{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T04:59:59Z","timestamp":1762491599536,"version":"build-2065373602"},"publisher-location":"Cham","reference-count":43,"publisher":"Springer Nature Switzerland","isbn-type":[{"value":"9783032093202","type":"print"},{"value":"9783032093219","type":"electronic"}],"license":[{"start":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T00:00:00Z","timestamp":1762560000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"},{"start":{"date-parts":[[2025,11,8]],"date-time":"2025-11-08T00:00:00Z","timestamp":1762560000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springernature.com\/gp\/researchers\/text-and-data-mining"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026]]},"DOI":"10.1007\/978-3-032-09321-9_17","type":"book-chapter","created":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T04:58:12Z","timestamp":1762491492000},"page":"243-257","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["MOSL: Integrating Multi-omics and\u00a0Machine Learning to\u00a0Predict Synthetic Lethality in\u00a0Cancer Cell Lines"],"prefix":"10.1007","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6824-172X","authenticated-orcid":false,"given":"Tan","family":"Pham","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-3268-024X","authenticated-orcid":false,"given":"Dang","family":"Vu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-0405-8205","authenticated-orcid":false,"given":"Tien","family":"Dang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5249-9702","authenticated-orcid":false,"given":"Binh T.","family":"Nguyen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3291-2413","authenticated-orcid":false,"given":"Tuan-Anh","family":"Tran","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,11,8]]},"reference":[{"key":"17_CR1","doi-asserted-by":"crossref","unstructured":"Arik, S.\u00d6., Pfister, T.: TabNet: attentive interpretable tabular learning. In: Proceedings of the AAAI Conference on Artificial Intelligence, vol.\u00a035, pp. 6679\u20136687 (2021)","DOI":"10.1609\/aaai.v35i8.16826"},{"key":"17_CR2","doi-asserted-by":"crossref","unstructured":"Aspden, J.L., Wallace, E.W., Whiffin, N.: Not all exons are protein coding: addressing a common misconception. Cell Genom. 3(4) (2023)","DOI":"10.1016\/j.xgen.2023.100296"},{"key":"17_CR3","doi-asserted-by":"crossref","unstructured":"Bender, A., Pringle, J.R.: Use of a screen for synthetic lethal and multicopy suppressee mutants to identify two new genes involved in morphogenesis in saccharomyces cerevisiae. Mol. Cell. Biol. (1991)","DOI":"10.1128\/MCB.11.3.1295"},{"key":"17_CR4","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman, L.: Random forests. Mach. Learn. 45, 5\u201332 (2001)","journal-title":"Mach. Learn."},{"issue":"14","key":"17_CR5","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1097\/01.COT.0000544205.33140.b8","volume":"40","author":"SK Butler","year":"2018","unstructured":"Butler, S.K.: Niraparib (zejula\u00ae). Oncol. Times 40(14), 20 (2018)","journal-title":"Oncol. Times"},{"key":"17_CR6","doi-asserted-by":"crossref","unstructured":"Chen, T., Guestrin, C.: XGBoost: a scalable tree boosting system. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 785\u2013794 (2016)","DOI":"10.1145\/2939672.2939785"},{"issue":"12","key":"17_CR7","doi-asserted-by":"publisher","first-page":"1144","DOI":"10.1016\/j.cels.2021.08.006","volume":"12","author":"B De Kegel","year":"2021","unstructured":"De Kegel, B., Quinn, N., Thompson, N.A., Adams, D.J., Ryan, C.J.: Comprehensive prediction of robust synthetic lethality between paralog pairs in cancer cell lines. Cell Syst. 12(12), 1144\u20131159 (2021)","journal-title":"Cell Syst."},{"key":"17_CR8","doi-asserted-by":"publisher","unstructured":"DepMap, B.: DepMap 24Q4 Public (2024). https:\/\/doi.org\/10.25452\/figshare.plus.27993248.v1, https:\/\/plus.figshare.com\/articles\/dataset\/DepMap_24Q4_Public\/27993248","DOI":"10.25452\/figshare.plus.27993248.v1"},{"key":"17_CR9","unstructured":"Devlin, J.: BERT: pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805 (2018)"},{"key":"17_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman, R.C., et al.: Bioconductor: open software development for computational biology and bioinformatics. Genome Biol. 5, 1\u201316 (2004)","journal-title":"Genome Biol."},{"key":"17_CR11","doi-asserted-by":"crossref","unstructured":"G\u00f6kba\u011f, B., Tang, S., Fan, K., Cheng, L., Li, L.: SLKB: synthetic lethality knowledge base for gene combination double knockout experiments. Cancer Res. 83(7_Supplement), 6581 (2023)","DOI":"10.1158\/1538-7445.AM2023-6581"},{"issue":"D1","key":"17_CR12","doi-asserted-by":"publisher","first-page":"D1011","DOI":"10.1093\/nar\/gkv1108","volume":"44","author":"J Guo","year":"2016","unstructured":"Guo, J., Liu, H., Zheng, J.: SynlethDB: synthetic lethality database toward discovery of selective and sensitive anticancer drug targets. Nucleic Acids Res. 44(D1), D1011\u2013D1017 (2016)","journal-title":"Nucleic Acids Res."},{"issue":"5340","key":"17_CR13","doi-asserted-by":"publisher","first-page":"1064","DOI":"10.1126\/science.278.5340.1064","volume":"278","author":"LH Hartwell","year":"1997","unstructured":"Hartwell, L.H., Szankasi, P., Roberts, C.J., Murray, A.W., Friend, S.H.: Integrating genetic approaches into the discovery of anticancer drugs. Science 278(5340), 1064\u20131068 (1997)","journal-title":"Science"},{"issue":"4","key":"17_CR14","doi-asserted-by":"publisher","first-page":"18","DOI":"10.1109\/5254.708428","volume":"13","author":"MA Hearst","year":"1998","unstructured":"Hearst, M.A., Dumais, S.T., Osuna, E., Platt, J., Scholkopf, B.: Support vector machines. IEEE Intell. Syst. Appl. 13(4), 18\u201328 (1998)","journal-title":"IEEE Intell. Syst. Appl."},{"issue":"18","key":"17_CR15","doi-asserted-by":"publisher","first-page":"1939","DOI":"10.1007\/s40265-018-1026-z","volume":"78","author":"SM Hoy","year":"2018","unstructured":"Hoy, S.M.: Talazoparib: first global approval. Drugs 78(18), 1939\u20131946 (2018)","journal-title":"Drugs"},{"issue":"5","key":"17_CR16","doi-asserted-by":"publisher","first-page":"1199","DOI":"10.1016\/j.cell.2014.07.027","volume":"158","author":"L Jerby-Arnon","year":"2014","unstructured":"Jerby-Arnon, L., et al.: Predicting cancer-specific vulnerability via data-driven detection of synthetic lethality. Cell 158(5), 1199\u20131209 (2014)","journal-title":"Cell"},{"key":"17_CR17","doi-asserted-by":"crossref","unstructured":"Kang, M., Ko, E., Mersha, T.B.: A roadmap for multi-omics data integration using deep learning. Brief. Bioinform. 23(1), bbab454 (2022)","DOI":"10.1093\/bib\/bbab454"},{"key":"17_CR18","unstructured":"Kipf, T.N., Welling, M.: Semi-supervised classification with graph convolutional networks. arXiv preprint arXiv:1609.02907 (2016)"},{"key":"17_CR19","unstructured":"Lee, J., Dabagia, M., Dyer, E., Rozell, C.: Hierarchical optimal transport for multimodal distribution alignment. Adv. Neural Inf. Process. Syst. 32 (2019)"},{"issue":"1","key":"17_CR20","doi-asserted-by":"publisher","first-page":"2546","DOI":"10.1038\/s41467-018-04647-1","volume":"9","author":"JS Lee","year":"2018","unstructured":"Lee, J.S., et al.: Harnessing synthetic lethality to predict the response to cancer treatment. Nat. Commun. 9(1), 2546 (2018)","journal-title":"Nat. Commun."},{"key":"17_CR21","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1007\/s11064-017-2460-0","volume":"44","author":"JM Lim","year":"2019","unstructured":"Lim, J.M., Kim, G., Levine, R.L.: Methionine in proteins: it\u2019s not just for protein initiation anymore. Neurochem. Res. 44, 247\u2013257 (2019)","journal-title":"Neurochem. Res."},{"key":"17_CR22","unstructured":"Lin, Z., et\u00a0al.: Language models of protein sequences at the scale of evolution enable accurate structure prediction. bioRxiv (2022)"},{"issue":"6","key":"17_CR23","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1097\/01.COT.0000515192.91956.8f","volume":"39","author":"L Lohr","year":"2017","unstructured":"Lohr, L.: Rucaparib (rubraca\u00ae). Oncol. Times 39(6), 19 (2017)","journal-title":"Oncol. Times"},{"issue":"1","key":"17_CR24","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1093\/genetics\/59.1.37","volume":"59","author":"JC Lucchesi","year":"1968","unstructured":"Lucchesi, J.C.: Synthetic lethality and semi-lethality among functionally related mutants of drosophila melanogaster. Genetics 59(1), 37 (1968)","journal-title":"Genetics"},{"key":"17_CR25","doi-asserted-by":"publisher","first-page":"S19","DOI":"10.1016\/S0959-8049(02)80599-8","volume":"38","author":"P Manley","year":"2002","unstructured":"Manley, P., et al.: Imatinib: a selective tyrosine kinase inhibitor. Eur. J. Cancer 38, S19\u2013S27 (2002)","journal-title":"Eur. J. Cancer"},{"issue":"D1","key":"17_CR26","doi-asserted-by":"publisher","first-page":"D933","DOI":"10.1093\/nar\/gkac958","volume":"51","author":"FJ Martin","year":"2023","unstructured":"Martin, F.J., et al.: Ensembl 2023. Nucleic Acids Res. 51(D1), D933\u2013D941 (2023)","journal-title":"Nucleic Acids Res."},{"issue":"9","key":"17_CR27","doi-asserted-by":"publisher","first-page":"3276","DOI":"10.1073\/pnas.0813414106","volume":"106","author":"KJ McManus","year":"2009","unstructured":"McManus, K.J., Barrett, I.J., Nouhi, Y., Hieter, P.: Specific synthetic lethal killing of rad54b-deficient human colorectal cancer cells by FEN1 silencing. Proc. Natl. Acad. Sci. 106(9), 3276\u20133281 (2009)","journal-title":"Proc. Natl. Acad. Sci."},{"key":"17_CR28","unstructured":"Nguyen, D.M.H., et al.: LoGra-med: long context multi-graph alignment for medical vision-language model (2024). https:\/\/arxiv.org\/abs\/2410.02615"},{"issue":"10","key":"17_CR29","doi-asserted-by":"publisher","first-page":"613","DOI":"10.1038\/nrg.2017.47","volume":"18","author":"NJ O\u2019Neil","year":"2017","unstructured":"O\u2019Neil, N.J., Bailey, M.L., Hieter, P.: Synthetic lethality and cancer. Nat. Rev. Genet. 18(10), 613\u2013623 (2017)","journal-title":"Nat. Rev. Genet."},{"issue":"1","key":"17_CR30","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1002\/pro.3978","volume":"30","author":"R Oughtred","year":"2021","unstructured":"Oughtred, R., et al.: The biogrid database: a comprehensive biomedical resource of curated protein, genetic, and chemical interactions. Protein Sci. 30(1), 187\u2013200 (2021)","journal-title":"Protein Sci."},{"key":"17_CR31","doi-asserted-by":"crossref","unstructured":"Sacha, T.: Imatinib in chronic myeloid leukemia: an overview. Mediterr. J. Hematol. Infect. Dis. 6(1) (2014)","DOI":"10.4084\/mjhid.2014.007"},{"issue":"D1","key":"17_CR32","doi-asserted-by":"publisher","first-page":"D1021","DOI":"10.1093\/nar\/gks1170","volume":"41","author":"EE Schmidt","year":"2013","unstructured":"Schmidt, E.E., Pelz, O., Buhlmann, S., Kerr, G., Horn, T., Boutros, M.: GenomeRNAi: a database for cell-based and in vivo RNAi phenotypes, 2013 update. Nucleic Acids Res. 41(D1), D1021\u2013D1026 (2013)","journal-title":"Nucleic Acids Res."},{"key":"17_CR33","doi-asserted-by":"crossref","unstructured":"Sennrich, R.: Neural machine translation of rare words with subword units. arXiv preprint arXiv:1508.07909 (2015)","DOI":"10.18653\/v1\/P16-1162"},{"issue":"1","key":"17_CR34","doi-asserted-by":"publisher","first-page":"118","DOI":"10.1093\/genetics\/41.1.118","volume":"41","author":"A Sturtevant","year":"1956","unstructured":"Sturtevant, A.: A highly specific complementary lethal system in drosophila melanogaster. Genetics 41(1), 118 (1956)","journal-title":"Genetics"},{"key":"17_CR35","doi-asserted-by":"crossref","unstructured":"Suzek, B.E., Wang, Y., Huang, H., McGarvey, P.B., Wu, C.H., Consortium, U.: UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches. Bioinformatics 31(6), 926\u2013932 (2015)","DOI":"10.1093\/bioinformatics\/btu739"},{"key":"17_CR36","doi-asserted-by":"publisher","first-page":"961611","DOI":"10.3389\/fgene.2022.961611","volume":"13","author":"S Tang","year":"2022","unstructured":"Tang, S., et al.: Synthetic lethal gene pairs: experimental approaches and predictive models. Front. Genet. 13, 961611 (2022)","journal-title":"Front. Genet."},{"key":"17_CR37","unstructured":"Vaswani, A.: Attention is all you need. Adv. Neural Inf. Process. Syst. (2017)"},{"key":"17_CR38","doi-asserted-by":"crossref","unstructured":"Wang, J., Wu, M., Huang, X., Wang, L., Zhang, S., Liu, H., Zheng, J.: SynlethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. Database 2022, baac030 (2022)","DOI":"10.1093\/database\/baac030"},{"key":"17_CR39","doi-asserted-by":"crossref","unstructured":"Wu, M., Li, X., Zhang, F., Li, X., Kwoh, C.K., Zheng, J.: In silico prediction of synthetic lethality by meta-analysis of genetic interactions, functions, and pathways in yeast and human cancer. Cancer Inform. 13, CIN\u2013S14026 (2014)","DOI":"10.4137\/CIN.S14026"},{"issue":"9","key":"17_CR40","doi-asserted-by":"publisher","first-page":"4591","DOI":"10.1109\/JBHI.2023.3284794","volume":"27","author":"S Xiao","year":"2023","unstructured":"Xiao, S., Lin, H., Wang, C., Wang, S., Rajapakse, J.C.: Graph neural networks with multiple prior knowledge for multi-omics data analysis. IEEE J. Biomed. Health Inform. 27(9), 4591\u20134600 (2023)","journal-title":"IEEE J. Biomed. Health Inform."},{"key":"17_CR41","doi-asserted-by":"crossref","unstructured":"Yin, Z., Qian, B., Yang, G., Guo, L.: Predicting synthetic lethal genetic interactions in breast cancer using decision tree. In: Proceedings of the 2019 6th International Conference on Biomedical and Bioinformatics Engineering, pp.\u00a01\u20136 (2019)","DOI":"10.1145\/3375923.3375933"},{"key":"17_CR42","doi-asserted-by":"publisher","unstructured":"Zhou, X., Pappas, N., Smith, N.A.: Multilevel text alignment with cross-document attention. In: Webber, B., Cohn, T., He, Y., Liu, Y. (eds.) Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP), pp. 5012\u20135025. Association for Computational Linguistics, Online (2020). https:\/\/doi.org\/10.18653\/v1\/2020.emnlp-main.407, https:\/\/aclanthology.org\/2020.emnlp-main.407\/","DOI":"10.18653\/v1\/2020.emnlp-main.407"},{"key":"17_CR43","unstructured":"Zhou, Z., Ji, Y., Li, W., Dutta, P., Davuluri, R., Liu, H.: DNABERT-2: efficient foundation model and benchmark for multi-species genome (2023)"}],"container-title":["Lecture Notes in Computer Science","Computational Collective Intelligence"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-032-09321-9_17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T04:58:16Z","timestamp":1762491496000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-032-09321-9_17"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,11,8]]},"ISBN":["9783032093202","9783032093219"],"references-count":43,"URL":"https:\/\/doi.org\/10.1007\/978-3-032-09321-9_17","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,11,8]]},"assertion":[{"value":"8 November 2025","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"ICCCI","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Computational Collective Intelligence","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Ho Chi Minh City","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Vietnam","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2025","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"12 November 2025","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"15 November 2025","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"17","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iccci2025","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/iccci.pwr.edu.pl\/2025\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}