{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T23:44:59Z","timestamp":1791935099675,"version":"4.3.4"},"reference-count":0,"publisher":"IOP Publishing","license":[{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"am","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T00:00:00Z","timestamp":1791849600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/iopscience.iop.org\/info\/page\/text-and-data-mining"}],"funder":[{"DOI":"10.13039\/100000183","name":"Army Research Office","doi-asserted-by":"publisher","award":["W911NF2510213"],"award-info":[{"award-number":["W911NF2510213"]}],"id":[{"id":"10.13039\/100000183","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["MP-TMPS-00005320"],"award-info":[{"award-number":["MP-TMPS-00005320"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["2317138"],"award-info":[{"award-number":["2317138"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS-2235451"],"award-info":[{"award-number":["DMS-2235451"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["PHY-2340791"],"award-info":[{"award-number":["PHY-2340791"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000057","name":"National Institute of General Medical Sciences","doi-asserted-by":"publisher","award":["R01GM151538"],"award-info":[{"award-number":["R01GM151538"]}],"id":[{"id":"10.13039\/100000057","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Phys. Biol."],"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>In microbial systems, many biochemical functions arise from pathways encoded and executed at the community level. The collective nature of these functions complicates bottom-up efforts to determine each species\u2019 contribution. Previous work has shown that regression over randomly sampled datasets of collective functions succeeds at predicting those functions. Building on this top-down idea, this paper asks whether regression can also reveal mechanistic insight into a cross-feeding relationship. For this, we propose extending the random sampling method to vary the growth environment, cultivating each community in the spent medium of another randomly constructed community. Using a model-based analysis, we illustrate that the mechanistic roles of species are structurally non-identifiable under the standard random sampling protocol, but become identifiable after the proposed modification, such that even a simple LASSO regression can recover them. More generally, our work suggests that the utility of machine-learning-based approaches can be greatly enhanced by a synergistic experimental design.<\/jats:p>","DOI":"10.1088\/1478-3975\/aeb3c4","type":"journal-article","created":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T22:53:02Z","timestamp":1791931982000},"source":"Crossref","is-referenced-by-count":0,"title":["Learning the mechanism of collective microbial function via random community-media pairing"],"prefix":"10.1088","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-5756-6611","authenticated-orcid":false,"given":"Luoqi","family":"Wang","sequence":"first","affiliation":[{"name":"The University of Chicago"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Seppe","family":"Kuehn","sequence":"additional","affiliation":[{"name":"The University of Chicago"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9558-1121","authenticated-orcid":false,"given":"Mikhail","family":"Tikhonov","sequence":"additional","affiliation":[{"name":"Washington University in St Louis"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"266","published-online":{"date-parts":[[2026,10,13]]},"container-title":["Physical Biology"],"original-title":[],"link":[{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1478-3975\/aeb3c4","content-type":"text\/html","content-version":"am","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1478-3975\/aeb3c4\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"text-mining"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1478-3975\/aeb3c4\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1478-3975\/aeb3c4\/pdf","content-type":"application\/pdf","content-version":"am","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,13]],"date-time":"2026-10-13T22:53:03Z","timestamp":1791931983000},"score":1,"resource":{"primary":{"URL":"https:\/\/iopscience.iop.org\/article\/10.1088\/1478-3975\/aeb3c4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,10,13]]},"references-count":0,"URL":"https:\/\/doi.org\/10.1088\/1478-3975\/aeb3c4","relation":{},"ISSN":["1478-3967","1478-3975"],"issn-type":[{"value":"1478-3967","type":"print"},{"value":"1478-3975","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,10,13]]}}}