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Simulations, although powerful in accurately replicating real-world systems, often remain inaccessible to non-technical users due to their complexity. Conversely, large language models (LLMs) provide intuitive, language-based interactions…

Computation and Language · Computer Science 2025-05-22 Jacob Kleiman , Kevin Frank , Joseph Voyles , Sindy Campagna

Large language models (LLMs) augmented with external tools are increasingly deployed as deep research agents that gather, reason over, and synthesize web information to answer complex queries. Although recent open-source systems achieve…

Artificial Intelligence · Computer Science 2026-02-24 Yi Wan , Jiuqi Wang , Liam Li , Jinsong Liu , Ruihao Zhu , Zheqing Zhu

Large Language Models (LLMs) like GPT-4 have revolutionized natural language processing, showing remarkable linguistic proficiency and reasoning capabilities. However, their application in strategic multi-agent decision-making environments…

Computation and Language · Computer Science 2024-05-29 Chuanhao Li , Runhan Yang , Tiankai Li , Milad Bafarassat , Kourosh Sharifi , Dirk Bergemann , Zhuoran Yang

With the advent of Large Language Models (LLMs), general-purpose agents have seen fundamental advancements. However, evaluating these agents presents unique challenges that distinguish them from static QA benchmarks. We observe that current…

Artificial Intelligence · Computer Science 2026-05-27 Pengyu Zhu , Li Sun , Philip S. Yu , Sen Su

As the strength of Large Language Models (LLMs) has grown over recent years, so too has interest in their use as the underlying models for autonomous agents. Although LLMs demonstrate emergent abilities and broad expertise across natural…

Artificial Intelligence · Computer Science 2024-12-06 Chris Sypherd , Vaishak Belle

Computational protein design is experiencing a transformation driven by AI/ML. However, the range of potential protein sequences and structures is astronomically vast, even for moderately sized proteins. Hence, achieving convergence between…

Distributed, Parallel, and Cluster Computing · Computer Science 2025-10-09 Aymen Alsaadi , Jonathan Ash , Mikhail Titov , Matteo Turilli , Andre Merzky , Shantenu Jha , Sagar Khare

The rapid advancement of Large Language Models (LLMs) has driven novel applications across diverse domains, with LLM-based agents emerging as a crucial area of exploration. This survey presents a comprehensive analysis of LLM-based agents…

Artificial Intelligence · Computer Science 2025-11-25 Ke Chen , Peiran Wang , Yaoning Yu , Xianyang Zhan , Haohan Wang

Large Language Models (LLMs) have rapidly transformed the landscape of artificial intelligence, enabling natural language interfaces and dynamic orchestration of software components. However, their reliance on probabilistic inference limits…

Machine Learning · Computer Science 2025-07-01 Claudionor Coelho , Yanen Li , Philip Tee

Large Language Models (LLMs) have achieved high accuracy on complex commonsense and mathematical problems that involve the composition of multiple reasoning steps. However, current compositional benchmarks testing these skills tend to focus…

Computation and Language · Computer Science 2026-05-26 Lisa Alazraki , Lihu Chen , Ana Brassard , Joe Stacey , Hossein A. Rahmani , Marek Rei

Large Language Models have demonstrated a remarkable capability in natural language and program generation and software development. However, the source code generated by the LLMs does not always meet quality requirements and may fail to…

Software Engineering · Computer Science 2026-01-26 Viktor Kjellberg , Miroslaw Staron , Farnaz Fotrousi

Protein language models (pLMs) excel in a variety of tasks that range from structure prediction to the design of functional enzymes. However, these models operate as black boxes, and their underlying working principles remain unclear. Here,…

Biomolecules · Quantitative Biology 2025-12-08 Andrea Hunklinger , Noelia Ferruz

Mathematical reasoning is a fundamental capability for large language models (LLMs), yet achieving high performance in this domain remains a significant challenge. The auto-regressive generation process often makes LLMs susceptible to…

Artificial Intelligence · Computer Science 2024-12-02 Xiaoxuan Lou , Chaojie Wang , Bo An

Large language models (LLMs) often struggle with complex reasoning tasks due to their limitations in addressing the vast reasoning space and inherent ambiguities of natural language. We propose the Mixture-of-Search-Agents (MoSA) paradigm,…

Artificial Intelligence · Computer Science 2025-02-27 Sen Yang , Yafu Li , Wai Lam , Yu Cheng

Protein language models learn powerful representations directly from sequences of amino acids. However, they are constrained to generate proteins with only the set of amino acids represented in their vocabulary. In contrast, chemical…

Biomolecules · Quantitative Biology 2023-08-21 Daniel Flam-Shepherd , Kevin Zhu , Alán Aspuru-Guzik

With the rise of large language models (LLMs), researchers are increasingly exploring their applications in var ious vertical domains, such as software engineering. LLMs have achieved remarkable success in areas including code generation…

Software Engineering · Computer Science 2025-04-15 Haolin Jin , Linghan Huang , Haipeng Cai , Jun Yan , Bo Li , Huaming Chen

The emergence of Large Language Models (LLMs) has reshaped agent systems. Unlike traditional rule-based agents with limited task scope, LLM-powered agents offer greater flexibility, cross-domain reasoning, and natural language interaction.…

Artificial Intelligence · Computer Science 2026-05-05 Guannan Liang , Qianqian Tong

Open-source pre-trained Large Language Models (LLMs) exhibit strong language understanding and generation capabilities, making them highly successful in a variety of tasks. However, when used as agents for dealing with complex problems in…

Computation and Language · Computer Science 2024-04-01 Qinhao Zhou , Zihan Zhang , Xiang Xiang , Ke Wang , Yuchuan Wu , Yongbin Li

Large language models (LLMs) have recently demonstrated remarkable capabilities to comprehend human intentions, engage in reasoning, and design planning-like behavior. To further unleash the power of LLMs to accomplish complex tasks, there…

Foundation models, such as large language models (LLMs), have been widely recognised as transformative AI technologies due to their capabilities to understand and generate content, including plans with reasoning capabilities. Foundation…

Artificial Intelligence · Computer Science 2024-04-04 Qinghua Lu , Liming Zhu , Xiwei Xu , Zhenchang Xing , Stefan Harrer , Jon Whittle

Scientific workflows in computational chemistry and materials science typically involve multiple interdependent steps, such as model preparation, system construction, simulation execution, and data analysis, that researchers have refined…