Predicting cellular responses to various perturbations is a critical focus in drug discovery and personalized therapeutics, with deep learning models playing a significant role in this endeavor. Single-cell datasets contain technical artifacts that may hinder the predictability of such models, which poses quality control issues highly regarded in this area. To address this, we propose Cradle-VAE, a causal generative framework tailored for single-cell gene perturbation modeling, enhanced with counterfactual reasoning-based artifact disentanglement. Throughout training, Cradle-VAE models the underlying latent distribution of technical artifacts and perturbation effects present in single-cell datasets. It employs counterfactual reasoning to effectively disentangle such artifacts by modulating the latent basal spaces and learns robust features for generating cellular response data with improved quality. Experimental results demonstrate that this approach improves not only treatment effect estimation performance but also generative quality as well.

MOTIVATION: Predicting cellular responses to genetic perturbations is essential for understanding biological systems and developing targeted therapeutic strategies. While variational autoencoders (VAEs) have shown promise in modeling perturbation responses, their limited explainability poses a significant challenge, as the learned features often lack clear biological meaning. Nevertheless, model explainability is one of the most important aspects in the realm of biological AI. One of the most effective ways to achieve explainability is incorporating the concept of gene regulatory networks (GRNs) in designing deep learning models such as VAEs. GRNs elicit the underlying causal relationships between genes and are capable of explaining the transcriptional responses caused by genetic perturbation treatments. RESULTS: We propose GPO-VAE, an explainable VAE enhanced by GRN-aligned Parameter Optimization that explicitly models gene regulatory networks in the latent space. Our key approach is to optimize the learnable parameters related to latent perturbation effects toward GRN-aligned explainability. Experimental results on perturbation prediction show our model achieves state-of-the-art performance in predicting transcriptional responses across multiple benchmark datasets. Furthermore, additional results on evaluating the GRN inference task reveal our model's ability to generate meaningful GRNs compared to other methods. According to qualitative analysis, GPO-VAE possesses the ability to construct biologically explainable GRNs that align with experimentally validated regulatory pathways. AVAILABILITY AND IMPLEMENTATION: GPO-VAE is available at https://github.com/dmis-lab/GPO-VAE.