News & ViewsPublished: 22 July 2025Recovering biological networksDavid Gomez-Cabrero ORCID: orcid.org/0000-0003-4186-37881 &Jesper N. Tegnér ORCID: orcid.org/0000-0002-9568-55881,2,3,4 Nature Machine Intelligence (2025)Cite this articleSubjectsComputational modelsComputational platforms and environmentsA unified optimization framework, CORNETO, introduces a versatile approach to knowledge-driven biological network inference, bringing machine learning sensibilities to systems biology.This is a preview of subscription content, access via your institutionAccess optionsAccess Nature and 54 other Nature Portfolio journalsGet Nature+, our best-value online-access subscription27,99 € / 30 dayscancel any timeLearn moreSubscribe to this journalReceive 12 digital issues and online access to articles118,99 € per yearonly 9,92 € per issueLearn moreBuy this articlePurchase on SpringerLinkInstant access to full article PDFBuy nowPrices may be subject to local taxes which are calculated during checkoutFig. 1: An example of a knowledge-driven biological network inference challenge in metabolic profiling for a single sample and multiple samples.ReferencesRodriguez-Mier, P., Garrido-Rodriguez, M., Gabor, A. & Saez-Rodriguez, J. Nat. Mach. Intell. https://doi.org/10.1038/s42256-025-01069-9 (2025).Article Google Scholar Orth, J. D., Thiele, I. & Palsson, B. O. Nat. Biotechnol. 28, 245–248 (2010).Google Scholar Liu, A. et al. npj Syst. Biol. Appl. 5, 1–10 (2019).Google Scholar Fleming, R. M. T. et al. Bioinformatics 39, btad450 (2023).Google Scholar Mohammadi, S., Davila-Velderrain, J. & Kellis, M. Cell Syst. 9, 559–568.e4 (2019).Google Scholar Li, M. M. et al. Nat. Methods 21, 1546–1557 (2024).Google Scholar Download referencesAuthor informationAuthors and AffiliationsBiological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaDavid Gomez-Cabrero & Jesper N. TegnérUnit of Computational Medicine, Center for Molecular Medicine, Department of Medicine Solna, Karolinska Institutet, Stockholm, SwedenJesper N. TegnérComputer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi ArabiaJesper N. TegnérScience for Life Laboratory, Solna, SwedenJesper N. TegnérAuthorsDavid Gomez-CabreroView author publicationsSearch author on:PubMed Google ScholarJesper N. TegnérView author publicationsSearch author on:PubMed Google ScholarCorresponding authorCorrespondence to David Gomez-Cabrero.Ethics declarationsCompeting interestsThe authors declare no competing interests.Rights and permissionsReprints and permissionsAbout this article