Semi-supervised Contrastive Learning for Bioactivity Prediction using Cell Painting Image Data

Abstract

Morphological profiling has recently demonstrated remarkable potential for identifying the biological activities of small molecules. Alongside the fully supervised and self-supervised machine learning methods recently proposed for bioactivity prediction from Cell Painting image data, we introduce here a semi-supervised contrastive (SemiSupCon) learning approach. This approach combines the strengths of using biological annotations in supervised contrastive learning and leveraging large unannotated image datasets with self-supervised contrastive learning. SemiSupCon enhances downstream prediction performance of classifying MeSH pharmacological classifications from PubChem, as well as mode of action and biological target annotations from the Drug Repurposing Hub across two publicly available Cell Painting datasets. Notably, our approach has effectively predicted the biological activities of several unannotated compounds, and these findings were validated through literature searches. This demonstrates that our approach can potentially expedite the exploration of biological activity based on Cell Painting image data with minimal human intervention.