********** TRAINING AND TESTING REPORT **********
Training file: training-data-set-70-NER.txt

best params:{'c1': 0.10113340120103063, 'c2': 0.0033520616552264585}
best CV score:0.8384402744923658
model size: 0.13M

Flat F1: 0.8139572492434117
             precision    recall  f1-score   support

         OD      1.000     1.000     1.000        21
         pH      1.000     1.000     1.000        10
  Technique      1.000     1.000     1.000        33
        Med      1.000     0.821     0.902        56
       Temp      1.000     0.800     0.889        15
       Vess      0.000     0.000     0.000         0
       Agit      0.000     0.000     0.000         7
      Phase      0.889     0.762     0.821        21
        Air      0.600     0.580     0.590        88
       Anti      0.929     1.000     0.963        13
     Strain      0.000     0.000     0.000         0
      Gtype      0.875     0.808     0.840        78
  Substrain      0.000     0.000     0.000         0
       Supp      0.868     0.824     0.845       136
   Gversion      1.000     0.500     0.667         6

avg / total      0.849     0.785     0.814       484


Top likely transitions:
Anti   -> Anti    6.979736
Temp   -> Temp    6.644918
Med    -> Med     6.194242
Phase  -> Phase   5.549513
Gversion -> Gversion 5.485685
Gtype  -> Gtype   5.024800
Technique -> Technique 4.906636
OD     -> OD      4.482383
Supp   -> Supp    4.124475
pH     -> pH      3.898677
Air    -> Air     3.753321
Agit   -> Agit    3.350922
O      -> O       2.808475
Substrain -> Gtype   2.383740
Technique -> Air     1.019176
Gtype  -> Supp    0.595133
O      -> Technique 0.556662
Gtype  -> pH      0.202960
O      -> Gtype   0.187132
Strain -> O       -0.001344
Supp   -> Air     -0.027506
Phase  -> Air     -0.036012
Technique -> O       -0.064347
Gversion -> O       -0.110791
O      -> Phase   -0.220765
OD     -> Supp    -0.247009
Supp   -> Gtype   -0.366993
O      -> Supp    -0.438435
Air    -> Supp    -0.467416
Phase  -> Supp    -0.498281
O      -> Med     -0.527835
Air    -> O       -0.596185
OD     -> Air     -0.607902
Phase  -> OD      -0.636259
O      -> Anti    -0.674001
Med    -> O       -0.799796
Phase  -> O       -0.800974
Temp   -> Med     -0.833967
O      -> OD      -0.834109
Technique -> pH      -1.039258
Supp   -> O       -1.104397
Supp   -> Med     -1.106592
Technique -> Gtype   -1.369941
OD     -> O       -1.469810
Gtype  -> O       -1.838819
Substrain -> O       -1.908444
O      -> Air     -2.015111
Med    -> Supp    -2.893255


Top unlikely transitions:
Anti   -> Anti    6.979736
Temp   -> Temp    6.644918
Med    -> Med     6.194242
Phase  -> Phase   5.549513
Gversion -> Gversion 5.485685
Gtype  -> Gtype   5.024800
Technique -> Technique 4.906636
OD     -> OD      4.482383
Supp   -> Supp    4.124475
pH     -> pH      3.898677
Air    -> Air     3.753321
Agit   -> Agit    3.350922
O      -> O       2.808475
Substrain -> Gtype   2.383740
Technique -> Air     1.019176
Gtype  -> Supp    0.595133
O      -> Technique 0.556662
Gtype  -> pH      0.202960
O      -> Gtype   0.187132
Strain -> O       -0.001344
Supp   -> Air     -0.027506
Phase  -> Air     -0.036012
Technique -> O       -0.064347
Gversion -> O       -0.110791
O      -> Phase   -0.220765
OD     -> Supp    -0.247009
Supp   -> Gtype   -0.366993
O      -> Supp    -0.438435
Air    -> Supp    -0.467416
Phase  -> Supp    -0.498281
O      -> Med     -0.527835
Air    -> O       -0.596185
OD     -> Air     -0.607902
Phase  -> OD      -0.636259
O      -> Anti    -0.674001
Med    -> O       -0.799796
Phase  -> O       -0.800974
Temp   -> Med     -0.833967
O      -> OD      -0.834109
Technique -> pH      -1.039258
Supp   -> O       -1.104397
Supp   -> Med     -1.106592
Technique -> Gtype   -1.369941
OD     -> O       -1.469810
Gtype  -> O       -1.838819
Substrain -> O       -1.908444
O      -> Air     -2.015111
Med    -> Supp    -2.893255


Top positive:
7.159086 Anti     b'-2:lemma:antibody'
6.913389 Phase    b'-2:lemma:phase'
5.627078 Supp     b'-2:lemma:shake'
5.394900 O        b'word:Cra'
5.354031 Gtype    b'-2:lemma:genotype/variation'
5.331542 Air      b'word:Aerobic'
4.964475 O        b'-2:lemma:_'
4.588915 Air      b'word:Anaerobic'
4.500360 O        b'lemma:at'
4.497528 Gtype    b'-2:lemma:affyexp'
4.493776 Technique b'word:ChIP-exo'
4.486242 Supp     b'lemma:nh4cl'
4.173716 Technique b'lemma:rna-seq'
4.159253 Med      b'word:LB'
4.068120 O        b'-1:lemma:lb'
4.026543 Technique b'word:ChIP-Seq'
3.976160 O        b'lemma:_'
3.976160 O        b'word:_'
3.832488 Supp     b'-2:lemma:media'
3.813912 Phase    b'lemma:mid-log'
3.813912 Phase    b'word:mid-log'
3.810208 Air      b'lemma:anaerobic'
3.784849 Technique b'word:ChIPSeq'
3.664161 O        b'lemma:1'
3.664161 O        b'word:1'
3.634425 Gtype    b'-2:lemma:genotype'
3.524441 O        b'lemma:-'
3.524441 O        b'word:-'
3.473200 O        b'+2:lemma:\xc2\xb0c'
3.399618 O        b'postag:VBG'
3.376140 Gtype    b'lemma:type'
3.376140 Gtype    b'word:type'
3.372885 Supp     b'lemma:arginine'
3.348323 Supp     b'+2:lemma:iptg'
3.336067 O        b'+2:lemma:crp'
3.319043 Gtype    b'+1:lemma:type'
3.319043 Gtype    b'+1:word:type'
3.307899 O        b'lemma:2'
3.307899 O        b'word:2'
3.287875 Supp     b'lemma:no3'
3.287875 Supp     b'word:NO3'
3.275273 Air      b'postag:RB'
3.238826 O        b'lemma:3'
3.238826 O        b'word:3'
3.216088 Supp     b'+2:lemma:rifampicin'
3.155825 Gtype    b'word:WT'
3.154878 Supp     b'lemma:pq'
3.154878 Supp     b'word:PQ'
3.115706 Gtype    b'lemma:wt'
3.062369 Gtype    b'lemma:\xce\xb4fur'
3.062369 Gtype    b'word:\xce\x94fur'
2.972567 O        b'word:A'
2.959706 Technique b'+2:lemma:ph5'
2.915197 O        b'-1:postag:NNS'
2.872122 Med      b'lemma:MOPS'
2.872122 Med      b'word:MOPS'
2.828014 Supp     b'+1:lemma:\xc2\xb5m'
2.828014 Supp     b'+1:word:\xc2\xb5M'
2.806128 O        b'+1:word:ChIP-Seq'
2.771879 O        b'lemma:.'
2.771879 O        b'postag:.'
2.771879 O        b'word:.'
2.735816 O        b'-1:lemma:ChIP-exo'
2.735172 Strain   b'lemma:k-12'
2.735172 Strain   b'word:K-12'
2.726238 Temp     b'-1:word:sample'
2.704067 O        b'lemma:b'
2.704067 O        b'word:B'
2.689190 O        b'lemma:for'
2.685095 Air      b'postag:JJ'
2.678157 O        b'lemma:with'
2.678157 O        b'word:with'
2.668181 Temp     b'-1:lemma:sample'
2.657068 O        b'-1:word:Anaerobic'
2.637694 Substrain b'-2:lemma:substr'
2.610759 O        b'lemma:rpob'
2.610759 O        b'word:RpoB'
2.590566 Gtype    b'lemma:\xce\xb4cra'
2.586579 O        b'-2:lemma:flagtag'
2.577584 Gtype    b'word:\xce\x94cra'
2.542397 Technique b'lemma:chipseq'
2.498185 Supp     b'lemma:Iron'
2.498185 Supp     b'word:Iron'
2.498185 Supp     b'+1:word:Deficient'
2.498185 Supp     b'-2:lemma:Anaerobic'
2.492478 Supp     b'-2:lemma:20'
2.474908 Supp     b'lemma:iptg'
2.474908 Supp     b'word:IPTG'
2.438780 Gtype    b'postag:JJ'
2.420552 Med      b'lemma:LB'
2.418995 Supp     b'-1:ner:SUPP'
2.392369 O        b'-1:word:tag'
2.363417 Supp     b'-1:word:Cra'
2.310521 O        b'lemma:culture'
2.306597 Gtype    b'-1:ner:GEN'
2.254639 Supp     b'lemma:2h'
2.254639 Supp     b'-1:lemma:additional'
2.254639 Supp     b'word:2h'
2.254639 Supp     b'-1:word:additional'
2.238631 Med      b'+2:lemma:b2'
2.233910 Med      b'+2:postag:CC'
2.226133 Gtype    b'lemma:\xce\xb4ompr'
2.226133 Gtype    b'word:\xce\x94ompR'
2.186776 Gtype    b'-2:lemma:delta'
2.142102 O        b'-1:word:Aerobic'
2.141809 O        b'-2:lemma:myc'
2.129595 O        b'word:OmpR'
2.119368 Air      b'lemma:anaeroibc'
2.119368 Air      b'word:Anaeroibc'
2.089575 O        b'+1:postag:RB'
2.035390 Air      b'-1:lemma:ChIP-Seq'
2.035390 Air      b'-1:word:ChIP-Seq'
2.017217 O        b'-2:lemma:='
2.016701 O        b'-2:lemma:fructose'
2.014096 Air      b'-2:lemma:IP'
2.007645 Med      b'+2:lemma:+'
1.994771 Gtype    b'lemma:wild-type'
1.979339 Technique b'-1:lemma:chip-exo'
1.966001 Gtype    b'lemma:pk4854'
1.966001 Gtype    b'word:PK4854'
1.938159 Air      b'-1:lemma:co2'
1.938159 Air      b'-1:word:CO2'
1.918390 Gtype    b'-1:postag:VBG'
1.904415 Substrain b'lemma:mg1655'
1.904415 Substrain b'word:MG1655'
1.882999 pH       b'+1:postag:CD'
1.882334 O        b'-2:lemma:overnight'
1.881129 O        b'word:Lrp'
1.872865 Gversion b'lemma:chip-seq'
1.843588 Phase    b'+2:lemma:o.d.'
1.833842 O        b'word:C'
1.825215 Air      b'word:anaerobic'
1.811259 O        b'lemma::'
1.811259 O        b'word::'
1.808351 O        b'lemma:chip'
1.800421 O        b'lemma:harbor'
1.800421 O        b'word:harboring'
1.780921 Air      b'-1:lemma:-'
1.780921 Air      b'-1:word:-'
1.780775 O        b'-2:lemma:medium'
1.779626 OD       b'lemma:0.3'
1.779626 OD       b'word:0.3'
1.758197 Gtype    b'lemma:dfnr'
1.758197 Gtype    b'word:dFNR'
1.755397 Gversion b'word:ChIP-Seq'
1.748846 O        b'-1:lemma:tag'
1.748556 Technique b'-2:lemma:wt'
1.735932 Air      b'lemma:aerobically'
1.735932 Air      b'word:aerobically'
1.725636 Temp     b'-2:lemma:keep'
1.724598 Med      b'+2:lemma:b1'
1.720992 Technique b'lemma:rnaseq'
1.720992 Technique b'word:RNASeq'
1.716252 Supp     b'-1:lemma:+'
1.716252 Supp     b'-1:word:+'
1.712543 O        b'-2:lemma:250'
1.708567 O        b'-1:word:ChIP-exo'
1.697789 Supp     b'lemma:acetate'
1.697789 Supp     b'word:acetate'
1.692471 Supp     b'lemma:nacl'
1.692471 Supp     b'word:NaCl'
1.685262 OD       b'-2:lemma:od450'
1.684244 Anti     b'-2:lemma:polymerase'
1.682797 Supp     b'-2:lemma:agent'
1.674278 O        b'lemma:gadx'
1.671694 O        b'lemma:rep2'
1.671694 O        b'word:rep2'
1.671694 O        b'lemma:rep1'
1.671694 O        b'word:rep1'
1.663419 O        b'-1:lemma:type'
1.663419 O        b'-1:word:type'
1.662512 O        b'lemma:trpr'
1.662512 O        b'word:TrpR'
1.658760 Med      b'lemma:media'
1.658760 Med      b'word:media'
1.656120 O        b'lemma:soxr'
1.656120 O        b'word:SoxR'
1.656120 O        b'lemma:soxs'
1.656120 O        b'word:SoxS'
1.653312 Supp     b'+1:word:was'
1.652658 Supp     b'-2:postag:VBG'
1.649601 Supp     b'+1:lemma:1'
1.649601 Supp     b'+1:word:1'
1.644028 Air      b'-2:lemma:cm20'
1.639074 O        b'lemma:ompr'
1.631831 O        b'+1:lemma:fnr-8myc'
1.631831 O        b'+1:word:Fnr-8myc'
1.613562 Temp     b'+1:lemma:\xc2\xb0c'
1.613562 Temp     b'+1:word:\xc2\xb0C'
1.611016 Vess     b'lemma:flask'
1.611016 Vess     b'-1:lemma:warm'
1.611016 Vess     b'word:flask'
1.611016 Vess     b'-1:word:warmed'
1.611016 Vess     b'-2:lemma:pre'
1.611016 Vess     b'+2:lemma:43'
1.606101 O        b'+1:lemma:od600'
1.606101 O        b'+1:word:OD600'
1.600519 O        b'+1:word:WT'
1.591721 pH       b'lemma:ph5'
1.591721 pH       b'+1:lemma:.5'
1.591721 pH       b'word:pH5'
1.591721 pH       b'+1:word:.5'
1.588862 O        b'postag::'
1.576308 Supp     b'+1:lemma:2'
1.576308 Supp     b'+1:word:2'
1.575115 Supp     b'lemma:Adenine'
1.575115 Supp     b'word:Adenine'
1.574178 O        b'+1:lemma:wt'
1.572183 Gtype    b'-1:lemma:\xe2\x88\x86'
1.572183 Gtype    b'-1:word:\xe2\x88\x86'
1.563692 O        b'+1:ner:MED'
1.547737 Gtype    b'+1:postag::'
1.543452 Supp     b'-2:lemma:for'
1.534933 Air      b'-2:lemma:nh4cl'
1.530724 O        b'+1:postag:NNP'
1.530723 O        b'postag:IN'
1.515611 O        b'+2:lemma:allow'
1.513158 Supp     b'lemma:fructose'
1.513158 Supp     b'word:fructose'
1.510344 O        b'lemma:from'
1.510344 O        b'word:from'
1.507445 Phase    b'postag:NN'
1.502926 O        b'lemma:CEL'
1.502926 O        b'word:CEL'
1.490514 Gtype    b'lemma:\xce\xb4oxyr'
1.490514 Gtype    b'word:\xce\x94oxyR'
1.476943 O        b'-2:ner:MED'
1.475717 Air      b'+2:postag:CD'
1.438545 Temp     b'-1:lemma:\xcf\x8332'
1.438545 Temp     b'-1:word:\xcf\x8332'
1.438385 O        b'lemma:purr'
1.438385 O        b'word:PurR'
1.433062 Supp     b'postag:NNP'
1.429404 Temp     b'-2:lemma:\xcf\x8332'
1.418237 Phase    b'-2:lemma:until'
1.408429 OD       b'+2:lemma:0.3'
1.397474 Temp     b'lemma:\xc2\xb0c'
1.397474 Temp     b'word:\xc2\xb0C'
1.393654 Supp     b'-2:lemma:10'
1.389868 O        b'-1:lemma:0.3'
1.389868 O        b'-1:word:0.3'
1.376539 Strain   b'+1:lemma:substr'
1.376539 Strain   b'+1:word:substr'
1.376539 Strain   b'-2:lemma:str'
1.368654 Technique b'lemma:ChIP-exo'
1.364857 Supp     b'-1:lemma:Cra'
1.364617 Supp     b'-1:lemma:with'
1.364617 Supp     b'-1:word:with'
1.342901 O        b'+1:lemma:coli'
1.342901 O        b'+1:word:coli'
1.333168 Supp     b'-2:lemma:argr'
1.331139 O        b'lemma:oxyr'
1.331139 O        b'word:OxyR'
1.327965 Supp     b'lemma:glucose'
1.327965 Supp     b'word:glucose'
1.320749 Agit     b'lemma:rpm'
1.320749 Agit     b'word:rpm'
1.311775 Med      b'-2:postag:JJ'
1.306611 Supp     b'+2:lemma:-lrb-'
1.305817 Temp     b'lemma:43'
1.305817 Temp     b'word:43'
1.303400 Gversion b'lemma:.2'
1.303400 Gversion b'-1:lemma:u00096'
1.303400 Gversion b'word:.2'
1.303400 Gversion b'-1:word:U00096'
1.300963 Gtype    b'-1:lemma:nsrr'
1.300963 Gtype    b'+1:lemma:flagtag'
1.300963 Gtype    b'-1:word:NsrR'
1.300963 Gtype    b'+1:word:Flagtag'
1.290749 O        b'+1:lemma:250'
1.290749 O        b'+1:word:250'
1.286304 O        b'-2:lemma:co2'
1.277313 Substrain b'+1:lemma:phtpg'
1.277313 Substrain b'+1:word:PhtpG'
1.271455 Med      b'lemma:minimal'
1.271455 Med      b'word:minimal'
1.265024 O        b'lemma:a'
1.264702 Gtype    b'+1:lemma:ph5'
1.264702 Gtype    b'+1:word:pH5'
1.264702 Gtype    b'+2:lemma:.5'
1.262898 O        b'word:GadX'
1.261116 O        b'-1:lemma:glucose'
1.261116 O        b'-1:word:glucose'
1.257695 Gversion b'-2:lemma:build'
1.257254 Gtype    b'-1:lemma:rpob'
1.257254 Gtype    b'-1:word:RpoB'
1.255290 Supp     b'-2:lemma:induce'
1.252217 Gtype    b'+2:lemma:glucose'
1.232404 Air      b'-2:lemma:%'
1.227757 Gtype    b'-1:postag:VBP'
1.222973 Air      b'lemma:aerobic'
1.221807 Gversion b'lemma:u00096'
1.221807 Gversion b'+1:lemma:.2'
1.221807 Gversion b'word:U00096'
1.221807 Gversion b'+1:word:.2'
1.220595 O        b'+1:word:were'
1.217284 Supp     b'-1:word:OmpR'
1.215085 Technique b'-1:lemma:input'
1.215085 Technique b'-1:word:Input'
1.214247 Anti     b'+1:lemma:antibody'
1.214247 Anti     b'+1:word:antibody'
1.213745 O        b'isLower'
1.213451 Air      b'+2:lemma:37'
1.212507 O        b'+2:postag:JJ'
1.211770 Gtype    b'lemma:\xe2\x88\x86'
1.211770 Gtype    b'word:\xe2\x88\x86'
1.211087 O        b'+1:lemma:0.2'
1.211087 O        b'+1:word:0.2'
1.206115 Med      b'+1:lemma:0.4'
1.206115 Med      b'+1:word:0.4'
1.204475 pH       b'lemma:5.5'
1.204475 pH       b'word:5.5'
1.204403 O        b'postag:VBN'
1.203362 O        b'+1:lemma:rifampicin'
1.203362 O        b'+1:word:rifampicin'
1.198584 Air      b'+2:lemma:%'
1.195795 Med      b'lemma:medium'
1.195795 Med      b'word:medium'
1.190664 Supp     b'lemma:Leu'
1.190664 Supp     b'word:Leu'
1.190664 Supp     b'-2:lemma:Lrp'
1.188832 pH       b'+1:lemma:5.5'
1.188832 pH       b'+1:word:5.5'
1.184383 Gtype    b'lemma:\xce\xb4soxs'
1.184383 Gtype    b'word:\xce\x94soxS'
1.182837 Gversion b'lemma:asm584v2'
1.182837 Gversion b'word:ASM584v2'
1.180741 O        b'+2:lemma:fructose'
1.177940 O        b'-2:lemma:min'
1.170962 O        b'-2:lemma:37'
1.157687 Med      b'lemma:m63'
1.157687 Med      b'word:M63'
1.155843 Air      b'+1:lemma:%'
1.155843 Air      b'+1:word:%'
1.153949 Gtype    b'lemma:arca8myc'
1.153949 Gtype    b'word:ArcA8myc'
1.153949 Gtype    b'-2:lemma:chip-arca'
1.146411 Air      b'-2:postag:CD'
1.141510 Temp     b'-1:lemma:37'
1.141510 Temp     b'-1:word:37'
1.137480 O        b'-1:lemma:pq'
1.137480 O        b'-1:word:PQ'
1.136779 Temp     b'-1:lemma:43'
1.136779 Temp     b'-1:word:43'
1.136649 Med      b'+2:lemma:then'
1.132608 O        b'+1:lemma:pq'
1.132608 O        b'+1:word:PQ'
1.129434 OD       b'+1:lemma:of'
1.129434 OD       b'+1:word:of'
1.124944 Gtype    b'+1:lemma:with'
1.124944 Gtype    b'+1:word:with'
1.122146 Med      b'isUpper'
1.121839 Gversion b'lemma:nc'
1.121839 Gversion b'word:NC'
1.121839 Gversion b'+2:lemma:000913'
1.116050 O        b'+1:lemma:\xe2\x88\x86'
1.116050 O        b'+1:word:\xe2\x88\x86'
1.113574 Gtype    b'lemma:\xce\xb4soxr'
1.113574 Gtype    b'word:\xce\x94soxR'
1.111055 O        b'-1:ner:_'
1.098439 Air      b'-2:lemma:0.3'
1.096063 O        b'lemma:ml'
1.095951 Substrain b'lemma:mg1655star'
1.095951 Substrain b'word:MG1655star'
1.095378 O        b'lemma:argr'
1.095378 O        b'word:ArgR'
1.084380 O        b'postag:VBD'
1.080536 Technique b'lemma:ChIP-Seq'
1.076385 Technique b'-1:lemma:IP'
1.076385 Technique b'-1:word:IP'
1.071052 Technique b'-2:lemma:Fur'
1.066629 O        b'-1:lemma:min'
1.066629 O        b'-1:word:min'
1.050785 Supp     b'+2:postag:IN'
1.048554 O        b'word:for'
1.040865 Gversion b'lemma:000913'
1.040865 Gversion b'word:000913'
1.040865 Gversion b'-2:lemma:nc'
1.040189 Gtype    b'+1:lemma:pq'
1.040189 Gtype    b'+1:word:PQ'
1.034042 O        b'+2:ner:_'
1.018924 Gversion b'-2:postag:VB'
1.014244 Supp     b'+2:postag:-LRB-'
1.012886 O        b'-1:lemma:into'
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0.979570 OD       b'word:OD450'
0.979570 OD       b'-1:word:At'
0.976988 Supp     b'-1:postag:CD'
0.975846 O        b'lemma:rnase'
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0.966841 O        b'-1:lemma:mg1655'
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0.941463 O        b'+1:lemma:mid-log'
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0.936854 O        b'lemma:affyexp'
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0.878105 Anti     b'postag:JJ'
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0.865398 Gtype    b'lemma:fnr8myc'
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