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GitHub Continuous Integration (CI) workflows increasingly integrate Large Language Models (LLMs) to automate review, triage, content generation, and repository maintenance. This creates a new attack surface: externally controllable workflow…

Cryptography and Security · Computer Science 2026-05-08 Bonan Ruan , Yeqi Fu , Chuqi Zhang , Jiahao Liu , Jun Zeng , Zhenkai Liang

Automatic differentiation (AD) enables powerful metasurface inverse design but requires extensive theoretical and programming expertise. We present a Model Context Protocol (MCP) assisted framework that allows researchers to conduct inverse…

Computational Physics · Physics 2026-04-13 Yi Huang , Bowen Zheng , Yunxi Dong , Hong Tang , Huan Zhao , S. M. Rakibul Hasan Shawon , Sensong An , Hualiang Zhang

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

The agent--tool interaction loop is a critical attack surface for modern Large Language Model (LLM) agents. Existing denial-of-service (DoS) attacks typically function at the user-prompt or retrieval-augmented generation (RAG) context layer…

Cryptography and Security · Computer Science 2026-03-12 Kaiyu Zhou , Yongsen Zheng , Yicheng He , Meng Xue , Xueluan Gong , Yuji Wang , Xuanye Zhang , Kwok-Yan Lam

The rapid deployment of Large language model (LLM) agents in critical domains like healthcare and finance necessitates robust security frameworks. To address the absence of standardized evaluation benchmarks for these agents in dynamic…

Cryptography and Security · Computer Science 2025-06-19 Yuchuan Fu , Xiaohan Yuan , Dongxia Wang

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

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

Standard Operating Procedures (SOPs) are critical for enterprise operations, yet existing language models struggle with SOP understanding and cross-domain generalization. Current methods fail because joint training cannot differentiate…

Computation and Language · Computer Science 2026-02-11 Siyuan Huang , Ziyu Wang , Chao Pan , Han Zhao

The evaluation of large language model refusal on malicious-coding tasks now spans at least thirteen publicly released prompt corpora (AdvBench, the CyberSecEval family, RMCBench, RedCode, MCGMark, JailbreakBench, CySecBench, MalwareBench,…

Cryptography and Security · Computer Science 2026-05-21 Richard J. Young , Gregory D. Moody

In this paper, we present the first comprehensive empirical study of specialized LLM-based detectors and compare them with traditional static analyzers at the project scale. Specifically, our study evaluates five latest and representative…

Software Engineering · Computer Science 2026-01-28 Fengjie Li , Jiajun Jiang , Dongchi Chen , Yingfei Xiong

Applications of Large Language Models~(LLMs) have evolved from simple text generators into complex software systems that integrate retrieval augmentation, tool invocation, and multi-turn interactions. Their inherent non-determinism,…

Software Engineering · Computer Science 2025-08-29 Wei Ma , Yixiao Yang , Qiang Hu , Shi Ying , Zhi Jin , Bo Du , Zhenchang Xing , Tianlin Li , Junjie Shi , Yang Liu , Linxiao Jiang

As large language models (LLMs) grow more capable, they face growing vulnerability to sophisticated jailbreak attacks. While developers invest heavily in alignment finetuning and safety guardrails, researchers continue publishing novel…

Cryptography and Security · Computer Science 2025-08-14 Boyuan Chen , Minghao Shao , Abdul Basit , Siddharth Garg , Muhammad Shafique

We investigate two questions in this paper: First, we ask to what extent "MPC friendly" models are already supported by major Machine Learning frameworks such as TensorFlow or PyTorch. Prior works provide protocols that only work on…

Cryptography and Security · Computer Science 2021-03-02 Anders Dalskov , Daniel Escudero , Marcel Keller

MITRE ATT&CK is a cybersecurity knowledge base that organizes threat actor and cyber-attack information into a set of tactics describing the reasons and goals threat actors have for carrying out attacks, with each tactic having a set of…

Today's AI agents are built on large language models (LLMs) equipped with tools to access and modify external environments, such as corporate file systems, API-accessible platforms and websites. AI agents offer the promise of automating…

Computers and Society · Computer Science 2026-03-26 Merlin Stein

Medical calculators are fundamental to quantitative, evidence-based clinical practice. However, their real-world use is an adaptive, multi-stage process, requiring proactive EHR data acquisition, scenario-dependent calculator selection, and…

Artificial Intelligence · Computer Science 2026-02-02 Yakun Zhu , Yutong Huang , Shengqian Qin , Zhongzhen Huang , Shaoting Zhang , Xiaofan Zhang

Regression testing activities greatly reduce the risk of faulty software release. However, the size of the test suites grows throughout the development process, resulting in time-consuming execution of the test suite and delayed feedback to…

Software Engineering · Computer Science 2023-11-21 Mostafa Mahdieh , Seyed-Hassan Mirian-Hosseinabadi , Mohsen Mahdieh

Large language models (LLMs) are increasingly prevalent in security research. Their unique characteristics, however, introduce challenges that undermine established paradigms of reproducibility, rigor, and evaluation. Prior work has…

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

Software architecture models capture early design decisions that strongly influence system quality attributes, including security. However, architecture-level security assessment and feedback are often absent in practice, allowing security…

Software Engineering · Computer Science 2026-03-26 Mahdi Jafari , Rahul Sharma , Sami Naim , Christopher Gerking , Ralf Reussner
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