{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,23]],"date-time":"2026-09-23T18:29:19Z","timestamp":1790188159120,"version":"4.1.0"},"reference-count":47,"publisher":"Oxford University Press (OUP)","issue":"Supplement_1","license":[{"start":{"date-parts":[[2022,6,27]],"date-time":"2022-06-27T00:00:00Z","timestamp":1656288000000},"content-version":"vor","delay-in-days":3,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Canadian Institute for Advanced Research AI","award":["RGPIN-2020-06189"],"award-info":[{"award-number":["RGPIN-2020-06189"]}]},{"name":"Canadian Institute for Advanced Research AI","award":["DGECR-2020-00294"],"award-info":[{"award-number":["DGECR-2020-00294"]}]},{"name":"NSERC Discovery Grant","award":["RGPIN-2018-06300"],"award-info":[{"award-number":["RGPIN-2018-06300"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,6,24]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>Molecular carcinogenicity is a preventable cause of cancer, but systematically identifying carcinogenic compounds, which involves performing experiments on animal models, is expensive, time consuming and low throughput. As a result, carcinogenicity information is limited and building data-driven models with good prediction accuracy remains a major challenge.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we propose CONCERTO, a deep learning model that uses a graph transformer in conjunction with a molecular fingerprint representation for carcinogenicity prediction from molecular structure. Special efforts have been made to overcome the data size constraint, such as multi-round pre-training on related but lower quality mutagenicity data, and transfer learning from a large self-supervised model. Extensive experiments demonstrate that our model performs well and can generalize to external validation sets. CONCERTO could be useful for guiding future carcinogenicity experiments and provide insight into the molecular basis of carcinogenicity.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The code and data underlying this article are available on github at https:\/\/github.com\/bowang-lab\/CONCERTO<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac266","type":"journal-article","created":{"date-parts":[[2022,4,14]],"date-time":"2022-04-14T07:10:15Z","timestamp":1649920215000},"page":"i84-i91","source":"Crossref","is-referenced-by-count":33,"title":["A graph neural network approach for molecule carcinogenicity prediction"],"prefix":"10.1093","volume":"38","author":[{"given":"Philip","family":"Fradkin","sequence":"first","affiliation":[{"name":"Department of Electrical & Computer Engineering, University of Toronto , Toronto, ON M5S 3G8, Canada"},{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Adamo","family":"Young","sequence":"additional","affiliation":[{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lazar","family":"Atanackovic","sequence":"additional","affiliation":[{"name":"Department of Electrical & Computer Engineering, University of Toronto , Toronto, ON M5S 3G8, Canada"},{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brendan","family":"Frey","sequence":"additional","affiliation":[{"name":"Department of Electrical & Computer Engineering, University of Toronto , Toronto, ON M5S 3G8, Canada"},{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Leo J","family":"Lee","sequence":"additional","affiliation":[{"name":"Department of Electrical & Computer Engineering, University of Toronto , Toronto, ON M5S 3G8, Canada"},{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Wang","sequence":"additional","affiliation":[{"name":"Vector Institute , Toronto, ON M5G 1M1, Canada"},{"name":"Department of Computer Science, University of Toronto , Toronto, ON M5S 2E4, Canada"},{"name":"Laboratory Medicine and Pathobiology, University of Toronto , Toronto, ON M5S 1A8, Canada"},{"name":"Peter Munk Cardiac Center, UHN , Toronto, ON M5G 2N2, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,6,27]]},"reference":[{"key":"2023041407565729900_","author":"Agarap","year":"2018"},{"key":"2023041407565729900_","doi-asserted-by":"crossref","first-page":"357","DOI":"10.2307\/2532549","article-title":"An index of tumorigenic potency","volume":"49","author":"Bailer","year":"1993","journal-title":"Biometrics"},{"key":"2023041407565729900_","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1038\/s41588-020-00727-5","article-title":"The critical roles of somatic mutations and environmental tumor-promoting agents in cancer risk","volume":"52","author":"Balmain","year":"2020","journal-title":"Nat. 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