TY - GEN
T1 - High precision rule based ppi extraction and per-pair basis performance evaluation
AU - Lee, Junkyu
AU - Kim, Seongsoon
AU - Lee, Sunwon
AU - Lee, Kyubum
AU - Kang, Jaewoo
PY - 2012
Y1 - 2012
N2 - Virtually all current PPI extraction studies focus on improving F-score, aiming to balance the performance on both precision and recall. However, in many realistic scenarios involving large corpora, one can benefit more from an extremely high precision PPI extraction tool than a high-recall counterpart. We also argue that the current per-instance basis performance evaluation method should be revisited. In order to address these problems, we introduce a new rulebased PPI extraction method equipped with a set of ultrahigh precision extraction rules. We also propose a new perpair basis performance metric, which is more pragmatic in practice. The proposed PPI extraction method achieves 95-96% per-pair and 94-97% per-instance precisions on the AIMed benchmark corpus.
AB - Virtually all current PPI extraction studies focus on improving F-score, aiming to balance the performance on both precision and recall. However, in many realistic scenarios involving large corpora, one can benefit more from an extremely high precision PPI extraction tool than a high-recall counterpart. We also argue that the current per-instance basis performance evaluation method should be revisited. In order to address these problems, we introduce a new rulebased PPI extraction method equipped with a set of ultrahigh precision extraction rules. We also propose a new perpair basis performance metric, which is more pragmatic in practice. The proposed PPI extraction method achieves 95-96% per-pair and 94-97% per-instance precisions on the AIMed benchmark corpus.
KW - Biomedical Text Mining
KW - Entity Relation Extraction
KW - Interaction Extraction
KW - PPI
KW - Text Mining
UR - http://www.scopus.com/inward/record.url?scp=84870552663&partnerID=8YFLogxK
U2 - 10.1145/2390068.2390082
DO - 10.1145/2390068.2390082
M3 - Conference contribution
AN - SCOPUS:84870552663
SN - 9781450317160
T3 - International Conference on Information and Knowledge Management, Proceedings
SP - 69
EP - 76
BT - DTMBIO'12 - Proceedings of the 6th ACM International Workshop on Data and Text Mining in Biomedical Informatics, Co-located with CIKM 2012
T2 - 6th ACM International Workshop on Data and Text Mining in Biomedical Informatics, DTMBIO 2012, in Conjunction with the 21st ACM International Conference on Information and Knowledge Management, CIKM 2012
Y2 - 29 October 2012 through 29 October 2012
ER -