arXiv subjects

Bingchen Duan

Publications and source records attributed to Bingchen Duan.

3 recordsLinked to original sources

arXiv2026

ProteoCraft: Protein Design as Proposal-Verification Search

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.

cs.CE↗

arXiv2026

Distilling the Thought, Watermarking the Answer: A Principle Semantic Guided Watermark for Large Reasoning Models

Reasoning Large Language Models (RLLMs) excelling in complex tasks present unique challenges for digital watermarking, as existing methods often disrupt logical coherence or incur high computational costs. Token-based watermarking techniques can corrupt the reasoning flow by applying pseudo-random biases, while semantic-aware approaches improve quality but introduce significant latency or require auxiliary models. This paper introduces ReasonMark, a novel watermarking framework specifically designed for reasoning-intensive LLMs. Our approach decouples generation into an undisturbed Thinking Phase and a watermarked Answering Phase. We propose a Criticality Score to identify semantically pivotal tokens from the reasoning trace, which are distilled into a Principal Semantic Vector (PSV). The PSV then guides a semantically-adaptive mechanism that modulates watermark strength based on token-PSV alignment, ensuring robustness without compromising logical integrity. Extensive experiments show ReasonMark surpasses state-of-the-art methods by reducing text Perplexity by 0.35, increasing translation BLEU score by 0.164, and raising mathematical accuracy by 0.67 points. These advancements are achieved alongside a 0.34% higher watermark detection AUC and stronger robustness to attacks, all with a negligible increase in latency. This work enables the traceable and trustworthy deployment of reasoning LLMs in real-world applications.

cs.AI↗

arXiv2025

A Survey on Proactive Defense Strategies Against Misinformation in Large Language Models

The widespread deployment of large language models (LLMs) across critical domains has amplified the societal risks posed by algorithmically generated misinformation. Unlike traditional false content, LLM-generated misinformation can be self-reinforcing, highly plausible, and capable of rapid propagation across multiple languages, which traditional detection methods fail to mitigate effectively. This paper introduces a proactive defense paradigm, shifting from passive post hoc detection to anticipatory mitigation strategies. We propose a Three Pillars framework: (1) Knowledge Credibility, fortifying the integrity of training and deployed data; (2) Inference Reliability, embedding self-corrective mechanisms during reasoning; and (3) Input Robustness, enhancing the resilience of model interfaces against adversarial attacks. Through a comprehensive survey of existing techniques and a comparative meta-analysis, we demonstrate that proactive defense strategies offer up to 63\% improvement over conventional methods in misinformation prevention, despite non-trivial computational overhead and generalization challenges. We argue that future research should focus on co-designing robust knowledge foundations, reasoning certification, and attack-resistant interfaces to ensure LLMs can effectively counter misinformation across varied domains.

cs.IR↗