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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

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Quantitative Methods · Quantitative Biology 2024-08-06 Mai Ha Vu , Rahmad Akbar , Philippe A. Robert , Bartlomiej Swiatczak , Victor Greiff , Geir Kjetil Sandve , Dag Trygve Truslew Haug

In recent years, large language models (e.g., Open AI's GPT-4, Meta's LLaMa, Google's PaLM) have become the dominant approach for building AI systems to analyze and generate language online. However, the automated systems that increasingly…

Computation and Language · Computer Science 2023-06-14 Gabriel Nicholas , Aliya Bhatia

Large Language Models (LLMs) have demonstrated remarkable proficiency in understanding and generating natural language. However, their capabilities wane in highly specialized domains underrepresented in the pretraining corpus, such as…

Machine Learning · Computer Science 2024-07-29 Junhong Shen , Neil Tenenholtz , James Brian Hall , David Alvarez-Melis , Nicolo Fusi

Large language models (LLMs), such as GPT-3 and GPT-4, have demonstrated exceptional performance in various natural language processing tasks and have shown the ability to solve certain reasoning problems. However, their reasoning…

Artificial Intelligence · Computer Science 2023-07-18 Adam Ishay , Zhun Yang , Joohyung Lee

We propose to utilize an instruction-tuned large language model (LLM) for guiding the text generation process in automatic speech recognition (ASR). Modern large language models (LLMs) are adept at performing various text generation tasks…

Audio and Speech Processing · Electrical Eng. & Systems 2025-01-08 Yosuke Higuchi , Tetsuji Ogawa , Tetsunori Kobayashi

Using AI to create autonomous researchers has the potential to accelerate scientific discovery. A prerequisite for this vision is understanding how well an AI model can identify the underlying structure of a black-box system from its…

Machine Learning · Computer Science 2025-05-26 Jiayi Geng , Howard Chen , Dilip Arumugam , Thomas L. Griffiths

Human decision-making belongs to the foundation of our society and civilization, but we are on the verge of a future where much of it will be delegated to artificial intelligence. The arrival of Large Language Models (LLMs) has transformed…

Artificial Intelligence · Computer Science 2025-06-23 Hao Li , Gengrui Zhang , Petter Holme , Shuyue Hu , Zhen Wang

Robots are increasingly common in industry and daily life, such as in nursing homes where they can assist staff. A key challenge is developing intuitive interfaces for easy communication. The use of Large Language Models (LLMs) like GPT-4…

Robotics · Computer Science 2024-08-01 Stanislau Stankevich , Wojciech Dudek

Large Language Models (LLMs) are transformer-based machine learning models that have shown remarkable performance in tasks for which they were not explicitly trained. Here, we explore the potential of LLMs to perform symbolic regression --…

Computation and Language · Computer Science 2026-04-17 Samiha Sharlin , Tyler R. Josephson

Large language models (LLMs), such as ChatGPT, have rapidly penetrated into people's work and daily lives over the past few years, due to their extraordinary conversational skills and intelligence. ChatGPT has become the fastest-growing…

Computation and Language · Computer Science 2024-09-04 Wenxuan Wang

Log analysis represents a critical sub-domain within AI applications that facilitates automatic approaches to fault and error management of large-scaled software systems, saving labors of traditional manual methods. While existing solutions…

Computation and Language · Computer Science 2025-08-27 Yuhe Ji , Yilun Liu , Feiyu Yao , Minggui He , Shimin Tao , Xiaofeng Zhao , Su Chang , Xinhua Yang , Weibin Meng , Yuming Xie , Boxing Chen , Shenglin Zhang , Yongqian Sun

Metadata play a crucial role in ensuring the findability, accessibility, interoperability, and reusability of datasets. This paper investigates the potential of large language models (LLMs), specifically GPT-4, to improve adherence to…

Artificial Intelligence · Computer Science 2025-02-24 Sowmya S. Sundaram , Benjamin Solomon , Avani Khatri , Anisha Laumas , Purvesh Khatri , Mark A. Musen

Current approaches to data discovery match keywords between metadata and queries. This matching requires researchers to know the exact wording that other researchers previously used, creating a challenging process that could lead to missing…

Human-Computer Interaction · Computer Science 2025-10-03 Maura E Halstead , Mark A. Green , Caroline Jay , Richard Kingston , David Topping , Alexander Singleton

While large language models (LLMs) have been successfully applied to various tasks, they still face challenges with hallucinations. Augmenting LLMs with domain-specific tools such as database utilities can facilitate easier and more precise…

Computation and Language · Computer Science 2024-04-10 Qiao Jin , Yifan Yang , Qingyu Chen , Zhiyong Lu

Effective biomedical data integration depends on automated term normalization, the mapping of natural language biomedical terms to standardized identifiers. This linking of terms to identifiers is essential for semantic interoperability.…

Computation and Language · Computer Science 2025-10-23 Suswitha Pericharla , Daniel B. Hier , Tayo Obafemi-Ajayi

Knob tuning plays a crucial role in optimizing databases by adjusting knobs to enhance database performance. However, traditional tuning methods often follow a Try-Collect-Adjust approach, proving inefficient and database-specific.…

Databases · Computer Science 2024-08-06 Yiyan Li , Haoyang Li , Zhao Pu , Jing Zhang , Xinyi Zhang , Tao Ji , Luming Sun , Cuiping Li , Hong Chen

Large language models (LLMs) have not only revolutionized natural language processing but also extended their prowess to various domains, marking a significant stride towards artificial general intelligence. The interplay between LLMs and…

Neural and Evolutionary Computing · Computer Science 2024-05-30 Xingyu Wu , Sheng-hao Wu , Jibin Wu , Liang Feng , Kay Chen Tan

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

Identifying logical errors in complex, incomplete or even contradictory and overall heterogeneous data like students' experimentation protocols is challenging. Recognizing the limitations of current evaluation methods, we investigate the…

Artificial Intelligence · Computer Science 2024-09-20 Arne Bewersdorff , Kathrin Seßler , Armin Baur , Enkelejda Kasneci , Claudia Nerdel
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