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To address this problem, extensive research efforts have been made to extract predefined features from the sequences. Based on these features, statistical algorithms are learned to classify the PPIs. However, such explicit features are usually costly to extract, and typically have limited coverage on the PPI information.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present an end-to-end framework, PIPR (Protein\u2013Protein Interaction Prediction Based on Siamese Residual RCNN), for PPI predictions using only the protein sequences. PIPR incorporates a deep residual recurrent convolutional neural network in the Siamese architecture, which leverages both robust local features and contextualized information, which are significant for capturing the mutual influence of proteins sequences. PIPR relieves the data pre-processing efforts that are required by other systems, and generalizes well to different application scenarios. Experimental evaluations show that PIPR outperforms various state-of-the-art systems on the binary PPI prediction problem. Moreover, it shows a promising performance on more challenging problems of interaction type prediction and binding affinity estimation, where existing approaches fall short.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The implementation is available at https:\/\/github.com\/muhaochen\/seq_ppi.git.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btz328","type":"journal-article","created":{"date-parts":[[2019,5,10]],"date-time":"2019-05-10T07:32:12Z","timestamp":1557473532000},"page":"i305-i314","source":"Crossref","is-referenced-by-count":336,"title":["Multifaceted protein\u2013protein interaction prediction based on Siamese residual RCNN"],"prefix":"10.1093","volume":"35","author":[{"given":"Muhao","family":"Chen","sequence":"first","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Chelsea J -T","family":"Ju","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Guangyu","family":"Zhou","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Xuelu","family":"Chen","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Tianran","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Kai-Wei","family":"Chang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Carlo","family":"Zaniolo","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]},{"given":"Wei","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA"}]}],"member":"286","published-online":{"date-parts":[[2019,7,5]]},"reference":[{"key":"2023062712360005700_btz328-B1","doi-asserted-by":"crossref","first-page":"3389","DOI":"10.1093\/nar\/25.17.3389","article-title":"Gapped BLAST and PSI-BLAST: a new generation of protein database search programs","volume":"25","author":"Altschul","year":"1997","journal-title":"Nucleic Acids Res"},{"key":"2023062712360005700_btz328-B2","doi-asserted-by":"crossref","first-page":"33","DOI":"10.1089\/clinomi.05.01.21","article-title":"Google\u2019s AI tool deepvariant promises significantly fewer genome errors","volume":"5","author":"Anderson","year":"2018","journal-title":"Clinical OMICs"},{"key":"2023062712360005700_btz328-B3","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J.\u00a0R. 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