Foundation Models for Biology How foundation models fit modern molecular biology and drug discovery — a practitioner's bridge. •Preface I · Foundations 1The Synthesis Premise 2The Landscape of Biological Problems 3Modern ML and Foundation Models, Quickly 4The Data: What Each Assay Measures 5Genetics for the ML Practitioner II · Molecular and therapeutic problems 6Target Discovery 7Function and Property Prediction 8Protein Structure Determination 9Protein and Binder Design 10Small-Molecule Drug Design 11Cell Engineering III · Genomic and regulatory problems 12From Sequence to Regulatory Function 13From Variant to Mechanism IV · Integration 14Multi-Modal Integration V · Doing it for real 15The Hard Realities of Biological Data 16Evaluating Models in Biology 17Closing the Loop with the Lab VI · Outlook 18Outlook: Open Frontiers Appendices ASingle-Cell Foundation Models BSpatial Omics CCell Imaging and Morphology DGlossary
