{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,6,19]],"date-time":"2025-06-19T04:08:13Z","timestamp":1750306093669,"version":"3.41.0"},"publisher-location":"New York, NY, USA","reference-count":36,"publisher":"ACM","license":[{"start":{"date-parts":[[2017,8,20]],"date-time":"2017-08-20T00:00:00Z","timestamp":1503187200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.acm.org\/publications\/policies\/copyright_policy#Background"}],"funder":[{"name":"National Institute of General Medical Sciences (NIH\/NIGMS)","award":["5P20GM103429"],"award-info":[{"award-number":["5P20GM103429"]}]},{"name":"the Science Technology Development Project from Jilin Province","award":["(20160101247JC)"],"award-info":[{"award-number":["(20160101247JC)"]}]},{"name":"the Premier Key-Discipline Enhancement Scheme from Guangdong Government, and China Scholarship Council"},{"name":"United States Food and Drug Administration (FDA)","award":["HHSF223201510172C"],"award-info":[{"award-number":["HHSF223201510172C"]}]},{"name":"the National Natural Science Foundation of China","award":["(61602207, 61572228, 61472158)"],"award-info":[{"award-number":["(61602207, 61572228, 61472158)"]}]},{"name":"the Premier Discipline Enhancement Scheme from Zhuhai Government"},{"name":"United States National Institutes of Health (NIH) Academic Research Enhancement Award","award":["1R15GM114739"],"award-info":[{"award-number":["1R15GM114739"]}]}],"content-domain":{"domain":["dl.acm.org"],"crossmark-restriction":true},"short-container-title":[],"published-print":{"date-parts":[[2017,8,20]]},"DOI":"10.1145\/3107411.3110418","type":"proceedings-article","created":{"date-parts":[[2017,8,24]],"date-time":"2017-08-24T11:58:11Z","timestamp":1503575891000},"page":"770-771","update-policy":"https:\/\/doi.org\/10.1145\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Protein-Protein Interaction Extraction Using Attention-Based Convolution Neural Networks"],"prefix":"10.1145","author":[{"given":"Hao","family":"Zhang","sequence":"first","affiliation":[{"name":"Jilin University, Changchun, China"}]},{"given":"Mary Qu","family":"Yang","sequence":"additional","affiliation":[{"name":"University of Arkansas, Little Rock &amp; Yale University, Little Rock, AR, USA"}]},{"given":"Xiaoyue","family":"Feng","sequence":"additional","affiliation":[{"name":"Jilin University, Changchun, China"}]},{"given":"William","family":"Yang","sequence":"additional","affiliation":[{"name":"Carnegie Mellon University, Pittsburgh, PA, USA"}]},{"given":"Weida","family":"Tong","sequence":"additional","affiliation":[{"name":"National Center for Toxicological United States Food and Drug Administration, Jefferson, AR, USA"}]},{"given":"Renchu","family":"Guan","sequence":"additional","affiliation":[{"name":"Jilin University &amp; University of Arkansas, Little Rock, Changchun, China"}]}],"member":"320","published-online":{"date-parts":[[2017,8,20]]},"reference":[{"key":"e_1_3_2_1_1_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-4-11"},{"key":"e_1_3_2_1_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.compbiolchem.2016.09.011"},{"key":"e_1_3_2_1_3_1","volume-title":"Proc Symp on Semantic Mining in Biomedicine","author":"Xiao J.","year":"2005","unstructured":"Xiao , J. , Su , J. , Zhou , G. and Tan , C . 2005. Protein-Protein Interaction Extraction: A Supervised Learning Approach . In Proc Symp on Semantic Mining in Biomedicine ( 2005 ), 51--59. Xiao, J., Su, J., Zhou, G. and Tan, C. 2005. Protein-Protein Interaction Extraction: A Supervised Learning Approach. In Proc Symp on Semantic Mining in Biomedicine (2005), 51--59."},{"key":"e_1_3_2_1_4_1","volume-title":"Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007)","author":"S\u00e6tre R.","year":"2008","unstructured":"S\u00e6tre , R. , Sagae , K. and Tsujii , J . 2008. Syntactic features for protein-protein interaction extraction . Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007) (Singapore, Jan. 2008 ), 6.1--6.14. S\u00e6tre, R., Sagae, K. and Tsujii, J. 2008. Syntactic features for protein-protein interaction extraction. Short Paper Proceedings of the 2nd International Symposium on Languages in Biology and Medicine (LBM 2007) (Singapore, Jan. 2008), 6.1--6.14."},{"key":"e_1_3_2_1_5_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-S3-S6"},{"key":"e_1_3_2_1_6_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000837"},{"key":"e_1_3_2_1_7_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bth451"},{"key":"e_1_3_2_1_8_1","first-page":"S4","article-title":"Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome biology, 9","volume":"2","author":"Krallinger M.","year":"2008","unstructured":"Krallinger , M. , Leitner , F. , Rodriguez-Penagos , C. and Valencia , A. 2008 . Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome biology, 9 , Suppl 2 (2008), S4 -- S4 . Krallinger, M., Leitner, F., Rodriguez-Penagos, C. and Valencia, A. 2008. Overview of the protein-protein interaction annotation extraction task of BioCreative II. Genome biology, 9, Suppl 2 (2008), S4--S4.","journal-title":"Suppl"},{"key":"e_1_3_2_1_9_1","volume-title":"Proceedings of the 11th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2006)","author":"Giuliano C.","year":"2006","unstructured":"Giuliano , C. , Lavelli , A. and Romano , L . 2006. Exploiting Shallow Linguistic Information for Relation Extraction from Biomedical Literature . Proceedings of the 11th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2006) (Trento, Italy , Apr. 2006 ), 3--7. Giuliano, C., Lavelli, A. and Romano, L. 2006. Exploiting Shallow Linguistic Information for Relation Extraction from Biomedical Literature. Proceedings of the 11th Conference of the European Chapter of the Association for Computational Linguistics (EACL 2006) (Trento, Italy, Apr. 2006), 3--7."},{"key":"e_1_3_2_1_10_1","unstructured":"Vishwanathan S.V.N. and Smola A. 2003. Fast Kernels for String and Tree Matching. Advances in neural information processing systems 15 (2003). Vishwanathan S.V.N. and Smola A. 2003. Fast Kernels for String and Tree Matching. Advances in neural information processing systems 15 (2003)."},{"key":"e_1_3_2_1_11_1","doi-asserted-by":"crossref","unstructured":"Collins M. and Duffy N. 2001. Convolution Kernels for Natural Language. Advances in Neural Information Processing Systems 14. 625--632. Collins M. and Duffy N. 2001. Convolution Kernels for Natural Language. Advances in Neural Information Processing Systems 14. 625--632.","DOI":"10.7551\/mitpress\/1120.003.0085"},{"key":"e_1_3_2_1_12_1","doi-asserted-by":"publisher","DOI":"10.1007\/11871842_32"},{"key":"e_1_3_2_1_13_1","first-page":"140","article-title":"A Spectrum Tree Kernel","volume":"22","author":"Kuboyama T.","year":"2007","unstructured":"Kuboyama , T. , Hirata , K. , Kashima , H., F. Aoki-Kinoshita , K. and Yasuda , H. 2007 . A Spectrum Tree Kernel . Information and Media Technologies , 22 , 2 (2007), 140 -- 147 . Kuboyama, T., Hirata, K., Kashima, H., F.Aoki-Kinoshita, K. and Yasuda, H. 2007. A Spectrum Tree Kernel. Information and Media Technologies, 22, 2 (2007), 140--147.","journal-title":"Information and Media Technologies"},{"key":"e_1_3_2_1_14_1","volume-title":"Proceedings of the Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL","author":"Erkan G.","year":"2007","unstructured":"Erkan , G. 2007 . Semi-supervised classification for extracting protein interaction sentences using dependency parsing . In Proceedings of the Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL (2007), 228--237. Erkan, G. 2007. Semi-supervised classification for extracting protein interaction sentences using dependency parsing. In Proceedings of the Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning (EMNLP-CoNLL (2007), 228--237."},{"key":"e_1_3_2_1_15_1","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-S11-S2"},{"key":"e_1_3_2_1_16_1","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btm544"},{"key":"e_1_3_2_1_17_1","doi-asserted-by":"crossref","unstructured":"Tikk D. Solt I. Thomas P. and Leser U. 2013. A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. BMC bioinformatics 14 1 (2013) 12. Tikk D. Solt I. Thomas P. and Leser U. 2013. A detailed error analysis of 13 kernel methods for protein-protein interaction extraction. BMC bioinformatics 14 1 (2013) 12.","DOI":"10.1186\/1471-2105-14-12"},{"key":"e_1_3_2_1_18_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/W16-2908"},{"key":"e_1_3_2_1_19_1","doi-asserted-by":"crossref","unstructured":"Miwa M. S\u00e6tre R. Miyao Y. and Tsujii J. 2009. Protein-protein interaction extraction by leveraging multiple kernels and parsers. International journal of medical informatics 78 12 (2009) e39--e46. Miwa M. S\u00e6tre R. Miyao Y. and Tsujii J. 2009. Protein-protein interaction extraction by leveraging multiple kernels and parsers. International journal of medical informatics 78 12 (2009) e39--e46.","DOI":"10.1016\/j.ijmedinf.2009.04.010"},{"key":"e_1_3_2_1_20_1","volume-title":"Second Joint Conference on Lexical and Computational Semantics (*SEM)","volume":"635","author":"Thomas P.","unstructured":"Thomas , P. , Neves , M. , Rockt\u00e4schel , T. and Leser , U . 2013. WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting . Second Joint Conference on Lexical and Computational Semantics (*SEM) , Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013) (Atlanta, Georgia, USA, Jun. 2013), 628-- 635 . Thomas, P., Neves, M., Rockt\u00e4schel, T. and Leser, U. 2013. WBI-DDI: Drug-Drug Interaction Extraction using Majority Voting. Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013) (Atlanta, Georgia, USA, Jun. 2013), 628--635."},{"key":"e_1_3_2_1_21_1","volume-title":"Proceedings of COLING 2014, the 25th International Conference on Computational Linguistics: Technical Papers","author":"Zeng D.","year":"2014","unstructured":"Zeng , D. , Liu , K. , Lai , S. , Zhou , G. and Zhao , J . 2014. Relation Classification via Convolutional Deep Neural Network . Proceedings of COLING 2014, the 25th International Conference on Computational Linguistics: Technical Papers ( Dublin, Ireland , Aug. 2014 ), 2335--2344. Zeng, D., Liu, K., Lai, S., Zhou, G. and Zhao, J. 2014. Relation Classification via Convolutional Deep Neural Network. Proceedings of COLING 2014, the 25th International Conference on Computational Linguistics: Technical Papers (Dublin, Ireland, Aug. 2014), 2335--2344."},{"key":"e_1_3_2_1_22_1","unstructured":"Santos C.N. dos Xiang B. and Zhou B. 2015. Classifying Relations by Ranking with Convolutional Neural Networks. arXiv preprint arXiv: abs\/1504.06580 (2015). Santos C.N. dos Xiang B. and Zhou B. 2015. Classifying Relations by Ranking with Convolutional Neural Networks. arXiv preprint arXiv: abs\/1504.06580 (2015)."},{"key":"e_1_3_2_1_23_1","volume-title":"Proceedings of the 1st Workshop on Vector Space Modeling for Natural Language Processing, VS@NAACL-HLT 2015","author":"Nguyen T.H.","year":"2015","unstructured":"Nguyen , T.H. and Grishman , R . 2015. Relation Extraction: Perspective from Convolutional Neural Networks . Proceedings of the 1st Workshop on Vector Space Modeling for Natural Language Processing, VS@NAACL-HLT 2015 , June 5, 2015 , Denver, Colorado, USA (2015), 39--48. Nguyen, T.H. and Grishman, R. 2015. Relation Extraction: Perspective from Convolutional Neural Networks. Proceedings of the 1st Workshop on Vector Space Modeling for Natural Language Processing, VS@NAACL-HLT 2015, June 5, 2015, Denver, Colorado, USA (2015), 39--48."},{"key":"e_1_3_2_1_24_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/D15-1062"},{"key":"e_1_3_2_1_25_1","unstructured":"Zhang D. and Wang D. 2015. Relation Classification via Recurrent Neural Network. arXiv preprint arXiv: abs\/1508.01006 (2015). Zhang D. and Wang D. 2015. Relation Classification via Recurrent Neural Network. arXiv preprint arXiv: abs\/1508.01006 (2015)."},{"key":"e_1_3_2_1_26_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/D16-1007"},{"key":"e_1_3_2_1_27_1","doi-asserted-by":"crossref","unstructured":"Xu Y. Mou L. Li G. Chen Y. Peng H. and Jin Z. 2015. Classifying Relations via Long Short Term Memory Networks along Shortest Dependency Path. arXiv preprint arXiv: abs\/1508.03720 (2015). Xu Y. Mou L. Li G. Chen Y. Peng H. and Jin Z. 2015. Classifying Relations via Long Short Term Memory Networks along Shortest Dependency Path. arXiv preprint arXiv: abs\/1508.03720 (2015).","DOI":"10.18653\/v1\/D15-1206"},{"key":"e_1_3_2_1_28_1","unstructured":"Xu Y. Jia R. Mou L. Li G. Chen Y. Lu Y. and Jin Z. 2016. Improved Relation Classification by Deep Recurrent Neural Networks with Data Augmentation. arXiv preprint arXiv: abs\/1601.03651 (2016). Xu Y. Jia R. Mou L. Li G. Chen Y. Lu Y. and Jin Z. 2016. Improved Relation Classification by Deep Recurrent Neural Networks with Data Augmentation. arXiv preprint arXiv: abs\/1601.03651 (2016)."},{"key":"e_1_3_2_1_29_1","volume-title":"Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, ACL 2016, August 7--12","author":"Cai R.","year":"2016","unstructured":"Cai , R. , Zhang , X. and Wang , H . 2016. Bidirectional Recurrent Convolutional Neural Network for Relation Classification . Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, ACL 2016, August 7--12 , 2016 , Berlin, Germany , Volume 1: Long Papers (2016). Cai, R., Zhang, X. and Wang, H. 2016. Bidirectional Recurrent Convolutional Neural Network for Relation Classification. Proceedings of the 54th Annual Meeting of the Association for Computational Linguistics, ACL 2016, August 7--12, 2016, Berlin, Germany, Volume 1: Long Papers (2016)."},{"key":"e_1_3_2_1_30_1","volume-title":"Proceedings of ACL 2016","author":"Wang L.","year":"2016","unstructured":"Wang , L. , Cao , Z. , de Melo , G. and Liu , Z . 2016. Relation Classification via Multi-Level Attention CNNs . Proceedings of ACL 2016 ( Berlin , 2016 ). Wang, L., Cao, Z., de Melo, G. and Liu, Z. 2016. Relation Classification via Multi-Level Attention CNNs. Proceedings of ACL 2016 (Berlin, 2016)."},{"key":"e_1_3_2_1_31_1","doi-asserted-by":"publisher","DOI":"10.18653\/v1\/W16-2922"},{"key":"e_1_3_2_1_32_1","first-page":"2016","volume-title":"Computational and Mathematical Methods in Medicine","author":"Liu S.","year":"2016","unstructured":"Liu , S. , Tang , B. , Chen , Q. and Wang , X . 2016. Drug-Drug Interaction Extraction via Convolutional Neural Networks . Computational and Mathematical Methods in Medicine , 2016 , ( 2016 ), 8. Liu, S., Tang, B., Chen, Q. and Wang, X. 2016. Drug-Drug Interaction Extraction via Convolutional Neural Networks. Computational and Mathematical Methods in Medicine, 2016, (2016), 8."},{"key":"e_1_3_2_1_33_1","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2015.2478467"},{"key":"e_1_3_2_1_34_1","article-title":"Natural Language Processing (Almost) from Scratch","author":"Collobert R.","year":"2011","unstructured":"Collobert , R. , Weston , J. , Bottou , L. , Karlen , M. , Kavukcuoglu , K. and Kuksa , P. 2011 . Natural Language Processing (Almost) from Scratch . Journal of Machine Learning Research, 12 , ( Nov. 2011), 2493--2537. Collobert, R., Weston, J., Bottou, L., Karlen, M., Kavukcuoglu, K. and Kuksa, P. 2011. Natural Language Processing (Almost) from Scratch. Journal of Machine Learning Research, 12, (Nov. 2011), 2493--2537.","journal-title":"Journal of Machine Learning Research, 12"},{"key":"e_1_3_2_1_35_1","unstructured":"Mikolov T. Chen K. Corrado G. and Dean J. 2013. Efficient Estimation of Word Representations in Vector Space. arXiv preprint arXiv: abs\/1301.3781 (2013). Mikolov T. Chen K. Corrado G. and Dean J. 2013. Efficient Estimation of Word Representations in Vector Space. arXiv preprint arXiv: abs\/1301.3781 (2013)."},{"key":"e_1_3_2_1_36_1","volume-title":"A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One","author":"Yang M.","year":"2016","unstructured":"Yang , M. , Elnitski , L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One , Public Library of Science , October 27, 2016 . Yang, M.,Elnitski, L. A Systems Biology Comparison of Ovarian Cancers Implicates Putative Somatic Driver Mutations through Protein-Protein Interaction Models. PLoS One, Public Library of Science, October 27, 2016."}],"event":{"name":"BCB '17: 8th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics","sponsor":["SIGBio ACM Special Interest Group on Bioinformatics"],"location":"Boston Massachusetts USA","acronym":"BCB '17"},"container-title":["Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics"],"original-title":[],"link":[{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3107411.3110418","content-type":"unspecified","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/dl.acm.org\/doi\/pdf\/10.1145\/3107411.3110418","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,18]],"date-time":"2025-06-18T03:30:25Z","timestamp":1750217425000},"score":1,"resource":{"primary":{"URL":"https:\/\/dl.acm.org\/doi\/10.1145\/3107411.3110418"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,20]]},"references-count":36,"alternative-id":["10.1145\/3107411.3110418","10.1145\/3107411"],"URL":"https:\/\/doi.org\/10.1145\/3107411.3110418","relation":{},"subject":[],"published":{"date-parts":[[2017,8,20]]},"assertion":[{"value":"2017-08-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}