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Large Language Models (LLMs) have demonstrated their transformative potential across numerous disciplinary studies, reshaping the existing research methodologies and fostering interdisciplinary collaboration. However, a systematic…

Computation and Language · Computer Science 2025-07-14 Lu Xiang , Yang Zhao , Yaping Zhang , Chengqing Zong

With the rapid development of artificial intelligence, large language models (LLMs) have shown promising capabilities in mimicking human-level language comprehension and reasoning. This has sparked significant interest in applying LLMs to…

Computation and Language · Computer Science 2023-11-06 Mingze Yuan , Peng Bao , Jiajia Yuan , Yunhao Shen , Zifan Chen , Yi Xie , Jie Zhao , Yang Chen , Li Zhang , Lin Shen , Bin Dong

With the rapid development of Large Language Models (LLMs), LLM-based agents have been widely adopted in various fields, becoming essential for autonomous decision-making and interactive tasks. However, current work typically relies on…

Artificial Intelligence · Computer Science 2026-02-25 Shangheng Du , Jiabao Zhao , Jinxin Shi , Zhentao Xie , Xin Jiang , Yanhong Bai , Liang He

This paper presents the Model Gateway, a management platform for managing machine learning (ML) and scientific computational models in the drug discovery pipeline. The platform supports Large Language Model (LLM) Agents and Generative…

Software Engineering · Computer Science 2025-12-08 Yan-Shiun Wu , Nathan A. Morin

Large Language Models (LLMs) demonstrate strong generalization and reasoning abilities, making them well-suited for complex decision-making tasks such as medical consultation (MC). However, existing LLM-based methods often fail to capture…

Computation and Language · Computer Science 2025-10-13 Zhihao Jia , Mingyi Jia , Junwen Duan , Jianxin Wang

Large language models (LLMs) are rapidly transforming materials science. This review examines recent LLM applications across the materials discovery pipeline, focusing on three key areas: mining scientific literature , predictive modelling,…

Computation and Language · Computer Science 2025-11-17 Fengxu Yang , Weitong Chen , Jack D. Evans

Optimization models developed by operations research (OR) experts are often deployed as decision-support systems in industrial settings. However, real-world environments are dynamic, with evolving business rules and unforeseen…

Artificial Intelligence · Computer Science 2026-05-28 Tinghan Ye , Arnaud Deza , Ved Mohan , El Mehdi Er Raqabi , Pascal Van Hentenryck

Optimization problems are pervasive in sectors from manufacturing and distribution to healthcare. However, most such problems are still solved heuristically by hand rather than optimally by state-of-the-art solvers because the expertise…

Artificial Intelligence · Computer Science 2025-08-29 Ali AhmadiTeshnizi , Wenzhi Gao , Herman Brunborg , Shayan Talaei , Connor Lawless , Madeleine Udell

While model serving has unlocked unprecedented capabilities, the high cost of serving large-scale models continues to be a significant barrier to widespread accessibility and rapid innovation. Compiler optimizations have long driven…

Machine Learning · Computer Science 2026-02-05 Annabelle Sujun Tang , Christopher Priebe , Rohan Mahapatra , Lianhui Qin , Hadi Esmaeilzadeh

Molecular property prediction (MPP) is a fundamental and crucial task in drug discovery. However, prior methods are limited by the requirement for a large number of labeled molecules and their restricted ability to generalize for unseen and…

Quantitative Methods · Quantitative Biology 2024-10-21 Yuyan Liu , Sirui Ding , Sheng Zhou , Wenqi Fan , Qiaoyu Tan

Recent regulatory initiatives like the European AI Act and relevant voices in the Machine Learning (ML) community stress the need to describe datasets along several key dimensions for trustworthy AI, such as the provenance processes and…

Digital Libraries · Computer Science 2024-05-27 Joan Giner-Miguelez , Abel Gómez , Jordi Cabot

Large language models (LLMs) are powerful artificial intelligence (AI) tools transforming how research is conducted. However, their use in research has been met with skepticism, due to concerns about hallucinations, biases and potential…

Artificial Intelligence · Computer Science 2025-07-08 Ruian Ke , Ruy M. Ribeiro

Large Language Models (LLMs) have recently demonstrated impressive capabilities across various real-world applications. However, due to the current text-in-text-out paradigm, it remains challenging for LLMs to handle dynamic and complex…

Artificial Intelligence · Computer Science 2024-10-25 Timothy Wei , Annabelle Miin , Anastasia Miin

Retrosynthesis, the process of breaking down a target molecule into simpler precursors through a series of valid reactions, stands at the core of organic chemistry and drug development. Although recent machine learning (ML) research has…

Artificial Intelligence · Computer Science 2026-05-12 Haorui Wang , Jeff Guo , Lingkai Kong , Rampi Ramprasad , Philippe Schwaller , Yuanqi Du , Chao Zhang

Large Language Models (LLMs) have swiftly emerged as vital resources for different applications in the biomedical and healthcare domains; however, these models encounter issues such as generating inaccurate information or hallucinations.…

Computation and Language · Computer Science 2024-05-06 Mingchen Li , Halil Kilicoglu , Hua Xu , Rui Zhang

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text.…

Machine Learning · Computer Science 2023-07-17 Chen Qian , Huayi Tang , Zhirui Yang , Hong Liang , Yong Liu

Drug discovery is a complex and resource-intensive process, making early prediction of approval outcomes critical for optimizing research investments. While classical machine learning and deep learning methods have shown promise in drug…

Foundation models are becoming valuable tools in medicine. Yet despite their promise, the best way to leverage Large Language Models (LLMs) in complex medical tasks remains an open question. We introduce a novel multi-agent framework, named…

Computation and Language · Computer Science 2024-10-31 Yubin Kim , Chanwoo Park , Hyewon Jeong , Yik Siu Chan , Xuhai Xu , Daniel McDuff , Hyeonhoon Lee , Marzyeh Ghassemi , Cynthia Breazeal , Hae Won Park

Evolutionary algorithms excel in solving complex optimization problems, especially those with multiple objectives. However, their stochastic nature can sometimes hinder rapid convergence to the global optima, particularly in scenarios…

Neural and Evolutionary Computing · Computer Science 2024-05-10 Zeyi Wang , Songbai Liu , Jianyong Chen , Kay Chen Tan

Large language models (LLMs) have large potential for molecular optimization, as they can gather external chemistry tools and enable collaborative interactions to iteratively refine molecular candidates. However, this potential remains…

Artificial Intelligence · Computer Science 2025-05-28 Hyomin Kim , Yunhui Jang , Sungsoo Ahn