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A drug molecule is a substance that changes the organism's mental or physical state. Every approved drug has an indication, which refers to the therapeutic use of that drug for treating a particular medical condition. While the Large…

Artificial Intelligence · Computer Science 2024-02-20 David Oniani , Jordan Hilsman , Chengxi Zang , Junmei Wang , Lianjin Cai , Jan Zawala , Yanshan Wang

Recent advancements in large language models (LLMs) have shown promise in medical applications such as disease diagnosis and treatment planning. However, most existing medical LLMs struggle with the deep reasoning required for complex…

Computation and Language · Computer Science 2025-07-31 Hongzhou Yu , Tianhao Cheng , Yingwen Wang , Wen He , Qing Wang , Ying Cheng , Yuejie Zhang , Rui Feng , Xiaobo Zhang

Large Language Models (LLMs) perform well in language tasks but often lack collaborative awareness and struggle to optimize global performance in multi-agent settings. We present a reinforcement learning-augmented LLM agent framework that…

Artificial Intelligence · Computer Science 2026-01-01 Dong Qiu , Duo Xu , Limengxi Yue

Large Language Models (LLMs) can generate code from natural language, but their performance is highly sensitive to prompt formulation. We propose a reinforcement-learning-based framework that models prompt refinement as a sequential…

Software Engineering · Computer Science 2026-05-20 Ali Mohammadi Esfahani , Nafiseh Kahani , Samuel A. Ajila

The ability to predict drug overdose risk from a patient's medical records is crucial for timely intervention and prevention. Traditional machine learning models have shown promise in analyzing longitudinal medical records for this task.…

Artificial Intelligence · Computer Science 2025-04-17 Md Sultan Al Nahian , Chris Delcher , Daniel Harris , Peter Akpunonu , Ramakanth Kavuluru

Large language models (LLMs) have shown remarkable performance on many tasks in different domains. However, their performance in closed-book biomedical machine reading comprehension (MRC) has not been evaluated in depth. In this work, we…

Computation and Language · Computer Science 2024-10-28 Shubham Vatsal , Ayush Singh

Open-source, multilingual medical large language models (LLMs) have the potential to serve linguistically diverse populations across different regions. Adapting generic LLMs for healthcare often requires continual pretraining, but this…

Computation and Language · Computer Science 2024-09-10 Meng Zhou , Surajsinh Parmar , Anubhav Bhatti

Large language models (LLMs) have garnered significant attention for their remarkable capabilities across various domains, whose vast parameter scales present challenges for practical deployment. Structured pruning is an effective method to…

Artificial Intelligence · Computer Science 2024-12-25 Gui Ling , Ziyang Wang , Yuliang Yan , Qingwen Liu

Molecular biologists frequently interpret gene lists derived from high-throughput experiments and computational analysis. This is typically done as a statistical enrichment analysis that measures the over- or under-representation of…

Genomics · Quantitative Biology 2024-07-08 Marcin P. Joachimiak , J. Harry Caufield , Nomi L. Harris , Hyeongsik Kim , Christopher J. Mungall

Data selection for finetuning Large Language Models (LLMs) can be framed as a budget-constrained optimization problem: maximizing a model's downstream performance under a strict training data budget. Solving this problem is generally…

Machine Learning · Computer Science 2025-10-01 Animesh Jha , Harshit Gupta , Ananjan Nandi

Optimization problems are prevalent across various scenarios. Formulating and then solving optimization problems described by natural language often requires highly specialized human expertise, which could block the widespread application…

Artificial Intelligence · Computer Science 2025-03-04 Caigao Jiang , Xiang Shu , Hong Qian , Xingyu Lu , Jun Zhou , Aimin Zhou , Yang Yu

The rapid development of large language models (LLMs) is reshaping operational paradigms across multidisciplinary domains. LLMs' emergent capability to synthesize policy-relevant insights across disciplinary boundaries suggests potential as…

Computers and Society · Computer Science 2025-04-22 Jinghan Ke , Zheng Zhou , Yuxuan Zhao

Large language models (LLMs) have shown remarkable in-context learning (ICL) capabilities, yet their potential for sequential decision-making remains underexplored. In this paper, we study the ICL capabilities of LLMs in sequential…

Machine Learning · Computer Science 2026-05-12 Minmin Zhang , Sina Aghaei , Soroush Saghafian

Aligning terminological resources, including ontologies, controlled vocabularies, taxonomies, and value sets is a critical part of data integration in many domains such as healthcare, chemistry, and biomedical research. Entity mapping is…

Goal-oriented de novo molecule design, namely generating molecules with specific property or substructure constraints, is a crucial yet challenging task in drug discovery. Existing methods, such as Bayesian optimization and reinforcement…

Computational Engineering, Finance, and Science · Computer Science 2025-02-28 Chuanliu Fan , Ziqiang Cao , Zicheng Ma , Nan Yu , Yimin Peng , Jun Zhang , Yiqin Gao , Guohong Fu

Large language models (LLMs) are in the ascendancy for research in drug discovery, offering unprecedented opportunities to reshape drug research by accelerating hypothesis generation, optimizing candidate prioritization, and enabling more…

Machine Learning · Computer Science 2026-04-06 Tianyu Liu , Sihan Jiang , Fan Zhang , Kunyang Sun , Teresa Head-Gordon , Hongyu Zhao

Pretrained large language models (LLMs) are currently state-of-the-art for solving the vast majority of natural language processing tasks. While many real-world applications still require fine-tuning to reach satisfactory levels of…

Data augmentation is an essential technique in natural language processing (NLP) for enriching training datasets by generating diverse samples. This process is crucial for improving the robustness and generalization capabilities of NLP…

Computation and Language · Computer Science 2025-10-16 Zaitian Wang , Jinghan Zhang , Xinhao Zhang , Kunpeng Liu , Pengfei Wang , Yuanchun Zhou

Large language models (LLMs) have demonstrated remarkable performance across a wide range of tasks. Advances in prompt engineering and fine-tuning techniques have further enhanced their ability to address complex reasoning challenges.…

Computation and Language · Computer Science 2024-12-16 Jing Bi , Yuting Wu , Weiwei Xing , Zhenjie Wei

In recent research advancements within the community, large language models (LLMs) have sparked great interest in creating autonomous agents. However, current prompt-based agents often heavily rely on large-scale LLMs. Meanwhile, although…

Computation and Language · Computer Science 2025-03-04 Xueyang Feng , Bo Lan , Quanyu Dai , Lei Wang , Jiakai Tang , Xu Chen , Zhenhua Dong , Ji-Rong Wen