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Studying protein mutations within amino acid sequences holds tremendous significance in life sciences. Protein language models (PLMs) have demonstrated strong capabilities in broad biological applications. However, due to architectural…

Large language models (LLMs) demonstrate exceptional performance on tasks requiring complex linguistic abilities, such as reference disambiguation and metaphor recognition/generation. Although LLMs possess impressive capabilities, their…

We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including: part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This…

Large Language Models (LLMs) are widely deployed in real-world applications, yet their internal mechanisms remain difficult to interpret and control, limiting our ability to diagnose and correct undesirable behaviors. Mechanistic…

With the widespread adoption of large language models (LLMs), understanding their personality representation mechanisms has become critical. As a novel paradigm in Personality Editing, most existing methods employ neuron-editing to locate…

Steering language models (LMs) by modifying internal activations is a popular approach for controlling text generation. Unsupervised dictionary learning methods, e.g., sparse autoencoders, can be scaled to produce many steering vectors, but…

Background: Identification of the interactions and regulatory relations between biomolecules play pivotal roles in understanding complex biological systems and the mechanisms underlying diverse biological functions. However, the collection…

Neurosymbolic approaches can add robustness to opaque neural systems by incorporating explainable symbolic representations. However, previous approaches have not used formal logic to contextualize queries to and validate outputs of large…

There is considerable interest in predicting the pathogenicity of protein variants in human genes. Due to the sparsity of high quality labels, recent approaches turn to \textit{unsupervised} learning, using Multiple Sequence Alignments…

Advances in Large Language Models (LLMs) have led to remarkable capabilities, yet their inner mechanisms remain largely unknown. To understand these models, we need to unravel the functions of individual neurons and their contribution to…

In recent years, protein-text models have gained significant attention for their potential in protein generation and understanding. Current approaches focus on integrating protein-related knowledge into large language models through…

Model pruning technique is vital for accelerating large language models by reducing their size and computational requirements. However, the generalizability of existing pruning methods across diverse datasets and tasks remains unclear.…

Autonomous tuning of particle accelerators is an active and challenging field of research with the goal of enabling novel accelerator technologies cutting-edge high-impact applications, such as physics discovery, cancer research and…

Exploring the application of large language models (LLMs) to graph learning is a emerging endeavor. However, the vast amount of information inherent in large graphs poses significant challenges to this process. This work focuses on the link…

Large Language Models (LLMs) play a crucial role in capturing structured semantics to enhance language understanding, improve interpretability, and reduce bias. Nevertheless, an ongoing controversy exists over the extent to which LLMs can…

Ambiguity is pervasive in real-world questions, yet large language models (LLMs) often respond with confident answers rather than seeking clarification. In this work, we show that question ambiguity is linearly encoded in the internal…

Learning effective protein representations is critical in a variety of tasks in biology such as predicting protein functions. Recent sequence representation learning methods based on Protein Language Models (PLMs) excel in sequence-based…

Neural language models (LMs) are typically trained using only lexical features, such as surface forms of words. In this paper, we argue this deprives the LM of crucial syntactic signals that can be detected at high confidence using existing…

In search settings, calibrating the scores during the ranking process to quantities such as click-through rates or relevance levels enhances a system's usefulness and trustworthiness for downstream users. While previous research has…

Cellular differentiation is governed by gene regulatory networks, the high-dimensional stochastic biochemical systems that determine the transcriptional landscape and mediate cellular responses to signals and perturbations. Although…