Author

Shupeng Cheng

University of Southern CaliforniaORCID 0009-0000-5888-5129Unclaimed ORCID profile · follow to get notified of new preprints

Biology Disciplines

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Bioinformatics· 1

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Organism:bacteria (other)· 1 Approach:contrastive learning· 1 Approach:deep learning· 1 Organism:multiple species· 1 Research Focus:sequence-to-function modeling· 1 Research Focus:software / tool· 1 Approach:transformer / foundation model· 1 Organism:virus· 1

Frequent Co-Authors

Athan Z. LiiD· 1 shared Ruishan LiuiD· 1 shared Shiyuan WangiD· 1 shared Yuxuan DuiD· 1 shared

Activity by Year

2026-2026 · peak 1/yr

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4 top collaborators · 6 mutual co-author links

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1 shared paperBioinformatics

Athan Z. LiORCID

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1 paper

Recent·Most cited

BioinformaticsbioRxivPreprintSep 28, 2026

✦ In-depth digest

A Taxonomy-Informed Sparse DNA Foundation Model for Microbial Genomics

Athan Z. Li, Shiyuan Wang, Shupeng Cheng…·Ruishan Liu

A sparse mixture-of-experts DNA model conditioned on hyperbolic taxonomy embeddings learns better microbial representations than its taxonomy-free twin and comes close to Evo2-7B in probing and fine-tuning at lower compute.

DOI 10.64898/2026.09.22.753215

multiple speciesbacteria (other)

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