Related papers: Structural Interpretations of Protein Language Mod…

Surface elasticity is central to understanding the mechanics and stability of surfaces and interfaces. It is characterized by quantities such as surface tension, residual surface stress, and surface stiffness, however their analytical…

Pretrained generative models have opened new frontiers in brain decoding by enabling the synthesis of realistic texts and images from non-invasive brain recordings. However, the reliability of such outputs remains questionable--whether they…

Accurate identification of protein binding sites is crucial for understanding biomolecular interaction mechanisms and for the rational design of drug targets. Traditional predictive methods often struggle to balance prediction accuracy with…

We introduce ProteinWorkshop, a comprehensive benchmark suite for representation learning on protein structures with Geometric Graph Neural Networks. We consider large-scale pre-training and downstream tasks on both experimental and…

We report a flexible language-model based deep learning strategy, applied here to solve complex forward and inverse problems in protein modeling, based on an attention neural network that integrates transformer and graph convolutional…

Proteins play a vital role in biological processes and are indispensable for living organisms. Accurate representation of proteins is crucial, especially in drug development. Recently, there has been a notable increase in interest in…

Understanding the function of individual neurons within language models is essential for mechanistic interpretability research. We propose $\textbf{Neuron to Graph (N2G)}$, a tool which takes a neuron and its dataset examples, and…

Accurate protein structure prediction from amino-acid sequences is critical to better understanding the protein function. Recent advances in this area largely benefit from more precise inter-residue distance and orientation predictions,…

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively…

Recent advancements in unsupervised protein language models (ProteinLMs), like ESM-1b and ESM-2, have shown promise in different protein prediction tasks. However, these models face challenges due to their high computational demands,…

Multimodal protein language models deliver strong performance on mutation-effect prediction, but training such models from scratch demands substantial computational resources. In this paper, we propose a fine-tuning framework called…

The advent of highly accurate protein structure prediction methods has fueled an exponential expansion of the protein structure database. Consequently, there is a rising demand for rapid and precise structural homolog search. Traditional…

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…

Protein-protein interactions (PPIs) are associated with various diseases, including cancer, infections, and neurodegenerative disorders. Obtaining three-dimensional structural information on these PPIs serves as a foundation to interfere…

Link prediction in knowledge graphs requires integrating structural information and semantic context to infer missing entities. While large language models offer strong generative reasoning capabilities, their limited exploitation of…

Predicting protein function from amino acid sequence remains a central challenge in data-scarce (low-$N$) regimes, limiting machine learning-guided protein design when only small amounts of assay-labeled sequence-function data are…

Predicting protein-protein interactions (PPIs) by learning informative representations from amino acid sequences is a challenging yet important problem in biology. Although various deep learning models in Siamese architecture have been…

Protein language models (pLMs) produce per-residue representations that capture evolutionary and structural information, yet their mean-pooled sequence embeddings are not explicitly trained to reflect functional, evolutionary or structural…

For learning graph representations, not all detailed structures within a graph are relevant to the given graph tasks. Task-relevant structures can be $localized$ or $sparse$ which are only involved in subgraphs or characterized by the…

GraphRAG conditions language models on subgraphs retrieved from knowledge graphs, encoded via message-passing GNNs. Because these encoders entangle node contributions through iterated neighborhood aggregation, there is no closed-form way to…