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Large language models (LLMs) are often used in environments where facts evolve, yet factual knowledge updates via fine-tuning on unstructured text often suffer from 1) reliance on compute-heavy paraphrasing augmentation and 2) the reversal…

Predicting problem-difficulty in large language models (LLMs) refers to estimating how difficult a task is according to the model itself, typically by training linear probes on its internal representations. In this work, we study the…

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…

Continual learning (CL) in large language models (LLMs) is an evolving domain that focuses on developing efficient and sustainable training strategies to adapt models to emerging knowledge and achieve robustness in dynamic environments. Our…

The parallels between protein sequences and natural language in their sequential structures have inspired the application of large language models (LLMs) to protein understanding. Despite the success of LLMs in NLP, their effectiveness in…

Protein language models (pLMs) pre-trained on vast protein sequence databases excel at various downstream tasks but often lack the structural knowledge essential for some biological applications. To address this, we introduce a method to…

Deep neural-network-based language models (LMs) are increasingly applied to large-scale protein sequence data to predict protein function. However, being largely black-box models and thus challenging to interpret, current protein LM…

Large Language Models (LLMs) stand at the forefront of a number of Natural Language Processing (NLP) tasks. Despite the widespread adoption of LLMs in NLP, much of their potential in broader fields remains largely unexplored, and…

Protein sequences are abundant in repeating segments, both as exact copies and as approximate segments with mutations. These repeats are important for protein structure and function, motivating decades of algorithmic work on repeat…

Structured pruning of modern large language models (LLMs) has emerged as a way of decreasing their high computational needs. Width pruning reduces the size of projection weight matrices (e.g., by removing attention heads) while maintaining…

Recently, foundation language models (LMs) have marked significant achievements in the domains of natural language processing (NLP) and computer vision (CV). Unlike traditional neural network models, foundation LMs obtain a great ability…

Large language models (LLMs) are increasingly costly to deploy, motivating extensive research on model pruning. However, most existing studies focus on instruction-following LLMs, leaving it unclear whether established pruning strategies…

We investigate the robustness of Large Language Models (LLMs) to structural interventions by deleting and swapping adjacent layers during inference. Surprisingly, models retain 72-95% of their original top-1 prediction accuracy without any…

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…

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…

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,…

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…

Large language models (LLMs) have achieved a milestone that undenia-bly changed many held beliefs in artificial intelligence (AI). However, there remains many limitations of these LLMs when it comes to true language understanding,…

Pre-trained language models (PLMs) have been the de facto paradigm for most natural language processing (NLP) tasks. This also benefits biomedical domain: researchers from informatics, medicine, and computer science (CS) communities propose…

In recent years, Large Language Models (LLMs) have emerged as a prominent area of interest across various research domains, including Process Mining (PM). Current applications in PM have predominantly centered on prompt engineering…