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Protein engineering is important for biomedical applications, but conventional approaches are often inefficient and resource-intensive. While deep learning (DL) models have shown promise, their training or implementation into protein…

Quantitative Methods · Quantitative Biology 2024-11-08 Yungeng Liu , Zan Chen , Yu Guang Wang , Yiqing Shen

We present a proof-of-principle study demonstrating the use of large language model (LLM) agents to automate a representative high energy physics (HEP) analysis. Using the Higgs boson diphoton cross-section measurement as a case study with…

Data Analysis, Statistics and Probability · Physics 2025-12-10 Eli Gendreau-Distler , Joshua Ho , Dongwon Kim , Luc Tomas Le Pottier , Haichen Wang , Chengxi Yang

Advancements in machine learning and artificial intelligence are transforming materials discovery. Yet, the availability of structured experimental data remains a bottleneck. The vast corpus of scientific literature presents a valuable and…

Artificial Intelligence · Computer Science 2023-12-20 Mehrad Ansari , Seyed Mohamad Moosavi

Large language model agents now act on codebases, browsers, operating systems, calendars, files, and tool ecosystems, but their evaluations often collapse behavior into final task success. AgentAtlas reframes agent evaluation as a…

Artificial Intelligence · Computer Science 2026-05-27 Parsa Mazaheri , Kasra Mazaheri

Large language models (LLMs) have sparked growing interest in machine learning research agents that can autonomously propose ideas and conduct experiments. However, existing benchmarks predominantly adopt an engineering-oriented…

Computation and Language · Computer Science 2026-02-26 Qiran Zou , Hou Hei Lam , Wenhao Zhao , Yiming Tang , Tingting Chen , Samson Yu , Tianyi Zhang , Chang Liu , Xiangyang Ji , Dianbo Liu

Large Language Model (LLM)-based autonomous agents are expected to play a vital role in the evolution of 6G networks, by empowering real-time decision-making related to management and service provisioning to end-users. This shift…

Artificial Intelligence · Computer Science 2025-09-04 Ilias Chatzistefanidis , Navid Nikaein

Large Language Models (LLMs) based autonomous agents demonstrate multifaceted capabilities to contribute substantially to economic production. However, existing benchmarks remain focused on single agentic capability, failing to capture…

Artificial Intelligence · Computer Science 2026-04-24 Keyu Li , Junhao Shi , Yang Xiao , Mohan Jiang , Jie Sun , Yunze Wu , Dayuan Fu , Shijie Xia , Xiaojie Cai , Tianze Xu , Weiye Si , Wenjie Li , Dequan Wang , Pengfei Liu

The discovery of novel small molecule drugs remains a critical scientific challenge with far-reaching implications for treating diseases and advancing human health. Traditional drug development--especially for small molecule…

Biomolecules · Quantitative Biology 2025-04-01 Bowen Gao , Yanwen Huang , Yiqiao Liu , Wenxuan Xie , Wei-Ying Ma , Ya-Qin Zhang , Yanyan Lan

AutoML (automated machine learning) has been extensively developed in the past few years for the model-centric approach. As for the data-centric approach, the processes to improve the dataset, such as fixing incorrect labels, adding…

Human-Computer Interaction · Computer Science 2021-11-25 Zac Yung-Chun Liu , Shoumik Roychowdhury , Scott Tarlow , Akash Nair , Shweta Badhe , Tejas Shah

Recent breakthroughs in Large Language Models (LLMs) have led to the emergence of agentic AI systems that extend beyond the capabilities of standalone models. By empowering LLMs to perceive external environments, integrate multimodal…

Artificial Intelligence · Computer Science 2025-03-24 Chengkai Huang , Junda Wu , Yu Xia , Zixu Yu , Ruhan Wang , Tong Yu , Ruiyi Zhang , Ryan A. Rossi , Branislav Kveton , Dongruo Zhou , Julian McAuley , Lina Yao

The development of automated experimental facilities and the digitization of experimental data have introduced numerous opportunities to radically advance chemical laboratories. As many laboratory tasks involve predicting and understanding…

New discoveries in chemistry and materials science, with increasingly expanding volume of requisite knowledge and experimental workload, provide unique opportunities for machine learning (ML) to take critical roles in accelerating research…

Modern disease classification often overlooks molecular commonalities hidden beneath divergent clinical presentations. This study introduces a transcriptomics-driven framework for discovering disease relationships by analyzing over 1300…

Genomics · Quantitative Biology 2025-08-08 Ke Chen , Haohan Wang

Large Language Models (LLMs) increasingly rely on agentic capabilities-iterative retrieval, tool use, and decision-making-to overcome the limits of static, parametric knowledge. Yet existing agentic frameworks treat external information as…

Computation and Language · Computer Science 2026-04-24 Yuanfu Sun , Kang Li , Dongzhe Fan , Jiajin Liu , Qiaoyu Tan

Machine learning (ML) methods have been developing rapidly, but configuring and selecting proper methods to achieve a desired performance is increasingly difficult and tedious. To address this challenge, automated machine learning (AutoML)…

Artificial Intelligence · Computer Science 2024-02-28 Zhenqian Shen , Yongqi Zhang , Lanning Wei , Huan Zhao , Quanming Yao

Drug discovery remains a formidable challenge: more than 90 percent of candidate molecules fail in clinical evaluation, and development costs often exceed one billion dollars per approved therapy. Disparate data streams, from genomics and…

Artificial Intelligence · Computer Science 2025-04-28 Kevin Song , Andrew Trotter , Jake Y. Chen

Autonomous agents have long been a prominent research focus in both academic and industry communities. Previous research in this field often focuses on training agents with limited knowledge within isolated environments, which diverges…

Artificial Intelligence · Computer Science 2025-03-04 Lei Wang , Chen Ma , Xueyang Feng , Zeyu Zhang , Hao Yang , Jingsen Zhang , Zhiyuan Chen , Jiakai Tang , Xu Chen , Yankai Lin , Wayne Xin Zhao , Zhewei Wei , Ji-Rong Wen

As large language models (LLMs) transition from static tools to fully agentic systems, their potential for transforming social science research has become increasingly evident. This paper introduces a structured framework for understanding…

Multiagent Systems · Computer Science 2026-05-19 Jennifer Haase , Sebastian Pokutta

Agent-based modeling (ABM) is a powerful computational approach for studying complex biological and biomedical systems, yet its widespread use remains limited by significant computational demands. As models become increasingly…

Quantitative Methods · Quantitative Biology 2025-04-17 Kerri-Ann Norton , Daniel Bergman , Harsh Vardhan Jain , Trachette Jackson

Scientific discovery is often slowed by the manual development of computational tools needed to analyze complex experimental data. Building such tools is costly and time-consuming because scientists must iteratively review literature, test…

Artificial Intelligence · Computer Science 2026-05-19 Alistair Turcan , Kexin Huang , Lei Li , Martin Jinye Zhang