HDS for BioNLP
Task 1
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Event Class gold (match) answer (match) recall prec. fscore
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Gene_expression 619 ( 453) 556 ( 453) 73.18 81.47 77.11
Transcription 101 ( 58) 113 ( 58) 57.43 51.33 54.21
Protein_catabolism 14 ( 7) 18 ( 7) 50.00 38.89 43.75
Localization 99 ( 50) 66 ( 50) 50.51 75.76 60.61
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=[SIMPLE ALL]= 833 ( 568) 753 ( 568) 68.19 75.43 71.63
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Binding 333 ( 135) 412 ( 135) 40.54 32.77 36.24
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Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Phosphorylation 160 ( 135) 178 ( 135) 84.38 75.84 79.88
Ubiquitination 30 ( 0) 0 ( 0) 0.00 0.00 0.00
Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[PROT-MOD ALL]= 191 ( 135) 178 ( 135) 70.68 75.84 73.17
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Regulation 288 ( 20) 140 ( 20) 6.94 14.29 9.35
Positive_regulation 1130 ( 176) 587 ( 176) 15.58 29.98 20.50
Negative_regulation 526 ( 120) 323 ( 120) 22.81 37.15 28.27
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=[REGULATION ALL]= 1944 ( 316) 1050 ( 316) 16.26 30.10 21.11
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==[EVENT TOTAL]== 3301 ( 1154) 2393 ( 1154) 34.96 48.22 40.53
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Event Class gold (match) answer (match) recall prec. fscore
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Gene_expression 619 ( 501) 556 ( 501) 80.94 90.11 85.28
Transcription 101 ( 66) 113 ( 66) 65.35 58.41 61.68
Protein_catabolism 14 ( 10) 18 ( 10) 71.43 55.56 62.50
Localization 99 ( 50) 66 ( 50) 50.51 75.76 60.61
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=[SIMPLE ALL]= 833 ( 627) 753 ( 627) 75.27 83.27 79.07
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Binding 333 ( 139) 412 ( 139) 41.74 33.74 37.32
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Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Phosphorylation 160 ( 135) 178 ( 135) 84.38 75.84 79.88
Ubiquitination 30 ( 0) 0 ( 0) 0.00 0.00 0.00
Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[PROT-MOD ALL]= 191 ( 135) 178 ( 135) 70.68 75.84 73.17
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Regulation 288 ( 21) 140 ( 21) 7.29 15.00 9.81
Positive_regulation 1130 ( 182) 587 ( 182) 16.11 31.01 21.20
Negative_regulation 526 ( 121) 323 ( 121) 23.00 37.46 28.50
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=[REGULATION ALL]= 1944 ( 324) 1050 ( 324) 16.67 30.86 21.64
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==[EVENT TOTAL]== 3301 ( 1225) 2393 ( 1225) 37.11 51.19 43.03
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Event Class gold (match) answer (match) recall prec. fscore
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Gene_expression 619 ( 511) 551 ( 503) 82.55 91.29 86.70
Transcription 101 ( 67) 110 ( 67) 66.34 60.91 63.51
Protein_catabolism 14 ( 10) 18 ( 10) 71.43 55.56 62.50
Localization 99 ( 55) 66 ( 52) 55.56 78.79 65.16
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=[SIMPLE ALL]= 833 ( 643) 745 ( 632) 77.19 84.83 80.83
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Binding 333 ( 147) 397 ( 146) 44.14 36.78 40.12
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Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Phosphorylation 160 ( 138) 176 ( 135) 86.25 76.70 81.20
Ubiquitination 30 ( 0) 0 ( 0) 0.00 0.00 0.00
Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[PROT-MOD ALL]= 191 ( 138) 176 ( 135) 72.25 76.70 74.41
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Regulation 288 ( 22) 139 ( 21) 7.64 15.11 10.15
Positive_regulation 1130 ( 190) 568 ( 189) 16.81 33.27 22.34
Negative_regulation 526 ( 127) 315 ( 123) 24.14 39.05 29.84
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=[REGULATION ALL]= 1944 ( 339) 1022 ( 333) 17.44 32.58 22.72
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==[EVENT TOTAL]== 3301 ( 1267) 2340 ( 1246) 38.38 53.25 44.61
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Event-Arg Type gold (match) answer (match) recall prec. fscore
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Theme-Gene_expression 619 ( 453) 556 ( 453) 73.18 81.47 77.11
Theme-Transcription 101 ( 58) 113 ( 58) 57.43 51.33 54.21
Theme-Protein_catabolism 14 ( 7) 18 ( 7) 50.00 38.89 43.75
Theme-Binding 418 ( 243) 421 ( 243) 58.13 57.72 57.93
Theme-Localization 99 ( 50) 66 ( 50) 50.51 75.76 60.61
Theme-Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Phosphorylation 160 ( 139) 178 ( 139) 86.88 78.09 82.25
Theme-Ubiquitination 25 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Regulation 257 ( 25) 140 ( 25) 9.73 17.86 12.59
Theme-Positive_regulation 1068 ( 199) 584 ( 199) 18.63 34.08 24.09
Theme-Negative_regulation 490 ( 136) 321 ( 136) 27.76 42.37 33.54
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=[THEME ALL]= 3252 ( 1310) 2397 ( 1310) 40.28 54.65 46.38
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Cause-Regulation 103 ( 0) 2 ( 0) 0.00 0.00 0.00
Cause-Positive_regulation 337 ( 8) 13 ( 8) 2.37 61.54 4.57
Cause-Negative_regulation 122 ( 5) 13 ( 5) 4.10 38.46 7.41
Cause-Protein_modification 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Phosphorylation 2 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Ubiquitination 8 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[CAUSE ALL]= 572 ( 13) 28 ( 13) 2.27 46.43 4.33
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==[PRIMARY ARG TOTAL]== 3824 ( 1323) 2425 ( 1323) 34.60 54.56 42.34
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Event-Arg Type gold (match) answer (match) recall prec. fscore
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Theme-Gene_expression 619 ( 501) 556 ( 501) 80.94 90.11 85.28
Theme-Transcription 101 ( 66) 113 ( 66) 65.35 58.41 61.68
Theme-Protein_catabolism 14 ( 10) 18 ( 10) 71.43 55.56 62.50
Theme-Binding 418 ( 259) 421 ( 259) 61.96 61.52 61.74
Theme-Localization 99 ( 50) 66 ( 50) 50.51 75.76 60.61
Theme-Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Phosphorylation 160 ( 139) 178 ( 139) 86.88 78.09 82.25
Theme-Ubiquitination 25 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Regulation 257 ( 27) 140 ( 27) 10.51 19.29 13.60
Theme-Positive_regulation 1068 ( 205) 584 ( 205) 19.19 35.10 24.82
Theme-Negative_regulation 490 ( 137) 321 ( 137) 27.96 42.68 33.79
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=[THEME ALL]= 3252 ( 1394) 2397 ( 1394) 42.87 58.16 49.35
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Cause-Regulation 103 ( 0) 2 ( 0) 0.00 0.00 0.00
Cause-Positive_regulation 337 ( 8) 13 ( 8) 2.37 61.54 4.57
Cause-Negative_regulation 122 ( 5) 13 ( 5) 4.10 38.46 7.41
Cause-Protein_modification 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Phosphorylation 2 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Ubiquitination 8 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[CAUSE ALL]= 572 ( 13) 28 ( 13) 2.27 46.43 4.33
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==[PRIMARY ARG TOTAL]== 3824 ( 1407) 2425 ( 1407) 36.79 58.02 45.03
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Event-Arg Type gold (match) answer (match) recall prec. fscore
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Theme-Gene_expression 619 ( 511) 551 ( 503) 82.55 91.29 86.70
Theme-Transcription 101 ( 67) 110 ( 67) 66.34 60.91 63.51
Theme-Protein_catabolism 14 ( 10) 18 ( 10) 71.43 55.56 62.50
Theme-Binding 418 ( 288) 404 ( 283) 68.90 70.05 69.47
Theme-Localization 99 ( 55) 66 ( 52) 55.56 78.79 65.16
Theme-Protein_modification 1 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Phosphorylation 160 ( 142) 176 ( 139) 88.75 78.98 83.58
Theme-Ubiquitination 25 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Theme-Regulation 257 ( 28) 139 ( 27) 10.89 19.42 13.96
Theme-Positive_regulation 1068 ( 217) 560 ( 215) 20.32 38.39 26.57
Theme-Negative_regulation 490 ( 143) 312 ( 138) 29.18 44.23 35.17
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=[THEME ALL]= 3252 ( 1461) 2336 ( 1434) 44.93 61.39 51.88
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Cause-Regulation 103 ( 0) 2 ( 0) 0.00 0.00 0.00
Cause-Positive_regulation 337 ( 8) 13 ( 8) 2.37 61.54 4.57
Cause-Negative_regulation 122 ( 5) 13 ( 5) 4.10 38.46 7.41
Cause-Protein_modification 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Phosphorylation 2 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Ubiquitination 8 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Acetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
Cause-Deacetylation 0 ( 0) 0 ( 0) 0.00 0.00 0.00
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=[CAUSE ALL]= 572 ( 13) 28 ( 13) 2.27 46.43 4.33
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==[PRIMARY ARG TOTAL]== 3824 ( 1474) 2364 ( 1447) 38.55 61.21 47.30
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Task 2
N/A
N/A
N/A
Task 3
N/A
N/A
N/A
Thank you for your participation!!