MODELLING BIOLOGICAL ASSAYS WITH ADAPTIVE DEEP KERNEL LEARNING

Prudencio Tossou, Basile Dura, Daniel Cohen, Mario Marchand, François Laviolette, Alexandre Lacoste

Keywords: few-shot learning, few-shot regression, deep kernel learning, biological assay modelling, drug discovery

TL;DR: We investigate the modelling of biological assays using deep kernel learning in few-shot settings.

Abstract: Due to the significant costs of data generation, many prediction tasks within drug discovery are by nature few-shot regression (FSR) problems, including accurate modelling of biological assays. Although a number of few-shot classification and reinforcement learning methods exist for similar applications, we find relatively few FSR methods meeting the performance standards required for such tasks under real-world constraints. Inspired by deep kernel learning, we develop a novel FSR algorithm that is better suited to these settings. Our algorithm consists of learning a deep network in combination with a kernel function and a differentiable kernel algorithm. As the choice of the kernel is critical, our algorithm learns to find the appropriate one for each task during inference. It thus performs more effectively with complex task distributions, outperforming current state-of-the-art algorithms on both toy and novel, real-world benchmarks that we introduce herein. By introducing novel benchmarks derived from biological assays, we hope that the community will progress towards the development of FSR algorithms suitable for use in noisy and uncertain environments such as drug discovery.