Related papers: Biologically Plausible Brain Graph Transformer

Motivation: Biological data and knowledge bases increasingly rely on Semantic Web technologies and the use of knowledge graphs for data integration, retrieval and federated queries. In the past years, feature learning methods that are…

Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and…

The brain can be regarded as a network: a connected system where nodes, or units, represent different specialized regions and links, or connections, represent communication pathways. From a functional perspective communication is coded by…

Interpretable graph neural networks (XGNNs ) are widely adopted in various scientific applications involving graph-structured data. Existing XGNNs predominantly adopt the attention-based mechanism to learn edge or node importance for…

Graph Transformers (GTs) have significantly advanced the field of graph representation learning by overcoming the limitations of message-passing graph neural networks (GNNs) and demonstrating promising performance and expressive power.…

The analysis of the brain surface modeled as a graph mesh is a challenging task. Conventional deep learning approaches often rely on data lying in the Euclidean space. As an extension to irregular graphs, convolution operations are defined…

Human brains lie at the core of complex neurobiological systems, where the neurons, circuits, and subsystems interact in enigmatic ways. Understanding the structural and functional mechanisms of the brain has long been an intriguing pursuit…

Transformers have attained outstanding performance across various modalities, owing to their simple but powerful scaled-dot-product (SDP) attention mechanisms. Researchers have attempted to migrate Transformers to graph learning, but most…

Graph Transformer is gaining increasing attention in the field of machine learning and has demonstrated state-of-the-art performance on benchmarks for graph representation learning. However, as current implementations of Graph Transformer…

Electronic Health Records (EHR) systematically organize patient health data through standardized medical codes, serving as a comprehensive and invaluable source for predictive modeling. Graph neural networks (GNNs) have demonstrated…

While concept-based interpretability methods have traditionally focused on local explanations of neural network predictions, we propose a novel framework and interactive tool that extends these methods into the domain of mechanistic…

Graph Representation Learning (GRL) is an influential methodology, enabling a more profound understanding of graph-structured data and aiding graph clustering, a critical task across various domains. The recent incursion of attention…

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, knowledge graph embedding models have been successfully applied in the transductive setting to tackle various challenging tasks including link prediction, and query answering. Yet, the transductive setting does not allow…

Our brain consists of biological neurons encoding information through accurate spike timing, yet both the architecture and learning rules of our brain remain largely unknown. Comparing to the recent development of backpropagation-based…

Graph embedding is a powerful method to represent graph neurological data (e.g., brain connectomes) in a low dimensional space for brain connectivity mapping, prediction and classification. However, existing embedding algorithms have two…

Encoder-decoder architectures are prominent building blocks of state-of-the-art solutions for tasks across multiple fields where deep learning (DL) or foundation models play a key role. Although there is a growing community working on the…

Interpretability is crucial to enhance trust in machine learning models for medical diagnostics. However, most state-of-the-art image classifiers based on neural networks are not interpretable. As a result, clinicians often resort to known…

We create a reusable Transformer, BrainBERT, for intracranial recordings bringing modern representation learning approaches to neuroscience. Much like in NLP and speech recognition, this Transformer enables classifying complex concepts,…

Graph data in real-world scenarios undergo rapid and frequent changes, making it challenging for existing graph models to effectively handle the continuous influx of new data and accommodate data withdrawal requests. The approach to…