{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T18:16:23Z","timestamp":1787940983820,"version":"build-2784847793"},"reference-count":31,"publisher":"Oxford University Press (OUP)","issue":"8","license":[{"start":{"date-parts":[[2026,8,10]],"date-time":"2026-08-10T00:00:00Z","timestamp":1786320000000},"content-version":"vor","delay-in-days":9,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"the National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62302495"],"award-info":[{"award-number":["62302495"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001809","name":"the National Natural Science Foundation of China","doi-asserted-by":"crossref","award":["62373348"],"award-info":[{"award-number":["62373348"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"crossref"}]},{"name":"the Natural Science Foundation of Xinjiang Uygur Autonomous Region","award":["2023D01E15"],"award-info":[{"award-number":["2023D01E15"]}]},{"name":"the Xinjiang Tianchi Talents Program","award":["E33B9401"],"award-info":[{"award-number":["E33B9401"]}]},{"name":"the Tianshan Talent Training Program","award":["2023TSYCLJ0021"],"award-info":[{"award-number":["2023TSYCLJ0021"]}]}],"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>Drug repositioning accelerates clinical translation by identifying new therapeutic indications for approved drugs. However, therapeutic associations in biomolecular networks often exist indirectly, through transitive chains and long-range mechanisms, rather than as directly observed links. Shallow methods are confined to direct similarity and miss such indirect associations, whereas deep graph neural networks suffer from over-smoothing and lose discriminative power in highly connected networks.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We propose a spatial-spectral collaborative framework. In the spatial domain, a wave-evolution process propagates similarity from local to global, capturing multi-hop transitive associations while preserving discriminative representations. In the spectral domain, network-specific spectral transforms model global connectivity for long-range dependencies over homogeneous similarity and heterogeneous drug-protein-disease networks, with the two views aligned by contrastive learning. On three benchmarks the method outperforms state-of-the-art baselines on most evaluation metrics; case studies on Alzheimer\u2019s and Parkinson\u2019s disease and molecular docking confirm its ability to recover non-explicit therapeutic associations.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability<\/jats:title>\n                    <jats:p>The source code and data are available at https:\/\/github.com\/Juniper-cola\/BIO_SSF.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btag553","type":"journal-article","created":{"date-parts":[[2026,8,9]],"date-time":"2026-08-09T11:33:12Z","timestamp":1786275192000},"source":"Crossref","is-referenced-by-count":0,"title":["Spatial-spectral fusion enables drug repositioning by capturing indirect and long-range associations in biological networks"],"prefix":"10.1093","volume":"42","author":[{"given":"Xiaobo","family":"Zhu","sequence":"first","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Urumqi 810011,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0184-307X","authenticated-orcid":false,"given":"Lei","family":"Wang","sequence":"additional","affiliation":[{"name":"China University of Mining and Technology , Xuzhou,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Runzhou","family":"Tang","sequence":"additional","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Urumqi 810011,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9974-148X","authenticated-orcid":false,"given":"Zhi-An","family":"Huang","sequence":"additional","affiliation":[{"name":"Research Office, City University of Hong Kong (Dongguan) , Dongguan 523000,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yu-an","family":"Huang","sequence":"additional","affiliation":[{"name":"School of Computing, Northwestern Polytechnical University , Xi\u2019an 710129,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Feng","family":"Tan","sequence":"additional","affiliation":[{"name":"AI and Quantum Lab , Darmstadt,","place":["Germany"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1591-8549","authenticated-orcid":false,"given":"Lun","family":"Hu","sequence":"additional","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Urumqi 810011,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhuhong","family":"You","sequence":"additional","affiliation":[{"name":"School of Computing, Northwestern Polytechnical University , Xi\u2019an 710129,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5974-7932","authenticated-orcid":false,"given":"Pengwei","family":"Hu","sequence":"additional","affiliation":[{"name":"Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences , Urumqi 810011,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,8,10]]},"reference":[{"key":"2026082813192803000_btag553-B1","doi-asserted-by":"crossref","first-page":"bbab319","DOI":"10.1093\/bib\/bbab319","article-title":"Drug repositioning based on the heterogeneous information fusion graph 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