7 accepted papers
The finite symmetric group $S_n$ provides a natural domain for permutations, yet learning probability distributions on $S_n$ is challenging due to its factorially growing size and discrete, non-Euclidean structure. Recent permutation diffusion methods define forward noising via shuffle-based random …
Discrete biological sequence optimization demands iterative refinement while satisfying strict syntactic constraints. Diffusion-based approaches provide strong progressive refinement but are not naturally aligned with discrete, grammar-constrained edit operations, whereas autoregressive LLMs readily…
Non-monotonic sequence generation methods, such as masked diffusion models, provide a flexible alternative to left-to-right autoregressive modeling by allowing tokens to be generated in non-fixed and prescribed orders. Despite their practical advantages, most existing non-monotonic models are order-…
Discrete diffusion models offer a flexible, controllable approach to structured sequence generation, yet they still lag behind causal language models in expressive power. A key limitation lies in their reliance on the Markovian assumption, which restricts each step to condition only on the current s…
Proteins play a critical role in carrying out biological functions, and their 3D structures are essential in determining their functions. Accurately predicting the conformation of protein side-chains given their backbones is important for applications in protein structure prediction, design and pro…
In silico prediction of the ligand binding pose to a given protein target is a crucial but challenging task in drug discovery. This work focuses on blind flexible self-docking, where we aim to predict the positions, orientations and conformations of docked molecules. Traditional physics-based method…
We are now witnessing significant progress of deep learning methods in a variety of tasks (or datasets) of proteins. However, there is a lack of a standard benchmark to evaluate the performance of different methods, which hinders the progress of deep learning in this field. In this paper, we propose…