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arXiv · 2401.09451

Diffusion-Driven Generative Framework for Molecular Conformation Prediction

Bobin Yang·Jie Deng·Zhenghan Chen·Ruoxue Wu
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Abstract

The task of deducing three-dimensional molecular configurations from their two-dimensional graph representations holds paramount importance in the fields of computational chemistry and pharmaceutical development. The rapid advancement of machine learning, particularly within the domain of deep generative networks, has revolutionized the precision of predictive modeling in this context. Traditional approaches often adopt a two-step strategy: initially estimating interatomic distances and subsequently refining the spatial molecular structure by solving a distance geometry problem. However, this sequential approach occasionally falls short in accurately capturing the intricacies of local atomic arrangements, thereby compromising the fidelity of the resulting structural models. Addressing these limitations, this research introduces a cutting-edge generative framework named DDGF. This framework is grounded in the principles of diffusion observed in classical non-equilibrium thermodynamics. DDGF views atoms as discrete entities and excels in guiding the reversal of diffusion, transforming a distribution of stochastic noise back into coherent molecular structures through a process akin to a Markov chain. This transformation commences with the initial representation of a molecular graph in an abstract latent space, culminating in the realization of three-dimensional structures via a sophisticated bilevel optimization scheme meticulously tailored to meet the specific requirements of the task. One of the formidable challenges in this modeling endeavor involves preserving roto-translational invariance to ensure that the generated molecular conformations adhere to the laws of physics. Extensive experimental evaluations confirm the efficacy of the proposed DDGF in comparison to state-of-the-art methods.

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Bobin Yang, Jie Deng, Zhenghan Chen, Ruoxue Wu. 2023-12-22. Diffusion-Driven Generative Framework for Molecular Conformation Prediction. https://arxiv.org/abs/2401.09451

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