{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,7]],"date-time":"2026-08-07T02:44:15Z","timestamp":1786070655464,"version":"3.56.0"},"reference-count":27,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T00:00:00Z","timestamp":1784937600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/2.zoppoz.workers.dev:443\/https\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Yuelushan Laboratory Breeding Program","award":["YLS-2026-ZY01001"],"award-info":[{"award-number":["YLS-2026-ZY01001"]}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62432011"],"award-info":[{"award-number":["62432011"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["62450002"],"award-info":[{"award-number":["62450002"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,8,3]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The scalable identification of bioactive compounds is essential for contemporary drug discovery. This process faces a key trade-off: structural screening offers scalability but lacks biological context, whereas high-content phenotypic profiling provides deep biological insights but is resource-intensive. The primary challenge is to extract robust biological signals from noisy data and encode them into representations that do not require biological data at inference.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>This study presents DECODE (DEcomposing Cellular Observations of Drug Effects), a framework that bridges this gap by empowering chemical representations with intrinsic biological semantics to enable structure-based in silico biological profiling. DECODE leverages limited paired transcriptomic and morphological data as supervisory signals during training, enabling the extraction of a measurement-invariant biological fingerprint from chemical structures and explicit filtering of modality-specific variation. Across held-out retrieval, scaffold-split and UMAP-clustering virtual-screening benchmarks, DECODE improves functional retrieval and early active-compound prioritization over baselines.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The codes and datasets of DECODE are available at https:\/\/2.zoppoz.workers.dev:443\/https\/github.com\/lian-xiao\/DECODE.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag517","type":"journal-article","created":{"date-parts":[[2026,7,25]],"date-time":"2026-07-25T11:36:30Z","timestamp":1784979390000},"source":"Crossref","is-referenced-by-count":0,"title":["Empowering chemical structures with biological insights for scalable phenotypic virtual screening"],"prefix":"10.1093","volume":"42","author":[{"given":"Xiaoqing","family":"Lian","sequence":"first","affiliation":[{"name":"State Key Laboratory 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Changsha 410128,","place":["China"]},{"name":"The Ministry of Education Key Laboratory of Fusion Computing of Supercomputing and Artificial Intelligence, Hunan University , Changsha 410082,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/2.zoppoz.workers.dev:443\/https\/orcid.org\/0009-0002-2656-6566","authenticated-orcid":false,"given":"Xibao","family":"Cai","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Chemo and Biosensing, College of Computer Science and Electronic Engineering, Hunan University , Changsha 410082,","place":["China"]},{"name":"Yuelushan Laboratory , Changsha 410128,","place":["China"]},{"name":"The Ministry of Education Key Laboratory of Fusion Computing of Supercomputing and Artificial Intelligence, Hunan University , Changsha 410082,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhixiang","family":"Cheng","sequence":"additional","affiliation":[{"name":"State 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