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Simulations, although powerful in accurately replicating real-world systems, often remain inaccessible to non-technical users due to their complexity. Conversely, large language models (LLMs) provide intuitive, language-based interactions…

Computation and Language · Computer Science 2025-05-22 Jacob Kleiman , Kevin Frank , Joseph Voyles , Sindy Campagna

Autonomous tuning of particle accelerators is an active and challenging field of research with the goal of enabling novel accelerator technologies cutting-edge high-impact applications, such as physics discovery, cancer research and…

Computation and Language · Computer Science 2024-05-16 Jan Kaiser , Annika Eichler , Anne Lauscher

Large Language Models (LLMs) have demonstrated remarkable capabilities in handling long texts and have almost perfect performance in traditional retrieval tasks. However, their performance significantly degrades when it comes to numerical…

Computation and Language · Computer Science 2024-12-05 Yijiong Yu

Large Language Models (LLMs) perform best with well-crafted prompts, yet prompt engineering remains manual, inconsistent, and inaccessible to non-experts. We introduce Promptomatix, an automatic prompt optimization framework that transforms…

Computation and Language · Computer Science 2025-07-28 Rithesh Murthy , Ming Zhu , Liangwei Yang , Jielin Qiu , Juntao Tan , Shelby Heinecke , Caiming Xiong , Silvio Savarese , Huan Wang

Scientific research increasingly relies on specialized computational tools, yet effectively utilizing these tools demands substantial domain expertise. While Large Language Models (LLMs) show promise in tool automation, they struggle to…

Artificial Intelligence · Computer Science 2025-07-29 Keyan Ding , Jing Yu , Junjie Huang , Yuchen Yang , Qiang Zhang , Huajun Chen

Frontier large language models (LLMs), such as GPT-5, Claude 4.5, Gemini 3, Llama 4, and DeepSeek-R1, represent a transformative class of AI tools capable of revolutionizing various aspects of healthcare by generating human-like responses…

The rapidly growing demand for high-quality data in Large Language Models (LLMs) has intensified the need for scalable, reliable, and semantically rich data preparation pipelines. However, current practices remain dominated by ad-hoc…

Computational Fluid Dynamics (CFD) is widely used in aerospace, energy, and biology to model fluid flow, heat transfer, and chemical reactions. While Large Language Models (LLMs) have transformed various domains, their application in CFD…

Artificial Intelligence · Computer Science 2025-02-04 Yuxuan Chen , Xu Zhu , Hua Zhou , Zhuyin Ren

In an era defined by the explosive growth of data and rapid technological advancements, Multimodal Large Language Models (MLLMs) stand at the forefront of artificial intelligence (AI) systems. Designed to seamlessly integrate diverse data…

LLM agents have incredible potential for scientific discovery applications. However, the performance of LLM agents on real-world, small molecule drug design (SMDD) tasks across diverse chemistries and targets is unclear. Current evaluation…

Artificial Intelligence · Computer Science 2026-05-26 Kevin Han , Renfei Zhang , Kathy Wei , Hamed Mahdavi , Niloofar Mireshghallah , Amir Barati Farimani

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…

Biomolecules · Quantitative Biology 2024-12-20 He Cao , Zijing Liu , Xingyu Lu , Yuan Yao , Yu Li

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

GitHub workflows or GitHub CI is a popular continuous integration platform that enables developers to automate various software engineering tasks by specifying them as workflows, i.e., YAML files with a list of jobs. However, engineering…

Software Engineering · Computer Science 2024-03-20 Xinyu Zhang , Siddharth Muralee , Sourag Cherupattamoolayil , Aravind Machiry

Large language models (LLMs) achieve strong performance in long-horizon decision-making tasks through multi-step interaction and reasoning at test time. While practitioners commonly believe a higher task success rate necessitates the use of…

Artificial Intelligence · Computer Science 2026-05-15 Yuanzhe Li , Jianing Deng , Jingtong Hu , Tianlong Chen , Song Wang , Huanrui Yang

Large Action Models (LAMs) for AI Agents offer incredible potential but face challenges due to the need for high-quality training data, especially for multi-steps tasks that involve planning, executing tool calls, and responding to…

We present sMolBoxes, a dataflow representation for the exploration and analysis of long molecular dynamics (MD) simulations. When MD simulations reach millions of snapshots, a frame-by-frame observation is not feasible anymore. Thus,…

Quantitative Methods · Quantitative Biology 2022-10-04 Pavol Ulbrich , Manuela Waldner , Katarína Furmanová , Sérgio M. Marques , David Bednář , Barbora Kozlikova , Jan Byška

ProMoAI is a novel tool that leverages Large Language Models (LLMs) to automatically generate process models from textual descriptions, incorporating advanced prompt engineering, error handling, and code generation techniques. Beyond…

Databases · Computer Science 2024-08-09 Humam Kourani , Alessandro Berti , Daniel Schuster , Wil M. P. van der Aalst

Existing AutoML systems have advanced the automation of machine learning (ML); however, they still require substantial manual configuration and expert input, particularly when handling multimodal data. We introduce MLZero, a novel…

Multimodal Large Language Models (MLLMs) hold significant promise for revolutionizing traditional education and reducing teachers' workload. However, accurately interpreting unconstrained STEM student handwritten solutions with intertwined…

Computer Vision and Pattern Recognition · Computer Science 2026-05-01 Weiyu Sun , Liangliang Chen , Yongnuo Cai , Huiru Xie , Yi Zeng , Ying Zhang

Multimodal large language models (MLLMs) have made impressive progress in many applications in recent years. However, chemical MLLMs that can handle cross-modal understanding and generation remain underexplored. To fill this gap, we propose…

Machine Learning · Computer Science 2025-08-05 Qian Tan , Dongzhan Zhou , Peng Xia , Wanhao Liu , Wanli Ouyang , Lei Bai , Yuqiang Li , Tianfan Fu
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