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Screening patients for enrollment is a well-known, labor-intensive bottleneck that leads to under-enrollment and, ultimately, trial failures. Recent breakthroughs in large language models (LLMs) offer a promising opportunity to use…

Computation and Language · Computer Science 2026-04-30 Ziyi Chen , Mengxian Lyu , Cheng Peng , Yonghui Wu

The use of generative artificial intelligence (AI) models is becoming ubiquitous in many fields. Though progress continues to be made, general purpose large language AI models (LLM) show a tendency to deliver creative answers, often called…

Molecular Networks · Quantitative Biology 2025-07-08 Pranta Saha , Joyce Reimer , Brook Byrns , Connor Burbridge , Neeraj Dhar , Jeffrey Chen , Steven Rayan , Gordon Broderick

With hundreds of thousands of language models available on Huggingface today, efficiently evaluating and utilizing these models across various downstream, tasks has become increasingly critical. Many existing methods repeatedly learn…

Computation and Language · Computer Science 2024-10-18 Richard Zhuang , Tianhao Wu , Zhaojin Wen , Andrew Li , Jiantao Jiao , Kannan Ramchandran

Large language models (LLMs) are a class of artificial intelligence models based on deep learning, which have great performance in various tasks, especially in natural language processing (NLP). Large language models typically consist of…

Quantitative Methods · Quantitative Biology 2025-02-04 Jiajia Liu , Mengyuan Yang , Yankai Yu , Haixia Xu , Tiangang Wang , Kang Li , Xiaobo Zhou

Large Language Models (LLMs) are prone to generating factually incorrect information when responding to queries that involve numerical and statistical data or other timely facts. In this paper, we present an approach for enhancing the…

Computation and Language · Computer Science 2024-09-24 Prashanth Radhakrishnan , Jennifer Chen , Bo Xu , Prem Ramaswami , Hannah Pho , Adriana Olmos , James Manyika , R. V. Guha

Understanding protein sequences is vital and urgent for biology, healthcare, and medicine. Labeling approaches are expensive yet time-consuming, while the amount of unlabeled data is increasing quite faster than that of the labeled data due…

Computation and Language · Computer Science 2021-11-01 Liang He , Shizhuo Zhang , Lijun Wu , Huanhuan Xia , Fusong Ju , He Zhang , Siyuan Liu , Yingce Xia , Jianwei Zhu , Pan Deng , Bin Shao , Tao Qin , Tie-Yan Liu

Sequential recommendation problems have received increasing attention in research during the past few years, leading to the inception of a large variety of algorithmic approaches. In this work, we explore how large language models (LLMs),…

Information Retrieval · Computer Science 2023-09-19 Jesse Harte , Wouter Zorgdrager , Panos Louridas , Asterios Katsifodimos , Dietmar Jannach , Marios Fragkoulis

Large Language Models (LLMs) are increasingly adopted as conversational assistants in genomics, where they are mainly used to reason over biological knowledge, annotations, and analysis outputs through natural language interfaces. However,…

Genomics · Quantitative Biology 2026-04-08 Weicai Long , Yusen Hou , Junning Feng , Houcheng Su , Shuo Yang , Donglin Xie , Yanlin Zhang

Proteins are fundamental to biology, executing diverse functions through complex physicochemical interactions, and they hold transformative potential across medicine, materials science, and environmental applications. Protein Language…

Biomolecules · Quantitative Biology 2025-06-11 Logan Hallee , Nikolaos Rafailidis , David B. Bichara , Jason P. Gleghorn

In this article, we evaluate four Large Language Models (LLMs) and their effectiveness at retrieving data within a specialized Retrieval-Augmented Generation (RAG) system, using a comprehensive food composition database. Our method is…

Computation and Language · Computer Science 2026-03-12 Maks Požarnik Vavken , Matevž Ogrinc , Tome Eftimov , Barbara Koroušić Seljak

Purpose: Large Language Models (LLMs) like GPT (Generative Pre-trained Transformer) from OpenAI and LLaMA (Large Language Model Meta AI) from Meta AI are increasingly recognized for their potential in the field of cheminformatics,…

Biomolecules · Quantitative Biology 2024-05-22 Shaghayegh Sadeghi , Alan Bui , Ali Forooghi , Jianguo Lu , Alioune Ngom

Predicting protein stability changes induced by single-point mutations has been a persistent challenge over the years, attracting immense interest from numerous researchers. The ability to precisely predict protein thermostability is…

Biomolecules · Quantitative Biology 2023-12-08 Yijie Zhang , Zhangyang Gao , Cheng Tan , Stan Z. Li

Large Language Models (LLMs) have made remarkable advancements in the field of natural language processing. However, their increasing size poses challenges in terms of computational cost. On the other hand, Small Language Models (SLMs) are…

Computation and Language · Computer Science 2023-08-03 Zhen Guo , Peiqi Wang , Yanwei Wang , Shangdi Yu

Protein language models (PLMs) have demonstrated remarkable capabilities in learning relationships between protein sequences and functions. However, finetuning these large models requires substantial computational resources, often with…

Machine Learning · Computer Science 2025-12-09 Shuo Zhang , Jian K. Liu

In recent years, large language models (LLM) have emerged as powerful tools for diverse natural language processing tasks. However, their potential for recommender systems under the generative recommendation paradigm remains relatively…

Information Retrieval · Computer Science 2023-07-11 Jianchao Ji , Zelong Li , Shuyuan Xu , Wenyue Hua , Yingqiang Ge , Juntao Tan , Yongfeng Zhang

This study investigates the mechanisms and factors influencing memorization in fine-tuned large language models (LLMs), with a focus on the medical domain due to its privacy-sensitive nature. We examine how different aspects of the…

Computation and Language · Computer Science 2025-08-06 Danil Savine

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

Retrieval-augmented large language models (LLMs) have been remarkably competent in various NLP tasks. However, it was observed by previous works that retrieval is not always helpful, especially when the LLM is already knowledgeable on the…

Computation and Language · Computer Science 2024-12-16 Chengkai Huang , Yu Xia , Rui Wang , Kaige Xie , Tong Yu , Julian McAuley , Lina Yao

Using tools by Large Language Models (LLMs) is a promising avenue to extend their reach beyond language or conversational settings. The number of tools can scale to thousands as they enable accessing sensory information, fetching updated…

Information Retrieval · Computer Science 2024-12-06 Mohammad Kachuee , Sarthak Ahuja , Vaibhav Kumar , Puyang Xu , Xiaohu Liu

Large Language Models (LLMs) have exhibited remarkable proficiency in comprehending and generating natural language. On the other hand, personalized LLM response generation holds the potential to offer substantial benefits for individuals…

Computation and Language · Computer Science 2025-01-15 Kai Zhang , Yejin Kim , Xiaozhong Liu