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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

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet,…

Computation and Language · Computer Science 2025-01-28 Ran Xu , Hejie Cui , Yue Yu , Xuan Kan , Wenqi Shi , Yuchen Zhuang , Wei Jin , Joyce Ho , Carl Yang

Large language models (LLMs) have shown strong empirical performance across pharmacology and drug discovery tasks, yet the internal mechanisms by which they encode pharmacological knowledge remain poorly understood. In this work, we…

Computation and Language · Computer Science 2026-03-05 Basil Hasan Khwaja , Dylan Chen , Guntas Toor , Anastasiya Kuznetsova

The increasing volume of scholarly publications requires advanced tools for efficient knowledge discovery and management. This paper introduces ongoing work on a system using Large Language Models (LLMs) for the semantic extraction of key…

Digital Libraries · Computer Science 2025-10-07 Samy Ateia , Udo Kruschwitz , Melanie Scholz , Agnes Koschmider , Moayad Almohaishi

Large language models (LLMs) have demonstrated broad utility across molecular domains, spanning drug discovery and materials design. Analyzing LLMs' latent representations is crucial for elucidating their underlying mechanisms, improving…

Machine Learning · Computer Science 2026-02-03 Zhuoran Li , Xu Sun , Wanyu Lin , Jiannong Cao

This survey paper delves into the emerging and critical area of symbolic knowledge distillation in Large Language Models (LLMs). As LLMs like Generative Pre-trained Transformer-3 (GPT-3) and Bidirectional Encoder Representations from…

Computation and Language · Computer Science 2024-08-21 Kamal Acharya , Alvaro Velasquez , Houbing Herbert Song

The deployment and application of Large Language Models (LLMs) is hindered by their memory inefficiency, computational demands, and the high costs of API inferences. Traditional distillation methods, which transfer the capabilities of LLMs…

Computation and Language · Computer Science 2024-11-21 Yifei Zhang , Bo Pan , Chen Ling , Yuntong Hu , Liang Zhao

The rapid evolution of artificial intelligence in drug discovery encounters challenges with generalization and extensive training, yet Large Language Models (LLMs) offer promise in reshaping interactions with complex molecular data. Our…

Biomolecules · Quantitative Biology 2024-12-20 He Cao , Zijing Liu , Xingyu Lu , Yuan Yao , Yu Li

Sequential Recommendation (SR) task involves predicting the next item a user is likely to interact with, given their past interactions. The SR models examine the sequence of a user's actions to discern more complex behavioral patterns and…

Information Retrieval · Computer Science 2025-04-22 Wujiang Xu , Qitian Wu , Zujie Liang , Jiaojiao Han , Xuying Ning , Yunxiao Shi , Wenfang Lin , Yongfeng Zhang

Large Language Models (LLMs) have exhibited impressive generation capabilities, but they suffer from hallucinations when solely relying on their internal knowledge, especially when answering questions that require less commonly known…

Computation and Language · Computer Science 2023-11-01 Wenting Zhao , Ye Liu , Tong Niu , Yao Wan , Philip S. Yu , Shafiq Joty , Yingbo Zhou , Semih Yavuz

Sequential recommender systems predict items that may interest users by modeling their preferences based on historical interactions. Traditional sequential recommendation methods rely on capturing implicit collaborative filtering signals…

Information Retrieval · Computer Science 2024-03-28 Shenghao Yang , Weizhi Ma , Peijie Sun , Qingyao Ai , Yiqun Liu , Mingchen Cai , Min Zhang

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…

This paper introduces a system that integrates large language models (LLMs) into the clinical trial retrieval process, enhancing the effectiveness of matching patients with eligible trials while maintaining information privacy and allowing…

Information Retrieval · Computer Science 2024-11-01 Georgios Peikos , Pranav Kasela , Gabriella Pasi

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

Large Language Models (LLMs) often generate inaccurate responses (hallucinations) when faced with questions beyond their knowledge scope. Retrieval-Augmented Generation (RAG) addresses this by leveraging external knowledge, but a critical…

Information Retrieval · Computer Science 2025-09-10 Haoxiang Jin , Ronghan Li , Zixiang Lu , Qiguang Miao

Sequential recommender systems have achieved significant success in modeling temporal user behavior but remain limited in capturing rich user semantics beyond interaction patterns. Large Language Models (LLMs) present opportunities to…

Large Language Models (LLMs) have achieved remarkable success in natural language tasks, yet understanding their reasoning processes remains a significant challenge. We address this by introducing XplainLLM, a dataset accompanying an…

Computation and Language · Computer Science 2024-09-24 Zichen Chen , Jianda Chen , Ambuj Singh , Misha Sra

In recent years, Large Language Models (LLMs) have demonstrated an impressive ability to encode knowledge during pre-training on large text corpora. They can leverage this knowledge for downstream tasks like question answering (QA), even in…

Computation and Language · Computer Science 2024-06-11 Juraj Vladika , Phillip Schneider , Florian Matthes

Large language models (LLMs) have achieved strong performance across a wide range of natural language processing tasks. However, deploying LLMs at scale for domain specific applications, such as job-person fit and explanation in job seeking…

Large Language Models (LLMs) have revolutionized various sectors, including healthcare where they are employed in diverse applications. Their utility is particularly significant in the context of rare diseases, where data scarcity,…

Computation and Language · Computer Science 2024-08-20 Qiuhao Lu , Rui Li , Andrew Wen , Jinlian Wang , Liwei Wang , Hongfang Liu