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Additionally, few efforts have been made to allow PPI predictors to discriminate between relative properties and intrinsic properties.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present a sequence-based approach, DeepTrio, for PPI prediction using mask multiple parallel convolutional neural networks. Experimental evaluations show that DeepTrio achieves a better performance over several state-of-the-art methods in terms of various quality metrics. Besides, DeepTrio is extended to provide additional insights into the contribution of each input neuron to the prediction results.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>We provide an online application at http:\/\/bis.zju.edu.cn\/deeptrio. The DeepTrio models and training data are deposited at https:\/\/github.com\/huxiaoti\/deeptrio.git.<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btab737","type":"journal-article","created":{"date-parts":[[2021,10,20]],"date-time":"2021-10-20T22:51:23Z","timestamp":1634770283000},"page":"694-702","source":"Crossref","is-referenced-by-count":61,"title":["DeepTrio: a ternary prediction system for protein\u2013protein interaction using mask multiple parallel convolutional neural networks"],"prefix":"10.1093","volume":"38","author":[{"given":"Xiaotian","family":"Hu","sequence":"first","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Cong","family":"Feng","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Yincong","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University , Hangzhou 310058, China"}]},{"given":"Andrew","family":"Harrison","sequence":"additional","affiliation":[{"name":"Department of Mathematical Sciences, University of Essex , Colchester CO4 3SQ, UK"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9677-1699","authenticated-orcid":false,"given":"Ming","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Bioinformatics, College of Life Sciences, Zhejiang University , Hangzhou 310058, China"},{"name":"Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine; Institute of Hematology, Zhejiang University , Hangzhou 310058, China"}]}],"member":"286","published-online":{"date-parts":[[2021,10,25]]},"reference":[{"key":"2023020108481975100_btab737-B1","author":"Abadi","year":"2016"},{"key":"2023020108481975100_btab737-B2","doi-asserted-by":"crossref","first-page":"831","DOI":"10.1038\/nbt.3300","article-title":"Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning","volume":"33","author":"Alipanahi","year":"2015","journal-title":"Nat. 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