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High-content perturbation experiments allow scientists to probe biomolecular systems at unprecedented resolution, but experimental and analysis costs pose significant barriers to widespread adoption. Machine learning has the potential to…

Artificial Intelligence · Computer Science 2025-03-03 Menghua Wu , Russell Littman , Jacob Levine , Lin Qiu , Tommaso Biancalani , David Richmond , Jan-Christian Huetter

Pre-trained large language models (LLMs) have become a cornerstone of modern natural language processing, with their capabilities extending across a wide range of applications and languages. However, the fine-tuning of multilingual LLMs,…

Computation and Language · Computer Science 2025-07-08 Wanru Zhao , Yihong Chen , Royson Lee , Xinchi Qiu , Yan Gao , Hongxiang Fan , Nicholas D. Lane

In this study, we expand upon the FLIP benchmark-designed for evaluating protein fitness prediction models in small, specialized prediction tasks-by assessing the performance of state-of-the-art large protein language models, including…

Machine Learning · Computer Science 2025-01-31 Manuel F. Mollon , Joaquin Gonzalez-Rodriguez , Alicia Lozano-Diez , Daniel Ramos , Doroteo T. Toledano

Emotion recognition from speech is a challenging task that requires capturing both linguistic and paralinguistic cues, with critical applications in human-computer interaction and mental health monitoring. Recent works have highlighted the…

Audio and Speech Processing · Electrical Eng. & Systems 2025-08-21 Hugo Thimonier , Antony Perzo , Renaud Seguier

The recent success of Large Language Models (LLM) in a wide range of Natural Language Processing applications opens the path towards novel Question Answering Systems over Knowledge Graphs leveraging LLMs. However, one of the main obstacles…

Artificial Intelligence · Computer Science 2025-08-26 Julio C. Rangel , Tarcisio Mendes de Farias , Ana Claudia Sima , Norio Kobayashi

Multimodal large language models (MLLMs) have shown remarkable performance in vision-language tasks. However, existing MLLMs are primarily trained on generic datasets, limiting their ability to reason on domain-specific visual cues such as…

Computer Vision and Pattern Recognition · Computer Science 2025-07-15 Hatef Otroshi Shahreza , Sébastien Marcel

Large Language Models (LLMs) have demonstrated profound impact on Natural Language Processing (NLP) tasks. However, their effective deployment across diverse domains often require domain-specific adaptation strategies, as generic models may…

Artificial Intelligence · Computer Science 2025-10-15 Jingyi Wang , Hongyuan Zhu , Ye Niu , Yunhui Deng

Protein language models have excelled in a variety of tasks, ranging from structure prediction to protein engineering. However, proteins are highly diverse in functions and structures, and current state-of-the-art models including the…

Biomolecules · Quantitative Biology 2023-02-27 Chang Ma , Haiteng Zhao , Lin Zheng , Jiayi Xin , Qintong Li , Lijun Wu , Zhihong Deng , Yang Lu , Qi Liu , Lingpeng Kong

Large Language Models (LLMs) are used for Register-Transfer Level (RTL) code generation, but they face two main challenges: functional correctness and Power, Performance, and Area (PPA) optimization. Iterative, feedback-based methods…

Neural and Evolutionary Computing · Computer Science 2025-10-27 Kyungjun Min , Kyumin Cho , Junhwan Jang , Seokhyeong Kang

Large Language Models (LLMs) represent a class of deep learning models adept at understanding natural language and generating coherent responses to various prompts or queries. These models far exceed the complexity of conventional neural…

Machine Learning · Computer Science 2024-12-05 Minghao Shao , Abdul Basit , Ramesh Karri , Muhammad Shafique

The rapid development of large language models (LLM) has greatly enhanced everyday applications. While many FPGA-based accelerators, with flexibility for fine-grained data control, exhibit superior speed and energy efficiency compared to…

Hardware Architecture · Computer Science 2026-03-24 Zifan He , Shengyu Ye , Rui Ma , Yang Wang , Jason Cong

Protein language models (PLMs) have transformed sequence-based protein analysis, yet most applications rely only on final-layer embeddings, which may overlook biologically meaningful information encoded in earlier layers. We systematically…

Quantitative Methods · Quantitative Biology 2025-12-02 Ajit Kumar , IndraPrakash Jha

Large Language Models (LLMs) are rapidly reshaping machine translation (MT), particularly by introducing instruction-following, in-context learning, and preference-based alignment into what has traditionally been a supervised…

Computation and Language · Computer Science 2026-04-29 Baban Gain , Dibyanayan Bandyopadhyay , Asif Ekbal , Trilok Nath Singh

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

Recently, there has been a significant upsurge of interest in leveraging large language models (LLMs) to assist scientific discovery. However, most LLMs only focus on general science, while they lack domain-specific knowledge, such as…

Computation and Language · Computer Science 2024-11-13 Liangtai Sun , Danyu Luo , Da Ma , Zihan Zhao , Baocai Chen , Zhennan Shen , Su Zhu , Lu Chen , Xin Chen , Kai Yu

Recent advancements in deep learning, particularly large language models (LLMs), made a significant impact on how researchers study microbiome and metagenomics data. Microbial protein and genomic sequences, like natural languages, form a…

Quantitative Methods · Quantitative Biology 2024-09-18 Binghao Yan , Yunbi Nam , Lingyao Li , Rebecca A. Deek , Hongzhe Li , Siyuan Ma

Large language models (LLMs), with their powerful generative capabilities and vast knowledge, empower various tasks in everyday life. However, these abilities are primarily concentrated in high-resource languages, leaving low-resource…

Computation and Language · Computer Science 2024-12-20 Shaolei Zhang , Kehao Zhang , Qingkai Fang , Shoutao Guo , Yan Zhou , Xiaodong Liu , Yang Feng

The biomedical domain has sparked a significant interest in the field of Natural Language Processing (NLP), which has seen substantial advancements with pre-trained language models (PLMs). However, comparing these models has proven…

Antibodies play a central role in the immune response by specifically recognizing and neutralizing antigens, and therapeutic antibodies have become major drugs for cancer and autoimmune diseases. However, their discovery still relies on…

Quantitative Methods · Quantitative Biology 2026-05-29 Xiao Luo

The advent of Multilingual Language Models (MLLMs) and Large Language Models has spawned innovation in many areas of natural language processing. Despite the exciting potential of this technology, its impact on developing high-quality…

Computation and Language · Computer Science 2024-03-06 Séamus Lankford , Haithem Afli , Andy Way
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