{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,18]],"date-time":"2026-08-18T02:50:52Z","timestamp":1787021452485,"version":"build-2736575974"},"update-to":[{"DOI":"10.12688\/f1000research.166682.1","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000}},{"DOI":"10.12688\/f1000research.166682.2","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000}}],"reference-count":25,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T00:00:00Z","timestamp":1775779200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100012024","name":"Multimedia University","doi-asserted-by":"publisher","award":["GrantNo.MMUE\/240128"],"award-info":[{"award-number":["GrantNo.MMUE\/240128"]}],"id":[{"id":"10.13039\/100012024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100024160","name":"ASPIRE\u2014the technology programme management pillar of Abu Dhabi\u2019s Advanced Technology Research Council","doi-asserted-by":"publisher","award":["AwardnumberVRI-20-10"],"award-info":[{"award-number":["AwardnumberVRI-20-10"]}],"id":[{"id":"10.13039\/100024160","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100006013","name":"United Arab Emirates University","doi-asserted-by":"publisher","award":["GrantNo.12R111"],"award-info":[{"award-number":["GrantNo.12R111"]}],"id":[{"id":"10.13039\/501100006013","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["f1000research.com"],"crossmark-restriction":false},"short-container-title":["F1000Res"],"abstract":"<ns3:p>Background Breast cancer is a leading cause of mortality among women worldwide. Accurate survival prediction can improve clinical decision-making and support personalized treatment planning. This study aims to develop an interpretable and effective deep learning model for breast cancer survival prediction using multi-omics data. Methods This study proposes a novel deep learning model combining Bi-directional Long Short-Term Memory (BiLSTM) and Convolutional Neural Network (CNN) architectures, integrated with Minimum Redundancy Maximum Relevance (MRMR) feature selection. The model was evaluated on two large datasets: METABRIC (n=1980) and TCGA-BRCA (n=1080), using clinical, copy number alteration (CNA), and gene expression data. Performance was assessed through metrics such as AUC-ROC and accuracy. Results The proposed model demonstrated superior performance compared to existing algorithms, achieving high AUC-ROC and accuracy values across all data modalities. The integration of BiLSTM and CNN architectures allowed the model to capture temporal and spatial patterns, improving prediction robustness. Notably, the model achieved an accuracy of 98% on the METABRIC dataset and 96% on the TCGA dataset. Conclusions The combination of BiLSTM, CNN, and MRMR offers an interpretable and accurate framework for breast cancer survival prediction using multi-omics data. This approach provides actionable insights for clinicians and highlights its potential for broader applications in oncology.<\/ns3:p>","DOI":"10.12688\/f1000research.166682.3","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T12:04:07Z","timestamp":1775822647000},"page":"765","update-policy":"https:\/\/doi.org\/10.12688\/f1000research.crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["An Improved Deep Learning Algorithm for Breast Cancer Survival Prediction Based on Multi-Omics Data"],"prefix":"10.12688","volume":"14","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7684-4184","authenticated-orcid":false,"given":"Nurul Athirah","family":"Nasarudin","sequence":"first","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences Al Ain Abu Dhabi 17666 United Arab Emirates University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fatma","family":"Al-Jasmi","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences Al Ain Abu Dhabi 17666 United Arab Emirates University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7995-4912","authenticated-orcid":false,"given":"Nor Hidayati","family":"Abdul Aziz","sequence":"additional","affiliation":[{"name":"Centre for Advanced Analytics, CoE for Artificial Intelligence Malacca Malacca 75450 Multimedia University"},{"name":"Faculty of Engineering & Technology Malacca Malacca 75450 Multimedia University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2119-6191","authenticated-orcid":false,"given":"Nor Azlina","family":"Ab Aziz","sequence":"additional","affiliation":[{"name":"Centre for Advanced Analytics, CoE for Artificial Intelligence Malacca Malacca 75450 Multimedia University"},{"name":"Faculty of Engineering & Technology Malacca Malacca 75450 Multimedia University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wasif","family":"Khan","sequence":"additional","affiliation":[{"name":"J. Crayton Pruitt Family Department of Biomedical Engineering, Herbert Wertheim College of Engineering Gainesville Florida 32 611 University of Florida"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yusuf","family":"Hendrawan","sequence":"additional","affiliation":[{"name":"Department of Biosystems Engineering, Faculty of Agricultural Technology Malang East Java 65145 Universitas Brawijaya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dimas Firmanda","family":"Al Riza","sequence":"additional","affiliation":[{"name":"Department of Biosystems Engineering, Faculty of Agricultural Technology Malang East Java 65145 Universitas Brawijaya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ayisha","family":"Manzoor","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences Al Ain Abu Dhabi 17666 United Arab Emirates University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1306-6618","authenticated-orcid":false,"given":"Bassam R.","family":"Ali","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences Al Ain Abu Dhabi 17666 United Arab Emirates University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1079-4559","authenticated-orcid":false,"given":"Mohd Saberi","family":"Mohamad","sequence":"additional","affiliation":[{"name":"Department of Genetics and Genomics, College of Medicine and Health Sciences Al Ain Abu Dhabi 17666 United Arab Emirates University"},{"name":"Centre for Advanced Analytics, CoE for Artificial Intelligence Malacca Malacca 75450 Multimedia University"},{"name":"Department of Biosystems Engineering, Faculty of Agricultural Technology Malang East Java 65145 Universitas Brawijaya"},{"name":"Faculty of Engineering & Technology Malacca Malacca 75450 Multimedia University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"2560","published-online":{"date-parts":[[2026,4,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"394-424","DOI":"10.3322\/caac.21492","article-title":"Global cancer statistics 2018: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries.","volume":"68","author":"F Bray","year":"2018","journal-title":"CA Cancer J. Clin."},{"key":"ref2","doi-asserted-by":"publisher","first-page":"5748-5803","DOI":"10.18632\/aging.202502","article-title":"Global incidence and mortality of breast cancer: a trend analysis.","volume":"13","author":"J Huang","year":"Feb. 2021","journal-title":"Aging."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"497-507","DOI":"10.1007\/s10549-020-06003-8","article-title":"International variation in breast cancer incidence and mortality in young women.","volume":"186","author":"V Sopik","year":"Apr. 2021","journal-title":"Breast Cancer Res. Treat."},{"key":"ref4","first-page":"Art. no. 4","article-title":"Extracting Rules from Feed Forward Neural Networks for Diagnosing Breast Cancer.","volume":"1","author":"F Paulin","year":"2009","journal-title":"Artif. Intell. Syst. Mach. Learn."},{"key":"ref5","doi-asserted-by":"publisher","first-page":"2719-2725","DOI":"10.1016\/j.csbj.2021.04.067","article-title":"DeepOmix: A scalable and interpretable multi-omics deep learning framework and application in cancer survival analysis.","volume":"19","author":"L Zhao","year":"Jan. 2021","journal-title":"Comput. Struct. Biotechnol. 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Risk Manag."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"346-352","DOI":"10.1038\/nature10983","article-title":"The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups.","volume":"486","author":"C Curtis","year":"Jun. 2012","journal-title":"Nature."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"106965","DOI":"10.1016\/j.knosys.2021.106965","article-title":"Multi-modal advanced deep learning architectures for breast cancer survival prediction.","volume":"221","author":"N Arya","year":"Jun. 2021","journal-title":"Knowl.-Based Syst."},{"key":"ref14","doi-asserted-by":"publisher","first-page":"68-77","DOI":"10.5114\/wo.2014.47136","article-title":"Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge.","volume":"1A","author":"K Tomczak","year":"2015","journal-title":"Contemp. Oncol. Onkol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"28-42","DOI":"10.1007\/978-3-031-08757-8_3","volume":"13352","author":"F Moreno-Barea","year":"2022 Jun","journal-title":"International Conference on Computational Science."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"113","DOI":"10.1038\/s42003-025-07552-8","article-title":"Single-cell RNA-seq data augmentation using generative Fourier transformer.","volume":"8","author":"N Nouri","year":"2025 Jan 22","journal-title":"Commun. Biol."},{"key":"ref15","doi-asserted-by":"publisher","first-page":"i446-i454","DOI":"10.1093\/bioinformatics\/btz342","article-title":"Deep learning with multimodal representation for pancancer prognosis prediction.","volume":"35","author":"A Cheerla","year":"Jul. 2019","journal-title":"Bioinformatics."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"13505","DOI":"10.1038\/s41598-021-92799-4","article-title":"Long-term cancer survival prediction using multimodal deep learning.","volume":"11","author":"L Vale-Silva","year":"Jun. 2021","journal-title":"Sci. Rep."},{"key":"ref17","doi-asserted-by":"publisher","first-page":"5993-6012","DOI":"10.1007\/s00500-021-05590-y","article-title":"A new imputation method based on genetic programming and weighted KNN for symbolic regression with incomplete data.","volume":"25","author":"B Al-Helali","year":"Apr. 2021","journal-title":"Soft. Comput."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"2278-2324","DOI":"10.1109\/5.726791","article-title":"Gradient-based learning applied to document recognition.","volume":"86","author":"Y Lecun","year":"Nov. 1998","journal-title":"Proc. IEEE."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"1735-1780","DOI":"10.1162\/neco.1997.9.8.1735","article-title":"Long Short-Term Memory.","volume":"9","author":"S Hochreiter","year":"Nov. 1997","journal-title":"Neural Comput."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"105151","DOI":"10.1016\/j.engappai.2022.105151","article-title":"Ensemble deep learning: A review.","volume":"115","author":"M Ganaie","year":"Oct. 2022","journal-title":"Eng. Appl. Artif. Intell."},{"key":"ref22","doi-asserted-by":"publisher","DOI":"10.48550\/arXiv.1412.6980","article-title":"Adam: A Method for Stochastic Optimization.","author":"D Kingma","year":"Jan. 30, 2017"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"85760-85769","DOI":"10.1109\/ACCESS.2023.3304242","article-title":"Deep Learning-Based Multi-Modal Ensemble Classification Approach for Human Breast Cancer Prognosis.","volume":"11","author":"E Jadoon","year":"2023","journal-title":"IEEE Access."}],"container-title":["F1000Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/f1000research.com\/articles\/14-765\/v3\/xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/14-765\/v3\/pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/f1000research.com\/articles\/14-765\/v3\/iparadigms","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,27]],"date-time":"2026-05-27T08:24:10Z","timestamp":1779870250000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/articles\/14-765\/v3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,4,10]]},"references-count":25,"URL":"https:\/\/doi.org\/10.12688\/f1000research.166682.3","relation":{"has-version":[{"id-type":"doi","id":"10.12688\/f1000research.166682.2","asserted-by":"subject"},{"id-type":"doi","id":"10.12688\/f1000research.166682.1","asserted-by":"subject"}],"has-review":[{"id-type":"doi","id":"10.5256\/f1000research.197690.r476836","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.197690.r474661","asserted-by":"subject"},{"id-type":"doi","id":"10.5256\/f1000research.197690.r476836","asserted-by":"object"},{"id-type":"doi","id":"10.5256\/f1000research.197690.r474661","asserted-by":"object"}]},"ISSN":["2046-1402"],"issn-type":[{"value":"2046-1402","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,4,10]]},"assertion":[{"value":"Indexed","URL":"https:\/\/f1000research.com\/articles\/14-765\/v3#article-reports","order":0,"name":"referee-status","label":"Referee status","group":{"name":"current-referee-status","label":"Current Referee Status"}},{"value":"10.5256\/f1000research.187135.r410019, Weng Howe Chan, Universiti Teknologi Malaysia, Johor Bahru, 05 Sep 2025, version 2, 1 approved, 1 approved with reservations","URL":"https:\/\/f1000research.com\/articles\/14-765\/v2#referee-response-410019","order":0,"name":"referee-response-410019","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.197690.r474661, Suhaila Zainudin, Universiti Kebangsaan Malaysia, Bangi, Selangor, 27 Apr 2026, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/14-765\/v3#referee-response-474661","order":1,"name":"referee-response-474661","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"10.5256\/f1000research.197690.r476836, Toni Arifin, Universitas Adhirajasa Reswara Sanjaya, Bandung, 25 Apr 2026, version 3, indexed","URL":"https:\/\/f1000research.com\/articles\/14-765\/v3#referee-response-476836","order":2,"name":"referee-response-476836","label":"Referee Report","group":{"name":"article-reports","label":"Article Reports"}},{"value":"This work was supported by the United Arab Emirates University through the Strategic Research Program (Grant No. 12R111) and the Fisabilillah Research Development Grant Scheme (Grant No. MMUE\/240128) awarded by Multimedia University. Additional support was provided by ASPIRE\u2014the technology programme management pillar of Abu Dhabi\u2019s Advanced Technology Research Council (ATRC)\u2014through the ASPIRE Precision Medicine Research Institute Abu Dhabi (ASPIRE-PMRIAD) under award number VRI-20-10.","order":3,"name":"grant-information","label":"Grant Information"},{"value":"This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.","order":0,"name":"copyright-info","label":"Copyright"}]}}