{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/deep-learning-in-single-cell-analysis","title":"Deep Learning in Single-Cell Analysis","arxiv_id":"2210.12385","date":"2022-10-22","proceeding":null,"authors":["Dylan Molho","Jiayuan Ding","Zhaoheng Li","Hongzhi Wen","Wenzhuo Tang","Yixin Wang","Julian Venegas","Wei Jin","Renming Liu","Runze Su","Patrick Danaher","Robert Yang","Yu Leo Lei","Yuying Xie","Jiliang Tang"],"abstract":"Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making analyses using conventional machine learning approaches challenging and impractical. In tackling these challenges, deep learning often demonstrates superior performance compared to traditional machine learning methods. In this work, we give a comprehensive survey on deep learning in single-cell analysis. We first introduce background on single-cell technologies and their development, as well as fundamental concepts of deep learning including the most popular deep architectures. We present an overview of the single-cell analytic pipeline pursued in research applications while noting divergences due to data sources or specific applications. We then review seven popular tasks spanning through different stages of the single-cell analysis pipeline, including multimodal integration, imputation, clustering, spatial domain identification, cell-type deconvolution, cell segmentation, and cell-type annotation. Under each task, we describe the most recent developments in classical and deep learning methods and discuss their advantages and disadvantages. Deep learning tools and benchmark datasets are also summarized for each task. Finally, we discuss the future directions and the most recent challenges. This survey will serve as a reference for biologists and computer scientists, encouraging collaborations.","url_abs":"https://arxiv.org/abs/2210.12385v2","url_pdf":"https://arxiv.org/pdf/2210.12385v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/omicsml/dance","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null},{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/cmzuo11/dcca","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok"}},{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/scverse/scvi-tools","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"jax","reach":{"status":"ok","spdx":"BSD-3-Clause"}},{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/vanvalenlab/deepcell-tf","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"tf","reach":{"status":"ok","spdx":"Apache-2.0"}},{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/wukevin/babel","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok"}},{"paper_slug":"deep-learning-in-single-cell-analysis","repo_url":"https://github.com/zjufanlab/scdeepsort","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"GPL-3.0"}}],"tasks":[{"task_slug":"cell-segmentation","task_name":"Cell Segmentation"},{"task_slug":"deep-learning","task_name":"Deep Learning"},{"task_slug":"imputation","task_name":"Imputation"},{"task_slug":"survey","task_name":"Survey"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2210.12385","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2210.12385"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. 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