Efficient Fine-Tuning of Single-Cell Foundation Models Enables Zero-Shot Molecular Perturbation Prediction

Predicting transcriptional responses to novel drugs provides a unique opportunity to accelerate biomedical research and advance drug discovery efforts. However, the inherent complexity and high dimensionality of cellular responses, combined with the extremely limited available experimental data, makes the task challenging. In this study, we leverage single-cell foundation models (FMs) pre-trained on tens of millions of single cells, encompassing multiple cell types, states, and disease annotations, to address molecular perturbation prediction. We introduce a drug-conditional adapter that allows efficient fine-tuning by training less than 1% of the original foundation model, thus enabling molecular conditioning while preserving the rich biological representation learned during pre-training. The proposed strategy allows not only the prediction of cellular responses to novel drugs, but also the zero-shot generalization to unseen cell lines. We establish a robust evaluation framework to assess model performance across different generalization tasks, demonstrating state-of-the-art results across all settings, with significant improvements in the few-shot and zero-shot generalization to new cell lines compared to existing baselines.

Learning Identifiable Factorized Causal Representations of Cellular Responses

The study of cells and their responses to genetic or chemical perturbations promises to accelerate the discovery of therapeutic targets. However, designing adequate and insightful models for such data is difficult because the response of a cell to perturbations essentially depends on its biological context (e.g., genetic background or cell type). For example, while discovering therapeutic targets, one may want to enrich for drugs that specifically target a certain cell type. This challenge emphasizes the need for methods that explicitly take into account potential interactions between drugs and contexts. Towards this goal, we propose a novel Factorized Causal Representation (FCR) learning method that reveals causal structure in single-cell perturbation data from several cell lines. Based on the framework of identifiable deep generative models, FCR learns multiple cellular representations that are disentangled, comprised of covariate-specific ($\mathbf{z}_x$), treatment-specific ($\mathbf{z}_{t}$), and interaction-specific ($\mathbf{z}_{tx}$) blocks. Based on recent advances in non-linear ICA theory, we prove the component-wise identifiability of $\mathbf{z}_{tx}$ and block-wise identifiability of $\mathbf{z}_t$ and $\mathbf{z}_x$. Then, we present our implementation of FCR, and empirically demonstrate that it outperforms state-of-the-art baselines in various tasks across four single-cell datasets.

Weakly Supervised Set-Consistency Learning Improves Morphological Profiling of Single-Cell Images

Optical Pooled Screening (OPS) is a powerful tool combining high-content microscopy with genetic engineering to investigate gene function in disease. The characterization of high-content images remains an active area of research and is currently undergoing rapid innovation through the application of self-supervised learning and vision transformers. In this study, we propose a set-level consistency learning algorithm, Set-DINO, that combines self-supervised learning with weak supervision to improve learned representations of perturbation effects in single-cell images. Our method leverages the replicate structure of OPS experiments (i.e., cells undergoing the same genetic perturbation, both within and across batches) as a form of weak supervision. We conduct extensive experiments on a large-scale OPS dataset with more than 5000 genetic perturbations, and demonstrate that Set-DINO helps mitigate the impact of confounders and encodes more biologically meaningful information. In particular, Set-DINO recalls known biological relationships with higher accuracy compared to commonly used methods for morphological profiling, suggesting that it can generate more reliable insights from drug target discovery campaigns leveraging OPS.

Toward the Identifiability of Comparative Deep Generative Models

Deep Generative Models (DGMs) are versatile tools for learning data representations while adequately incorporating domain knowledge such as the specification of conditional probability distributions. Recently proposed DGMs tackle the important task of comparing data sets from different sources. One such example is the setting of contrastive analysis that focuses on describing patterns that are enriched in a target data set compared to a background data set. The practical deployment of those models often assumes that DGMs naturally infer interpretable and modular latent representations, which is known to be an issue in practice. Consequently, existing methods often rely on ad-hoc regularization schemes, although without any theoretical grounding. Here, we propose a theory of identifiability for comparative DGMs by extending recent advances in the field of non-linear independent component analysis. We show that, while these models lack identifiability across a general class of mixing functions, they surprisingly become identifiable when the mixing function is piece-wise affine (e.g., parameterized by a ReLU neural network). We also investigate the impact of model misspecification, and empirically show that previously proposed regularization techniques for fitting comparative DGMs help with identifiability when the number of latent variables is not known in advance. Finally, we introduce a novel methodology for fitting comparative DGMs that improves the treatment of multiple data sources via multi-objective optimization and that helps adjust the hyperparameter for the regularization in an interpretable manner, using constrained optimization. We empirically validate our theory and new methodology using simulated data as well as a recent data set of genetic perturbations in cells profiled via single-cell RNA sequencing.