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We present a modular framework powered by large language models (LLMs) that automates and streamlines key tasks across the early-stage computational drug discovery pipeline. By combining LLM reasoning with domain-specific tools, the…

Recent work has demonstrated the promise of orchestrating large language models (LLMs) within evolutionary and agentic optimization systems. However, the mechanisms driving these optimization gains remain poorly understood. In this work, we…

Computation and Language · Computer Science 2026-04-22 Xinhao Zhang , Xi Chen , François Portet , Maxime Peyrard

Generating challenging instances is crucial for the evaluation and advancement of combinatorial optimization solvers. In this work, we introduce EALG (Evolutionary Adversarial Generation of Language Model-Guided Generators), a novel…

Artificial Intelligence · Computer Science 2025-06-04 Ruibo Duan , Yuxin Liu , Xinyao Dong , Chenglin Fan

The discovery of symbolic solutions -- mathematical expressions, logical rules, and algorithmic structures -- is fundamental to advancing scientific and engineering progress. However, traditional methods often struggle with search…

Artificial Intelligence · Computer Science 2025-11-17 Ping Guo , Qingfu Zhang , Xi Lin

Machine learning and Bayesian optimization (BO) algorithms can significantly accelerate the optimization of chemical reactions. Transfer learning can bolster the effectiveness of BO algorithms in low-data regimes by leveraging pre-existing…

Machine Learning · Computer Science 2025-04-15 Roshan Patel , Saeed Moayedpour , Louis De Lescure , Lorenzo Kogler-Anele , Alan Cherney , Sven Jager , Yasser Jangjou

This study analyzes the multiple functions of Large Language Models (LLMs) in transforming research and development (R&D) processes. By automating knowledge discovery, boosting hypothesis creation, integrating transdisciplinary insights,…

Computation and Language · Computer Science 2025-11-25 Raha Aghaei , Ali A. Kiaei , Mahnaz Boush , Mahan Rofoosheh , Mohammad Zavvar

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

Traditional query optimization relies on cost-based optimizers that estimate execution cost (e.g., runtime, memory, and I/O) using predefined heuristics and statistical models. Improving these heuristics requires substantial engineering…

Databases · Computer Science 2026-02-12 Mehmet Hamza Erol , Xiangpeng Hao , Federico Bianchi , Ciro Greco , Jacopo Tagliabue , James Zou

The burgeoning field of Large Language Models (LLMs), exemplified by sophisticated models like OpenAI's ChatGPT, represents a significant advancement in artificial intelligence. These models, however, bring forth substantial challenges in…

Scientific research faces high costs and inefficiencies with traditional methods, but the rise of deep learning and large language models (LLMs) offers innovative solutions. This survey reviews transformer-based LLM applications across…

Machine Learning · Computer Science 2025-09-16 Kaiyuan Tian , Linbo Qiao , Baihui Liu , Gongqingjian Jiang , Shanshan Li , Dongsheng Li

The rapid advancement of Large Language Models (LLMs) poses a significant challenge to existing mathematical reasoning benchmarks. However, these benchmarks tend to become easier over time as LLMs can learn from the published benchmarks.…

Artificial Intelligence · Computer Science 2025-10-07 Shengbo Wang , Mingwei Liu , Zike Li , Anji Li , Yanlin Wang , Xin Peng , Zibin Zheng

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an…

Machine Learning · Computer Science 2025-01-20 Yinkai Wang , Jiaxing He , Yuanqi Du , Xiaohui Chen , Jianan Canal Li , Li-Ping Liu , Xiaolin Xu , Soha Hassoun

The rapid evolution of Large Language Models (LLMs) has markedly expanded their application across diverse domains, transforming how complex problems are approached and solved. Initially conceived to predict subsequent words in texts, these…

Artificial Intelligence · Computer Science 2024-07-11 Sumedh Rasal , E. J. Hauer

Evolutionary agentic systems intensify the trade-off between computational efficiency and reasoning capability by repeatedly invoking large language models (LLMs) during inference. This setting raises a central question: how can an agent…

Computation and Language · Computer Science 2026-04-27 Pretam Ray , Pratik Prabhanjan Brahma , Zicheng Liu , Emad Barsoum

This paper introduces an approach that integrates self-adaptive Evolution Strategies (ES) with Large Language Models (LLMs) to enhance the explainability of complex optimization processes. By employing a self-adaptive ES equipped with a…

Neural and Evolutionary Computing · Computer Science 2024-08-06 Jill Baumann , Oliver Kramer

Recent decades have witnessed great advancements in multiobjective evolutionary algorithms (MOEAs) for multiobjective optimization problems (MOPs). However, these progressively improved MOEAs have not necessarily been equipped with scalable…

Neural and Evolutionary Computing · Computer Science 2023-02-28 Songbai Liu , Qiuzhen Lin , Jianqiang Li , Kay Chen Tan

Automated feature engineering plays a critical role in improving predictive model performance for tabular learning tasks. Traditional automated feature engineering methods are limited by their reliance on pre-defined transformations within…

Machine Learning · Computer Science 2026-05-12 Nikhil Abhyankar , Parshin Shojaee , Chandan K. Reddy

Large Language Models (LLMs) are a class of generative AI models built using the Transformer network, capable of leveraging vast datasets to identify, summarize, translate, predict, and generate language. LLMs promise to revolutionize…

Information Retrieval · Computer Science 2024-03-05 Chunhe Ni , Jiang Wu , Hongbo Wang , Wenran Lu , Chenwei Zhang

The integration of Large Language Models (LLMs) into the drug discovery and development field marks a significant paradigm shift, offering novel methodologies for understanding disease mechanisms, facilitating drug discovery, and optimizing…

Quantitative Methods · Quantitative Biology 2024-09-10 Yizhen Zheng , Huan Yee Koh , Maddie Yang , Li Li , Lauren T. May , Geoffrey I. Webb , Shirui Pan , George Church
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