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

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report_Run_4_v12.txt 17.1 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt

best params:{'c1': 0.10934136756341511, 'c2': 0.11233592223188592}
best CV score:0.880070585228673
model size: 0.16M

Flat F1: 0.7987637165072743
             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      0.909     0.690     0.784        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      0.882     0.788     0.832        85
  Substrain      0.000     0.000     0.000         0
       Supp      0.848     0.791     0.819       134
   Gversion      0.000     0.000     0.000         0

avg / total      0.850     0.758     0.799       451


Top likely transitions:
OD     -> OD      4.835421
Med    -> Med     4.432130
Temp   -> Temp    4.381858
Supp   -> Supp    4.249606
Anti   -> Anti    4.153912
Agit   -> Agit    3.968681
Air    -> Air     3.831359
Gtype  -> Gtype   3.677992
Gversion -> Gversion 3.265155
O      -> O       3.210778
Phase  -> Phase   3.136151
Technique -> Technique 2.609081
pH     -> pH      2.036266
Substrain -> Gtype   0.689009
Air    -> O       0.614440
O      -> Supp    0.599670
O      -> Technique 0.575931
Gtype  -> Supp    0.484890
O      -> Gtype   0.452540
Technique -> Air     0.313681
Gtype  -> Air     0.150938
Med    -> O       0.101880
Supp   -> O       0.080361
Gtype  -> pH      0.018366
O      -> Strain  -0.000117
Supp   -> Temp    -0.004625
Air    -> Agit    -0.004733
O      -> OD      -0.005112
Anti   -> Med     -0.010247
pH     -> Supp    -0.019865
Gversion -> Air     -0.021135
Technique -> Gversion -0.026379
Vess   -> O       -0.027766
Gtype  -> OD      -0.029261
O      -> Substrain -0.033985
Air    -> Technique -0.035861
O      -> Phase   -0.036615
OD     -> O       -0.041954
Gversion -> Gtype   -0.044992
OD     -> Supp    -0.048485
O      -> Gversion -0.055499
Phase  -> Gtype   -0.077815
Anti   -> Temp    -0.081500
Phase  -> Med     -0.087481
Temp   -> Med     -0.102584
Anti   -> Supp    -0.104656
Gtype  -> Phase   -0.110657
Supp   -> pH      -0.119733
Agit   -> Air     -0.121190
Gtype  -> Temp    -0.124907


Top unlikely transitions:
OD     -> O       -0.041954
Gversion -> Gtype   -0.044992
OD     -> Supp    -0.048485
O      -> Gversion -0.055499
Phase  -> Gtype   -0.077815
Anti   -> Temp    -0.081500
Phase  -> Med     -0.087481
Temp   -> Med     -0.102584
Anti   -> Supp    -0.104656
Gtype  -> Phase   -0.110657
Supp   -> pH      -0.119733
Agit   -> Air     -0.121190
Gtype  -> Temp    -0.124907
OD     -> Technique -0.148325
Supp   -> Air     -0.175860
Anti   -> Gtype   -0.176413
Phase  -> OD      -0.183709
Supp   -> Anti    -0.184780
Air    -> Med     -0.197230
O      -> Agit    -0.219762
Gtype  -> Gversion -0.221487
Phase  -> Supp    -0.230211
Air    -> Supp    -0.237948
Phase  -> Technique -0.238586
Gversion -> Supp    -0.239381
Technique -> Supp    -0.246780
Supp   -> Phase   -0.249929
Technique -> OD      -0.257903
Air    -> Phase   -0.275963
Agit   -> O       -0.288627
Anti   -> O       -0.319981
Supp   -> Gversion -0.332251
OD     -> Air     -0.336991
Air    -> Temp    -0.361852
Gtype  -> Technique -0.399331
Supp   -> Technique -0.405956
Phase  -> O       -0.432789
Technique -> Gtype   -0.440396
Supp   -> Gtype   -0.441214
Technique -> pH      -0.443537
Gtype  -> Anti    -0.491458
O      -> Med     -0.522931
Gtype  -> Med     -0.545579
Gversion -> O       -0.619815
O      -> Air     -0.714655
Gtype  -> O       -0.835271
Technique -> O       -0.871817
Supp   -> Med     -0.890595
Med    -> Supp    -0.986516
Substrain -> O       -1.034601


Top positive:
2.709537 Gtype    b'word[:1]:\xce\x94'
2.682016 Technique b'word[:2]:Ch'
2.639969 O        b'word[:2]:re'
2.530056 O        b'lemma:_'
2.530056 O        b'word[:1]:_'
2.530056 O        b'word:_'
2.312646 Air      b'lemma:anaerobic'
2.190494 O        b'lemma:2'
2.190494 O        b'word:2'
2.027500 O        b'word:A'
1.983858 Air      b'word[:2]:An'
1.950019 Air      b'word[:2]:Ae'
1.950019 Air      b'word:Aerobic'
1.947205 Gtype    b'lemma:wt'
1.940543 Gtype    b'word[:1]:W'
1.844619 Supp     b'-1:word:Cra'
1.822143 Air      b'word[:1]:A'
1.818988 O        b'word[:1]:S'
1.775674 Technique b'word[:2]:RN'
1.765741 O        b'lemma:1'
1.765741 O        b'word:1'
1.724942 Phase    b'lemma:mid-log'
1.724942 Phase    b'word:mid-log'
1.723723 Supp     b'word[:1]:I'
1.723541 Gtype    b'word[:1]:d'
1.713163 O        b'postag::'
1.713163 O        b'postag[:1]::'
1.712969 Supp     b'+1:lemma:\xc2\xb5m'
1.712969 Supp     b'+1:word:\xc2\xb5M'
1.705742 O        b'lemma:3'
1.705742 O        b'word:3'
1.679949 Gtype    b'hGreek'
1.676513 Air      b'word[:1]:a'
1.653704 Supp     b'-1:postag:CC'
1.616788 O        b'-1:lemma:tag'
1.599401 Air      b'word[:2]:an'
1.579379 O        b'isLower'
1.575060 O        b'-1:word:tag'
1.543882 O        b'word[:1]:G'
1.542332 Substrain b'word[:2]:MG'
1.517878 Anti     b'word[:2]:an'
1.501383 O        b'lemma:a'
1.478818 Supp     b'word[:2]:ni'
1.475795 Supp     b'-1:lemma:with'
1.475795 Supp     b'-1:word:with'
1.470736 Gtype    b'word[:2]:Fl'
1.468144 Gversion b'word[:2]:00'
1.466264 Gtype    b'symb'
1.463246 Gtype    b'word[:1]:w'
1.451800 O        b'lemma:.'
1.451800 O        b'postag:.'
1.451800 O        b'postag[:1]:.'
1.451800 O        b'word:.'
1.449609 pH       b'+1:postag:CD'
1.443950 Supp     b'lemma:Iron'
1.443950 Supp     b'word[:2]:Ir'
1.443950 Supp     b'word:Iron'
1.443950 Supp     b'+1:word:Deficient'
1.440541 O        b'postag:IN'
1.440541 O        b'postag[:1]:I'
1.440541 O        b'postag[:2]:IN'
1.432941 O        b'word[:2]:ch'
1.423481 O        b'word[:2]:ge'
1.416303 O        b'word[:1]:-'
1.412935 Strain   b'+1:lemma:substr'
1.412935 Strain   b'+1:word:substr'
1.409982 O        b'lemma:with'
1.409982 O        b'word:with'
1.409286 Substrain b'word[:1]:M'
1.405314 O        b'lemma:-'
1.405314 O        b'word:-'
1.400041 Technique b'word[:1]:R'
1.397927 O        b'word[:2]:Rp'
1.391254 O        b'word[:1]:B'
1.385270 Technique b'word[:1]:C'
1.383408 O        b'word[:1]:C'
1.375474 Supp     b'lemma:pq'
1.375474 Supp     b'word[:2]:PQ'
1.375474 Supp     b'word:PQ'
1.368840 Gtype    b'word[:2]:PK'
1.361629 Supp     b'word[:2]:gl'
1.355258 Supp     b'lemma:arginine'
1.351941 Gtype    b'lemma:arca8myc'
1.351941 Gtype    b'word:ArcA8myc'
1.348800 pH       b'word[:2]:pH'
1.345187 O        b'+1:lemma:pq'
1.345187 O        b'+1:word:PQ'
1.341451 Gtype    b'-1:lemma:\xe2\x88\x86'
1.341451 Gtype    b'-1:word:\xe2\x88\x86'
1.330835 Supp     b'word[:2]:Fe'
1.329888 Gtype    b'word[:1]:t'
1.324689 O        b'-1:word:Aerobic'
1.311273 Phase    b'word[:2]:ex'
1.293669 Air      b'word:anaerobic'
1.281678 OD       b'word[:1]:O'
1.279382 Air      b'+1:postag:IN'
1.278560 O        b'postag:CC'
1.278560 O        b'postag[:2]:CC'
1.274647 O        b'-1:lemma:lb'
1.274647 O        b'-1:word:LB'
1.273896 Phase    b'word[:1]:e'
1.263423 O        b'word[:2]:Cr'
1.244847 Gtype    b'word[:2]:WT'
1.244847 Gtype    b'word:WT'
1.236647 Gtype    b'word[:1]:F'
1.232072 Technique b'lemma:ChIP-exo'
1.218565 Supp     b'lemma:acetate'
1.218565 Supp     b'word:acetate'
1.218411 O        b'word:Cra'
1.214505 Med      b'isUpper'
1.210174 Gtype    b'word[:2]:Ar'
1.197926 Supp     b'word[:1]:N'
1.194956 Air      b'word:Anaerobic'
1.192780 O        b'+1:word:were'
1.191655 Supp     b'-1:lemma:Cra'
1.188100 Med      b'word[:1]:L'
1.185467 O        b'+1:postag:RB'
1.185391 Gversion b'-1:lemma:nc'
1.185391 Gversion b'-1:word:NC'
1.182343 Med      b'word[:1]:M'
1.178948 Gtype    b'word[:2]:cr'
1.165949 pH       b'word[:1]:p'
1.163893 O        b'word[:1]:R'
1.163629 O        b'word[:1]:c'
1.155830 Phase    b'lemma:stationary'
1.155830 Phase    b'word:stationary'
1.142993 O        b'+1:postag:NNP'
1.134168 O        b'word[:1]:E'
1.133170 O        b'-1:lemma:glucose'
1.133170 O        b'-1:word:glucose'
1.132500 Supp     b'word[:2]:ac'
1.130901 O        b'+1:word:ChIP-Seq'
1.120305 Gtype    b'lemma:flag-tag'
1.120305 Gtype    b'-1:lemma:c-terminal'
1.120305 Gtype    b'word:Flag-tag'
1.120305 Gtype    b'-1:word:C-terminal'
1.110588 Supp     b'postag:NNP'
1.109954 Technique b'symb'
1.108629 Supp     b'+1:lemma:1'
1.108629 Supp     b'+1:word:1'
1.105428 O        b'lemma:b'
1.105428 O        b'word:B'
1.104286 Gtype    b'lemma:type'
1.104286 Gtype    b'word[:2]:ty'
1.104286 Gtype    b'word:type'
1.089168 Gtype    b'word[:1]:f'
1.087372 Gversion b'lemma:nc'
1.087372 Gversion b'word[:2]:NC'
1.087372 Gversion b'word:NC'
1.083150 O        b'-1:lemma:0.3'
1.083150 O        b'-1:word:0.3'
1.081216 O        b'lemma:Custom'
1.081216 O        b'word:Custom'
1.074470 O        b'-1:lemma:anaerobic'
1.073417 Gtype    b'lemma:nsrr'
1.073417 Gtype    b'word[:2]:Ns'
1.073417 Gtype    b'word:NsrR'
1.073408 Gtype    b'-1:postag:VBG'
1.057426 Supp     b'lemma:rifampicin'
1.057426 Supp     b'word:rifampicin'
1.055166 Med      b'+1:lemma:0.4'
1.055166 Med      b'+1:word:0.4'
1.052666 Supp     b'word[:2]:ri'
1.044391 Anti     b'word[:1]:a'
1.039713 Supp     b'lemma:nacl'
1.039713 Supp     b'word:NaCl'
1.030612 Gversion b'lemma:asm584v2'
1.030612 Gversion b'word[:2]:AS'
1.030612 Gversion b'word:ASM584v2'
1.030597 Gversion b'lemma:chip-seq'
1.029930 Med      b'word[:1]:m'
1.029515 Gtype    b'+1:postag::'
1.026311 Med      b'lemma:MOPS'
1.026311 Med      b'word[:2]:MO'
1.026311 Med      b'word:MOPS'
1.021842 O        b'-1:lemma:ChIP-exo'
1.020313 Med      b'+1:postag:CD'
1.017584 Anti     b'+1:lemma:antibody'
1.017584 Anti     b'+1:word:antibody'
1.017141 O        b'isNumber'
1.015378 O        b'+1:lemma:od600'
1.015378 O        b'+1:word:OD600'
1.014672 Gversion b'word:ChIP-Seq'
1.011776 Strain   b'lemma:k-12'
1.011776 Strain   b'word[:2]:K-'
1.011776 Strain   b'word:K-12'
1.008575 Agit     b'+1:lemma:rpm'
1.008575 Agit     b'+1:word:rpm'
1.005191 O        b'word[:2]:Cu'
1.002792 Technique b'-1:lemma:chip-exo'
1.000546 Air      b'postag:RB'
1.000546 Air      b'postag[:1]:R'
1.000546 Air      b'postag[:2]:RB'
0.992188 Supp     b'-1:lemma:+'
0.992188 Supp     b'-1:word:+'
0.991416 Gtype    b'word[:1]:P'
0.986807 O        b'lemma:rpob'
0.986807 O        b'word:RpoB'
0.985164 Supp     b'+1:lemma:mm'
0.985164 Supp     b'+1:word:mM'


Top negative:
-0.277257 O        b'-1:lemma:iptg'
-0.277257 O        b'-1:word:IPTG'
-0.279683 O        b'-1:lemma:37'
-0.279683 O        b'-1:word:37'
-0.279732 O        b'word[:2]:ce'
-0.280808 O        b'lemma:sodium'
-0.280808 O        b'word:Sodium'
-0.283552 O        b'lemma:37'
-0.283552 O        b'word[:2]:37'
-0.283552 O        b'word:37'
-0.285904 O        b'-1:lemma:cra'
-0.287226 O        b'lemma:fructose'
-0.287226 O        b'word:fructose'
-0.287570 O        b'word[:2]:gl'
-0.288146 O        b'+1:word:C'
-0.288657 O        b'postag:RB'
-0.288657 O        b'postag[:1]:R'
-0.288657 O        b'postag[:2]:RB'
-0.290394 O        b'+1:lemma:phosphate'
-0.290394 O        b'+1:word:phosphate'
-0.291469 Anti     b'+1:lemma:anti-fur'
-0.291469 Anti     b'+1:word:anti-Fur'
-0.291608 Med      b'-1:postag:CD'
-0.292517 O        b'+1:lemma:antibody'
-0.292517 O        b'+1:word:antibody'
-0.293015 Temp     b'postag:NN'
-0.293202 O        b'word:cells'
-0.295080 Substrain b'isLower'
-0.301504 Technique b'-1:postag::'
-0.301563 O        b'+1:lemma:rep2'
-0.301563 O        b'+1:word:rep2'
-0.303285 Gtype    b'-1:lemma:mg1655'
-0.303285 Gtype    b'-1:word:MG1655'
-0.312135 pH       b'isUpper'
-0.315986 O        b'word[:1]:\xce\x94'
-0.318042 O        b'-1:lemma:control'
-0.318042 O        b'-1:word:control'
-0.320219 O        b'word[:1]:F'
-0.320234 O        b'-1:lemma:mm'
-0.320234 O        b'-1:word:mM'
-0.325890 Phase    b'postag[:1]:J'
-0.325890 Phase    b'postag[:2]:JJ'
-0.329319 Air      b'isUpper'
-0.337579 O        b'lemma:of'
-0.337579 O        b'word[:2]:of'
-0.337579 O        b'word:of'
-0.338232 O        b'lemma:30'
-0.338232 O        b'word:30'
-0.338512 Gtype    b'+1:postag:CD'
-0.340489 pH       b'isNumber'
-0.349750 Phase    b'postag:JJ'
-0.351290 O        b'-1:postag:IN'
-0.351993 Gtype    b'postag[:1]:V'
-0.351993 Gtype    b'postag[:2]:VB'
-0.352349 OD       b'symb'
-0.354429 Gtype    b'+1:lemma:-rrb-'
-0.354429 Gtype    b'+1:word:-RRB-'
-0.356978 O        b'-1:lemma:chip-exo'
-0.365676 Air      b'postag[:1]:N'
-0.365676 Air      b'postag[:2]:NN'
-0.369913 O        b'+1:lemma:at'
-0.369913 O        b'+1:word:at'
-0.374701 Supp     b'-1:lemma:-lrb-'
-0.374701 Supp     b'-1:word:-LRB-'
-0.385565 Supp     b'+1:postag:VBN'
-0.385693 O        b'word[:1]:4'
-0.396082 Technique b'isNumber'
-0.396613 Med      b'-1:postag:NN'
-0.398175 O        b'word[:1]:0'
-0.400398 Air      b'isLower'
-0.400541 O        b'+1:lemma:1m'
-0.400541 O        b'+1:word:1M'
-0.406455 O        b'+1:lemma:until'
-0.406455 O        b'+1:word:until'
-0.406467 O        b'lemma:0.3'
-0.406467 O        b'word:0.3'
-0.406862 Supp     b'-1:postag:NNP'
-0.407709 Vess     b'hUpper'
-0.407709 Vess     b'hLower'
-0.409808 Air      b'-1:lemma:or'
-0.409808 Air      b'-1:word:or'
-0.411518 Supp     b'-1:postag:-LRB-'
-0.413893 O        b'word[:2]:mg'
-0.416294 O        b'-1:lemma:\xe2\x88\x86'
-0.416294 O        b'-1:word:\xe2\x88\x86'
-0.416443 O        b'-1:lemma:dissolve'
-0.416443 O        b'+1:lemma:methanol'
-0.416443 O        b'-1:word:dissolved'
-0.416443 O        b'+1:word:methanol'
-0.416730 O        b'-1:lemma:rpob'
-0.416730 O        b'-1:word:RpoB'
-0.420106 O        b'lemma:mid-log'
-0.420106 O        b'word:mid-log'
-0.424246 Supp     b'postag:JJ'
-0.424315 Med      b'+1:postag:IN'
-0.425368 O        b'lemma:2h'
-0.425368 O        b'-1:lemma:additional'
-0.425368 O        b'word[:2]:2h'
-0.425368 O        b'word:2h'
-0.425368 O        b'-1:word:additional'
-0.427387 Supp     b'postag[:1]:J'
-0.427387 Supp     b'postag[:2]:JJ'
-0.432272 O        b'-1:lemma:ph'
-0.432272 O        b'-1:word:pH'
-0.437208 Agit     b'symb'
-0.450378 Air      b'+1:postag:JJ'
-0.451134 Med      b'symb'
-0.452272 O        b'-1:lemma:nsrr'
-0.452272 O        b'-1:word:NsrR'
-0.452987 O        b'-1:lemma:1'
-0.452987 O        b'-1:word:1'
-0.453419 OD       b'hUpper'
-0.453419 OD       b'hLower'
-0.455390 O        b'-1:lemma:30'
-0.455390 O        b'-1:word:30'
-0.458645 Strain   b'isLower'
-0.473382 O        b'+1:word:ChIP-exo'
-0.477433 O        b'word[:1]:M'
-0.478284 Air      b'-1:postag:JJ'
-0.481981 Med      b'-1:postag:IN'
-0.490205 O        b'-1:lemma:final'
-0.490205 O        b'-1:word:final'
-0.498623 O        b'+1:lemma:mm'
-0.498623 O        b'+1:word:mM'
-0.504915 O        b'-1:lemma:IP'
-0.504915 O        b'-1:word:IP'
-0.508549 O        b'+1:postag:IN'
-0.527183 O        b'-1:lemma:until'
-0.527183 O        b'-1:word:until'
-0.534060 O        b'+1:lemma:+'
-0.534060 O        b'+1:word:+'
-0.536386 O        b'-1:lemma:co2'
-0.536386 O        b'-1:word:CO2'
-0.546923 Technique b'isLower'
-0.549653 O        b'+1:lemma:g/l'
-0.549653 O        b'+1:word:g/L'
-0.556331 Agit     b'hUpper'
-0.556331 Agit     b'hLower'
-0.566036 O        b'-1:lemma:fresh'
-0.566036 O        b'-1:word:fresh'
-0.589166 O        b'word[:2]:pH'
-0.606308 Gtype    b'isNumber'
-0.608954 O        b'-1:lemma:ml'
-0.608954 O        b'-1:word:ml'
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