Dose–response prediction for in-vitro drug combination datasets: a probabilistic approach

In this paper we propose PIICM, a probabilistic framework for dose–response prediction in high-throughput drug combination datasets. PIICM utilizes a permutation invariant version of the intrinsic co-regionalization model for multi-output Gaussian process regression, to predict dose–response surfaces in untested drug combination experiments. Coupled with an observation model that incorporates experimental uncertainty, PIICM is able to learn from noisily observed cell-viability measurements in settings where the underlying dose–response experiments are of varying quality, utilize different experimental designs, and the resulting training dataset is sparsely observed. We show that the model can accurately predict dose–response in held out experiments, and the resulting function captures relevant features indicating synergistic interaction between drugs. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-023-05256-6.