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Protein-specific large language models (Protein LLMs) are revolutionizing protein science by enabling more efficient protein structure prediction, function annotation, and design. While existing surveys focus on specific aspects or…

We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution has been a dominating paradigm in this field which has an…

Machine Learning · Computer Science 2025-01-20 Yinkai Wang , Jiaxing He , Yuanqi Du , Xiaohui Chen , Jianan Canal Li , Li-Ping Liu , Xiaolin Xu , Soha Hassoun

Code large language models (Code LLMs) are powerful but costly to train, with scaling laws predicting performance from model size, data, and compute. However, different programming languages (PLs) have varying impacts during pre-training…

Computation and Language · Computer Science 2025-12-16 Jian Yang , Shawn Guo , Lin Jing , Wei Zhang , Aishan Liu , Chuan Hao , Zhoujun Li , Wayne Xin Zhao , Xianglong Liu , Weifeng Lv , Bryan Dai

Protein language models (PLMs) have shown promise in improving the understanding of protein sequences, contributing to advances in areas such as function prediction and protein engineering. However, training these models from scratch…

Machine Learning · Computer Science 2024-12-19 Shivasankaran Vanaja Pandi , Bharath Ramsundar

The rapid advancement of large language models (LLMs) has led to significant improvements in natural language processing but also poses challenges due to their high computational and energy demands. This paper introduces a series of…

Computation and Language · Computer Science 2024-06-27 Dylan Hillier , Leon Guertler , Cheston Tan , Palaash Agrawal , Chen Ruirui , Bobby Cheng

In recent years, Large Language Models (LLMs) have made significant strides towards Artificial General Intelligence. However, training these models from scratch requires substantial computational resources and vast amounts of text data. In…

Computation and Language · Computer Science 2024-10-03 Wenzhen Zheng , Wenbo Pan , Xu Xu , Libo Qin , Li Yue , Ming Zhou

Test-Time Scaling (TTS) is an important method for improving the performance of Large Language Models (LLMs) by using additional computation during the inference phase. However, current studies do not systematically analyze how policy…

Computation and Language · Computer Science 2025-02-11 Runze Liu , Junqi Gao , Jian Zhao , Kaiyan Zhang , Xiu Li , Biqing Qi , Wanli Ouyang , Bowen Zhou

Current multimodal language model (MLM) training approaches overlook the influence of instruction templates. Previous research deals with this problem by leveraging hand-crafted or model-generated templates, failing to investigate the…

Computer Vision and Pattern Recognition · Computer Science 2025-04-09 Shijian Wang , Linxin Song , Jieyu Zhang , Ryotaro Shimizu , Jiarui Jin , Ao Luo , Yuan Lu , Li Yao , Cunjian Chen , Julian McAuley , Wentao Zhang , Hanqian Wu

Traditional scaling laws in natural language processing suggest that increasing model size and training data enhances performance. However, recent studies reveal deviations, particularly in large language models, where performance…

Machine Learning · Computer Science 2025-07-16 Zhengyu Chen , Siqi Wang , Teng Xiao , Yudong Wang , Shiqi Chen , Xunliang Cai , Junxian He , Jingang Wang

While scaling laws for Large Language Models (LLMs) traditionally focus on proxy metrics like pretraining loss, predicting downstream task performance has been considered unreliable. This paper challenges that view by proposing a direct…

Machine Learning · Computer Science 2025-12-10 Jakub Krajewski , Amitis Shidani , Dan Busbridge , Sam Wiseman , Jason Ramapuram

Language is essentially a complex, intricate system of human expressions governed by grammatical rules. It poses a significant challenge to develop capable AI algorithms for comprehending and grasping a language. As a major approach,…

Research on scaling large language models (LLMs) has primarily focused on model parameters and training data size, overlooking the role of vocabulary size. We investigate how vocabulary size impacts LLM scaling laws by training models…

Computation and Language · Computer Science 2024-11-04 Chaofan Tao , Qian Liu , Longxu Dou , Niklas Muennighoff , Zhongwei Wan , Ping Luo , Min Lin , Ngai Wong

While scaling laws for large language models (LLMs) during pre-training have been extensively studied, their behavior under reinforcement learning (RL) post-training remains largely unexplored. This paper presents a systematic empirical…

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

[Context and motivation] Large language models (LLMs) show notable results in natural language processing (NLP) tasks for requirements engineering (RE). However, their use is compromised by high computational cost, data sharing risks, and…

Software Engineering · Computer Science 2025-10-27 Mohammad Amin Zadenoori , Vincenzo De Martino , Jacek Dabrowski , Xavier Franch , Alessio Ferrari

Guided by the belief of the scaling law, large language models (LLMs) have achieved impressive performance in recent years. However, scaling law only gives a qualitative estimation of loss, which is influenced by various factors such as…

Computation and Language · Computer Science 2024-09-16 Chuhan Wu , Ruiming Tang

Pretraining large language models (LLMs) is resource-intensive, often requiring months of training time even with high-end GPU clusters. There are two approaches of mitigating such computational demands: reusing smaller models to train…

Machine Learning · Computer Science 2025-06-17 Seng Pei Liew , Takuya Kato , Sho Takase

The current trend of scaling language models involves increasing both parameter count and training dataset size. Extrapolating this trend suggests that training dataset size may soon be limited by the amount of text data available on the…

In recent years, multimodal large language models (MLLMs) have shown strong potential in real-world applications. They are developing rapidly due to their remarkable ability to comprehend multimodal information and their inherent powerful…

Computer Vision and Pattern Recognition · Computer Science 2024-08-02 Bozhou Li , Hao Liang , Zimo Meng , Wentao Zhang

The recent advancements of Small Language Models (SLMs) have opened new possibilities for efficient code generation. SLMs offer lightweight and cost-effective alternatives to Large Language Models (LLMs), making them attractive for use in…

Software Engineering · Computer Science 2026-01-21 Md Mahade Hasan , Muhammad Waseem , Kai-Kristian Kemell , Jussi Rasku , Juha Ala-Rantala , Pekka Abrahamsson