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The Model Context Protocol (MCP) has emerged as a widely adopted mechanism for connecting large language models to external tools and resources. While MCP promises seamless extensibility and rich integrations, it also introduces a…

Cryptography and Security · Computer Science 2025-07-10 Zhihao Li , Kun Li , Boyang Ma , Minghui Xu , Yue Zhang , Xiuzhen Cheng

Bioinformatics web servers are critical resources in modern biomedical research, facilitating interactive exploration of datasets through custom-built interfaces with rich visualization capabilities. However, this human-centric design…

Other Quantitative Biology · Quantitative Biology 2026-02-25 Matthias Flotho , Ian Ferenc Diks , Philipp Flotho , Leidy-Alejandra G. Molano , Pascal Hirsch , Andreas Keller

We present M^3-Bench, the first benchmark for evaluating multimodal tool use under the Model Context Protocol. The benchmark targets realistic, multi-hop and multi-threaded workflows that require visual grounding and textual reasoning,…

Artificial Intelligence · Computer Science 2026-02-05 Yang Zhou , Mingyu Zhao , Zhenting Wang , Difei Gu , Bangwei Guo , Ruosong Ye , Ligong Han , Can Jin , Dimitris N. Metaxas

The Model Context Protocol (MCP) enhances large language models (LLMs) by integrating external tools, enabling dynamic aggregation of real-time data to improve task execution. However, its non-isolated execution context introduces critical…

Computation and Language · Computer Science 2025-08-11 Haoran Shi , Hongwei Yao , Shuo Shao , Shaopeng Jiao , Ziqi Peng , Zhan Qin , Cong Wang

Model Context Protocols (MCPs) provide a unified platform for agent systems to discover, select, and orchestrate tools across heterogeneous execution environments. As MCP-based systems scale to incorporate larger tool catalogs and multiple…

Cryptography and Security · Computer Science 2026-02-19 Yuval Felendler , Parth A. Gandhi , Idan Habler , Yuval Elovici , Asaf Shabtai

The Model Context Protocol (MCP) aims to create a standard for how Large Language Models use tools. However, most current research focuses on selecting tools from an existing pool. A more fundamental, yet largely overlooked, problem is how…

Software Engineering · Computer Science 2026-02-12 Chaoqian Ouyang , Ling Yue , Shimin Di , Libin Zheng , Linan Yue , Shaowu Pan , Jian Yin , Min-Ling Zhang

Effective multi-agent systems cannot be designed by selecting prompts or communication graphs in isolation. Agent behavior depends on the information an agent receives, while the usefulness of a communication edge depends on how the…

Artificial Intelligence · Computer Science 2026-05-28 Yi Ding , Zijie Xuan , Haowei Zhou , Zhenyu Ju , Xiaoxiao Dong , Jingwen Zhang , Xingyu Zhu , Leixin Sun , Haochi Zhang

The Model Context Protocol (MCP) is rapidly emerging as the middleware for LLM-based applications, offering a standardized interface for tool integration. However, its built-in security mechanisms are minimal: while schemas and declarations…

Cryptography and Security · Computer Science 2025-12-04 Biwei Yan , Yue Zhang , Minghui Xu , Hao Wu , Yechao Zhang , Kun Li , Guoming Zhang , Xiuzhen Cheng

Aiming at the problems of computational inefficiency and insufficient interpretability faced by large models in complex tasks such as multi-round reasoning and multi-modal collaboration, this study proposes a three-layer collaboration…

Computation and Language · Computer Science 2025-09-23 Luyan Zhang

Healthcare AI systems have historically faced challenges in merging contextual reasoning, long-term state management, and human-verifiable workflows into a cohesive framework. This paper introduces a completely innovative architecture and…

Artificial Intelligence · Computer Science 2025-12-08 Zag ElSayed , Craig Erickson , Ernest Pedapati

As Agentic AI gain mainstream adoption, the industry invests heavily in model capabilities, achieving rapid leaps in reasoning and quality. However, these systems remain largely confined to data silos, and each new integration requires…

Cryptography and Security · Computer Science 2025-05-20 Sonu Kumar , Anubhav Girdhar , Ritesh Patil , Divyansh Tripathi

The variety of data in data lakes presents significant challenges for data analytics, as data scientists must simultaneously analyze multi-modal data, including structured, semi-structured, and unstructured data. While Large Language Models…

Databases · Computer Science 2025-05-19 Chao Zhang , Shaolei Zhang , Quehuan Liu , Sibei Chen , Tong Li , Ju Fan

The Model Context Protocol (MCP) has rapidly emerged as a universal standard for connecting AI assistants to external tools and data sources. While MCP simplifies integration between AI applications and various services, it introduces…

Cryptography and Security · Computer Science 2026-03-25 Charoes Huang , Xin Huang , Ngoc Phu Tran , Amin Milani Fard

Large language models are increasingly expected to serve as general-purpose agents that interact with external, stateful tool environments. The Model Context Protocol (MCP) and broader agent skills offer a unified interface for connecting…

Model Context Protocol (MCP) enables agents to interact with external tools, yet empirical research on MCP is hindered by the lack of large-scale, accessible datasets. We present MCPZoo, the largest and most comprehensive dataset of MCP…

Cryptography and Security · Computer Science 2025-12-29 Mengying Wu , Pei Chen , Geng Hong , Baichao An , Jinsong Chen , Binwang Wan , Xudong Pan , Jiarun Dai , Min Yang

Large Language Models (LLMs) based agent systems have made great strides in real-world applications beyond traditional NLP tasks. This paper proposes a new LLM-based Multi-Agent System (LLM-MAS) benchmark, Collab-Overcooked, built on the…

Computation and Language · Computer Science 2025-12-02 Haochen Sun , Shuwen Zhang , Lujie Niu , Lei Ren , Hao Xu , Hao Fu , Fangkun Zhao , Caixia Yuan , Xiaojie Wang

Large language models and autonomous AI agents have evolved rapidly, resulting in a diverse array of evaluation benchmarks, frameworks, and collaboration protocols. Driven by the growing need for standardized evaluation and integration, we…

Artificial Intelligence · Computer Science 2026-03-10 Mohamed Amine Ferrag , Norbert Tihanyi , Merouane Debbah

Information seeking is a fundamental requirement for humans. However, existing LLM agents rely heavily on open-web search, which exposes two fundamental weaknesses: online content is noisy and unreliable, and many real-world tasks require…

Computation and Language · Computer Science 2025-10-07 Yaxin Du , Yuanshuo Zhang , Xiyuan Yang , Yifan Zhou , Cheng Wang , Gongyi Zou , Xianghe Pang , Wenhao Wang , Menglan Chen , Shuo Tang , Zhiyu Li , Feiyu Xiong , Siheng Chen

Temporal reasoning and planning are essential capabilities for large language models (LLMs), yet most existing benchmarks evaluate them in isolation and under limited forms of complexity. To address this gap, we introduce the Temporal…

Artificial Intelligence · Computer Science 2025-10-14 Zifeng Ding , Sikuan Yan , Zhangdie Yuan , Xianglong Hu , Fangru Lin , Andreas Vlachos

Large language models (LLMs) are essential tools that users employ across various scenarios, so evaluating their performance and guiding users in selecting the suitable service is important. Although many benchmarks exist, they mainly focus…

Computation and Language · Computer Science 2024-09-23 Jiayin Wang , Fengran Mo , Weizhi Ma , Peijie Sun , Min Zhang , Jian-Yun Nie
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