Compressing Chemistry Reveals Functional Groups

We introduce the first formal large-scale assessment of the utility of traditional chemical functional groups as used in chemical explanations. Our assessment employs a fundamental principle from computational learning theory: a good explanation of data should also compress the data. We introduce an unsupervised learning algorithm based on the Minimum Message Length (MML) principle that searches for substructures that compress around three million biologically relevant molecules. We demonstrate that the discovered substructures contain most human-curated functional groups as well as novel larger patterns with more specific functions. We also run our algorithm on 24 specific bioactivity prediction datasets to discover dataset-specific functional groups. Fingerprints constructed from dataset-specific functional groups are shown to significantly outperform other fingerprint representations, including the MACCS and Morgan fingerprint, when training ridge regression models on bioactivity regression tasks.

Learning Logical Rules using Minimum Message Length

Unifying probabilistic and logical learning is a key challenge in AI. We introduce a Bayesian inductive logic programming approach that learns minimum message length programs from noisy data. Our approach balances hypothesis complexity and data fit through priors, which explicitly favour more general programs, and a likelihood that favours accurate programs. Our experiments on several domains, including game playing and drug design, show that our method significantly outperforms previous methods, notably those that learn minimum description length programs. Our results also show that our approach is data-efficient and insensitive to example balance, including the ability to learn from exclusively positive examples.