Mechanisms Matter: Transportability of Cellular Perturbation Effects

Shi-ang Qi, Paidamoyo Chapfuwa

Keywords: Cellular perturbation effect; transportability; Perturb-seq; causal mechanisms

TL;DR: We formalize cellular perturbation response prediction as a causal transportability problem, using a novel causal simulator and diversity-aware metrics on Perturb-seq datasets to reveal fundamental limits of cross-context generalization.

Abstract: Predicting cellular responses to genetic or chemical perturbations across biological contexts is central to drug development and disease understanding. Despite increases in data and model scale, deep learning models have not consistently outperformed simple baselines. Leveraging causal transportability theory, we show that cross-context generalization is governed by shared causal mechanisms, not merely distributional similarity. To enable controlled evaluation, we develop a causal simulator that generates realistic semi-synthetic Perturb-seq datasets with tunable mechanistic divergence, providing benchmarks with known ground-truth causal structure. Further, we adapt the Vendi diversity score to the perturbation setting as a diagnostic for mode collapse, a failure mode invisible to standard per-perturbation metrics. Extensive experiments across four deep learning models and six simple baselines on semi-synthetic and real Perturb-seq datasets reveal a cross-context generalization gap: performance under cross-context splits drops substantially, often to simple baseline levels. Notably, even on synthetic data with fully specified causal structure, no model generalized across contexts with different causal mechanisms. These results underscore the need for cross-context evaluation, diversity-aware metrics, and mechanistically grounded inductive biases.

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Submission Number: 94