Molecular Fingerprints for Robust and Efficient ML-Driven Molecular Generation

We propose a novel molecular fingerprint-based variational autoencoder applied for molecular generation on real-world drug molecules. We define more suitable and pharma-relevant baseline metrics and tests, focusing on the generation of diverse, drug-like, novel small molecules and scaffolds. When we apply these molecular generation metrics to our novel model, we observe a substantial improvement in chemical synthetic accessibility ($\Delta\bar{{SAS}}$ = -0.83) and in computational efficiency up to 5.9x in comparison to an existing state-of-the-art SMILES-based architecture.

Phenotype Detection in Real World Data via Online MixEHR Algorithm

Understanding patterns of diagnoses, medications, procedures, and laboratory tests from electronic health records (EHRs) and health insurer claims is important for understanding disease risk and for efficient clinical development, which often require rules-based curation in collaboration with clinicians. We extended an unsupervised phenotyping algorithm, mixEHR, to an online version allowing us to use it on order of magnitude larger datasets including a large, US-based claims dataset and a rich regional EHR dataset. In addition to recapitulating previously observed disease groups, we discovered clinically meaningful disease subtypes and comorbidities. This work scaled up an effective unsupervised learning method, reinforced existing clinical knowledge, and is a promising approach for efficient collaboration with clinicians.