GenMol: A Drug Discovery Generalist with Discrete Diffusion

• URL: http://arxiv.org/abs/2501.06158v1
• Date: Fri, 10 Jan 2025 18:30:05 GMT
• Title: GenMol: A Drug Discovery Generalist with Discrete Diffusion
• Authors: Seul Lee, Karsten Kreis, Srimukh Prasad Veccham, Meng Liu, Danny Reidenbach, Yuxing Peng, Saee Paliwal, Weili Nie, Arash Vahdat,
• Abstract summary: Generalist Molecular generative model (GenMol) is a versatile framework that addresses various aspects of the drug discovery pipeline. Under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimize molecules by replacing fragments with masked tokens. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation.
• Score: 43.29814519270451
• License:
• Abstract: Drug discovery is a complex process that involves multiple scenarios and stages, such as fragment-constrained molecule generation, hit generation and lead optimization. However, existing molecular generative models can only tackle one or two of these scenarios and lack the flexibility to address various aspects of the drug discovery pipeline. In this paper, we present Generalist Molecular generative model (GenMol), a versatile framework that addresses these limitations by applying discrete diffusion to the Sequential Attachment-based Fragment Embedding (SAFE) molecular representation. GenMol generates SAFE sequences through non-autoregressive bidirectional parallel decoding, thereby allowing utilization of a molecular context that does not rely on the specific token ordering and enhanced computational efficiency. Moreover, under the discrete diffusion framework, we introduce fragment remasking, a strategy that optimizes molecules by replacing fragments with masked tokens and regenerating them, enabling effective exploration of chemical space. GenMol significantly outperforms the previous GPT-based model trained on SAFE representations in de novo generation and fragment-constrained generation, and achieves state-of-the-art performance in goal-directed hit generation and lead optimization. These experimental results demonstrate that GenMol can tackle a wide range of drug discovery tasks, providing a unified and versatile approach for molecular design.

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