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Protein language models (pLMs) have demonstrated success at generating functional proteins across vast sequence spaces but lack the ability to design high-fitness variants on demand. Here, we iteratively guide pLMs toward user-defined…

In this paper, we introduce \textbf{Share}d \textbf{Lo}w \textbf{R}ank \textbf{A}daptation (ShareLoRA), a Large Language Model (LLM) fine-tuning technique that balances parameter efficiency, adaptability, and robustness without compromising…

We report a mixture of expert strategy to create fine-tuned large language models using a deep layer-wise token-level approach based on low-rank adaptation (LoRA). Starting with a set of pre-trained LoRA adapters, our gating strategy uses…

Adapting large language models (LLMs) to downstream tasks via full fine-tuning is increasingly impractical due to its computational and memory demands. Parameter-efficient fine-tuning (PEFT) approaches such as Low-Rank Adaptation (LoRA)…

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…

Less than 1% of protein sequences are structurally and functionally annotated. Natural Language Processing (NLP) community has recently embraced self-supervised learning as a powerful approach to learn representations from unlabeled text,…

Time series modeling holds significant importance in many real-world applications and has been extensively studied. While pre-trained foundation models have made impressive strides in the fields of natural language processing (NLP) and…

Unlocking the next generation of biotechnology and therapeutic innovation demands overcoming the inherent complexity and resource-intensity of conventional protein engineering methods. Recent GenAI-powered computational techniques often…

It is a common practice in natural language processing to pre-train a single model on a general domain and then fine-tune it for downstream tasks. However, when it comes to Large Language Models, fine-tuning the entire model can be…

Low-resource languages (LRLs) face significant challenges in natural language processing (NLP) due to limited data. While current state-of-the-art large language models (LLMs) still struggle with LRLs, smaller multilingual models (mLMs)…

[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…

Proteins adopt multiple structural conformations to perform their diverse biological functions, and understanding these conformations is crucial for advancing drug discovery. Traditional physics-based simulation methods often struggle with…

In recent years, large language models (LLMs) have achieved remarkable success in natural language processing (NLP). LLMs require an extreme amount of parameters to attain high performance. As models grow into the trillion-parameter range,…

Parameter-efficient fine-tuning (PEFT) is essential for adapting large language models (LLMs), with low-rank adaptation (LoRA) being the most popular approach. However, LoRA suffers from slow convergence, and some recent LoRA variants, such…

Large language models (LLMs) have garnered significant interest in natural language processing (NLP), particularly their remarkable performance in various downstream tasks in resource-rich languages. Recent studies have highlighted the…

The fine-tuning of Large Language Models (LLMs) is pivotal for achieving optimal performance across diverse downstream tasks. However, while full fine-tuning delivers superior results, it entails significant computational and resource…

Low-rank Adaptation (LoRA) has gained popularity as a fine-tuning approach for Large Language Models (LLMs) due to its low resource requirements and good performance. While a plethora of work has investigated improving LoRA serving…

We propose ProtLLM, a versatile cross-modal large language model (LLM) for both protein-centric and protein-language tasks. ProtLLM features a unique dynamic protein mounting mechanism, enabling it to handle complex inputs where the natural…

Although the advancements of pre-trained Large Language Models have significantly accelerated recent progress in NLP, their ever-increasing size poses significant challenges for conventional fine-tuning, especially in memory-intensive…

Phenotype-driven gene prioritization is a critical process in the diagnosis of rare genetic disorders for identifying and ranking potential disease-causing genes based on observed physical traits or phenotypes. While traditional approaches…