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Large language models (LLMs) are introducing a paradigm shift in molecular discovery by enabling text-guided interaction with chemical spaces through natural language, symbolic notations, with emerging extensions to incorporate multi-modal…

Machine Learning · Computer Science 2025-05-23 Ziqing Wang , Kexin Zhang , Zihan Zhao , Yibo Wen , Abhishek Pandey , Han Liu , Kaize Ding

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) have made great strides in areas such as language processing and computer vision. Despite the emergence of diverse techniques to improve few-shot learning capacity, current LLMs fall short in handling the…

Biomolecules · Quantitative Biology 2024-05-14 Xianggen Liu , Yan Guo , Haoran Li , Jin Liu , Shudong Huang , Bowen Ke , Jiancheng Lv

The use of Large Language Models (LLMs) for program code generation has gained substantial attention, but their biases and limitations with non-English prompts challenge global inclusivity. This paper investigates the complexities of…

Computation and Language · Computer Science 2025-05-13 Mingda Li , Abhijit Mishra , Utkarsh Mujumdar

Many recent prompting strategies for large language models (LLMs) query the model multiple times sequentially -- first to produce intermediate results and then the final answer. However, using these methods, both decoder and model are…

Computation and Language · Computer Science 2023-11-10 Luca Beurer-Kellner , Mark Niklas Müller , Marc Fischer , Martin Vechev

Designing de-novo molecules with desired property profiles requires efficient exploration of the vast chemical space ranging from $10^{23}$ to $10^{60}$ possible synthesizable candidates. While various deep generative models have been…

Machine Learning · Computer Science 2025-08-25 Kamran Chitsaz , Roshan Balaji , Quentin Fournier , Nirav Pravinbhai Bhatt , Sarath Chandar

Large Language Models (LLMs) have the potential to accelerate small molecule drug design due to their ability to reason about information from diverse sources and formats. However, their practical utility remains unclear due to the lack of…

Large Language Models (LLMs) have demonstrated remarkable performance across diverse tasks and exhibited impressive reasoning abilities by applying zero-shot Chain-of-Thought (CoT) prompting. However, due to the evolving nature of sentence…

Computation and Language · Computer Science 2024-02-09 Feihu Jin , Yifan Liu , Ying Tan

Large Language models (LLMs) have emerged as powerful tools for addressing challenges across diverse domains. Notably, recent studies have demonstrated that large language models significantly enhance the efficiency of biomolecular analysis…

Computation and Language · Computer Science 2025-03-07 Jiyue Jiang , Zikang Wang , Yuheng Shan , Heyan Chai , Jiayi Li , Zixian Ma , Xinrui Zhang , Yu Li

Large Language Models (LLMs) have demonstrated great performance in few-shot In-Context Learning (ICL) for a variety of generative and discriminative chemical design tasks. The newly expanded context windows of LLMs can further improve ICL…

Retrained large language models (LLMs) have become extensively used across various sub-disciplines of natural language processing (NLP). In NLP, text classification problems have garnered considerable focus, but still faced with some…

Computation and Language · Computer Science 2023-12-05 Zhiqiang Wang , Yiran Pang , Yanbin Lin

Despite their ability to understand chemical knowledge, large language models (LLMs) remain limited in their capacity to propose novel molecules with desired functions (e.g., drug-like properties). In addition, the molecules that LLMs…

Large language models (LLMs) have shown remarkable capabilities in Natural Language Processing (NLP), especially in domains where labeled data is scarce or expensive, such as clinical domain. However, to unlock the clinical knowledge hidden…

Computation and Language · Computer Science 2023-09-18 Sonish Sivarajkumar , Mark Kelley , Alyssa Samolyk-Mazzanti , Shyam Visweswaran , Yanshan Wang

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

Language models (LLMs) offer potential as a source of knowledge for agents that need to acquire new task competencies within a performance environment. We describe efforts toward a novel agent capability that can construct cues (or…

Machine Learning · Computer Science 2022-11-22 James R. Kirk , Robert E. Wray , Peter Lindes , John E. Laird

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

Large language models (LLMs) are very proficient text generators. We leverage this capability of LLMs to generate task-specific data via zero-shot prompting and promote cross-lingual transfer for low-resource target languages. Given…

Computation and Language · Computer Science 2024-07-16 Barah Fazili , Ashish Sunil Agrawal , Preethi Jyothi

Pretrained large language models (LLMs) are widely used in many sub-fields of natural language processing (NLP) and generally known as excellent few-shot learners with task-specific exemplars. Notably, chain of thought (CoT) prompting, a…

Computation and Language · Computer Science 2023-01-31 Takeshi Kojima , Shixiang Shane Gu , Machel Reid , Yutaka Matsuo , Yusuke Iwasawa

Recent breakthroughs in large language models (LLMs) have opened the door to in-depth investigation of their potential in tabular data modeling. However, effectively utilizing advanced LLMs in few-shot and even zero-shot scenarios is still…

Machine Learning · Computer Science 2025-08-14 Peng Wang , Dongsheng Wang , He Zhao , Hangting Ye , Dandan Guo , Yi Chang

We introduce a large language model (LLM) based approach to answer complex questions requiring multi-hop numerical reasoning over financial reports. While LLMs have exhibited remarkable performance on various natural language and reasoning…

Computation and Language · Computer Science 2023-11-28 Karmvir Singh Phogat , Chetan Harsha , Sridhar Dasaratha , Shashishekar Ramakrishna , Sai Akhil Puranam
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