REVIEW article
Front. Bioinform.
Sec. Single Cell Bioinformatics
This article is part of the Research TopicAI in Single-Cell BiologyView all 3 articles
Applications of AI to single-cell and spatial transcriptomics: current state-of-the-art and challenges
Provisionally accepted
- Western University, London, Canada
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Artificial intelligence (AI) has become a common tool for bioinformatics, with hundreds of methods published in recent years. Due to the training data demands of deep-learning algorithms, high-throughput single-cell and spatial transcriptomics is one of the most popular areas for these applications. Here we review how AI is being used for single-cell and spatial transcriptomics analysis, and how these approaches compare to alternative statistical or heuristic-based methods. We explored 10 common analysis tasks: dimensionality reduction, cross-dataset integration, data denoising, data augmentation, deconvolution, cell-cell interactions, transcriptional velocity, transcriptomic-chromatin accessibility integration, and integrating single-cell and spatial transcriptomics modalities. We highlight which algorithms are likely to be useful for discovery researchers, and which are not yet ready for general research use.
Keywords: cell-cell interactions, cross-dataset integration, Data augmentation, Data denoising, deconvolution, dimensionality reduction, integrating single-cell and spatial transcriptomics modalities, transcriptional velocity
Received: 29 Sep 2025; Accepted: 08 Dec 2025.
Copyright: © 2025 Tchatchoua Ngassam, Niu, Shydlouskaya and Andrews. 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: Tallulah Suzanne Andrews
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