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Masked language modeling (MLM) is one of the key sub-tasks in vision-language pretraining. In the cross-modal setting, tokens in the sentence are masked at random, and the model predicts the masked tokens given the image and the text. In…

Computation and Language · Computer Science 2021-09-07 Yonatan Bitton , Gabriel Stanovsky , Michael Elhadad , Roy Schwartz

Matrix-based preconditioned optimizers, such as Muon, have recently been shown to be more efficient than scalar-based optimizers for training large-scale neural networks, including large language models (LLMs). Recent benchmark studies of…

Machine Learning · Computer Science 2026-02-02 Yifeng Liu , Angela Yuan , Quanquan Gu

In this study, we delve into the efficacy of transformers within pre-trained language models (PLMs) when repurposed as encoders for Automatic Speech Recognition (ASR). Our underlying hypothesis posits that, despite being initially trained…

Audio and Speech Processing · Electrical Eng. & Systems 2024-09-27 Keyu An , Shiliang Zhang , Zhijie Yan

The anti-cancer immune response relies on the bindings between T-cell receptors (TCRs) and antigens, which elicits adaptive immunity to eliminate tumor cells. This ability of the immune system to respond to novel various neoantigens arises…

Quantitative Methods · Quantitative Biology 2025-11-11 Xing Fang , Chenpeng Yu , Shiye Tian , Hui Liu

Explorations in fine-tuning Vision-Language Models (VLMs), such as Low-Rank Adaptation (LoRA) from Parameter Efficient Fine-Tuning (PEFT), have made impressive progress. However, most approaches rely on explicit weight updates, overlooking…

Machine Learning · Computer Science 2025-12-30 Mingyuan Zhang , Yue Bai , Yifan Wang , Yiyang Huang , Yun Fu

Protein language models (PLMs) have emerged as powerful tools to detect complex patterns of protein sequences. However, the capability of PLMs to fully capture information on protein sequences might be limited by focusing on single…

Machine Learning · Computer Science 2025-05-27 Hazem Alsamkary , Mohamed Elshaffei , Mohamed Elkerdawy , Ahmed Elnaggar

The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…

Biomolecules · Quantitative Biology 2022-08-24 Noelia Ferruz , Birte Höcker

Pre-trained large-scale language models (LLMs) excel at producing coherent articles, yet their outputs may be untruthful, toxic, or fail to align with user expectations. Current approaches focus on using reinforcement learning with human…

Computation and Language · Computer Science 2024-06-06 Dehong Xu , Liang Qiu , Minseok Kim , Faisal Ladhak , Jaeyoung Do

Recent advances in pre-trained language models (PLMs) have demonstrated their capabilities in capturing universal knowledge, making them promising for radar signal processing applications. Nevertheless, directly fine-tuning PLMs on radar…

Signal Processing · Electrical Eng. & Systems 2026-05-01 Qiying Hu , Yaowen Li , Shengyi Zhang , Chuan Huang , Yu Liu , You He

Evaluating the quality of machine-generated natural language content is a challenging task in Natural Language Processing (NLP). Recently, large language models (LLMs) like GPT-4 have been employed for this purpose, but they are…

Computation and Language · Computer Science 2024-12-23 Daniil Larionov , Steffen Eger

Genomic language models (gLMs) face a fundamental efficiency challenge: either maintain separate specialized models for each biological modality (DNA and RNA) or develop large multi-modal architectures. Both approaches impose significant…

Genomics · Quantitative Biology 2025-08-08 Shiyi Du , Litian Liang , Jiayi Li , Carl Kingsford

The rapid advancement of pre-trained language models (PLMs) has demonstrated promising results for various code-related tasks. However, their effectiveness in detecting real-world vulnerabilities remains a critical challenge. While existing…

Cryptography and Security · Computer Science 2025-11-25 Youpeng Li , Weiliang Qi , Xuyu Wang , Fuxun Yu , Xinda Wang

This study investigates the mechanisms and factors influencing memorization in fine-tuned large language models (LLMs), with a focus on the medical domain due to its privacy-sensitive nature. We examine how different aspects of the…

Computation and Language · Computer Science 2025-08-06 Danil Savine

Accurate prediction of enzymatic activity from amino acid sequences could drastically accelerate enzyme engineering for applications such as bioremediation and therapeutics development. In recent years, Protein Language Model (PLM)…

Quantitative Methods · Quantitative Biology 2025-05-07 Duncan F. Muir , Parker Grosjean , Margaux M. Pinney , Michael J. Keiser

Pre-trained Language Models (PLMs) can be accurately fine-tuned for downstream text processing tasks. Recently, researchers have introduced several parameter-efficient fine-tuning methods that optimize input prompts or adjust a small number…

Computation and Language · Computer Science 2024-06-07 Saeed Najafi , Alona Fyshe

Evolutionary algorithms excel in solving complex optimization problems, especially those with multiple objectives. However, their stochastic nature can sometimes hinder rapid convergence to the global optima, particularly in scenarios…

Neural and Evolutionary Computing · Computer Science 2024-05-10 Zeyi Wang , Songbai Liu , Jianyong Chen , Kay Chen Tan

This paper investigates different pretraining approaches to spoken language identification. The paper is based on our submission to the Oriental Language Recognition 2021 Challenge. We participated in two tracks of the challenge:…

Audio and Speech Processing · Electrical Eng. & Systems 2022-05-17 Tanel Alumäe , Kunnar Kukk

Safe reinforcement learning (RL) agents accomplish given tasks while adhering to specific constraints. Employing constraints expressed via easily-understandable human language offers considerable potential for real-world applications due to…

Machine Learning · Computer Science 2024-05-16 Xingzhou Lou , Junge Zhang , Ziyan Wang , Kaiqi Huang , Yali Du

The conditional generation of proteins with desired functions is a key goal for generative models. Existing methods based on prompting of protein language models (PLMs) can generate proteins conditioned on a target functionality, such as a…

Biomolecules · Quantitative Biology 2025-06-13 Jason Yang , Aadyot Bhatnagar , Jeffrey A. Ruffolo , Ali Madani

Parameter-Efficient Fine-Tuning (PEFT) methods like Low-Rank Adaptation (LoRA) optimize federated training by reducing computational and communication costs. We propose RoLoRA, a federated framework using alternating optimization to…

Machine Learning · Computer Science 2025-11-06 Shuangyi Chen , Yuanxin Guo , Yue Ju , Harik Dalal , Zhongwen Zhu , Ashish Khisti
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