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Designing proteins that satisfy natural language functional requirements is a central goal in protein engineering. A straightforward baseline is to fine-tune generic instruction-tuned LLMs as direct text-to-sequence generators, but this is…

Quantitative Methods · Quantitative Biology 2026-04-21 Yutang Ge , Guojiang Zhao , Sihang Li , Zheng Cheng , Zifeng Zhao , Hanchen Xia , Guolin Ke , Linfeng Zhang , Zhifeng Gao , Yuguang Wang

A number of flexible tactic-based logical frameworks are nowadays available that can implement a wide range of mathematical theories using a common higher-order metalanguage. Used as proof assistants, one of the advantages of such powerful…

Logic in Computer Science · Computer Science 2010-03-26 João Marcos

We investigate how large language models can be used as research tools in scientific computing while preserving mathematical rigor. We propose a human-in-the-loop workflow for interactive theorem proving and discovery with LLMs. Human…

Human-Computer Interaction · Computer Science 2025-12-12 Chenyi Li , Zhijian Lai , Dong An , Jiang Hu , Zaiwen Wen

Lead optimization in drug discovery requires efficiently navigating vast chemical space through iterative cycles to enhance molecular properties while preserving structural similarity to the original lead compound. Despite recent advances,…

Machine Learning · Computer Science 2025-09-29 Ziqing Wang , Yibo Wen , William Pattie , Xiao Luo , Weimin Wu , Jerry Yao-Chieh Hu , Abhishek Pandey , Han Liu , Kaize Ding

Chain-of-Thought (CoT) prompting has proven to be effective in enhancing the reasoning capabilities of Large Language Models (LLMs) with at least 100 billion parameters. However, it is ineffective or even detrimental when applied to…

Computation and Language · Computer Science 2023-10-24 Chengcheng Han , Xiaowei Du , Che Zhang , Yixin Lian , Xiang Li , Ming Gao , Baoyuan Wang

This work introduces Symbolic-Aided Chain-of-Thought (CoT), an improved approach to standard CoT, for logical reasoning in large language models (LLMs). The key idea is to integrate lightweight symbolic representations into few-shot…

Artificial Intelligence · Computer Science 2025-10-07 Phuong Minh Nguyen , Tien Huu Dang , Naoya Inoue

AI-assisted research compresses ideation, implementation, evaluation, and manuscript writing into a single interactive loop. This compression is useful, but it also creates a publication risk: paper claims can become easier to state than to…

Artificial Intelligence · Computer Science 2026-05-28 Yihan Xia , Taotao Wang

We present an in-context learning agent for formal theorem-proving in environments like Lean and Coq. Current state-of-the-art models for the problem are finetuned on environment-specific proof data. By contrast, our approach, called COPRA,…

Machine Learning · Computer Science 2024-08-09 Amitayush Thakur , George Tsoukalas , Yeming Wen , Jimmy Xin , Swarat Chaudhuri

LLMs can perform multi-step reasoning through Chain-of-Thought (CoT), but they cannot reliably verify their own logic. Even when they reach correct answers, the underlying reasoning may be flawed, undermining trust in high-stakes scenarios.…

Artificial Intelligence · Computer Science 2025-11-07 Yu Feng , Nathaniel Weir , Kaj Bostrom , Sam Bayless , Darion Cassel , Sapana Chaudhary , Benjamin Kiesl-Reiter , Huzefa Rangwala

Recent advances in large language models (LLMs) have popularized test-time scaling, where models generate additional reasoning tokens before producing final answers. These approaches have demonstrated significant performance improvements on…

Artificial Intelligence · Computer Science 2026-01-13 Wenxun Wu , Yuanyang Li , Guhan Chen , Linyue Wang , Hongyang Chen

Theorem proving is a fundamental aspect of mathematics, spanning from informal reasoning in natural language to rigorous derivations in formal systems. In recent years, the advancement of deep learning, especially the emergence of large…

Artificial Intelligence · Computer Science 2024-08-23 Zhaoyu Li , Jialiang Sun , Logan Murphy , Qidong Su , Zenan Li , Xian Zhang , Kaiyu Yang , Xujie Si

As knowledge and semantics on the web grow increasingly complex, enhancing Large Language Models (LLMs)' comprehension and reasoning capabilities has become particularly important. Chain-of-Thought (CoT) prompting has been shown to enhance…

Artificial Intelligence · Computer Science 2026-01-21 Ke Chen , Jiandian Zeng , Zihao Peng , Guo Li , Guangxue Zhang , Tian Wang

Formal verification is a promising method for producing reliable software, but the difficulty of manually writing verification proofs severely limits its utility in practice. Recent methods have automated some proof synthesis by guiding a…

Software Engineering · Computer Science 2024-12-18 Alex Sanchez-Stern , Abhishek Varghese , Zhanna Kaufman , Dylan Zhang , Talia Ringer , Yuriy Brun

Neural theorem proving has advanced rapidly in the past year, reaching IMO gold-medalist capabilities and producing formal proofs that span thousands of lines. Although such proofs are mechanically verified by formal systems like Lean,…

Machine Learning · Computer Science 2025-10-20 Alex Gu , Bartosz Piotrowski , Fabian Gloeckle , Kaiyu Yang , Aram H. Markosyan

Automated theorem proving (ATP) has become an appealing domain for exploring the reasoning ability of the recent successful generative language models. However, current ATP benchmarks mainly focus on symbolic inference, but rarely involve…

Traditional automated theorem provers for first-order logic depend on speed-optimized search and many handcrafted heuristics that are designed to work best over a wide range of domains. Machine learning approaches in literature either…

Artificial Intelligence · Computer Science 2021-12-21 Eser Aygün , Laurent Orseau , Ankit Anand , Xavier Glorot , Vlad Firoiu , Lei M. Zhang , Doina Precup , Shibl Mourad

Reinforcement Learning with Verifiable Rewards (RLVR) has become a central post-training paradigm for improving the reasoning capabilities of large language models. Yet existing methods share a common blind spot: they optimize policies…

Machine Learning · Computer Science 2026-04-29 Huaiyang Wang , Xiaojie Li , Deqing Wang , Haoyi Zhou , Zixuan Huang , Yaodong Yang , Jianxin Li , Yikun Ban

We present a tool for modelling and reasoning with knowledge from various diverse (and possibly conflicting) viewpoints. The theoretical underpinnings are provided by enhancing base logics by standpoints according to a recently introduced…

Artificial Intelligence · Computer Science 2023-05-02 Florian Emmrich , Lucía Gómez Álvarez , Hannes Strass

Proust is a small Racket program offering rudimentary interactive assistance in the development of verified proofs for propositional and predicate logic. It is constructed in stages, some of which are done by students before using it to…

Programming Languages · Computer Science 2016-11-30 Prabhakar Ragde

While Reinforcement Learning for Verifiable Rewards (RLVR) is powerful for training large reasoning models, its training dynamics harbor a critical challenge: RL overfitting, where models gain training rewards but lose generalization. Our…

Artificial Intelligence · Computer Science 2025-11-07 Zeng Zhiyuan , Jiashuo Liu , Zhangyue Yin , Ge Zhang , Wenhao Huang , Xipeng Qiu