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Large language models (LLMs) are having transformative impacts across a wide range of scientific fields, particularly in the biomedical sciences. Just as the goal of Natural Language Processing is to understand sequences of words, a major…

Genomics · Quantitative Biology 2024-09-24 Gonzalo Benegas , Chengzhong Ye , Carlos Albors , Jianan Canal Li , Yun S. Song

Large Language Models (LLMs) have demonstrated impressive capabilities across a range of scientific tasks including mathematics, physics, and chemistry. Despite their successes, the effectiveness of LLMs in handling complex statistical…

Computation and Language · Computer Science 2024-10-11 Yizhang Zhu , Shiyin Du , Boyan Li , Yuyu Luo , Nan Tang

As LLMs have become increasingly popular, they have been used in almost every field. But as the application for LLMs expands from generic fields to narrow, focused science domains, there exists an ever-increasing gap in ways to evaluate…

Computation and Language · Computer Science 2023-10-18 Anurag Acharya , Sai Munikoti , Aaron Hellinger , Sara Smith , Sridevi Wagle , Sameera Horawalavithana

Large Language Models (LLMs) are revolutionizing bioinformatics, enabling advanced analysis of DNA, RNA, proteins, and single-cell data. This survey provides a systematic review of recent advancements, focusing on genomic sequence modeling,…

Computation and Language · Computer Science 2026-03-03 Zhenyu Wang , Zikang Wang , Jiyue Jiang , Pengan Chen , Xiangyu Shi , Yu Li

Predictive analysis is a cornerstone of modern decision-making, with applications in various domains. Large Language Models (LLMs) have emerged as powerful tools in enabling nuanced, knowledge-intensive conversations, thus aiding in complex…

Computation and Language · Computer Science 2025-05-26 Qin Chen , Yuanyi Ren , Xiaojun Ma , Yuyang Shi

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

Recent advancements in Large Language Models (LLMs) have pushed the boundaries of natural language processing, especially in long-context understanding. However, the evaluation of these models' long-context abilities remains a challenge due…

Computation and Language · Computer Science 2025-04-24 Cunxiang Wang , Ruoxi Ning , Boqi Pan , Tonghui Wu , Qipeng Guo , Cheng Deng , Guangsheng Bao , Xiangkun Hu , Zheng Zhang , Qian Wang , Yue Zhang

Large language models (LLMs) have become important tools in solving biological problems, offering improvements in accuracy and adaptability over conventional methods. Several benchmarks have been proposed to evaluate the performance of…

Large Language Models (LLMs) have demonstrated remarkable capabilities across a wide range of general-domain tasks. However, their effectiveness in specialized fields, such as construction, remains underexplored. In this paper, we introduce…

Computation and Language · Computer Science 2025-08-25 Yanzhao Wu , Lufan Wang , Rui Liu

Large language models (LLMs) have demonstrated impressive capabilities in natural language understanding and generation, but the quality bar for medical and clinical applications is high. Today, attempts to assess models' clinical knowledge…

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose…

Computation and Language · Computer Science 2025-11-25 Yanjun Lyu , Zihao Wu , Lu Zhang , Jing Zhang , Yiwei Li , Wei Ruan , Zhengliang Liu , Zeyu Zhang , Xiang Li , Rongjie Liu , Chao Huang , Wentao Li , Tianming Liu , Dajiang Zhu

Large Language Models (LLMs) perform well on standard reasoning and question-answering benchmarks, yet such evaluations often fail to capture their ability to handle long-tail, expertise-intensive knowledge in real-world professional…

This paper introduces AQA-Bench, a novel benchmark to assess the sequential reasoning capabilities of large language models (LLMs) in algorithmic contexts, such as depth-first search (DFS). The key feature of our evaluation benchmark lies…

Computation and Language · Computer Science 2025-06-23 Siwei Yang , Bingchen Zhao , Cihang Xie

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

We introduce KoLasSimpleQA, the first benchmark evaluating the multilingual factual ability of Large Language Models (LLMs). Inspired by existing research, we created the question set with features such as single knowledge point coverage,…

Computation and Language · Computer Science 2025-05-23 Bowen Jiang , Runchuan Zhu , Jiang Wu , Zinco Jiang , Yifan He , Junyuan Gao , Jia Yu , Rui Min , Yinfan Wang , Haote Yang , Songyang Zhang , Dahua Lin , Lijun Wu , Conghui He

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…

Quantitative Methods · Quantitative Biology 2024-04-04 Junyoung Kim , Jingye Yang , Kai Wang , Chunhua Weng , Cong Liu

The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…

Machine Learning · Computer Science 2024-09-25 Tianyu Liu , Yijia Xiao , Xiao Luo , Hua Xu , W. Jim Zheng , Hongyu Zhao

We introduce TeleQnA, the first benchmark dataset designed to evaluate the knowledge of Large Language Models (LLMs) in telecommunications. Comprising 10,000 questions and answers, this dataset draws from diverse sources, including…

Information Theory · Computer Science 2023-10-24 Ali Maatouk , Fadhel Ayed , Nicola Piovesan , Antonio De Domenico , Merouane Debbah , Zhi-Quan Luo

Large Language Models (LLMs) have demonstrated remarkable performance across various disciplines and tasks. However, benchmarking their capabilities with multilingual spoken queries remains largely unexplored. In this study, we introduce…

Computation and Language · Computer Science 2025-05-27 Firoj Alam , Md Arid Hasan , Shammur Absar Chowdhury

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and…

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