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This article introduces a deep convolutional neural network (DCNN) equipped with various feature embeddings to battle the limitations of the existing machine learning-based PPI extraction methods. The proposed model learns and optimises word embeddings based on the publicly available word vectors and also exploits position embeddings to identify the locations of the target protein names in sentences. Furthermore, it can employ various linguistic feature embeddings to improve the PPI extraction. The intensive experiments using AIMed data set known as the most difficult collection not only show the superiority of the suggested model but also indicate important implications in optimising the network parameters and hyperparameters.<\/jats:p>","DOI":"10.1177\/0165551516673485","type":"journal-article","created":{"date-parts":[[2016,11,14]],"date-time":"2016-11-14T21:25:12Z","timestamp":1479158712000},"page":"60-73","update-policy":"https:\/\/doi.org\/10.1177\/sage-journals-update-policy","source":"Crossref","is-referenced-by-count":38,"title":["Extraction of protein\u2013protein interactions (PPIs) from the literature by deep convolutional neural networks with various feature embeddings"],"prefix":"10.1177","volume":"44","author":[{"given":"Sung-Pil","family":"Choi","sequence":"first","affiliation":[{"name":"Department of Library and Information Science, Kyonggi University, South Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"179","published-online":{"date-parts":[[2016,11,1]]},"reference":[{"key":"bibr1-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.artmed.2004.07.016"},{"key":"bibr2-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2007.11.008"},{"key":"bibr3-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-9-S11-S2"},{"key":"bibr4-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.ijmedinf.2009.04.010"},{"key":"bibr5-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000837"},{"key":"bibr6-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.jbi.2012.02.004"},{"key":"bibr7-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.ymeth.2015.03.026"},{"key":"bibr8-0165551516673485","doi-asserted-by":"publisher","DOI":"10.1016\/j.ipm.2007.07.013"},{"key":"bibr9-0165551516673485","first-page":"298473","volume":"2014","author":"Zhou D","year":"2014","journal-title":"Comput Math Method M"},{"key":"bibr10-0165551516673485","unstructured":"Hendrickx I, Kim SN, Kozareva Z, et al. 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