{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:55:19Z","timestamp":1791222919595,"version":"4.1.0"},"reference-count":54,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T00:00:00Z","timestamp":1791158400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["61802246"],"award-info":[{"award-number":["61802246"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Shanghai Natural Science Foundation","award":["24ZR1421600"],"award-info":[{"award-number":["24ZR1421600"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>Microorganisms exert profound influences on both natural ecosystems and human society. As the cornerstone of microbial research, metagenomics relies on the precise analysis of large-scale, multi-source genomic data. However, discriminating among diverse sequence types remains a formidable challenge. To address this, we present CamFi (Codon-aware Multi-scale Feature Fusion), a unified framework integrating overlapping nucleotide-triplet representations with multi-scale dilated convolutions for classifying prokaryotic chromosomes, eukaryotic chromosomes, plasmids, and viruses. Benchmark evaluations demonstrate strong mean F1 scores of 97.70% for eukaryotic chromosomes and 94.13% for plasmids. On the CAMI II marine dataset, CamFi achieved a weighted F1 of 82.65%, ranking second among six methods based on reported aggregate metrics. In a balanced four-class benchmark, CamFi attained a macro-F1 of 93.77%, compared with DeepMicroClass (90.03%) and the XGBoost stage of 4CAC (64.66%). These results establish CamFi as a competitive approach for unified metagenomic contig classification under the evaluated conditions.<\/jats:p>","DOI":"10.1371\/journal.pone.0359090","type":"journal-article","created":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T17:25:18Z","timestamp":1791221118000},"page":"e0359090","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Codon-aware multi-scale feature fusion for metagenomic sequence classification"],"prefix":"10.1371","volume":"21","author":[{"given":"Yan","family":"Qian","sequence":"first","affiliation":[{"name":"Shanghai University","place":["Shanghai, People\u2019s Republic of China"],"department":["School of Mechatronic Engineering and Automation"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quanjie","family":"Song","sequence":"additional","affiliation":[{"name":"Shanghai University","place":["Shanghai, People\u2019s Republic of China"],"department":["School of Mechatronic Engineering and Automation"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinyi","family":"Xie","sequence":"additional","affiliation":[{"name":"Shanghai University","place":["Shanghai, People\u2019s Republic of China"],"department":["School of Mechatronic Engineering and Automation"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9976-147X","authenticated-orcid":true,"given":"Li","family":"Deng","sequence":"additional","affiliation":[{"name":"Shanghai University","place":["Shanghai, People\u2019s Republic of China"],"department":["School of Mechatronic Engineering and Automation"]},{"name":"Shanghai Key Laboratory of Power Station Automation Technology","place":["Shanghai, People\u2019s Republic of China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2026,10,5]]},"reference":[{"issue":"5879","key":"pone.0359090.ref001","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1126\/science.1153213","article-title":"The microbial engines that drive Earth\u2019s biogeochemical cycles","volume":"320","author":"PG Falkowski","year":"2008","journal-title":"Science"},{"issue":"5664","key":"pone.0359090.ref002","doi-asserted-by":"crossref","first-page":"1622","DOI":"10.1126\/science.1093892","article-title":"Oceanography. 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