Related papers: PepDoRA: A Unified Peptide Language Model via Weig…

Recent advances in Language Models have enabled the protein modeling community with a powerful tool since protein sequences can be represented as text. Specifically, by taking advantage of Transformers, sequence-to-property prediction will…

Peptide classification tasks, such as predicting toxicity and HIV inhibition, are fundamental to bioinformatics and drug discovery. Traditional approaches rely heavily on handcrafted encodings of one-dimensional (1D) peptide sequences,…

Parameter-efficient fine-tuning (PEFT) is a flexible and efficient method for adapting large language models (LLMs) to downstream tasks. Among these methods, weight-decomposed low-rank adaptation (DoRA) is a promising approach that…

Therapeutic peptides have emerged as a pivotal modality in modern drug discovery, occupying a chemically and topologically rich space. While accurate prediction of their physicochemical properties is essential for accelerating peptide…

Despite their exceptional performance on various tasks after fine-tuning, pre-trained language models (PLMs) face significant challenges due to growing privacy concerns with data in centralized training methods. We consider federated…

Parameter-efficient fine-tuning methods, such as LoRA, reduces the number of trainable parameters. However, they often suffer from scalability issues and differences between their learning pattern and full fine-tuning. To overcome these…

Low-rank adaptation (LoRA) has been developed as an efficient approach for adapting large language models (LLMs) by fine-tuning two low-rank matrices, thereby reducing the number of trainable parameters. However, prior research indicates…

Low Rank Adaptation (LoRA) is a popular Parameter Efficient Fine Tuning (PEFT) method that effectively adapts large pre-trained models for downstream tasks. LoRA parameterizes model updates using low-rank matrices at each layer,…

Functional peptides have the potential to treat a variety of diseases. Their good therapeutic efficacy and low toxicity make them ideal therapeutic agents. Artificial intelligence-based computational strategies can help quickly identify new…

Accurate identification of bioactive peptides (BPs) and protein post-translational modifications (PTMs) is essential for understanding protein function and advancing therapeutic discovery. However, most computational methods remain limited…

Various parameter-efficient fine-tuning (PEFT) techniques have been proposed to enable computationally efficient fine-tuning while maintaining model performance. However, existing PEFT methods are still limited by the growing number of…

Parameter-Efficient Fine-Tuning (PEFT) of text-to-image models has become an increasingly popular technique with many applications. Among the various PEFT methods, Low-Rank Adaptation (LoRA) and its variants have gained significant…

Contemporary large language models (LLMs), such as GPT-4 and Llama, have harnessed extensive computational power and diverse text corpora to achieve remarkable proficiency in interpreting and generating domain-specific content, including…

Large language models (LLMs) have demonstrated significant success in natural language processing (NLP) tasks and have shown promising results in other domains such as protein sequence generation. However, there remain salient differences…

Low-rank adaptation (LoRA) has become the default approach to fine-tune large language models (LLMs) due to its significant reduction in trainable parameters. However, trainable parameter demand for LoRA increases with increasing model…

Pre-trained Language Models (PLMs) have demonstrated their superiority and versatility in modern Natural Language Processing (NLP), effectively adapting to various downstream tasks through further fine-tuning. Federated Parameter-Efficient…

Fine-tuning Large Language Models (LLMs) remains structurally uncertain despite parameter-efficient methods such as Low-Rank Adaptation (LoRA), as the layer-specific roles of internal representations are poorly understood, leading to…

While overparameterization in machine learning models offers great benefits in terms of optimization and generalization, it also leads to increased computational requirements as model sizes grow. In this work, we show that by leveraging the…

Parameter-efficient fine-tuning (PEFT) is a popular method for tailoring pre-trained large language models (LLMs), especially as the models' scale and the diversity of tasks increase. Low-rank adaptation (LoRA) is based on the idea that the…

Representation learning for proteins has primarily focused on the global understanding of protein sequences regardless of their length. However, shorter proteins (known as peptides) take on distinct structures and functions compared to…