Publications (22)
Minimal-Action Discrete Schrödinger Bridge Matching for Peptide Sequence Design
Shrey Goel, Pranam Chatterjee
Generative modeling of peptide sequences requires navigating a discrete and highly constrained space in which many intermediate states are chemically implausible or unstable. Exist…
PepMLM: Target Sequence-Conditioned Generation of Therapeutic Peptide Binders via Span Masked Language Modeling
Tianlai Chen, Madeleine Dumas, Rio Watson +17
Target proteins that lack accessible binding pockets and conformational stability have posed increasing challenges for drug development. Induced proximity strategies, such as PROTA…
TR2-D2: Tree Search Guided Trajectory-Aware Fine-Tuning for Discrete Diffusion
Sophia Tang, Yuchen Zhu, Molei Tao +1
Reinforcement learning with stochastic optimal control offers a promising framework for diffusion fine-tuning, where a pre-trained diffusion model is optimized to generate paths th…
Rethinking Benchmarks and Models for Enzyme Specificity Prediction
Elizabeth H. Mahood, Natália KomornÃková, Tomáš Pluskal +1
Artificial Intelligence has had a profound impact on the biological sciences, and in particular has accelerated research on protein form and function. Enzymes are no exception: a s…
Path Planning for Masked Diffusion Model Sampling
Fred Zhangzhi Peng, Zachary Bezemek, Sawan Patel +5
Any order generation of discrete data using masked diffusion models (MDMs) offers a compelling alternative to traditional autoregressive models, especially in domains that lack a n…
SF-Cluster: Frustration-Guided MSA Subsampling for Alternative Protein Conformation Recovery
Hanqun Cao, Zijun Gao, Chunbin Gu +3
Deep-learning structure predictors are sensitive to their multiple sequence alignment (MSA) input, making MSA subsampling a practical route to recovering alternative conformations.…