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Poster
in
Workshop: Machine Learning for Genomics Explorations (MLGenX)

ShortListing Model: A Streamlined Simplex Diffusion for Biological Sequence Generation

Yuxuan Song · Zhe Zhang · Yu Pei · Jingjing Gong · Mingxuan Wang · Hao Zhou · Jingjing Liu · Wei-Ying Ma


Abstract:

Generative modeling of discrete variables is challenging yet crucial for applications in natural language processing and biological sequence design. We introduce the Shortlisting Model (SLM), a novel simplex-based diffusion model inspired by progressive candidate pruning. SLM operates on simplex centroids, reducing complexity and enhancing scalability. Additionally, SLM incorporates a flexible implementation of classifier-free guidance, enhancing unconditional generation performance. Extensive experiments in DNA promoter and enhancer design, and protein design demonstrate SLM's competitive performance and scalability.

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