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Leveraging artificial intelligence for automatic retrosynthesis speeds up organic pathway planning in digital laboratories. However, existing deep learning approaches are unexplainable, like "black box" with few insights, notably limiting…

Machine Learning · Computer Science 2023-10-13 Yu Wang , Chao Pang , Yuzhe Wang , Yi Jiang , Junru Jin , Sirui Liang , Quan Zou , Leyi Wei

Molecule generation and optimization is a fundamental task in chemical domain. The rapid development of intelligent tools, especially large language models (LLMs) with powerful knowledge reserves and interactive capabilities, has provided…

Machine Learning · Computer Science 2026-02-10 Haoran Liu , Zheni Zeng , Yukun Yan , Yuxuan Chen , Yunduo Xiao

Generative Large Language Models (LLMs) are a promising approach to structuring knowledge contained within the corpora of research literature produced by large-scale and long-running scientific collaborations. Within experimental particle…

High Energy Physics - Experiment · Physics 2025-09-09 James McGreivy , Blaise Delaney , Anja Beck , Mike Williams

Large Language Model (LLM)-based agents show promise for e-commerce conversational shopping, yet existing implementations lack the interaction depth and contextual breadth required for complex product research. Meanwhile, the Deep Research…

Artificial Intelligence · Computer Science 2026-03-02 Jiangyuan Wang , Kejun Xiao , Huaipeng Zhao , Tao Luo , Xiaoyi Zeng

Code reproduction is a cornerstone of scientific validity, yet it remains a formidable challenge in computer networking research due to the scarcity of open-source implementations and the complexity of heterogeneous system architectures.…

Networking and Internet Architecture · Computer Science 2026-02-17 Yining Jiang , Yunxin Xu , Wenyun Xu , Yufan Zhu , Tangtang He , Haiying Huang , Letian Zhu , Qingyu Song , Qiang Su , Lizhao You , Lu Tang , Wanjin Feng , Yuchao Zhang , Linghe Kong , Qiao Xiang , Jiwu Shu

Microwell microfluidics has been utilized for single-cell analysis to reveal heterogeneity in gene expression, signaling pathways, and phenotypic responses for identifying rare cell types, understanding disease progression, and developing…

Neurons and Cognition · Quantitative Biology 2025-10-17 Dinh-Nguyen Nguyen , Sadia Shakil , Raymond Kai-Yu Tong , Ngoc-Duy Dinh

Computer-aided synthesis planning (CASP) has long been envisioned as a complementary tool for synthetic chemists. However, existing frameworks often lack mechanisms to allow interaction with human experts, limiting their ability to…

Artificial Intelligence · Computer Science 2025-12-19 Nguyen Xuan-Vu , Daniel Armstrong , Milena Wehrbach , Andres M Bran , Zlatko Jončev , Philippe Schwaller

Large Language Models (LLMs) have the potential to revolutionize automated traceability by overcoming the challenges faced by previous methods and introducing new possibilities. However, the optimal utilization of LLMs for automated…

Software Engineering · Computer Science 2023-08-02 Alberto D. Rodriguez , Katherine R. Dearstyne , Jane Cleland-Huang

On-demand Polymer discovery is essential for various industries, ranging from biomedical to reinforcement materials. Experiments with polymers have a long trial-and-error process, leading to use of extensive resources. For these processes,…

Computation and Language · Computer Science 2026-02-12 Vani Nigam , Achuth Chandrasekhar , Amir Barati Farimani

The development of synthesis procedures remains a fundamental challenge in materials discovery, with procedural knowledge scattered across decades of scientific literature in unstructured formats that are challenging for systematic…

We aim at designing language agents with greater autonomy for crystal materials discovery. While most of existing studies restrict the agents to perform specific tasks within predefined workflows, we aim to automate workflow planning given…

Artificial Intelligence · Computer Science 2025-06-10 Lianhao Zhou , Hongyi Ling , Keqiang Yan , Kaiji Zhao , Xiaoning Qian , Raymundo Arróyave , Xiaofeng Qian , Shuiwang Ji

Real-world path planning tasks typically involve multiple constraints beyond simple route optimization, such as the number of routes, maximum route length, depot locations, and task-specific requirements. Traditional approaches rely on…

Computation and Language · Computer Science 2026-03-23 Dylan Shim , Minghan Wei

Large language models (LLMs) are rapidly transforming various domains, including biomedicine and healthcare, and demonstrate remarkable potential from scientific research to new drug discovery. Graph-based retrieval-augmented generation…

Quantitative Methods · Quantitative Biology 2025-11-14 Guofeng Meng , Li Shen , Qiuyan Zhong , Wei Wang , Haizhou Zhang , Xiaozhen Wang

The proliferation of large language models (LLMs) and their integration into multi-agent systems has paved the way for sophisticated automation in various domains. This paper introduces AutoGenesisAgent, a multi-agent system that…

Multiagent Systems · Computer Science 2024-04-29 Jeremy Harper

Large language models (LLMs) have demonstrated remarkable capabilities across a range of text-generation tasks. However, LLMs still struggle with problems requiring multi-step decision-making and environmental feedback, such as online…

Artificial Intelligence · Computer Science 2025-02-18 Zhenfang Chen , Delin Chen , Rui Sun , Wenjun Liu , Chuang Gan

In silico tools are important for generating novel hypotheses and exploring alternatives in de novo metabolic pathway design. However, while many computational frameworks have been proposed for retrobiosynthesis, few successful examples of…

Machine Learning · Computer Science 2026-04-16 Peter Zhiping Zhang , Jeffrey D. Varner

In this study, we introduced a new benchmark consisting of a curated dataset and a defined evaluation process to assess the compositional reasoning capabilities of large language models within the chemistry domain. We designed and validated…

Computation and Language · Computer Science 2025-08-07 Mohammad Khodadad , Ali Shiraee Kasmaee , Mahdi Astaraki , Nicholas Sherck , Hamidreza Mahyar , Soheila Samiee

The performance of large language models (LLMs) depends on how they are prompted, with choices spanning both the high-level prompting pattern (e.g., Zero-Shot, CoT, ReAct, ReWOO) and the specific prompt content (instructions and few-shot…

Machine Learning · Computer Science 2025-11-05 Claudio Spiess , Mandana Vaziri , Louis Mandel , Martin Hirzel

Large language models (LLMs) are becoming increasingly applied beyond natural language processing, demonstrating strong capabilities in complex scientific tasks that traditionally require human expertise. This progress has extended into…

Materials Science · Physics 2026-02-26 Dong Hyeon Mok , Seoin Back , Victor Fung , Guoxiang Hu

The rapid progress of large language models (LLMs) has opened new opportunities for education. While learners can interact with academic papers through LLM-powered dialogue, limitations still exist: the lack of structured organization and…

Human-Computer Interaction · Computer Science 2026-04-02 Yuheng Yang , Wenjia Jiang , Yang Wang , Yi Song , Yiwei Wang , Chi Zhang
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