217 O        b'isLower'
2.349451 OD       b'word[:1]:O'
2.325310 Air      b'lemma:anaerobic'
2.308276 Air      b'word[:2]:An'
2.302010 O        b'postag::'
2.198277 O        b'lemma:2'
2.198277 O        b'word:2'
2.169367 Air      b'word[:2]:Ae'
2.169367 Air      b'word:Aerobic'
2.123019 O        b'word:A'
2.076492 Air      b'postag:RB'
2.043571 O        b'lemma:_'
2.043571 O        b'word[:1]:_'
2.043571 O        b'word:_'
2.029395 Air      b'word[:1]:A'
2.002141 O        b'postag:CC'
1.942490 O        b'lemma:1'
1.942490 O        b'word:1'
1.937470 O        b'word[:1]:S'
1.896723 Gtype    b'hGreek'
1.887387 Air      b'word[:1]:a'
1.887291 O        b'postag:VBN'
1.861797 Supp     b'-1:word:Cra'
1.851009 Gtype    b'word[:1]:W'
1.850161 O        b'word[:1]:G'
1.829782 Technique b'word[:2]:RN'
1.823057 O        b'lemma:.'
1.823057 O        b'postag:.'
1.823057 O        b'word:.'
1.783472 Gtype    b'-2:lemma:genotype/variation'
1.743688 O        b'isNumber'
1.737426 Supp     b'word[:1]:I'
1.735984 O        b'lemma:3'
1.735984 O        b'word:3'
1.735450 Gtype    b'lemma:wt'
1.732890 Phase    b'-2:lemma:phase'
1.713773 O        b'+2:lemma:\xc2\xb0c'
1.626531 O        b'lemma:-'
1.626531 O        b'word:-'
1.621002 Gtype    b'word[:1]:d'
1.585833 Substrain b'word[:2]:MG'
1.567249 Med      b'+2:postag:CC'
1.561495 Gtype    b'-2:lemma:delta'
1.538812 Gtype    b'-1:lemma:\xe2\x88\x86'
1.538812 Gtype    b'-1:word:\xe2\x88\x86'
1.529675 O        b'-2:lemma:medium'
1.528642 Phase    b'lemma:mid-log'
1.528642 Phase    b'word:mid-log'
1.525710 Supp     b'lemma:arginine'
1.515052 Med      b'isUpper'
1.509156 Anti     b'+2:lemma:antibody'
1.498445 Air      b'word[:2]:an'
1.448455 Gtype    b'word[:2]:Fl'
1.445971 O        b'word[:1]:B'
1.442694 Substrain b'word[:1]:M'
1.424126 Technique b'word[:1]:R'
1.419379 Supp     b'-1:lemma:with'
1.419379 Supp     b'-1:word:with'
1.408287 O        b'-1:word:Aerobic'
1.401018 O        b'+2:postag:JJ'
1.385158 Supp     b'-1:postag:CC'
1.377203 pH       b'word[:2]:pH'
1.376034 O        b'word[:2]:Rp'
1.370982 Supp     b'+2:lemma:iptg'
1.365225 O        b'lemma:a'
1.363156 Gtype    b'word[:1]:w'
1.362194 Gtype    b'lemma:type'
1.362194 Gtype    b'word[:2]:ty'
1.362194 Gtype    b'word:type'
1.335730 Supp     b'word[:1]:N'
1.328524 Gtype    b'word[:2]:PK'
1.323973 Supp     b'word[:2]:ni'
1.321948 Anti     b'word[:2]:an'
1.321538 Supp     b'lemma:acetate'
1.321538 Supp     b'word:acetate'
1.318423 O        b'word[:2]:ch'
1.318176 Air      b'+1:postag:IN'
1.315132 O        b'lemma:with'
1.315132 O        b'word:with'
1.314507 pH       b'+1:postag:CD'
1.302202 Supp     b'word[:2]:Fe'
1.295539 Supp     b'word[:2]:gl'
1.282771 Gtype    b'word[:1]:F'
1.281044 O        b'+2:lemma:cra'
1.274682 O        b'postag:DT'
1.272939 O        b'word[:2]:ge'
1.271317 Med      b'word[:1]:L'
1.265104 Technique b'word[:1]:C'
1.259599 Supp     b'-2:lemma:for'
1.259424 Supp     b'lemma:pq'
1.259424 Supp     b'word[:2]:PQ'
1.259424 Supp     b'word:PQ'
1.253382 O        b'-1:lemma:tag'
1.226505 O        b'-1:lemma:anaerobic'
1.220019 Gtype    b'+2:lemma:glucose'
1.217394 Gtype    b'-2:postag:DT'
1.200992 O        b'word[:1]:-'
1.197803 Supp     b'+1:lemma:\xc2\xb5m'
1.197803 Supp     b'+1:word:\xc2\xb5M'
1.197777 O        b'word[:1]:R'
1.178925 Med      b'word[:1]:M'
1.178705 pH       b'word[:1]:p'
1.165105 Air      b'word:Anaerobic'
1.151652 Gtype    b'word[:1]:t'
1.150537 O        b'word[:1]:C'
1.139639 O        b'-2:lemma:flagtag'
1.135644 Technique b'lemma:ChIP-exo'
1.134050 O        b'-1:word:tag'
1.133929 O        b'+1:postag:RB'
1.129756 Anti     b'+1:lemma:antibody'
1.129756 Anti     b'+1:word:antibody'
1.121198 Supp     b'lemma:Iron'
1.121198 Supp     b'word[:2]:Ir'
1.121198 Supp     b'word:Iron'
1.121198 Supp     b'+1:word:Deficient'
1.121198 Supp     b'-2:lemma:Anaerobic'
1.114176 Med      b'word[:1]:m'
1.100461 Supp     b'word[:2]:ac'
1.099208 Gtype    b'symb'
1.094239 Temp     b'isUpper'
1.093800 O        b'+2:lemma:of'
1.088664 Gtype    b'lemma:\xe2\x88\x86'
1.088664 Gtype    b'word[:1]:\xe2\x88\x86'
1.088664 Gtype    b'word:\xe2\x88\x86'
1.071215 O        b'+1:word:ChIP-Seq'
1.066491 Agit     b'+2:lemma:at'
1.066258 Gtype    b'-2:lemma:affyexp'
1.060022 Gtype    b'word[:2]:WT'
1.060022 Gtype    b'word:WT'
1.053727 O        b'-2:lemma:myc'
1.050067 Technique b'symb'
1.039357 Air      b'-2:lemma:%'
1.038444 Gtype    b'lemma:nsrr'
1.038444 Gtype    b'word[:2]:Ns'
1.038444 Gtype    b'word:NsrR'
1.033615 OD       b'-1:postag:IN'
1.032571 Supp     b'-1:lemma:Cra'
1.027117 O        b'lemma:b'
1.027117 O        b'word:B'
1.026841 Phase    b'word[:2]:ex'
1.020258 Temp     b'+2:postag:DT'
1.005720 Med      b'word[:1]:g'
1.003046 Phase    b'word[:1]:e'
0.988531 Technique b'+2:lemma:ph5'
0.982847 Med      b'lemma:MOPS'
0.982847 Med      b'word[:2]:MO'
0.982847 Med      b'word:MOPS'
0.982044 Gtype    b'word[:1]:P'
0.978963 Supp     b'+1:lemma:1'
0.978963 Supp     b'+1:word:1'
0.977470 O        b'+1:postag:VBN'
0.972345 Gversion b'lemma:chip-seq'
0.965776 O        b'-1:lemma:0.3'
0.965776 O        b'-1:word:0.3'
0.961310 O        b'word[:1]:c'
0.961310 Gversion b'word:ChIP-Seq'
0.954008 Supp     b'-2:lemma:media'
0.953354 O        b'word[:1]:E'
0.952860 OD       b'word[:2]:0.'
0.951986 Gversion b'word[:2]:00'
0.951986 Gversion b'-2:lemma:nc'
0.951757 Temp     b'isNumber'
0.944374 O        b'-1:lemma:glucose'
0.944374 O        b'-1:word:glucose'
0.939001 Anti     b'word[:1]:a'
0.933490 Gtype    b'word[:1]:f'
0.932192 Technique b'lemma:rna-seq'
0.927167 O        b'word[:2]:Cr'
0.924784 O        b'+1:postag:NNP'
0.923460 Temp     b'lemma:43'
0.923460 Temp     b'word[:2]:43'
0.923460 Temp     b'word:43'
0.922823 Gversion b'postag:NN'
0.920025 O        b'word:Cra'
0.919393 Gtype    b'-2:lemma:genotype'
0.916703 O        b'-1:postag:NNS'
0.914905 Temp     b'-1:lemma:43'
0.914905 Temp     b'-1:word:43'
0.914011 Supp     b'lemma:fructose'
0.914011 Supp     b'word:fructose'
0.910162 Gtype    b'+2:lemma:a'
0.909270 O        b'-1:lemma:ChIP-exo'
0.906917 O        b'-1:lemma:lb'
0.906917 O        b'-1:word:LB'
0.905676 Temp     b'-2:lemma:30'
0.905544 O        b'lemma::'
0.905544 O        b'word[:1]::'
0.905544 O        b'word::'
0.903768 O        b'-2:lemma:min'
0.902708 Gtype    b'lemma:flag-tag'
0.902708 Gtype    b'-1:lemma:c-terminal'
0.902708 Gtype    b'word:Flag-tag'
0.902708 Gtype    b'-1:word:C-terminal'
0.895846 Gtype    b'-1:postag:VBG'


Top negative:
-0.213281 Gtype    b'postag:VBG'
-0.213927 O        b'lemma:30'
-0.213927 O        b'word:30'
-0.214268 O        b'+1:lemma:1m'
-0.214268 O        b'+1:word:1M'
-0.214268 O        b'-2:lemma:vol'
-0.214305 Technique b'isLower'
-0.215229 O        b'+2:lemma:tag'
-0.224496 O        b'lemma:0.3'
-0.224496 O        b'word:0.3'
-0.225047 O        b'word[:2]:ae'
-0.225048 O        b'+2:lemma:10'
-0.225327 O        b'+1:lemma:.'
-0.225327 O        b'+1:postag:.'
-0.225327 O        b'+1:word:.'
-0.226893 O        b'lemma:media'
-0.226893 O        b'word:media'
-0.227738 O        b'-1:lemma:final'
-0.227738 O        b'-1:word:final'
-0.236792 Supp     b'-1:postag:NN'
-0.237178 O        b'lemma:aerobically'
-0.237178 O        b'word:aerobically'
-0.237751 Temp     b'-2:postag:NN'
-0.238106 O        b'+1:lemma:mm'
-0.238106 O        b'+1:word:mM'
-0.238950 Med      b'+2:postag:VBN'
-0.239931 Supp     b'-2:lemma:treat'
-0.242306 Supp     b'+2:lemma:-rrb-'
-0.244385 O        b'-2:lemma:fresh'
-0.248124 O        b'-1:word:the'
-0.250659 O        b'-1:lemma:control'
-0.250659 O        b'-1:word:control'
-0.252294 Vess     b'hUpper'
-0.252294 Vess     b'hLower'
-0.260164 Gtype    b'-2:postag:CD'
-0.261752 Supp     b'-1:lemma:-lrb-'
-0.261752 Supp     b'-1:word:-LRB-'
-0.264366 O        b'-1:lemma:dissolve'
-0.264366 O        b'+1:lemma:methanol'
-0.264366 O        b'-1:word:dissolved'
-0.264366 O        b'+1:word:methanol'
-0.265460 O        b'+2:lemma:b'
-0.272617 O        b'+1:lemma:until'
-0.272617 O        b'+1:word:until'
-0.273572 Gtype    b'word[:1]:h'
-0.274523 O        b'+1:postag:-RRB-'
-0.278891 O        b'word[:2]:mg'
-0.284692 O        b'-2:lemma:rpob'
-0.286507 Supp     b'-1:postag:-LRB-'
-0.287758 Gtype    b'+1:postag:CD'
-0.288985 O        b'+1:lemma:+'
-0.288985 O        b'+1:word:+'
-0.291255 Supp     b'+2:postag:CC'
-0.293167 Anti     b'isUpper'
-0.295610 Air      b'symb'
-0.297086 Med      b'+1:postag:IN'
-0.297472 Anti     b'+2:lemma:polyclonal'
-0.301599 Supp     b'+1:postag:-LRB-'
-0.303534 O        b'word[:2]:pH'
-0.308953 O        b'+2:lemma:250'
-0.312066 O        b'-2:postag::'
-0.312712 O        b'-1:lemma:1'
-0.312712 O        b'-1:word:1'
-0.314265 Supp     b'+2:postag:-RRB-'
-0.320230 Supp     b'+1:lemma:-lrb-'
-0.320230 Supp     b'+1:word:-LRB-'
-0.322105 Supp     b'isLower'
-0.323396 O        b'+2:lemma:fnr'
-0.323418 O        b'-2:lemma:anaerobically'
-0.325030 O        b'-1:lemma:mm'
-0.325030 O        b'-1:word:mM'
-0.330509 O        b'-2:lemma:IP'
-0.332858 Gtype    b'-2:lemma:\xe2\x88\x86'
-0.339609 OD       b'hUpper'
-0.339609 OD       b'hLower'
-0.339859 O        b'-1:lemma:30'
-0.339859 O        b'-1:word:30'
-0.350738 O        b'postag:VBP'
-0.351658 O        b'+2:lemma:.'
-0.351658 O        b'+2:postag:.'
-0.352921 O        b'-1:lemma:rpob'
-0.352921 O        b'-1:word:RpoB'
-0.353783 Anti     b'+1:lemma:anti-fur'
-0.353783 Anti     b'+1:word:anti-Fur'
-0.354236 O        b'-1:postag:IN'
-0.356640 O        b'+2:lemma:add'
-0.363002 O        b'+1:lemma:g/l'
-0.363002 O        b'+1:word:g/L'
-0.363879 O        b'-2:lemma:pahse'
-0.364619 Air      b'isLower'
-0.365203 Supp     b'+1:lemma:,'
-0.365203 Supp     b'+1:postag:,'
-0.365203 Supp     b'+1:word:,'
-0.365874 O        b'-2:lemma:supplement'
-0.369104 O        b'-1:lemma:ph'
-0.369104 O        b'-1:word:pH'
-0.371371 Supp     b'isNumber'
-0.371775 O        b'+2:lemma:a'
-0.372992 O        b'-2:postag:-LRB-'
-0.377752 O        b'-1:lemma:nsrr'
-0.377752 O        b'-1:word:NsrR'
-0.378984 O        b'-1:lemma:IP'
-0.378984 O        b'-1:word:IP'
-0.385721 O        b'+2:lemma:at'
-0.390304 O        b'-2:lemma:dpd'
-0.398681 O        b'-1:lemma:co2'
-0.398681 O        b'-1:word:CO2'
-0.401830 Supp     b'-2:postag:JJ'
-0.414842 O        b'+2:lemma:-rrb-'
-0.419511 O        b'-1:lemma:vol'
-0.419511 O        b'-1:word:vol'
-0.419511 O        b'-2:lemma:1/100'
-0.419511 O        b'+2:lemma:1m'
-0.426146 Supp     b'+2:postag:NNP'
-0.441021 Gtype    b'isNumber'
-0.444323 O        b'word[:2]:gl'
-0.446407 O        b'-2:lemma:until'
-0.457555 Agit     b'symb'
-0.459022 Phase    b'postag:JJ'
-0.462341 O        b'+1:postag:VBG'
-0.464267 Med      b'-1:postag:NN'
-0.468286 O        b'lemma:mid-log'
-0.468286 O        b'word:mid-log'
-0.472613 O        b'+1:lemma:at'
-0.472613 O        b'+1:word:at'
-0.477062 pH       b'isLower'
-0.477743 Agit     b'hUpper'
-0.477743 Agit     b'hLower'
-0.479686 O        b'+2:lemma:+'
-0.484984 Temp     b'postag:NN'
-0.499704 O        b'word[:2]:ri'
-0.501394 O        b'-2:lemma:media'
-0.507911 O        b'lemma:wt'
-0.526226 O        b'-2:lemma:phase'
-0.529104 Supp     b'-1:postag:NNP'
-0.529212 Phase    b'-1:postag:JJ'
-0.533189 O        b'lemma:rifampicin'
-0.533189 O        b'word:rifampicin'
-0.534646 O        b'word[:1]:K'
-0.547839 O        b'-1:lemma:2'
-0.547839 O        b'-1:word:2'
-0.552833 O        b'lemma:of'
-0.552833 O        b'word[:2]:of'
-0.552833 O        b'word:of'
-0.571985 Phase    b'hUpper'
-0.571985 Phase    b'hLower'
-0.583528 O        b'word[:2]:fl'
-0.593059 O        b'+1:lemma:2.0'
-0.593059 O        b'+1:word:2.0'
-0.609973 Med      b'symb'
-0.616268 O        b'-1:lemma:sample'
-0.631905 O        b'+2:lemma:rifampicin'
-0.641208 Air      b'-1:postag:JJ'
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-0.764889 O        b'+1:word:1'
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-1.012812 O        b'word[:2]:30'
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-1.093793 O        b'+1:lemma:2'
-1.093793 O        b'+1:word:2'
-1.142191 O        b'word[:1]:P'
-1.483645 O        b'-1:postag:VBG'
-1.592855 O        b'-1:lemma::'
-1.592855 O        b'-1:word::'
-1.768431 O        b'word[:2]:Ch'
-1.920566 O        b'-1:lemma:_'
-1.920566 O        b'-1:word:_'