Beam Enumeration: Probabilistic Explainability For Sample Efficient Self-conditioned Molecular Design

Published: 28 Oct 2023, Last Modified: 28 Oct 2023NeurIPS2023-AI4Science PosterEveryoneRevisionsBibTeX
Keywords: Molecular generative models, reinforcement learning, natural language processing, drug discovery, sample-efficiency, explainability
TL;DR: novel algorithm to extract molecular substructures from language-based molecular generative models to jointly address explainability and sample efficiency.
Abstract: Generative molecular design has moved from proof-of-concept to real-world applicability, as marked by the surge in very recent papers reporting experimental validation. Key challenges in explainability and sample efficiency present opportunities to enhance generative design to directly optimize expensive high-fidelity oracles and provide actionable insights to domain experts. Here, we propose Beam Enumeration to exhaustively enumerate the most probable sub-sequences from language-based molecular generative models and show that molecular substructures can be extracted. When coupled with reinforcement learning, extracted substructures become meaningful, providing a source of explainability and improving sample efficiency through self-conditioned generation. Beam Enumeration is generally applicable to any language-based molecular generative model and notably further improves the performance of the recently reported Augmented Memory algorithm, which achieved the new state-of-the-art on the Practical Molecular Optimization benchmark for sample efficiency. The combined algorithm generates more high reward molecules and faster, given a fixed oracle budget. Beam Enumeration is the first method to jointly address explainability and sample efficiency for molecular design.
Submission Number: 15