{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,25]],"date-time":"2026-03-25T02:33:22Z","timestamp":1774406002078,"version":"3.50.1"},"reference-count":23,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2024,11,5]],"date-time":"2024-11-05T00:00:00Z","timestamp":1730764800000},"content-version":"vor","delay-in-days":4,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000060","name":"National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["AI134678"],"award-info":[{"award-number":["AI134678"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,11,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Accurate protein function prediction is crucial for understanding biological processes and advancing biomedical research. However, the rapid growth of protein sequences far outpaces the experimental characterization of their functions, necessitating the development of automated computational methods.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We present InterLabelGO+, a hybrid approach that integrates a deep learning-based method with an alignment-based method for improved protein function prediction. InterLabelGO+ incorporates a novel loss function that addresses label dependency and imbalance and further enhances performance through dynamic weighting of the alignment-based component. A preliminary version of InterLabelGO+ achieved a strong performance in the CAFA5 challenge, ranking sixth out of 1625 participating teams. Comprehensive evaluations on large-scale protein function prediction tasks demonstrate InterLabelGO+\u2019s ability to accurately predict Gene Ontology terms across various functional categories and evaluation metrics.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The source code and datasets for InterLabelGO+ are freely available on GitHub at https:\/\/github.com\/QuanEvans\/InterLabelGO. A web-server is available at https:\/\/seq2fun.dcmb.med.umich.edu\/InterLabelGO\/. The software is implemented in Python and PyTorch, and is supported on Linux and macOS.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btae655","type":"journal-article","created":{"date-parts":[[2024,11,2]],"date-time":"2024-11-02T00:21:20Z","timestamp":1730506880000},"source":"Crossref","is-referenced-by-count":8,"title":["InterLabelGO+: unraveling label correlations in protein function prediction"],"prefix":"10.1093","volume":"40","author":[{"given":"Quancheng","family":"Liu","sequence":"first","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor, MI, 48109,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7290-1324","authenticated-orcid":false,"given":"Chengxin","family":"Zhang","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor, MI, 48109,","place":["USA"]},{"name":"Department of Biological Chemistry , University of Michigan , Ann Arbor, MI, 48109,","place":["USA"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5821-4226","authenticated-orcid":false,"given":"Lydia","family":"Freddolino","sequence":"additional","affiliation":[{"name":"Department of Computational Medicine and Bioinformatics , University of Michigan , Ann Arbor, MI, 48109,","place":["USA"]},{"name":"Department of Biological Chemistry , University of Michigan , Ann Arbor, MI, 48109,","place":["USA"]}]}],"member":"286","published-online":{"date-parts":[[2024,11,5]]},"reference":[{"key":"2024111606014854700_btae655-B1","article-title":"The gene ontology knowledgebase in 2023","volume":"224","author":"Aleksander","year":"2023","journal-title":"Genetics"},{"key":"2024111606014854700_btae655-B2","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene ontology: tool for the unification of biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat 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