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

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report_Run_8_v13.txt 16.8 KB
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********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70.txt

best params:{'c1': 0.12475431096451621, 'c2': 0.013861677898849787}
best CV score:0.8708258755708097
model size: 0.13M

Flat F1: 0.7686691050567419
             precision    recall  f1-score   support

         OD      0.818     0.818     0.818        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     0.828     0.906        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      0.556     0.362     0.439        69
       Anti      1.000     1.000     1.000        11
     Strain      0.000     0.000     0.000         1
      Gtype      0.867     0.847     0.857        85
  Substrain      0.000     0.000     0.000         0
       Supp      0.586     0.813     0.681       134
   Gversion      0.000     0.000     0.000         0

avg / total      0.769     0.787     0.769       451


Top likely transitions:
Agit   -> Agit    6.648242
Temp   -> Temp    6.282260
OD     -> OD      5.656317
Med    -> Med     5.374931
Supp   -> Supp    5.024760
Gversion -> Gversion 4.860700
Anti   -> Anti    4.808761
Phase  -> Phase   4.070172
Air    -> Air     4.046984
Gtype  -> Gtype   3.891102
O      -> O       3.673937
Technique -> Technique 3.298287
pH     -> pH      2.863141
Substrain -> Gtype   0.869714
O      -> Technique 0.537319
Air    -> O       0.264430
O      -> Gtype   0.222368
Temp   -> O       0.130509
Gtype  -> Supp    0.079007
Technique -> Air     0.075090
Med    -> O       0.071813
O      -> Anti    0.041836
O      -> Supp    0.033164
Supp   -> O       -0.011764
Phase  -> O       -0.027870
OD     -> O       -0.058085
Gversion -> O       -0.096750
O      -> Phase   -0.097534
Air    -> Supp    -0.189966
Technique -> pH      -0.218375
Temp   -> Med     -0.224152
O      -> Med     -0.332474
O      -> OD      -0.383967
Gtype  -> Med     -0.624502
Gtype  -> Technique -0.734455
Technique -> O       -0.940389
O      -> Air     -1.114206
Gtype  -> O       -1.304969
Substrain -> O       -1.345412
Med    -> Supp    -2.177917


Top unlikely transitions:
Agit   -> Agit    6.648242
Temp   -> Temp    6.282260
OD     -> OD      5.656317
Med    -> Med     5.374931
Supp   -> Supp    5.024760
Gversion -> Gversion 4.860700
Anti   -> Anti    4.808761
Phase  -> Phase   4.070172
Air    -> Air     4.046984
Gtype  -> Gtype   3.891102
O      -> O       3.673937
Technique -> Technique 3.298287
pH     -> pH      2.863141
Substrain -> Gtype   0.869714
O      -> Technique 0.537319
Air    -> O       0.264430
O      -> Gtype   0.222368
Temp   -> O       0.130509
Gtype  -> Supp    0.079007
Technique -> Air     0.075090
Med    -> O       0.071813
O      -> Anti    0.041836
O      -> Supp    0.033164
Supp   -> O       -0.011764
Phase  -> O       -0.027870
OD     -> O       -0.058085
Gversion -> O       -0.096750
O      -> Phase   -0.097534
Air    -> Supp    -0.189966
Technique -> pH      -0.218375
Temp   -> Med     -0.224152
O      -> Med     -0.332474
O      -> OD      -0.383967
Gtype  -> Med     -0.624502
Gtype  -> Technique -0.734455
Technique -> O       -0.940389
O      -> Air     -1.114206
Gtype  -> O       -1.304969
Substrain -> O       -1.345412
Med    -> Supp    -2.177917


Top positive:
5.778785 Anti     b'-2:lemma:antibody'
5.099975 Technique b'lemma[:2]:Ch'
4.743651 O        b'-2:lemma:_'
4.315336 Gtype    b'lemma[:1]:\xce\xb4'
4.248364 O        b'lemma[:2]:re'
4.215292 Air      b'word:Aerobic'
3.511204 O        b'postag:CC'
3.394617 O        b'postag:IN'
3.322867 O        b'lemma:2'
3.322867 O        b'word:2'
3.302849 O        b'-2:lemma:medium'
3.302673 Substrain b'lemma[:2]:mg'
3.165450 Technique b'lemma[:2]:rn'
3.016068 Med      b'+2:postag:CC'
2.985942 Air      b'word:Anaerobic'
2.966163 O        b'lemma:1'
2.966163 O        b'word:1'
2.923025 O        b'lemma:3'
2.923025 O        b'word:3'
2.877232 Phase    b'-2:lemma:phase'
2.867093 Supp     b'-1:word:Cra'
2.833973 Supp     b'lemma:arginine'
2.812849 O        b'+2:lemma:\xc2\xb0c'
2.760554 Air      b'postag:RB'
2.740030 O        b'lemma[:1]:h'
2.731812 Gtype    b'-2:lemma:genotype/variation'
2.708235 Air      b'lemma[:2]:an'
2.604774 O        b'postag::'
2.584655 Anti     b'+2:lemma:antibody'
2.582878 O        b'lemma:-'
2.582878 O        b'word:-'
2.571693 O        b'word:Cra'
2.568004 O        b'lemma:_'
2.568004 O        b'lemma[:1]:_'
2.568004 O        b'word:_'
2.567283 O        b'-1:lemma:ChIP-exo'
2.560556 O        b'word:A'
2.539743 Gtype    b'word:WT'
2.513546 O        b'lemma:.'
2.513546 O        b'postag:.'
2.513546 O        b'word:.'
2.499439 Gtype    b'lemma:type'
2.499439 Gtype    b'lemma[:2]:ty'
2.499439 Gtype    b'word:type'
2.460970 Air      b'lemma:anaerobic'
2.408658 O        b'+1:postag:RB'
2.388183 Phase    b'lemma:mid-log'
2.388183 Phase    b'word:mid-log'
2.384478 Supp     b'lemma[:2]:gl'
2.383895 O        b'postag:VBN'
2.382299 Air      b'lemma[:2]:ae'
2.358041 O        b'lemma:with'
2.358041 O        b'word:with'
2.353625 Supp     b'+2:lemma:iptg'
2.350953 Phase    b'lemma[:2]:ex'
2.322692 Technique b'word:ChIPSeq'
2.304893 Gtype    b'-2:lemma:delta'
2.289460 O        b'+2:lemma:fructose'
2.285493 O        b'+2:lemma:cra'
2.276073 O        b'lemma[:2]:ge'
2.256719 Supp     b'-1:postag:CC'
2.250185 Air      b'lemma[:1]:a'
2.234168 Gtype    b'lemma[:2]:pk'
2.207665 O        b'-1:lemma:tag'
2.164408 Technique b'lemma:chipseq'
2.073628 O        b'+2:lemma:70'
2.050739 Supp     b'lemma:pq'
2.050739 Supp     b'lemma[:2]:pq'
2.050739 Supp     b'word:PQ'
2.001826 Air      b'+1:postag:IN'
1.975647 O        b'isLower'
1.936376 O        b'-1:word:Aerobic'
1.920820 Gtype    b'-1:lemma:\xe2\x88\x86'
1.920820 Gtype    b'-1:word:\xe2\x88\x86'
1.908896 O        b'-1:lemma:anaerobic'
1.889420 pH       b'+1:postag:CD'
1.888509 Supp     b'lemma[:1]:n'
1.886729 O        b'postag:DT'
1.858376 Supp     b'lemma:Iron'
1.858376 Supp     b'lemma[:2]:Ir'
1.858376 Supp     b'word:Iron'
1.858376 Supp     b'+1:word:Deficient'
1.858376 Supp     b'-2:lemma:Anaerobic'
1.853608 O        b'lemma:chip'
1.838366 Gversion b'lemma:chip-seq'
1.831815 O        b'-1:word:tag'
1.820620 Anti     b'lemma[:2]:an'
1.815550 Gtype    b'lemma[:1]:w'
1.809178 Gtype    b'hGreek'
1.792293 Gversion b'word:ChIP-Seq'
1.775178 Gtype    b'-2:postag:DT'
1.768307 O        b'+1:word:ChIP-Seq'
1.764667 Supp     b'-1:lemma:with'
1.764667 Supp     b'-1:word:with'
1.722957 Supp     b'lemma:acetate'
1.722957 Supp     b'word:acetate'
1.713832 Technique b'-1:lemma:chip-exo'
1.710287 Med      b'isUpper'
1.709780 O        b'lemma:b'
1.709780 O        b'word:B'
1.704621 Technique b'word:ChIP-Seq'
1.694028 Phase    b'lemma[:1]:e'
1.689430 Gtype    b'+1:lemma:type'
1.689430 Gtype    b'+1:word:type'
1.679770 Supp     b'lemma[:1]:I'
1.670552 Supp     b'+2:lemma:rifampicin'
1.664056 O        b'lemma[:1]:b'
1.661667 Substrain b'lemma[:1]:m'
1.647294 Gtype    b'lemma:wt'
1.647294 Gtype    b'lemma[:2]:wt'
1.634965 O        b'-2:lemma:myc'
1.622392 pH       b'lemma[:2]:ph'
1.620704 Supp     b'-2:lemma:agent'
1.618245 Technique b'lemma[:2]:ch'
1.617020 O        b'+2:postag:JJ'
1.593807 Supp     b'+1:lemma:\xc2\xb5m'
1.593807 Supp     b'+1:word:\xc2\xb5M'
1.593155 O        b'lemma:a'
1.582387 O        b'+1:postag:NNP'
1.579370 Temp     b'-1:word:sample'
1.576150 Gtype    b'+2:lemma:glucose'
1.562990 O        b'+1:lemma:pq'
1.562990 O        b'+1:word:PQ'
1.555511 Gtype    b'lemma[:2]:wi'
1.554537 Gtype    b'lemma[:1]:f'
1.545677 Temp     b'-1:lemma:sample'
1.540501 Med      b'lemma:MOPS'
1.540501 Med      b'lemma[:1]:M'
1.540501 Med      b'lemma[:2]:MO'
1.540501 Med      b'word:MOPS'
1.522098 OD       b'lemma[:1]:o'
1.509875 Med      b'lemma[:1]:m'
1.505327 Phase    b'-2:lemma:until'
1.505027 O        b'-1:lemma:lb'
1.505027 O        b'-1:word:LB'
1.497714 Gtype    b'-1:postag:VBG'
1.492176 Agit     b'+2:lemma:at'
1.486489 O        b'isNumber'
1.464199 Gtype    b'-2:lemma:affyexp'
1.453424 Supp     b'lemma[:2]:30'
1.450691 Gversion b'lemma[:2]:00'
1.450691 Gversion b'-2:lemma:nc'
1.450278 Technique b'lemma:ChIP-exo'
1.448397 O        b'-1:lemma:media'
1.448397 O        b'-1:word:media'
1.443477 Supp     b'lemma[:2]:ni'
1.440399 O        b'lemma:Custom'
1.440399 O        b'lemma[:2]:Cu'
1.440399 O        b'word:Custom'
1.429606 Supp     b'-1:lemma:Cra'
1.425430 Supp     b'-2:lemma:media'
1.418079 Med      b'+2:lemma:b2'
1.404067 O        b'-1:lemma:glucose'
1.404067 O        b'-1:word:glucose'
1.396114 Phase    b'+2:lemma:o.d.'
1.387435 Gtype    b'lemma:\xe2\x88\x86'
1.387435 Gtype    b'lemma[:1]:\xe2\x88\x86'
1.387435 Gtype    b'word:\xe2\x88\x86'
1.349810 Temp     b'-2:lemma:\xcf\x8332'
1.346540 Supp     b'lemma:fructose'
1.346540 Supp     b'word:fructose'
1.343114 Technique b'lemma[:1]:C'
1.341281 Gversion b'-2:lemma:build'
1.336703 O        b'-2:lemma:flagtag'
1.328773 Med      b'lemma:broth'
1.328773 Med      b'-1:lemma:L'
1.328773 Med      b'lemma[:2]:br'
1.328773 Med      b'word:broth'
1.328773 Med      b'-1:word:L'
1.325888 Supp     b'+1:lemma:1'
1.325888 Supp     b'+1:word:1'
1.321862 Anti     b'+1:lemma:antibody'
1.321862 Anti     b'+1:word:antibody'
1.316632 O        b'+2:lemma:polyclonal'
1.311992 O        b'-1:lemma:0.3'
1.311992 O        b'-1:word:0.3'
1.295781 Gtype    b'lemma[:2]:de'
1.284876 Gtype    b'-2:lemma:genotype'
1.277004 Supp     b'-2:lemma:condition'
1.273482 Supp     b'-2:lemma:induce'
1.271728 Air      b'-1:postag::'
1.268149 Phase    b'lemma:stationary'
1.268149 Phase    b'word:stationary'
1.262573 Technique b'-1:lemma:input'
1.262573 Technique b'-1:word:Input'
1.259324 Gversion b'-2:postag:VB'
1.259137 Supp     b'lemma[:2]:ac'
1.259012 O        b'+1:lemma:mid-log'
1.259012 O        b'+1:word:mid-log'
1.253088 Temp     b'-1:lemma:43'
1.253088 Temp     b'-1:word:43'
1.253040 Gtype    b'lemma:nsrr'
1.253040 Gtype    b'lemma[:2]:ns'
1.253040 Gtype    b'word:NsrR'
1.237967 O        b'lemma:0.4'
1.237967 O        b'word:0.4'
1.236427 O        b'-1:lemma:type'
1.236427 O        b'-1:word:type'
1.229582 O        b'lemma:ompr'
1.229582 O        b'word:OmpR'


Top negative:
-0.226109 O        b'+1:word:+'
-0.228043 Supp     b'-1:lemma:-lrb-'
-0.228043 Supp     b'-1:word:-LRB-'
-0.230436 O        b'-1:lemma:37'
-0.230436 O        b'-1:word:37'
-0.231705 O        b'-2:lemma:rpob'
-0.238413 Supp     b'-2:lemma:treat'
-0.244411 O        b'+1:lemma:supplement'
-0.244411 O        b'+1:word:supplemented'
-0.245251 Supp     b'-1:postag:-LRB-'
-0.247310 O        b'+2:lemma:at'
-0.248881 Supp     b'-2:lemma:grow'
-0.251177 O        b'lemma[:1]:I'
-0.254376 Supp     b'+2:lemma:glucose'
-0.259696 O        b'-1:lemma:ph'
-0.259696 O        b'-1:word:pH'
-0.264998 O        b'-2:postag:-LRB-'
-0.269895 O        b'lemma[:2]:0.'
-0.271060 O        b'lemma:media'
-0.271060 O        b'word:media'
-0.271346 O        b'lemma:of'
-0.271346 O        b'lemma[:2]:of'
-0.271346 O        b'word:of'
-0.271681 Med      b'-1:postag:CD'
-0.273156 Supp     b'lemma[:1]:a'
-0.280251 O        b'lemma:glucose'
-0.280251 O        b'word:glucose'
-0.283644 O        b'+1:lemma:1m'
-0.283644 O        b'+1:word:1M'
-0.283644 O        b'-2:lemma:vol'
-0.283702 Med      b'+1:postag:NN'
-0.284709 O        b'+2:lemma:a'
-0.285197 Anti     b'+2:lemma:polyclonal'
-0.289677 O        b'lemma:30'
-0.289677 O        b'word:30'
-0.295454 O        b'-2:lemma:of'
-0.296935 Phase    b'+1:postag:NN'
-0.298375 Phase    b'-2:postag:NN'
-0.304558 O        b'+1:lemma:until'
-0.304558 O        b'+1:word:until'
-0.306703 O        b'-1:lemma:30'
-0.306703 O        b'-1:word:30'
-0.313912 Supp     b'+2:postag:NNP'
-0.316964 O        b'+1:lemma:mm'
-0.316964 O        b'+1:word:mM'
-0.318525 O        b'lemma:0.3'
-0.318525 O        b'word:0.3'
-0.320042 Supp     b'+1:lemma:-lrb-'
-0.320042 Supp     b'+1:word:-LRB-'
-0.320535 Gtype    b'-2:postag:CD'
-0.321989 O        b'-2:lemma:dpd'
-0.322258 O        b'lemma:2h'
-0.322258 O        b'-1:lemma:additional'
-0.322258 O        b'lemma[:2]:2h'
-0.322258 O        b'word:2h'
-0.322258 O        b'-1:word:additional'
-0.322790 O        b'-1:lemma:final'
-0.322790 O        b'-1:word:final'
-0.324434 Air      b'+2:lemma:95'
-0.331328 O        b'-2:lemma:anaerobically'
-0.334146 O        b'+1:lemma:g/l'
-0.334146 O        b'+1:word:g/L'
-0.335082 Supp     b'+1:postag:-LRB-'
-0.338290 O        b'-2:lemma:fresh'
-0.339212 O        b'+2:lemma:250'
-0.341268 O        b'-2:postag::'
-0.342136 Gtype    b'isNumber'
-0.347416 Temp     b'isLower'
-0.350883 O        b'-1:lemma:nsrr'
-0.350883 O        b'-1:word:NsrR'
-0.354035 O        b'lemma[:2]:ph'
-0.354572 O        b'+2:lemma:10'
-0.357789 O        b'-1:postag:IN'
-0.359009 O        b'lemma[:2]:gl'
-0.359220 Anti     b'+1:lemma:anti-fur'
-0.359220 Anti     b'+1:word:anti-Fur'
-0.360276 O        b'lemma[:1]:0'
-0.369156 Gtype    b'postag:VBG'
-0.370735 O        b'lemma[:1]:p'
-0.372427 Supp     b'hGreek'
-0.376173 O        b'-1:lemma:co2'
-0.376173 O        b'-1:word:CO2'
-0.379578 Air      b'-1:postag:JJ'
-0.395494 O        b'-2:lemma:pahse'
-0.402449 O        b'-1:lemma:IP'
-0.402449 O        b'-1:word:IP'
-0.408327 O        b'-1:lemma:dissolve'
-0.408327 O        b'+1:lemma:methanol'
-0.408327 O        b'-1:word:dissolved'
-0.408327 O        b'+1:word:methanol'
-0.412183 Supp     b'-1:postag:NNP'
-0.420616 O        b'-1:lemma:mm'
-0.420616 O        b'-1:word:mM'
-0.429595 Supp     b'-2:postag:JJ'
-0.430195 O        b'-1:lemma:grow'
-0.435625 Med      b'-1:postag:NN'
-0.448459 O        b'lemma[:1]:k'
-0.448610 O        b'-2:lemma:supplement'
-0.466479 O        b'-1:lemma:1'
-0.466479 O        b'-1:word:1'
-0.469602 O        b'-2:lemma:until'
-0.479898 O        b'lemma[:1]:d'
-0.497095 OD       b'isUpper'
-0.504384 O        b'+2:lemma:-rrb-'
-0.509042 O        b'+2:lemma:.'
-0.509042 O        b'+2:postag:.'
-0.509708 O        b'lemma[:1]:L'
-0.515769 Supp     b'+1:lemma:,'
-0.515769 Supp     b'+1:postag:,'
-0.515769 Supp     b'+1:word:,'
-0.523080 O        b'+2:lemma:mid-log'
-0.538428 O        b'+2:lemma:tag'
-0.544421 O        b'+1:lemma:at'
-0.544421 O        b'+1:word:at'
-0.547856 Air      b'isLower'
-0.550244 Supp     b'lemma[:1]:s'
-0.559046 O        b'+2:postag:-RRB-'
-0.569716 O        b'lemma[:1]:n'
-0.570198 Gtype    b'-2:lemma:\xe2\x88\x86'
-0.579000 Gtype    b'lemma[:1]:a'
-0.583274 Anti     b'+2:postag:JJ'
-0.584013 O        b'+2:lemma:+'
-0.587165 O        b'-2:postag:DT'
-0.588343 Anti     b'isUpper'
-0.593932 Temp     b'postag:NN'
-0.629429 Technique b'postag:NN'
-0.641599 O        b'+1:postag:VBG'
-0.642253 O        b'-2:postag:RB'
-0.645675 O        b'-2:lemma:glucose'
-0.646300 O        b'-2:lemma:aerobically'
-0.655586 Phase    b'hUpper'
-0.655586 Phase    b'hLower'
-0.667822 Supp     b'symb'
-0.684950 O        b'lemma:mid-log'
-0.684950 O        b'word:mid-log'
-0.696963 Air      b'postag:CD'
-0.697392 Gtype    b'lemma[:1]:c'
-0.708226 O        b'+1:postag:IN'
-0.709735 Agit     b'hUpper'
-0.709735 Agit     b'hLower'
-0.719991 Supp     b'+2:postag:CD'
-0.734493 O        b'postag:VBP'
-0.737825 O        b'+1:lemma:2.0'
-0.737825 O        b'+1:word:2.0'
-0.739276 O        b'-2:lemma:phase'
-0.744487 O        b'-1:lemma:vol'
-0.744487 O        b'-1:word:vol'
-0.744487 O        b'-2:lemma:1/100'
-0.744487 O        b'+2:lemma:1m'
-0.745820 O        b'-1:lemma:2'
-0.745820 O        b'-1:word:2'
-0.779133 O        b'lemma[:2]:me'
-0.791240 Med      b'-2:postag:VBN'
-0.811108 pH       b'isLower'
-0.815019 O        b'lemma[:2]:ri'
-0.822304 O        b'lemma[:2]:ae'
-0.845031 Air      b'symb'
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-0.858500 O        b'lemma:rifampicin'
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-0.868974 O        b'+1:word:in'
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-0.989258 Supp     b'+2:lemma:fructose'
-0.999898 Gtype    b'isUpper'
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-1.027901 O        b'+1:lemma:1'
-1.027901 O        b'+1:word:1'
-1.080125 O        b'-1:lemma:sample'
-1.081087 Med      b'symb'
-1.103669 Anti     b'postag:NNP'
-1.119102 Supp     b'lemma[:1]:c'
-1.161510 Gtype    b'+2:lemma:cra'
-1.168776 O        b'postag:RB'
-1.179031 Gversion b'isLower'
-1.264564 Air      b'postag:NN'
-1.303121 Phase    b'-1:postag:JJ'
-1.313129 O        b'-2:lemma:0.3'
-1.354086 O        b'+2:lemma:then'
-1.362965 O        b'-2:lemma:rifampicin'
-1.372070 O        b'lemma[:2]:30'
-1.477845 O        b'+1:lemma:2'
-1.477845 O        b'+1:word:2'
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-1.790036 O        b'-1:postag:VBG'
-1.878256 O        b'-2:lemma:media'
-1.903402 Supp     b'+2:lemma:1'
-1.998576 Phase    b'postag:JJ'
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-2.297320 O        b'-1:lemma::'
-2.297320 O        b'-1:word::'
-2.625976 O        b'lemma[:2]:fl'
-2.846763 O        b'-1:lemma:_'
-2.846763 O        b'-1:word:_'