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.
Yunxiang MO, Tianshi Zheng The Hong Kong University of Science and Technology, Qing Zong, Jiayu Liu, Baixuan Xu Hong Kong University of Science and Technology, Yauwai Yim, Chunkit Chan, Jiaxin Bai Hong Kong Baptist University 等 9 位作者
Multimodal abductive reasoning — the generation and selection of explanatory hypotheses from partial observations — is a cornerstone of intelligence. Current evaluations of such ability in vision–language models (VLMs) are largely confined to static, single-agent tasks. Inspired by Dixit, we introduce DixitWorld, a comprehensive evaluation suite designed to deconstruct this challenge. DixitWorld features two core components: DixitArena, a dynamic, multi-agent environment that evaluates both hypothesis generation (a “storyteller” crafting cryptic clues) and hypothesis selection (“listeners” choosing the target image from decoys) under imperfect information; and DixitBench, a static QA benchmark that isolates the listener’s task for efficient, controlled evaluation. Results from DixitArena reveal distinct, role-dependent behaviors: smaller open-source models often excel as creative storytellers, producing imaginative yet less discriminative clues, whereas larger proprietary models demonstrate superior overall performance, particularly as listeners. Performance on DixitBench strongly correlates with listener results in DixitArena, validating it as a reliable proxy for hypothesis selection. Our findings reveal a key trade-off between generative creativity and discriminative understanding in multimodal abductive reasoning, a central challenge for developing more balanced and capable vision-language agents.
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cs.CL · cs.MA · cs.CV
Proceedings of the 64th Annual Meeting of the Association for Computational Linguistics (Volume 2: Short Papers) · 2026 · 正式发表