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Jian-Wen Xie

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#machine learning Preprint Oct 2026

InstructPro2: Natural Language and Biological Grounding Guided De Novo Protein Design

The ability to generate proteins with desired functions is a central goal of computational biology. Although natural language can express diverse design objectives, existing protein generation methods often support only narrow tasks or make limited use of biological constraints. We develop InstructPro2 to translate nat...

Charles Novak, Zhenqiao Song, Chuan Li et al. · 0 citations
#machine learning Preprint Oct 2026

TurboPairFormer: Fast and Stable Protein Folding Model Training with an Optimized Triangle Attention Kernel

Triangular attention is a core computation in AlphaFold3-style biomolecular models, with cubic cost in token count. Its shared pair bias adds a gradient reduction across attention slices to the usual reductions over queries and keys. The open-source backends we examine handle these reductions through repeated probabili...

Yi-De Ran, Chelsea Lowman, J. Domanski et al. · 0 citations

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