Understanding biology with machine learning: compression, intelligibility, and dependency

Machine learning (ML) is increasingly used to interrogate biological systems whose complexity resists law-like, deductive explanation. As a result, embeddings, clusters, and attributions are often overinterpreted, dependencies are left implicit, and claims about explainability are often insufficiently bounded. In this work, we present a framework for contextualizing how machine learning contributes to scientific understanding in biology via compression, qualitative intelligibility, and dependency models. Compression is achieved when inductive biases encode biological structure, reducing the effective hypothesis space and yielding representations aligned with known biology. Qualitative intelligibility is supported when high-dimensional measurements are mapped to human-graspable objects, such as embeddings, clusters, and trajectories, that enable accurate qualitative reasoning without exact calculation. Dependency modelling is realized when learned models make explicit the pattern of relations among system components and thereby guide prediction and intervention. We examine how these principles manifest in successful ML applications and discuss considerations that emerge from this framework. Overall, when viewed through these lenses, ML can transform predictive success into intervention-guiding knowledge in the life sciences.