arXiv:2608.23114cs.LGcs.AI2026-08

分解细胞扰动响应,提升未知扰动预测精度

DeMixPert: Decomposed Response Modeling with Gaussian Mixtures for OOD Single-Cell Perturbation Prediction

论文配图:DeMixPert: Decomposed Response Modeling with Gaussian Mixtures for OOD Single-Cell Perturbation Prediction
图 1 · 摘自论文原文
  • 将扰动响应拆分为基础状态、特异性变化和群体变异三部分
  • 在未见扰动下实现更优的单细胞表达预测性能
  • 适合研究基因调控与药物开发的计算生物学家

预测未知遗传扰动下的全转录组响应仍是重大计算挑战,因准确预测需同时恢复扰动特异的转录变化和细胞异质性反应。现有方法常将确定性响应结构与随机群体变异混淆,导致主导共享模式掩盖微弱扰动信号,影响分布建模。为此,我们提出DeMixPert:基于高斯混合的去耦响应建模方法,用于分布外(OOD)单细胞扰动预测。DeMixPert将扰动诱导变化分解为依赖基础状态的系统性响应、扰动特异性响应及群体水平变异。系统性成分由对照细胞表达编码的基础状态获得,扰动特异性成分则通过预训练目标嵌入实现未见目标泛化。群体变异采用高斯原型可逆网络建模,并根据基础状态与扰动条件自适应组合可复用的高斯原型,生成条件特定的变异分布。采样后的变异与系统性和特异性成分结合,再与基础状态联合解码,重建扰动后细胞基因表达。实验表明,DeMixPert能有效捕捉异质性单细胞扰动响应,在未见扰动设置下表现优异。代码将在发表后公开。

原文摘要 · Abstract (English)

Predicting transcriptome-wide responses to unseen genetic perturbations remains a major computational challenge because accurate prediction requires recovering both perturbation-specific transcriptional shifts and heterogeneous cellular responses. Existing methods often entangle deterministic response structure with stochastic population-level variation, causing dominant shared patterns to mask weaker perturbation-specific signals and impair distributional modeling. To address these challenges, we propose \textbf{DeMixPert}, an approach for Decomposed response Modeling with Gaussian Mixtures for Out-Of-Distribution (OOD) single-cell Perturbation prediction. DeMixPert decomposes perturbation-induced changes into a basal-state-dependent systematic response, a perturbation-specific response, and population-level variation. The systematic component is derived from the basal state encoded from control-cell expression, whereas the perturbation-specific component is inferred from pretrained target embeddings for unseen-target generalization. DeMixPert models population-level variation using a Gaussian prototype Invertible Network and adaptively combines reusable Gaussian prototypes according to the basal state and perturbation condition. The resulting mixture is mapped to a condition-specific variation distribution. Sampled variations are integrated with the systematic and perturbation-specific components, followed by joint decoding with the basal state to reconstruct perturbed-cell gene expression. Experimental results show that DeMixPert effectively captures heterogeneous single-cell perturbation responses and achieves superior performance across unseen-perturbation settings. The source code is made publicly available upon publication.

单细胞扰动预测高斯混合基因调控

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