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Large Language Model (LLM) agents have shown significant autonomous capabilities in dynamically searching and incorporating relevant tools or Model Context Protocol (MCP) servers for individual queries. However, fixed context windows limit…

Computation and Language · Computer Science 2025-07-30 Elias Lumer , Anmol Gulati , Vamse Kumar Subbiah , Pradeep Honaganahalli Basavaraju , James A. Burke

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

Constraint Programming (CP) and Machine Learning (ML) face challenges in text generation due to CP's struggle with implementing "meaning'' and ML's difficulty with structural constraints. This paper proposes a solution by combining both…

Computation and Language · Computer Science 2024-09-26 Florian Régin , Elisabetta De Maria , Alexandre Bonlarron

The Model Context Protocol (MCP) plays a crucial role in extending the capabilities of Large Language Models (LLMs) by enabling integration with external tools and data sources. However, the standard MCP specification presents significant…

Cryptography and Security · Computer Science 2025-06-03 Manish Bhatt , Vineeth Sai Narajala , Idan Habler

Large Language Model (LLM) coding agents typically explore codebases through repeated file-reading and grep-searching, consuming thousands of tokens per query without structural understanding. We present Codebase-Memory, an open-source…

Software Engineering · Computer Science 2026-03-31 Martin Vogel , Falk Meyer-Eschenbach , Severin Kohler , Elias Grünewald , Felix Balzer

While Transformer language models (LMs) are state-of-the-art for information extraction, long text introduces computational challenges requiring suboptimal preprocessing steps or alternative model architectures. Sparse attention LMs can…

Computation and Language · Computer Science 2022-12-01 Joel Stremmel , Brian L. Hill , Jeffrey Hertzberg , Jaime Murillo , Llewelyn Allotey , Eran Halperin

The integration of Large Language Models (LLMs) into network operations (AIOps) is hindered by two fundamental challenges: the stochastic grounding problem, where LLMs struggle to reliably parse unstructured, vendor-specific CLI output, and…

Networking and Internet Architecture · Computer Science 2026-02-02 Devansh Lodha , Mohit Panchal , Sameer G. Kulkarni

Large Language Model (LLM) agents face security vulnerabilities spanning AI-specific and traditional software domains, yet current research addresses these separately. This study bridges this gap through comparative evaluation of Function…

Cryptography and Security · Computer Science 2025-07-10 Tarek Gasmi , Ramzi Guesmi , Ines Belhadj , Jihene Bennaceur

Tool-using LLM agents increasingly coordinate real workloads by selecting and chaining third-party tools based on text-visible metadata such as tool names, descriptions, and return messages. We show that this convenience creates a…

Computation and Language · Computer Science 2026-02-17 Yohan Lee , Jisoo Jang , Seoyeon Choi , Sangyeop Kim , Seungtaek Choi

Modern process simulators enable detailed process design, simulation, and optimization; however, constructing and interpreting simulations is time-consuming and requires expert knowledge. This limits early exploration by inexperienced…

Chemical Physics · Physics 2026-05-22 Jingkang Liang , Niklas Groll , Gürkan Sin

Large language model (LLM) agents rely on external tools to solve complex tasks, but real-world toolsets often contain redundant tools with overlapping names and descriptions, introducing ambiguity and reducing selection accuracy. LLMs also…

Computation and Language · Computer Science 2026-05-12 Marianne Menglin Liu , Daniel Garcia , Fjona Parllaku , Vikas Upadhyay , Syed Fahad Allam Shah , Dan Roth

The Model Context Protocol (MCP) has become a widely adopted interface for LLM agents to invoke external tools, yet learned monitoring of MCP tool-call traffic remains underexplored. In this article, the proposed detector is presented as an…

Cryptography and Security · Computer Science 2026-05-25 Sultan Zavrak

Large Language Models (LLMs) have demonstrated impressive quality when applied to predictive tasks such as relevance ranking and semantic search. However, deployment of such LLMs remains prohibitively expensive for industry applications…

Conversational modeling using Large Language Models (LLMs) requires a nuanced understanding of context to generate coherent and contextually relevant responses. In this paper, we present Token Trails, a novel approach that leverages…

Computation and Language · Computer Science 2024-04-04 Md. Kowsher , Ritesh Panditi , Nusrat Jahan Prottasha , Prakash Bhat , Anupam Kumar Bairagi , Mohammad Shamsul Arefin

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…

The remarkable capability of large language models (LLMs) has led to the wide application of LLM-based agents in various domains. To standardize interactions between LLM-based agents and their environments, model context protocol (MCP)…

Cryptography and Security · Computer Science 2025-09-26 Ping He , Changjiang Li , Binbin Zhao , Tianyu Du , Shouling Ji

The Model Context Protocol (MCP), introduced by Anthropic in November 2024 and now governed by the Linux Foundation's Agentic AI Foundation, has rapidly become the de facto standard for connecting large language model (LLM)-based agents to…

Cryptography and Security · Computer Science 2026-04-08 Nirajan Acharya , Gaurav Kumar Gupta

Background: Conducting Multi Vocal Literature Reviews (MVLRs) is often time and effort-intensive. Researchers must review and filter a large number of unstructured sources, which frequently contain sparse information and are unlikely to be…

Software Engineering · Computer Science 2025-09-17 Santiago Matalonga , Domenico Amalfitano , Jean Carlo Rossa Hauck , Martín Solari , Guilherme H. Travassos

Despite various approaches being employed to detect vulnerabilities, the number of reported vulnerabilities shows an upward trend over the years. This suggests the problems are not caught before the code is released, which could be caused…

Cryptography and Security · Computer Science 2025-02-14 Karl Tamberg , Hayretdin Bahsi

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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