{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T23:38:25Z","timestamp":1761176305743,"version":"build-2065373602"},"reference-count":0,"publisher":"IOS Press","isbn-type":[{"value":"9781643686318","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,10,21]],"date-time":"2025-10-21T00:00:00Z","timestamp":1761004800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,10,21]]},"abstract":"<jats:p>Understanding protein functions enables deciphering cellular mechanisms and improving healthcare outcomes, from disease diagnosis to targeted therapy. We present GOMIX, an ensemble learning method for predicting the functions of newly discovered proteins, packaged within an easy-to-use web application. By combining seven complementary base predictors\u2013including sequence homology and protein language models, GOMIX achieves competitive or state-of-the-art performance in the CAFA-3 challenge. Unlike existing solutions, GOMIX is entirely open-source, modular, and computationally low-resource. The code is publicly available at https:\/\/github.com\/disi-unibo-nlp\/gomix (MIT License).<\/jats:p>","DOI":"10.3233\/faia251439","type":"book-chapter","created":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T10:02:30Z","timestamp":1761127350000},"source":"Crossref","is-referenced-by-count":0,"title":["Predicting Protein Functions with Ensemble Deep Learning and Protein Language Models"],"prefix":"10.3233","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9845-0231","authenticated-orcid":false,"given":"Giacomo","family":"Frisoni","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering (DISI), University of Bologna, Cesena Campus, Via dell\u2019Universit\u00e0 50, I-47522 Cesena, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1834-953X","authenticated-orcid":false,"given":"Marcello","family":"Fuschi","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering (DISI), University of Bologna, Cesena Campus, Via dell\u2019Universit\u00e0 50, I-47522 Cesena, Italy"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3663-7877","authenticated-orcid":false,"given":"Gianluca","family":"Moro","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering (DISI), University of Bologna, Cesena Campus, Via dell\u2019Universit\u00e0 50, I-47522 Cesena, Italy"}]}],"member":"7437","container-title":["Frontiers in Artificial Intelligence and Applications","ECAI 2025"],"original-title":[],"link":[{"URL":"https:\/\/ebooks.iospress.nl\/pdf\/doi\/10.3233\/FAIA251439","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,22]],"date-time":"2025-10-22T10:02:31Z","timestamp":1761127351000},"score":1,"resource":{"primary":{"URL":"https:\/\/ebooks.iospress.nl\/doi\/10.3233\/FAIA251439"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,10,21]]},"ISBN":["9781643686318"],"references-count":0,"URL":"https:\/\/doi.org\/10.3233\/faia251439","relation":{},"ISSN":["0922-6389","1879-8314"],"issn-type":[{"value":"0922-6389","type":"print"},{"value":"1879-8314","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,10,21]]}}}