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

Track: Main track (up to 8 pages)

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.

Submission Number: 28