3 papers
cs.LG2026
Reading the Cell, Designing the Cure: Perturbation-Conditioned Molecular Diffusion for Function-Oriented Drug Design
Ziyu Xu, Zijian Zhang, Liang Wang +3
When reliable target structures are unavailable at scale or phenotypes arise from dysregulated pathways, transcriptomic perturbations provide a system-level functional readout for…
q-bio.BM2025
EnzyControl: Adding Functional and Substrate-Specific Control for Enzyme Backbone Generation
Chao Song, Zhiyuan Liu, Han Huang +6
Designing enzyme backbones with substrate-specific functionality is a critical challenge in computational protein engineering. Current generative models excel in protein design but…
cs.LG2025
3D-GSRD: 3D Molecular Graph Auto-Encoder with Selective Re-mask Decoding
Chang Wu, Zhiyuan Liu, Wen Shu +6
Masked graph modeling (MGM) is a promising approach for molecular representation learning (MRL).However, extending the success of re-mask decoding from 2D to 3D MGM is non-trivial,…