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Large Language Models (LLMs) have made significant progress in open-ended dialogue, yet their inability to retain and retrieve relevant information from long-term interactions limits their effectiveness in applications requiring sustained…

Designing protein sequences that fold into a target 3D structure, known as protein inverse folding, is a fundamental challenge in protein engineering. While recent deep learning methods have achieved impressive performance by recovering…

Biomolecules · Quantitative Biology 2025-06-03 Mengdi Liu , Xiaoxue Cheng , Zhangyang Gao , Hong Chang , Cheng Tan , Shiguang Shan , Xilin Chen

Large language models (LLMs), when guided by explicit textual plans, can perform reliable step-by-step reasoning during problem-solving. However, generating accurate and effective textual plans remains challenging due to LLM hallucinations…

Computation and Language · Computer Science 2026-01-01 Sijia Chen , Di Niu

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Artificial Intelligence · Computer Science 2025-04-21 Yijia Xiao , Edward Sun , Yiqiao Jin , Qifan Wang , Wei Wang

While most efforts to improve LLM-based tool-using agents focus on the agent itself - through larger models, better prompting, or fine-tuning - agent performance increasingly plateaus due to the quality of the tool interfaces these agents…

Artificial Intelligence · Computer Science 2026-04-30 Ruocheng Guo , Kaiwen Dong , Xiang Gao , Kamalika Das

The global demand for sustainable protein sources has accelerated the need for intelligent tools that can rapidly process and synthesise domain-specific scientific knowledge. In this study, we present a proof-of-concept multi-agent…

Artificial Intelligence · Computer Science 2025-06-26 Alexander D. Kalian , Jaewook Lee , Stefan P. Johannesson , Lennart Otte , Christer Hogstrand , Miao Guo

Despite the remarkable success of large language models (LLMs) on traditional natural language processing tasks, their planning ability remains a critical bottleneck in tackling complex multi-step reasoning tasks. Existing approaches mainly…

Computation and Language · Computer Science 2024-10-07 Jiaxin Wen , Jian Guan , Hongning Wang , Wei Wu , Minlie Huang

Large Language Models (LLMs) have demonstrated impressive capability in many natural language tasks. However, the auto-regressive generation process makes LLMs prone to produce errors, hallucinations and inconsistent statements when…

Artificial Intelligence · Computer Science 2024-07-23 Chaojie Wang , Yanchen Deng , Zhiyi Lyu , Liang Zeng , Jujie He , Shuicheng Yan , Bo An

LLMs have demonstrated commendable performance across diverse domains. Nevertheless, formulating high-quality prompts to assist them in their work poses a challenge for non-AI experts. Existing research in prompt engineering suggests…

Computation and Language · Computer Science 2024-09-23 Ming Wang , Yuanzhong Liu , Xiaoyu Liang , Yijie Huang , Daling Wang , Xiaocui Yang , Sijia Shen , Shi Feng , Xiaoming Zhang , Chaofeng Guan , Yifei Zhang

The ability to automatically generate accurate protocols for scientific experiments would represent a major step towards the automation of science. Large Language Models (LLMs) have impressive capabilities on a wide range of tasks, such as…

Computation and Language · Computer Science 2023-10-17 Odhran O'Donoghue , Aleksandar Shtedritski , John Ginger , Ralph Abboud , Ali Essa Ghareeb , Justin Booth , Samuel G Rodriques

This paper introduces a novel framework that leverages large language models (LLMs) for machine translation (MT). We start with one conjecture: an ideal translation should contain complete and accurate information for a strong enough LLM to…

Computation and Language · Computer Science 2024-11-06 Jianqiao Wangni

The constitutional framework of alignment aims to align large language models (LLMs) with value-laden principles written in natural language (such as to avoid using biased language). Prior work has focused on parameter fine-tuning…

Computation and Language · Computer Science 2026-01-27 Henry Bell , Caroline Zhang , Mohammed Mobasserul Haque , Dhaval Potdar , Samia Zaman , Brandon Fain

Automated planning using a symbolic planning language, such as PDDL, is a general approach to producing optimal plans to achieve a stated goal. However, creating suitable machine understandable descriptions of the planning domain, problem,…

Artificial Intelligence · Computer Science 2025-10-10 Owen Burns , Dana Hughes , Katia Sycara

User modeling in large e-commerce platforms aims to optimize user experiences by incorporating various customer activities. Traditional models targeting a single task often focus on specific business metrics, neglecting the comprehensive…

Information Retrieval · Computer Science 2025-02-28 Mingdai Yang , Fan Yang , Yanhui Guo , Shaoyuan Xu , Tianchen Zhou , Yetian Chen , Simone Shao , Jia Liu , Yan Gao

LLMs have recently been used to generate Python programs representing generalized plans in PDDL planning, i.e., plans that generalize across the tasks of a given PDDL domain. Previous work proposed a framework consisting of three steps: the…

Artificial Intelligence · Computer Science 2026-03-23 Katharina Stein , Nils Hodel , Daniel Fišer , Jörg Hoffmann , Michael Katz , Alexander Koller

Large Language Models (LLMs) have shown remarkable performance in various natural language processing tasks but face challenges in mathematical reasoning, where complex problem-solving requires both linguistic understanding and mathematical…

Computation and Language · Computer Science 2025-03-20 Shuguang Chen , Guang Lin

Real-world path planning tasks typically involve multiple constraints beyond simple route optimization, such as the number of routes, maximum route length, depot locations, and task-specific requirements. Traditional approaches rely on…

Computation and Language · Computer Science 2026-03-23 Dylan Shim , Minghan Wei

Pre-trained language models (PrLM) has been shown powerful in enhancing a broad range of downstream tasks including various dialogue related ones. However, PrLMs are usually trained on general plain text with common language model (LM)…

Computation and Language · Computer Science 2021-08-03 Yi Xu , Hai Zhao

There is a growing interest in applying pre-trained large language models (LLMs) to planning problems. However, methods that use LLMs directly as planners are currently impractical due to several factors, including limited correctness of…

Artificial Intelligence · Computer Science 2023-11-03 Lin Guan , Karthik Valmeekam , Sarath Sreedharan , Subbarao Kambhampati

Large language models (LLMs) have been increasingly used to interact with external environments (e.g., games, compilers, APIs) as goal-driven agents. However, it remains challenging for these language agents to quickly and efficiently learn…

Artificial Intelligence · Computer Science 2023-10-11 Noah Shinn , Federico Cassano , Edward Berman , Ashwin Gopinath , Karthik Narasimhan , Shunyu Yao