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Protein research is crucial in various fundamental disciplines, but understanding their intricate structure-function relationships remains challenging. Recent Large Language Models (LLMs) have made significant strides in comprehending…

Computational Engineering, Finance, and Science · Computer Science 2025-01-24 Chao Wang , Hehe Fan , Ruijie Quan , Yi Yang

In recent years, there has been remarkable progress in leveraging Language Models (LMs), encompassing Pre-trained Language Models (PLMs) and Large-scale Language Models (LLMs), within the domain of mathematics. This paper conducts a…

Computation and Language · Computer Science 2025-01-03 Wentao Liu , Hanglei Hu , Jie Zhou , Yuyang Ding , Junsong Li , Jiayi Zeng , Mengliang He , Qin Chen , Bo Jiang , Aimin Zhou , Liang He

Biomedical research requires large, diverse samples to produce unbiased results. Automated methods for matching variables across datasets can accelerate this process. Research in this area has been limited, primarily focusing on lexical…

Computation and Language · Computer Science 2024-11-06 Zexu Li , Suraj P. Prabhu , Zachary T. Popp , Shubhi S. Jain , Vijetha Balakundi , Ting Fang Alvin Ang , Rhoda Au , Jinying Chen

Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial intelligence-driven protein design. However, we lack a sufficient understanding of how…

Machine Learning · Computer Science 2022-06-29 Erik Nijkamp , Jeffrey Ruffolo , Eli N. Weinstein , Nikhil Naik , Ali Madani

The realization of autonomous scientific experimentation is currently limited by LLMs' struggle to grasp the strict procedural logic and accuracy required by biological protocols. To address this fundamental challenge, we present…

Computation and Language · Computer Science 2026-01-22 Yuyang Liu , Liuzhenghao Lv , Xiancheng Zhang , Jingya Wang Li Yuan , Yonghong Tian

Large Language Models (LLMs) have transformed artificial intelligence by excelling in complex natural language processing tasks. Their ability to generate human-like text has opened new possibilities for market research, particularly in…

Artificial Intelligence · Computer Science 2026-04-20 Mengxin Wang , Dennis J. Zhang , Heng Zhang

Prompt engineering has proven to be a crucial step in leveraging pretrained large language models (LLMs) in solving various real-world tasks. Numerous solutions have been proposed that seek to automate prompt engineering by using the model…

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

Large Language Models (LLMs) excel in various tasks, but they rely on carefully crafted prompts that often demand substantial human effort. To automate this process, in this paper, we propose a novel framework for discrete prompt…

Computation and Language · Computer Science 2025-05-02 Qingyan Guo , Rui Wang , Junliang Guo , Bei Li , Kaitao Song , Xu Tan , Guoqing Liu , Jiang Bian , Yujiu Yang

Understanding biological processes, drug development, and biotechnological advancements requires a detailed analysis of protein structures and functions, a task that is inherently complex and time-consuming in traditional protein research.…

Artificial Intelligence · Computer Science 2025-04-21 Yijia Xiao , Edward Sun , Yiqiao Jin , Qifan Wang , Wei Wang

Automated heuristic design (AHD) has gained considerable attention for its potential to automate the development of effective heuristics. The recent advent of large language models (LLMs) has paved a new avenue for AHD, with initial efforts…

Neural and Evolutionary Computing · Computer Science 2024-07-16 Rui Zhang , Fei Liu , Xi Lin , Zhenkun Wang , Zhichao Lu , Qingfu Zhang

The exponential growth of text-based data in domains such as healthcare, education, and social sciences has outpaced the capacity of traditional qualitative analysis methods, which are time-intensive and prone to subjectivity. Large…

Recent advancements in large language models (LLMs) have sparked considerable interest in automated theorem proving and a prominent line of research integrates stepwise LLM-based provers into tree search. In this paper, we introduce a novel…

Artificial Intelligence · Computer Science 2025-05-20 Junyu Lai , Jiakun Zhang , Shuo Xu , Taolue Chen , Zihang Wang , Yao Yang , Jiarui Zhang , Chun Cao , Jingwei Xu

As Large language models (LLMs) become increasingly integrated into our lives, their inherent social biases remain a pressing concern. Detecting and evaluating these biases can be challenging because they are often implicit rather than…

Computation and Language · Computer Science 2025-10-29 Katherine Abramski , Giulio Rossetti , Massimo Stella

Large language models (LLMs) have displayed an impressive ability to harness natural language to perform complex tasks. In this work, we explore whether we can leverage this learned ability to find and explain patterns in data.…

Machine Learning · Computer Science 2023-01-30 Chandan Singh , John X. Morris , Jyoti Aneja , Alexander M. Rush , Jianfeng Gao

We consider enhancing large language models (LLMs) for complex planning tasks. While existing methods allow LLMs to explore intermediate steps to make plans, they either depend on unreliable self-verification or external verifiers to…

Artificial Intelligence · Computer Science 2025-02-27 Hongyi Ling , Shubham Parashar , Sambhav Khurana , Blake Olson , Anwesha Basu , Gaurangi Sinha , Zhengzhong Tu , James Caverlee , Shuiwang Ji

Prompts are the interface for eliciting the capabilities of large language models (LLMs). Understanding their structure and components is critical for analyzing LLM behavior and optimizing performance. However, the field lacks a…

Computation and Language · Computer Science 2026-01-27 Sullam Jeoung , Yueyan Chen , Yi Zhang , Shuai Wang , Haibo Ding , Lin Lee Cheong

Large language models (LLMs) have empowered AI agents to tackle increasingly complex tasks. However, most existing agents remain limited to static planning and brittle interactions, falling short of true collaboration or adaptive reasoning.…

Artificial Intelligence · Computer Science 2025-10-14 William Nguyen , Vinh Luong , Christopher Nguyen

Scientific names of organisms consist of a genus name and a species epithet, with the latter often reflecting aspects such as morphology, ecology, distribution, and cultural background. Traditionally, researchers have manually labeled…

Computation and Language · Computer Science 2026-01-13 Keito Inoshita , Kota Nojiri , Haruto Sugeno , Takumi Taga

Since the adoption of large language models (LLMs) for text evaluation has become increasingly prevalent in the field of natural language processing (NLP), a series of existing works attempt to optimize the prompts for LLM evaluators to…

Computation and Language · Computer Science 2025-06-03 Bosi Wen , Pei Ke , Yufei Sun , Cunxiang Wang , Xiaotao Gu , Jinfeng Zhou , Jie Tang , Hongning Wang , Minlie Huang
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