arXiv:2602.00423cs.LG2026-02

提出轻量级方法scBatchProx,稳定异构批次下细胞类型识别性能。

scBatchProx: Federated-Inspired Refinement for Stable Cell-Type Discriminability under Heterogeneous Batch Compositions

  • 借鉴联邦学习思想,对预计算嵌入进行保守更新。
  • 在不平衡扰动下,保持受影响细胞类型的F1值更稳定。
  • 适合动态单细胞数据系统中持续集成新数据场景。

单细胞整合流程通常先构建低维细胞嵌入,再通过后处理方法减少批次效应。当批次间细胞类型组成不一致时,某些群体可能在特定批次中缺失或代表性不足,导致该过程不稳定。这一问题在动态单细胞数据系统中尤为严重,因新批次的引入会同时改变技术条件和细胞类型组成。本文提出scBatchProx,一种轻量级后处理优化方法,用于在异构且动态演化的场景中稳定单细胞潜在表示。scBatchProx直接作用于预计算嵌入,将每个批次或研究视为联邦学习中的客户端,通过批次条件化的FiLM适配器学习局部更新,并结合近端与身份保持正则化,使更新更保守。在多批次和跨研究数据集上的实验表明,scBatchProx能提升下游细胞类型分类性能。在受控不平衡扰动下,当部分细胞类型被降采样或移除时,scBatchProx仍能维持更高的受影响细胞类型F1值。在累积重训练和持续整合设置中,随着新数据不断到来,scBatchProx仍保持有效性。结果表明,保守的联邦启发式优化可帮助在批次组成随数据集变化及时间推移时,维持稳定的单细胞嵌入。

原文摘要 · Abstract (English)

Single-cell integration workflows often construct low-dimensional cell embeddings and then refine them with post-hoc methods to reduce batch effects. This refinement process can become unstable when cell-type compositions vary across batches, with some populations underrepresented or absent in particular batches. The problem becomes more consequential in dynamic single-cell data systems, where newly acquired batches can change both technical conditions and cell-type composition. Such instability can reduce downstream cell-type classification performance and weaken stability under imbalance perturbations. We introduce scBatchProx, a lightweight post-hoc refinement method for stabilizing single-cell latent embeddings in these heterogeneous and evolving settings. scBatchProx operates directly on precomputed embeddings and treats each batch or study as a client in a federated-inspired optimization procedure. A batch-conditioned FiLM adapter learns local latent updates, while proximal and identity-preserving regularization keep these updates conservative. Experiments on multi-batch and cross-study single-cell datasets show that scBatchProx improves downstream cell-type classification across different upstream embeddings. In controlled imbalance perturbations, scBatchProx maintains more stable affected-cell-type F1 when selected populations are downsampled or ablated from one batch. In cumulative retraining and continual integration settings, scBatchProx remains effective as new datasets arrive over time. Together, these results suggest that conservative, federated-inspired refinement can help maintain stable single-cell embeddings as batch compositions change across datasets and over time.

单细胞分析批次效应联邦学习嵌入优化

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