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Related papers: MCPmed: A Call for MCP-Enabled Bioinformatics Web …

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Bioinformatics tools are essential for complex computational biology tasks, yet their integration with emerging AI-agent frameworks is hindered by incompatible interfaces, heterogeneous input-output formats, and inconsistent parameter…

Quantitative Methods · Quantitative Biology 2025-10-03 Florensia Widjaja , Zhangtianyi Chen , Juexiao Zhou

Large language model (LLM)-powered agents are increasingly used to plan and execute scientific workflows, yet most research cyberinfrastructure (CI) exposes heterogeneous APIs and implements security models that present barriers for use by…

Current AI agents create significant barriers for users by requiring extensive processing to understand web pages, making AI-assisted web interaction slow and expensive. This paper introduces webMCP (Web Machine Context & Procedure), a…

Networking and Internet Architecture · Computer Science 2025-08-14 D. Perera

With the rise of LLMs, a large number of Model Context Protocol (MCP) services have emerged since the end of 2024. However, the effectiveness and efficiency of MCP servers have not been well studied. To study these questions, we propose an…

Information Retrieval · Computer Science 2025-04-21 Zhiling Luo , Xiaorong Shi , Xuanrui Lin , Jinyang Gao

Background: Large language models (LLMs) show promise in medicine, but their deployment in hospitals is limited by restricted access to electronic health record (EHR) systems. The Model Context Protocol (MCP) enables integration between…

Artificial Intelligence · Computer Science 2025-09-22 Kanato Masayoshi , Masahiro Hashimoto , Ryoichi Yokoyama , Naoki Toda , Yoshifumi Uwamino , Shogo Fukuda , Ho Namkoong , Masahiro Jinzaki

The Model Context Protocol (MCP) has recently emerged as a standardized interface for connecting language models with external tools and data. As the ecosystem rapidly expands, the lack of a structured, comprehensive view of existing MCP…

Cryptography and Security · Computer Science 2025-07-01 Zhiwei Lin , Bonan Ruan , Jiahao Liu , Weibo Zhao

Model Context Protocol (MCP) servers contain a collection of thousands of open-source standardized tools, linking LLMs to external systems; however, existing datasets and benchmarks lack realistic, human-like user queries, remaining a…

Artificial Intelligence · Computer Science 2026-03-02 Shubh Laddha , Lucas Changbencharoen , Win Kuptivej , Surya Shringla , Archana Vaidheeswaran , Yash Bhaskar

Large Language Models (LLMs) are increasingly augmented with external tools through standardized interfaces like the Model Context Protocol (MCP). However, current MCP implementations face critical limitations: they typically require local…

Cryptography and Security · Computer Science 2026-03-11 Arash Ahmadi , Sarah Sharif , Yaser M. Banad

The rapid expansion of the model context protocol (MCP) ecosystem enables large language model (LLM)-based agents to access a wide range of external tools via a standardized interface. However, identifying appropriate MCP servers for a…

Software Engineering · Computer Science 2026-04-21 Shiyu He , Zhiman Chen , Yuqi Zhao , Neng Zhang , Ran Mo , Yutao Ma

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) 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

The integration of large language models (LLMs) into scientific research is accelerating the realization of autonomous ``AI Scientists.'' While recent advancements have empowered AI to formulate hypotheses and design experiments, a critical…

Quantum Physics · Physics 2026-05-27 Masaki Shiraishi , Ikko Hamamura , Tatsuya Ishigaki , Tadashi Kadowaki

Large Language Models (LLMs) increasingly rely on external tools to perform complex, realistic tasks, yet their ability to utilize the rapidly expanding Model Contextual Protocol (MCP) ecosystem remains limited. Existing MCP research covers…

Artificial Intelligence · Computer Science 2026-04-17 Wenhao Wang , Peizhi Niu , Zhao Xu , Zhaoyu Chen , Jian Du , Yaxin Du , Xianghe Pang , Keduan Huang , Yanfeng Wang , Qiang Yan , Siheng Chen

The Model Context Protocol has emerged as a transformative standard for connecting large language models to external data sources and tools, rapidly gaining adoption across major AI providers and development platforms. However, existing…

Artificial Intelligence · Computer Science 2025-08-21 Ziyang Luo , Zhiqi Shen , Wenzhuo Yang , Zirui Zhao , Prathyusha Jwalapuram , Amrita Saha , Doyen Sahoo , Silvio Savarese , Caiming Xiong , Junnan Li

Large Language Models (LLMs) remain static in functionality after training, and extending their capabilities requires integration with external data, computation, and services. The Model Context Protocol (MCP) has emerged as a standard…

Networking and Internet Architecture · Computer Science 2025-10-16 Enhan Li , Hongyang Du , Kaibin Huang

Backgrounds: Artificial intelligence (AI) is transforming healthcare, yet translating AI models from theoretical frameworks to real-world clinical applications remains challenging. The Mayo Clinic Platform (MCP) was established to address…

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

Large language models (LLMs) are evolving into agentic systems that reason, plan, and operate external tools. The Model Context Protocol (MCP) is a key enabler of this transition, offering a standardized interface for connecting LLMs with…

Computation and Language · Computer Science 2026-03-06 Xuanjun Zong , Zhiqi Shen , Lei Wang , Yunshi Lan , Chao Yang

We introduce MCP-Bench, a benchmark for evaluating large language models (LLMs) on realistic, multi-step tasks that demand tool use, cross-tool coordination, precise parameter control, and planning/reasoning for solving tasks. Built on the…

Computation and Language · Computer Science 2025-08-29 Zhenting Wang , Qi Chang , Hemani Patel , Shashank Biju , Cheng-En Wu , Quan Liu , Aolin Ding , Alireza Rezazadeh , Ankit Shah , Yujia Bao , Eugene Siow

The Model Context Protocol (MCP) has emerged as a standardized interface enabling seamless integration between Large Language Models (LLMs) and external data sources and tools. While MCP significantly reduces development complexity and…

Cryptography and Security · Computer Science 2025-10-29 Bin Wang , Zexin Liu , Hao Yu , Ao Yang , Yenan Huang , Jing Guo , Huangsheng Cheng , Hui Li , Huiyu Wu
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