Related papers: GRAPE: Heterogeneous Graph Representation Learning…

Optimizing power control in multi-cell cellular networks with deep learning enables such a non-convex problem to be implemented in real-time. When channels are time-varying, the deep neural networks (DNNs) need to be re-trained frequently,…

Stem cells can precisely and robustly undergo cellular differentiation and lineage commitment, referred to as stemness. However, how the gene network underlying stemness regulation reliably specifies cell fates is not well understood. To…

Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI…

One of the main goals of developmental biology is to reveal the gene regulatory networks (GRNs) underlying the robust differentiation of multipotent progenitors into precisely specified cell types. Most existing methods to infer GRNs from…

Gene Regulatory Network (GRN) plays an important role in knowing insight of cellular life cycle. It gives information about at which different environmental conditions genes of particular interest get over expressed or under expressed.…

Graph Neural Networks (GNNs) often struggle with heterophilic data, where connected nodes may have dissimilar labels, as they typically assume homophily and rely on local message passing. To address this, we propose creating alternative…

Retrieving gene functional networks from knowledge databases presents a challenge due to the mismatch between disease networks and subtype-specific variations. Current solutions, including statistical and deep learning methods, often fail…

Multi-scale biomedical knowledge networks are expanding with emerging experimental technologies that generates multi-scale biomedical big data. Link prediction is increasingly used especially in bipartite biomedical networks to identify…

Predicting drug-gene associations is crucial for drug development and disease treatment. While graph neural networks (GNN) have shown effectiveness in this task, they face challenges with data sparsity and efficient contrastive learning…

Under circumstances of heterophily, where nodes with different labels tend to be connected based on semantic meanings, Graph Neural Networks (GNNs) often exhibit suboptimal performance. Current studies on graph heterophily mainly focus on…

Recent years have witnessed the emerging success of graph neural networks (GNNs) for modeling structured data. However, most GNNs are designed for homogeneous graphs, in which all nodes and edges belong to the same types, making them…

Graph Neural Networks (GNNs) often assume strong homophily for graph classification, seldom considering heterophily, which means connected nodes tend to have different class labels and dissimilar features. In real-world scenarios, graphs…

Gene regulatory networks (GRNs) play a central role in cellular decision-making. Understanding their structure and how it impacts their dynamics constitutes thus a fundamental biological question. GRNs are frequently modeled as Boolean…

Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biological processes, including development,…

Graph neural networks (GNNs) and heterogeneous graph neural networks (HGNNs) are prominent techniques for homogeneous and heterogeneous graph representation learning, yet their performance in an end-to-end supervised framework greatly…

Graph Contrastive Learning (GCL) is a powerful self-supervised learning framework that performs data augmentation through graph perturbations, with growing applications in the analysis of biological networks such as Gene Regulatory Networks…

Graph neural networks (GNNs) have shown advantages in graph-based analysis tasks. However, most existing methods have the homogeneity assumption and show poor performance on heterophilic graphs, where the linked nodes have dissimilar…

The Gene Regulatory Network (GRN) of biological cells governs a number of key functionalities that enables them to adapt and survive through different environmental conditions. Close observation of the GRN shows that the structure and…

Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…

Real data collected from different applications that have additional topological structures and connection information are amenable to be represented as a weighted graph. Considering the node labeling problem, Graph Neural Networks (GNNs)…