ORIGINAL RESEARCH article
Front. Artif. Intell.
Sec. Medicine and Public Health
This article is part of the Research TopicArtificial Intelligence for Computational Biology and Health Informatics ChallengesView all articles
Computational Understanding of non-coding RNA Pairwise Interactions
Provisionally accepted
- Department of Computer Science, Faculty of Science and Technology, University of Milan, Milan, Italy
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Non-coding RNAs (ncRNAs) govern a vast network of regulatory interactions within the cells, yet their pairwise relationships remain largely uncharted due to the complexity of RNA structure and the limits of current experimental methods. We present CUPID (Computational Understanding of Pairwise Interactions in ncRNA Data), a deep learning framework that predicts ncRNA-ncRNA interactions directly from primary sequence information. CUPID uses embeddings from a pre-trained RNA language model combined with a feed-forward classifier to identify patterns linked to molecular pairing. This approach avoids reliance on thermodynamic models or manual feature design and, unlike previously proposed models, is able to generalize across different types of ncRNAs, including long non-coding, circular, micro-, and small nuclear RNAs. By learning the hidden rules that govern RNA recognition, CUPID provides a scalable tool for exploring ncRNA interaction networks and advancing our understanding of RNA-based regulation.
Keywords: artificial intelligence, bioinformatics, deep learning, Fine-tuning, Large language models, machine learning, non-coding RNA
Received: 18 Nov 2025; Accepted: 28 Jan 2026.
Copyright: © 2026 Nicolini, Stacchietti, Casiraghi and Valentini. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Giorgio Valentini
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