{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,13]],"date-time":"2026-02-13T15:30:45Z","timestamp":1770996645438,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"4","license":[{"start":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T00:00:00Z","timestamp":1756252800000},"content-version":"vor","delay-in-days":57,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100009500","name":"Bangladesh University of Engineering and Technology","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100009500","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2025,7,2]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The subcellular localization of messenger RNAs (mRNAs) plays a crucial role in gene regulation, ensuring precise spatial and temporal control of protein synthesis. Traditional computational approaches for mRNA localization have primarily relied on single-label classification models, which fail to capture the inherent multi-label nature of mRNA localization. Recent advancements have introduced deep learning-based multi-label prediction frameworks; however, existing methods often lack an effective way to model the relationships between multiple localizations. In this paper, we propose Localization with Supervised Contrastive Learning (LOCAS), a novel approach for multi-label mRNA subcellular localization prediction. LOCAS integrates an RNA language model (RiNALMo) to generate high-quality sequence embeddings and employs supervised contrastive learning (SCL) to refine the embedding space, ensuring biologically meaningful clustering of RNA sequences. To handle overlapping labels, we introduce an overlap-threshold-based similarity measure during contrastive training. Finally, we leverage an ML-Decoder, which utilizes a cross-attention mechanism to enhance multi-label classification performance. We evaluate LOCAS on two benchmark datasets, RNALocate and RNALocate V2.0, demonstrating state-of-the-art performance across all evaluation metrics. Extensive ablation studies validate the effectiveness of our approach, highlighting the contributions of contrastive learning and ML-decoder in improving multi-label classification. Our results suggest that integrating RNA sequence representation learning with SCL offers a powerful and scalable solution for mRNA localization prediction.<\/jats:p>","DOI":"10.1093\/bib\/bbaf441","type":"journal-article","created":{"date-parts":[[2025,8,27]],"date-time":"2025-08-27T11:13:33Z","timestamp":1756293213000},"source":"Crossref","is-referenced-by-count":2,"title":["LOCAS: multilabel mRNA localization with supervised contrastive learning"],"prefix":"10.1093","volume":"26","author":[{"given":"Abrar","family":"Rahman Abir","sequence":"first","affiliation":[{"name":"Department of Computer Science and Engineering , Bangladesh University of Engineering and Technology, Dhaka-1000,","place":["Bangladesh"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Md","family":"Toki Tahmid","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , Bangladesh University of Engineering and Technology, Dhaka-1000,","place":["Bangladesh"]}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M","family":"Saifur Rahman","sequence":"additional","affiliation":[{"name":"Department of Computer Science and Engineering , Bangladesh University of Engineering and Technology, Dhaka-1000,","place":["Bangladesh"]}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2025,8,27]]},"reference":[{"key":"2025082707132505200_ref1","doi-asserted-by":"publisher","first-page":"408","DOI":"10.1016\/0012-1606(83)90290-7","article-title":"Localization of actin messenger RNA during early ascidian development","volume":"99","author":"Jeffery","year":"1983","journal-title":"Dev Biol"},{"key":"2025082707132505200_ref2","doi-asserted-by":"publisher","first-page":"1212","DOI":"10.1126\/science.1176488","article-title":"Subcellular mRNA localization in animal cells and why it 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