Organizations: School of Computer Science and Engineering, South China University of Technology, Guangzhou, China · School of Future Technology, South China University of Technology, Guangzhou, China
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.
Predicting transcriptional responses to specific perturbations is critical for understanding cellular regulatory mechanisms and accelerating drug discovery. Single-cell RNA sequencing destroys each measured cell, yielding only unpaired populations of control and perturbed cells. However, existing methods typically model perturbation prediction at the single-cell level and assume cell-to-cell correspondence, which conflicts with the unpaired nature of the observed data. To address this challenge, we propose PopPert, a framework that explicitly parameterizes population-level joint gene expression distributions for collective transcriptional state modeling. Given a control population distribution and a perturbation condition, PopPert predicts perturbation-induced changes in distribution parameters, eliminating the need for cell-level correspondence and reducing sensitivity to single-cell noise. To effectively capture gene co-expression patterns, PopPert leverages a low-rank Gaussian Copula to model cross-gene statistical dependencies and construct the joint gene expression distribution, additionally allowing sampling of synthetic perturbed single-cell profiles. Across multiple single-cell benchmarks spanning both genetic and chemical perturbations, PopPert achieves superior overall performance in differential expression recovery, perturbation effect estimation, and population-level distribution matching. These results establish population-level joint distribution learning as an effective paradigm for predicting transcriptional responses from unpaired single-cell populations. Code for PopPert is publicly available at https://github.com/whd1125/PopPert.
Handong Wang, Jiaxin Qi, Haochen Feng +1
Computer Network Information Center, Chinese Academy of Sciences · University of Chinese Academy of Sciences
Predicting transcriptional responses to genetic perturbations is fundamental to functional genomics and therapeutic discovery. Recent deep learning models have shown promise in single-cell perturbation response prediction, but they typically generate each response in isolation, without explicitly leveraging related perturbations. We introduce PT-RAG (Perturbation-aware Two-stage Retrieval-Augmented Generation), a plug-in retrieval-and-conditioning module for generative cellular perturbation response. PT-RAG augments an existing perturbation-response backbone with learned access to related perturbation contexts. The key challenge is that relevance is not fixed in this setting: functionally related genes may elicit different effects across cell types. PT-RAG addresses this with a two-stage retrieval mechanism: GenePT-based semantic retrieval first identifies K candidate perturbations, after which a differentiable Gumbel-Softmax selector adaptively selects retrieved contexts conditioned on the control cell state, the query perturbation, and each candidate perturbation. We evaluate PT-RAG on two backbones, a STATE-style generator used as a frozen random reservoir and a fully trained scGPT, across cross-cell-type and cross-perturbation generalization tasks. PT-RAG consistently improves distributional similarity and often overall predictive quality; for example, on scGPT cross-cell-type results, the 2-Wasserstein distance drops by 5.9% relative to scGPT alone. The code to reproduce our experiments is available at https://github.com/difra100/PT-RAG_NIPS.
Andrea Giuseppe Di Francesco, Andrea Rubbi, Rishabh Jain +1
Sapienza University of Rome, Rome, Italy · ISTI-CNR, Institute of Information Science and Technologies, Pisa, Italy · University of Cambridge, Cambridge, United Kingdom +1
Predicting cellular transcriptional responses to genetic perturbations is a central problem in single-cell biology, especially in the zero-shot setting where the perturbed gene or gene combination is unseen during training. A major difficulty is that perturbation effects are not determined by expression state alone: they depend on how the perturbed gene product influences other genes and proteins, how those downstream factors act on cis-regulatory elements, and which regulatory programs are active in the current cell state. To better capture this biological complexity, we propose CisTransCell, a cell-conditioned multi-modal framework for single-cell perturbation prediction that augments each gene with two complementary priors: a regulatory-sequence prior that captures how the gene is controlled, and a coding-sequence prior that captures what the gene product does. By integrating these priors with cellular expression state, CisTransCell models perturbation response as a cascade from gene function to regulatory control to downstream transcriptional change. Experiments on benchmark single-cell perturbation datasets show that CisTransCell achieves strong performance in zero-shot perturbation prediction.
Wei Zhang, Xun Jiang, Yuesi Xi +1
1L3S Research Center, Leibniz Universität Hannover, Germany · School of Clinical Medicine & Laboratory Medicine, Jiangsu University, China · Institute for Information Processing (tnt), Leibniz Universität Hannover, Germany.