Scaling recipes for single-cell RNA sequencing foundation models: when do scaling laws hold?

Abstract

Deep learning models exhibit empirical scaling laws whereby performance changes predictably with model size, dataset size, and training compute. Although these relationships are well established in domains such as language and image modelling, their applicability to biological data remains unclear. Here, we investigate scaling behaviour in foundation models trained on large collections of single-cell transcriptomes. We show that pre-training loss decreases systematically with model capacity and training compute, exhibiting a power-law dependence on model size. The strength and regularity of these trends differ between model formulations. We identify and quantify empirical relationships linking the optimal learning rate and depth-to-width ratio to model size and depth or compute. These results demonstrate that scaling principles extend to transcriptomic modelling. More broadly, they provide a quantitative framework for estimating the expected returns from additional resources and selecting suitable hyperparameters and architectures, thereby supporting the development of increasingly capable foundation models for omics data.