Yanchao Li, Yusu Zhang, Jiaqing Xie, Yi Ban, Ben Gao, Zhongyu Huang, Tianfan Fu, Yuqiang Li
Parallel decoding speeds up masked diffusion language models by writing several tokens per forward pass. Published commit rules choose these tokens by testing the predicted distributions. Under sampling the written tokens are drawn, and these tests do not see them. We find that answer quality follows the reliability of the tokens actually written. An answer's log probability splits into this reliability and the dependence within each step. We propose PACT, a training-free commit rule that draws the tokens first, certifies the set it will write and spaces the positions of each step apart. This certificate holds at every temperature, and we show that no rule with the same guarantee commits more positions. Experiments use four models of the LLaDA and Dream families and HumanEval, MBPP, GSM8K, MATH500 and IFEval benchmarks. PACT reaches the quality of published commit rules with fewer forward passes. Spacing removes positions from each step, yet it usually lowers the total cost because later steps then write more tokens. At the same speed, published decoders also write a word twice in a row far more often than PACT. These results suggest that commit rules should certify the tokens they write. Code is available at https://github.com/LiZaiyuan0619/PACT.
Fang Wu, Hongbin Lin, Bingchen Duan, Yuchen Wang, Li Erran Li, Yanjie Huang, Mingxuan Cao, Yijun Ma 等 27 位作者
Protein-protein interactions underpin nearly all biological processes. Yet, designing proteins with desired interactions remains challenging due to the structural complexity governing molecular recognition. This study views protein design as a search optimization problem over a combinatorial sequence space under expensive structural evaluation. Toward this goal, we introduce a novel tree-based search framework, ProteoCraft, that employs approximate structural gradients from diffusion-based structure predictors as effective proposal policies to specify where the search should explore. Complete no-gradient inference of folding models separately assigns values to the resulting sequences, determining what is good. ProteoCraft allocates this verification budget through a coarse-to-fine paradigm: multi-site edits first explore distinct sequence basins, then verified promising states undergo strict single-site refinement. Across fourteen de novo binder-design settings spanning eight target proteins, five immune-relevant TCR-facing targets, and four localized CDR redesign tasks, ProteoCraft improves design quality and high-confidence yield. These improvements persist under independent AF2-IG and Rosetta-based interface evaluation. Prospective experimental validation further yielded an 82.9% binding hit rate for PD-L1 miniproteins, with a best measured KD of 0.879 nM, and confirmed binding of designed IFNAR2 VHH. Our code is available at https://github.com/smiles724/ProteoCraft_v1.