Tabular Foundation Models Are Competitive Cellular Perturbation Predictors Across Biological Scales

Authors

Palla, G., Hillsley, A., Kim, Y.-J., Royer, L. A.

Abstract

Predicting how cells respond to genetic and chemical perturbations is a central challenge in drug discovery and functional genomics. A growing ecosystem of specialized single-cell foundation models has been developed to address this problem, yet their practical advantage over domain-agnostic approaches remains unclear. Here we evaluate the power of Tabular Foundation Models such as TabICL and TabPFN, general-purpose pre-trained regression models, against domain-specific architectures including PRESAGE, scGPT, scLAMBDA, STACK and Prophet across four complementary evaluation settings: cell-level in-context cross-cell-type prediction, pseudobulk perturbation prediction on five Perturb-seq datasets of cell-lines, a genome-wide CRISPR screen in primary human CD4+ T cells, and embryo-level cell-type composition prediction in a zebrafish developmental perturbation atlas. In the cell-level cross-cell type perturbation prediction, Tabular Foundation Models perform on par or better than specialized models. On pseudobulk perturbation prediction, Tabular Foundation Models consistently outperform specialized baselines across multiple evaluation metrics and datasets. On whole-emrbryo cell-type composition prediction, Tabular Foundation Models are competitive with specialized baselines. These results demonstrate that general-purpose tabular in-context learning provides a strong and scalable alternative to bespoke biological architectures for perturbation response modeling across cell systems and scales.

Preprint server: bioRxiv
The authors list and abstract were imported from bioRxiv on 02 Jul 2026.

Stats

1-terrible, 9-excellent. How would you rate this preprint? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.