BioNLP'09 Shared Task on
Event Extraction
in conjunction with
BioNLP, a NAACL-HLT 2009
workshop, June 4-5 2009, Boulder, Colorado
Final Evaluation Results
of Universidade de Aveiro
Task 1
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 56) 89 ( 56) 32.18 62.92 42.59
Binding 347 ( 38) 138 ( 38) 10.95 27.54 15.67
Gene_expression 722 ( 300) 427 ( 300) 41.55 70.26 52.22
Transcription 137 ( 21) 112 ( 21) 15.33 18.75 16.87
Protein_catabolism 14 ( 5) 8 ( 5) 35.71 62.50 45.45
Phosphorylation 135 ( 57) 84 ( 57) 42.22 67.86 52.05
==[EVT-TOTAL]== 1529 ( 477) 858 ( 477) 31.20 55.59 39.97
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Regulation 291 ( 20) 165 ( 20) 6.87 12.12 8.77
Positive_regulation 983 ( 49) 218 ( 49) 4.98 22.48 8.16
Negative_regulation 379 ( 22) 111 ( 22) 5.80 19.82 8.98
==[REG-TOTAL]== 1653 ( 91) 494 ( 91) 5.51 18.42 8.48
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==[ALL-TOTAL]== 3182 ( 568) 1352 ( 568) 17.85 42.01 25.06
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 62) 88 ( 62) 35.63 70.45 47.33
Binding 347 ( 47) 138 ( 47) 13.54 34.06 19.38
Gene_expression 722 ( 335) 427 ( 335) 46.40 78.45 58.31
Transcription 137 ( 46) 112 ( 46) 33.58 41.07 36.95
Protein_catabolism 14 ( 5) 8 ( 5) 35.71 62.50 45.45
Phosphorylation 135 ( 67) 84 ( 67) 49.63 79.76 61.19
==[EVT-TOTAL]== 1529 ( 562) 857 ( 562) 36.76 65.58 47.11
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Regulation 291 ( 23) 165 ( 23) 7.90 13.94 10.09
Positive_regulation 983 ( 56) 218 ( 56) 5.70 25.69 9.33
Negative_regulation 379 ( 25) 111 ( 25) 6.60 22.52 10.20
==[REG-TOTAL]== 1653 ( 104) 494 ( 104) 6.29 21.05 9.69
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==[ALL-TOTAL]== 3182 ( 666) 1351 ( 666) 20.93 49.30 29.38
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 62) 88 ( 62) 35.63 70.45 47.33
Binding 347 ( 47) 138 ( 47) 13.54 34.06 19.38
Gene_expression 722 ( 335) 427 ( 335) 46.40 78.45 58.31
Transcription 137 ( 46) 112 ( 46) 33.58 41.07 36.95
Protein_catabolism 14 ( 5) 8 ( 5) 35.71 62.50 45.45
Phosphorylation 135 ( 67) 84 ( 67) 49.63 79.76 61.19
==[EVT-TOTAL]== 1529 ( 562) 857 ( 562) 36.76 65.58 47.11
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Regulation 291 ( 23) 165 ( 23) 7.90 13.94 10.09
Positive_regulation 983 ( 56) 218 ( 56) 5.70 25.69 9.33
Negative_regulation 379 ( 25) 111 ( 25) 6.60 22.52 10.20
==[REG-TOTAL]== 1653 ( 104) 494 ( 104) 6.29 21.05 9.69
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==[ALL-TOTAL]== 3182 ( 666) 1351 ( 666) 20.93 49.30 29.38
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 56) 89 ( 56) 32.18 62.92 42.59
Binding 398 ( 67) 149 ( 67) 16.83 44.97 24.50
Gene_expression 722 ( 300) 427 ( 300) 41.55 70.26 52.22
Transcription 137 ( 21) 112 ( 21) 15.33 18.75 16.87
Protein_catabolism 14 ( 5) 8 ( 5) 35.71 62.50 45.45
Phosphorylation 135 ( 57) 84 ( 57) 42.22 67.86 52.05
==[EVT-TOTAL]== 1580 ( 506) 869 ( 506) 32.03 58.23 41.32
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Regulation 338 ( 22) 165 ( 22) 6.51 13.33 8.75
Positive_regulation 1186 ( 84) 218 ( 84) 7.08 38.53 11.97
Negative_regulation 416 ( 22) 111 ( 22) 5.29 19.82 8.35
==[REG-TOTAL]== 1940 ( 128) 494 ( 128) 6.60 25.91 10.52
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==[ALL-TOTAL]== 3520 ( 634) 1363 ( 634) 18.01 46.52 25.97
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Event Class gold (match) answer (match) recall prec. fscore
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Localization 174 ( 62) 88 ( 62) 35.63 70.45 47.33
Binding 398 ( 78) 149 ( 78) 19.60 52.35 28.52
Gene_expression 722 ( 335) 427 ( 335) 46.40 78.45 58.31
Transcription 137 ( 46) 112 ( 46) 33.58 41.07 36.95
Protein_catabolism 14 ( 5) 8 ( 5) 35.71 62.50 45.45
Phosphorylation 135 ( 67) 84 ( 67) 49.63 79.76 61.19
==[EVT-TOTAL]== 1580 ( 593) 868 ( 593) 37.53 68.32 48.45
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Regulation 338 ( 25) 165 ( 25) 7.40 15.15 9.94
Positive_regulation 1186 ( 94) 218 ( 94) 7.93 43.12 13.39
Negative_regulation 416 ( 27) 111 ( 27) 6.49 24.32 10.25
==[REG-TOTAL]== 1940 ( 146) 494 ( 146) 7.53 29.55 12.00
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==[ALL-TOTAL]== 3520 ( 739) 1362 ( 739) 20.99 54.26 30.27
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Task 2
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Task 3
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