{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T20:28:47Z","timestamp":1772915327912,"version":"3.50.1"},"reference-count":32,"publisher":"World Scientific Pub Co Pte Ltd","issue":"01","funder":[{"DOI":"10.13039\/501100014188","name":"Ministry of Science and ICT, South Korea","doi-asserted-by":"publisher","award":["RS-2023-00208892"],"award-info":[{"award-number":["RS-2023-00208892"]}],"id":[{"id":"10.13039\/501100014188","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2026,2]]},"abstract":"<jats:p>Predicting metastasis in early stages of cancer plays a crucial role in effectively controlling cancer progression and thereby improving patient survival outcomes. Although several computational methods have been developed to predict cancer metastasis, most focus on lymph node metastasis. Distant metastasis is more difficult to detect or predict than lymph node metastasis. In this study, we developed a multilayer perceptron (MLP) model to predict distant cancer metastases. We constructed a weighted gene interaction network and computed sample-specific differential gene correlations for individual cancer samples. The MLP model was trained on sample-specific differential gene correlations and tested on independent datasets of differential gene correlations from samples that were not used in training the model. The MLP model is capable of predicting whether or not distant metastasis will occur and potential distant metastatic sites. In independent testing, it predicted distant metastasis with a high performance (AUC of 0.95) and predicted metastatic sites with an average AUC of 0.97. In comparison of our model with other state-of-the-art methods using the same data set, our model showed better performance than the others. The prediction model developed in this study may help clinicians determine site-specific testing and treatment options.<\/jats:p>","DOI":"10.1142\/s0219720025500246","type":"journal-article","created":{"date-parts":[[2025,11,28]],"date-time":"2025-11-28T10:20:24Z","timestamp":1764325224000},"source":"Crossref","is-referenced-by-count":0,"title":["Predicting distant cancer metastasis using a weighted gene interaction network and sample-specific differential correlations"],"prefix":"10.1142","volume":"24","author":[{"ORCID":"https:\/\/orcid.org\/0009-0002-3515-3421","authenticated-orcid":false,"given":"Jiahui","family":"Kang","sequence":"first","affiliation":[{"name":"Department of Computer Engineering, Inha University, 100 Inha-ro, Incheon 22212, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9900-6741","authenticated-orcid":false,"given":"Kyungsook","family":"Han","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, Inha University, 100 Inha-ro, Incheon 22212, Republic of Korea"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"219","published-online":{"date-parts":[[2026,2,17]]},"reference":[{"issue":"16","key":"S0219720025500246BIB001","doi-asserted-by":"crossref","first-page":"3029","DOI":"10.1002\/cncr.33587","volume":"127","author":"Bray F","year":"2021","journal-title":"Cancer"},{"issue":"3","key":"S0219720025500246BIB002","first-page":"229","volume":"74","author":"Bray F","year":"2024","journal-title":"CA: Cancer J Clin"},{"issue":"5","key":"S0219720025500246BIB003","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1016\/j.apsb.2015.07.005","volume":"5","author":"Guan X","year":"2015","journal-title":"Acta Pharma Sin B"},{"issue":"1","key":"S0219720025500246BIB004","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1038\/s41591-020-01195-4","volume":"27","author":"Ganesh K","year":"2021","journal-title":"Nat Med"},{"issue":"1","key":"S0219720025500246BIB005","doi-asserted-by":"crossref","first-page":"1519","DOI":"10.1038\/s41467-024-45307-x","volume":"15","author":"Mani K","year":"2024","journal-title":"Nat Commun"},{"key":"S0219720025500246BIB006","doi-asserted-by":"crossref","first-page":"36","DOI":"10.3389\/fonc.2018.00036","volume":"8","author":"Jones D","year":"2018","journal-title":"Front Oncol"},{"issue":"14","key":"S0219720025500246BIB007","doi-asserted-by":"crossref","first-page":"2942","DOI":"10.1200\/JCO.2004.08.181","volume":"22","author":"Hamaoka T","year":"2004","journal-title":"J Clin Oncol"},{"issue":"2","key":"S0219720025500246BIB008","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1002\/pros.1053","volume":"47","author":"Djavan B","year":"2001","journal-title":"The Prostate"},{"issue":"3421","key":"S0219720025500246BIB009","doi-asserted-by":"crossref","first-page":"571","DOI":"10.1016\/S0140-6736(00)49915-0","volume":"133","author":"Paget S","year":"1889","journal-title":"The Lancet"},{"key":"S0219720025500246BIB010","doi-asserted-by":"crossref","first-page":"913602","DOI":"10.3389\/fmolb.2022.913602","volume":"9","author":"Albaradei S","year":"2022","journal-title":"Front Mol Biosci"},{"key":"S0219720025500246BIB011","doi-asserted-by":"crossref","unstructured":"Jha A, Khan Y, Sahay R, d\u2019Aquin M, Metastatic site prediction in breast cancer using omics knowledge graph and pattern mining with Kirchhoff\u2019s law traversal, bioRxiv, 2020.","DOI":"10.1101\/2020.07.14.203208"},{"issue":"5","key":"S0219720025500246BIB012","doi-asserted-by":"crossref","first-page":"473","DOI":"10.2174\/0115748936338628241104110200","volume":"20","author":"Mamatkarimov D","year":"2025","journal-title":"Curr Bioinform"},{"issue":"12","key":"S0219720025500246BIB013","doi-asserted-by":"crossref","first-page":"e1000601","DOI":"10.1371\/journal.pcbi.1000601","volume":"5","author":"Kar G","year":"2009","journal-title":"PLoS Comput Biol"},{"issue":"10","key":"S0219720025500246BIB014","doi-asserted-by":"crossref","first-page":"1113","DOI":"10.1038\/ng.2764","volume":"45","author":"Weinstein JN","year":"2013","journal-title":"Nat Genet"},{"issue":"1","key":"S0219720025500246BIB015","doi-asserted-by":"crossref","first-page":"D730","DOI":"10.1093\/nar\/gkae1113","volume":"53","author":"Szklarczyk D","year":"2025","journal-title":"Nucl Acids Res"},{"key":"S0219720025500246BIB016","doi-asserted-by":"crossref","DOI":"10.1037\/11491-005","volume-title":"The Proof and Measurement of Association between Two Things","author":"Spearman C","year":"1961"},{"key":"S0219720025500246BIB017","first-page":"1","volume":"1695","author":"Csardi G","year":"2006","journal-title":"Complex Syst"},{"issue":"11","key":"S0219720025500246BIB018","doi-asserted-by":"crossref","first-page":"3747","DOI":"10.1073\/pnas.0400087101","volume":"101","author":"Barrat A","year":"2004","journal-title":"Proc Natl Acad Sci"},{"key":"S0219720025500246BIB019","doi-asserted-by":"crossref","DOI":"10.1103\/PhysRevE.70.056131","volume-title":"Analysis of Weighted Networks","author":"Newman MEJ","year":"2004"},{"issue":"1","key":"S0219720025500246BIB020","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1080\/0022250X.1972.9989806","volume":"2","author":"Bonacich P","year":"1972","journal-title":"J Math Sociol"},{"issue":"4","key":"S0219720025500246BIB021","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1007\/BF02289527","volume":"31","author":"Sabidussi G","year":"1966","journal-title":"Psychometrika"},{"issue":"2","key":"S0219720025500246BIB022","doi-asserted-by":"crossref","first-page":"163","DOI":"10.1080\/0022250X.2001.9990249","volume":"25","author":"Brandes U","year":"2001","journal-title":"J Math Sociol"},{"key":"S0219720025500246BIB023","doi-asserted-by":"crossref","first-page":"107965","DOI":"10.1016\/j.patcog.2021.107965","volume":"118","author":"Tarekegn AN","year":"2021","journal-title":"Pattern Recognit"},{"key":"S0219720025500246BIB024","first-page":"1301","volume-title":"2008 IEEE Int Joint Conf Neural Networks (IEEE World Congress on Computational Intelligence)","author":"Tepvorachai G","year":"2008"},{"key":"S0219720025500246BIB025","doi-asserted-by":"crossref","DOI":"10.1007\/b107408","volume-title":"Data Mining and Knowledge Discovery Handbook","volume":"2","author":"Maimon O","year":"2005"},{"issue":"9","key":"S0219720025500246BIB026","doi-asserted-by":"crossref","first-page":"1757","DOI":"10.1016\/j.patcog.2004.03.009","volume":"37","author":"Boutell MR","year":"2004","journal-title":"Pattern Recognit"},{"issue":"3","key":"S0219720025500246BIB027","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1007\/s10994-011-5256-5","volume":"85","author":"Read J","year":"2011","journal-title":"Mach Learn"},{"issue":"1","key":"S0219720025500246BIB028","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1186\/s12859-023-05578-5","volume":"24","author":"Behdenna A","year":"2023","journal-title":"BMC Bioinform"},{"issue":"4","key":"S0219720025500246BIB029","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1145\/2523813","volume":"46","author":"Gama J","year":"2014","journal-title":"ACM Comput Surv"},{"key":"S0219720025500246BIB030","unstructured":"Brown O, Curtis A, Goodwin J, Principles for evaluation of AI\/ML model performance and robustness, preprint, arXiv:2107.02868, 2021."},{"issue":"11","key":"S0219720025500246BIB031","doi-asserted-by":"crossref","first-page":"2498","DOI":"10.1101\/gr.1239303","volume":"13","author":"Shannon P","year":"2003","journal-title":"Genome Res"},{"key":"S0219720025500246BIB032","first-page":"4765","volume-title":"Advances in Neural Information Processing Systems","author":"Lundberg SM","year":"2017"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720025500246","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,3,7]],"date-time":"2026-03-07T02:59:19Z","timestamp":1772852359000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/10.1142\/S0219720025500246"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,2]]},"references-count":32,"journal-issue":{"issue":"01","published-print":{"date-parts":[[2026,2]]}},"alternative-id":["10.1142\/S0219720025500246"],"URL":"https:\/\/doi.org\/10.1142\/s0219720025500246","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,2]]},"article-number":"2550024"}}