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Inverse molecular generation is an essential task for drug discovery, and generative models offer a very promising avenue, especially when diffusion models are used. Despite their great success, existing methods are inherently limited by the lack of a semantic latent space that can not be navigated and perform targeted exploration to generate molecules with desired properties. Here, we present a property-guided diffusion model for generating desired molecules, which incorporates a sophisticated diffusion process capturing intricate interactions of nodes and edges within molecular graphs and leverages a time-dependent molecular property classifier to integrate desired properties into the diffusion sampling process. Furthermore, we extend our model to a multi-property-guided paradigm. Experimental results underscore the competitiveness of our approach in molecular generation, highlighting its superiority in generating desired molecules without the need for additional optimization steps.
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3M-Diffusion: Latent Multi-Modal Diffusion for Language-Guided Molecular Structure Generation
Generating molecular structures with desired properties is a critical task with broad applications in drug discovery and materials design. We propose 3M-Diffusion, a novel multi-modal molecular graph generation method, to generate diverse, ideally novel molecular structures with desired properties. 3M-Diffusion encodes molecular graphs into a graph latent space which it then aligns with the text space learned by encoder based LLMs from textual descriptions. It then reconstructs the molecular structure and atomic attributes based on the given text descriptions using the molecule decoder. It then learns a probabilistic mapping from the text space to the latent molecular graph space using a diffusion model. The results of our extensive experiments on several datasets demonstrate that 3M-Diffusion can generate high-quality, novel and diverse molecular graphs that semantically match the textual description provided. The code is available on github.
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- Award ID(s):
- 2020243
- PAR ID:
- 10566043
- Publisher / Repository:
- openreview.net
- Date Published:
- Subject(s) / Keyword(s):
- Materials discovery Large Language Models Machine Learning
- Format(s):
- Medium: X
- Location:
- Philadelphia, PA, USA
- Sponsoring Org:
- National Science Foundation
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Accepted Manuscript1.0
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