A survey of diffusion models for biomolecule generation, organized around DDPM and score-based frameworks, equivariance, 56 application models, benchmarks, and future directions for autonomous protein engineering.
Sifting through the Noise: A Survey of Diffusion Probabilistic Models and Their Applications to Biomolecules
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abstract
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular structures and sequences. Their growing ubiquity makes it imperative for researchers in these fields to understand them. This paper serves as a general overview for the theory behind these models and the current state of research. We first introduce diffusion models and discuss common motifs used when applying them to biomolecules. We then present the significant outcomes achieved through the application of these models in generative and predictive tasks. This survey aims to provide readers with a comprehensive understanding of the increasingly critical role of diffusion models.
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2025 1verdicts
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From thermodynamics to protein design: Diffusion models for biomolecule generation towards autonomous protein engineering
A survey of diffusion models for biomolecule generation, organized around DDPM and score-based frameworks, equivariance, 56 application models, benchmarks, and future directions for autonomous protein engineering.