Gene Incremental Learning for Single-Cell Transcriptomics

Classes, as fundamental elements of Computer Vision, have been extensively studied within incremental learning frameworks. In contrast, tokens, which play essential roles in many research fields, exhibit similar characteristics of growth, yet investigations into their incremental learning remain significantly scarce. This research gap primarily stems from the holistic nature of tokens in language, which imposes significant challenges on the design of incremental learning frameworks for them. To overcome this obstacle, in this work, we turn to a type of token, gene, for a large-scale biological dataset—single-cell transcriptomics—to formulate a pipeline for gene incremental learning and establish corresponding evaluations. We found that the forgetting problem also exists in gene incremental learning, thus we adapted existing class incremental learning methods to mitigate the forgetting of genes. Through extensive experiments, we demonstrated the soundness of our framework design and evaluations, as well as the effectiveness of the method adaptations. Finally, we provide a complete benchmark for gene incremental learning in single-cell transcriptomics.

Authors

• Jiaxin Qi Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
• Yan Cui Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China
• Jianqiang Huang Computer Network Information Center, Chinese Academy of Sciences, Beijing, China Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Hangzhou, China University of Chinese Academy of Sciences, Beijing, China
• Gaogang Xie Computer Network Information Center, Chinese Academy of Sciences, Beijing, China University of Chinese Academy of Sciences, Beijing, China

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