SAVE: A Generalizable Framework for Multi-Condition Single-Cell Generation with Gene Block Attention

Computer Science > Artificial Intelligence [Submitted on 18 Apr 2026] SAVE: A Generalizable Framework for Multi-Condition Single-Cell Generation with Gene Block Attention Jiahao Li, Jiayi Dong, Peng Ye, Xiaochi Zhou, Haohai Lu, Fei Wang Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing methods often treat genes as independent tokens, overlooking their high-level biological relationships and leading to poor performance. We introduce SAVE, a unified generative framework based on conditional Transformers for multi-condition single-cell modeling. SAVE leverages a coarse-grained representation by grouping semantically related genes into blocks, capturing higher-order dependencies among gene modules. A Flow Matching mechanism and condition-masking strategy further enhance flexible simulation and enable generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative generalization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological interpretation. Our code is publicly available at this https URL Comments: Accepted to ICLR 2026 Subjects: Artificial Intelligence (cs.AI) Cite as: arXiv:2604.16776 [cs.AI]   (or arXiv:2604.16776v1 [cs.AI] for this version)   https://doi.org/10.48550/arXiv.2604.16776 Focus to learn more Submission history From: Jiahao Li [view email] [v1] Sat, 18 Apr 2026 01:45:16 UTC (31,949 KB) Access Paper: HTML (experimental) view license Current browse context: cs.AI < prev   |   next > new | recent | 2026-04 Change to browse by: cs References & Citations NASA ADS Google Scholar Semantic Scholar Export BibTeX Citation Bookmark Bibliographic Tools Bibliographic and Citation Tools Bibliographic Explorer Toggle Bibliographic Explorer (What is the Explorer?) Connected Papers Toggle Connected Papers (What is Connected Papers?) Litmaps Toggle Litmaps (What is Litmaps?) scite.ai Toggle scite Smart Citations (What are Smart Citations?) Code, Data, Media Demos Related Papers About arXivLabs Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)