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Recent improvements in large language models (LLMs) have had a dramatic effect on capabilities and productivity across many disciplines involving critical thinking and writing. The development of the model context protocol (MCP) provides a…

We present a refined approach to biomedical question-answering (QA) services by integrating large language models (LLMs) with Multi-BERT configurations. By enhancing the ability to process and prioritize vast amounts of complex biomedical…

Computation and Language · Computer Science 2024-10-18 Cheng Qian , Xianglong Shi , Shanshan Yao , Yichen Liu , Fengming Zhou , Zishu Zhang , Junaid Akram , Ali Braytee , Ali Anaissi

Current LLM agents are proficient at calling isolated APIs but struggle with the "last mile" of commercial software automation. In real-world scenarios, tools are not independent; they are atomic, interdependent, and prone to environmental…

Artificial Intelligence · Computer Science 2026-05-21 Yuanyang Li , Xue Yang , Longyue Wang , Weihua Luo , Hongyang Chen

Large language models (LLMs) such as ChatGPT have gained considerable interest across diverse research communities. Their notable ability for text completion and generation has inaugurated a novel paradigm for language-interfaced problem…

Quantitative Methods · Quantitative Biology 2024-02-22 Hengchuang Yin , Zhonghui Gu , Fanhao Wang , Yiparemu Abuduhaibaier , Yanqiao Zhu , Xinming Tu , Xian-Sheng Hua , Xiao Luo , Yizhou Sun

Large language models translate natural language into database queries, yet context window limitations prevent direct deployment in reporting systems where complete datasets exhaust available tokens. The Model Context Protocol specification…

Software Engineering · Computer Science 2025-10-08 Scott Frees

Traditional bibliography databases require users to navigate search forms and manually copy citation data. Language models offer an alternative: a natural-language interface where researchers write text with informal citation fragments,…

Digital Libraries · Computer Science 2026-02-03 Stefan Szeider

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

Advancements in large language models (LLMs) have unlocked remarkable capabilities. While deploying these models typically requires server-grade GPUs and cloud-based inference, the recent emergence of smaller open-source models and…

Model Context Protocol (MCP) have quickly become the interface layer between LLM agents and external tools, yet they also introduce unsafe data flows that existing analyzers handle poorly. Vulnerabilities manifest in two directions:…

Software Engineering · Computer Science 2026-05-11 Xinyi Hou , Yanjie Zhao , Haoyu Wang

The biomedical literature contains a vast collection of omics studies, yet most published data remain functionally inaccessible for computational reuse. When raw data are deposited in public repositories, essential information for…

Genomics · Quantitative Biology 2026-03-16 Alexandre Hutton , Jesse G. Meyer

Modern AI technologies for drug discovery are distributed across heterogeneous platforms-including web applications, desktop environments, and code libraries-leading to fragmented workflows, inconsistent interfaces, and high integration…

The Model Context Protocol (MCP) replaces static, developer-controlled API integrations with more dynamic, user-driven agent systems, which also introduces new security risks. As MCP adoption grows across community servers and major…

Cryptography and Security · Computer Science 2025-11-27 Herman Errico , Jiquan Ngiam , Shanita Sojan

Large Language Models (LLMs) exhibit strong general-purpose reasoning abilities but lack access to wireless environment information due to the absence of native sensory input and domain-specific priors. Previous attempts to apply LLMs in…

Networking and Internet Architecture · Computer Science 2025-05-06 Zongxi Liu , Hongyang Du

The Model Context Protocol (MCP) is a new and emerging technology that extends the functionality of large language models, improving workflows but also exposing users to a new attack surface. Several studies have highlighted related…

Cryptography and Security · Computer Science 2026-04-14 Tobias Mattsson , Samuel Nyberg , Anton Borg , Ricardo Britto

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

Large language models (LLMs) that have been trained on a corpus that includes large amount of code exhibit a remarkable ability to understand HTML code. As web interfaces are primarily constructed using HTML, we design an in-depth study to…

Computation and Language · Computer Science 2023-12-12 Faria Huq , Jeffrey P. Bigham , Nikolas Martelaro

The Model Context Protocol (MCP) is an open and standardized interface that enables large language models (LLMs) to interact with external tools and services, and is increasingly adopted by AI agents. However, the security of MCP-based…

Cryptography and Security · Computer Science 2026-03-10 Yuhang Huang , Boyang Ma , Biwei Yan , Xuelong Dai , Yechao Zhang , Minghui Xu , Kaidi Xu , Yue Zhang

The Model Context Protocol (MCP) enables large language models to invoke external tools through natural-language descriptions, forming the foundation of many AI agent applications. However, MCP does not enforce consistency between…

Cryptography and Security · Computer Science 2026-02-04 Zhihao Li , Boyang Ma , Xuelong Dai , Minghui Xu , Yue Zhang , Biwei Yan , Kun Li

While Large Language Models (LLMs) have achieved remarkable performance, they remain vulnerable to jailbreak. The integration of Large Language Models (LLMs) with external tools via protocols such as the Model Context Protocol (MCP)…

Cryptography and Security · Computer Science 2026-01-09 Wenpeng Xing , Zhonghao Qi , Yupeng Qin , Yilin Li , Caini Chang , Jiahui Yu , Changting Lin , Zhenzhen Xie , Meng Han

While powerful and well-established, tools like ParaView present a steep learning curve that discourages many potential users. This work introduces ParaView-MCP, an autonomous agent that integrates modern multimodal large language models…

Human-Computer Interaction · Computer Science 2025-05-13 Shusen Liu , Haichao Miao , Peer-Timo Bremer
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