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Graph neural networks (GNNs) are powerful graph-based deep-learning models that have gained significant attention and demonstrated remarkable performance in various domains, including natural language processing, drug discovery, and…

Knowledge Graph(KG) has gained traction as a machine-readable organization of real-world knowledge for analytics using artificial intelligence systems. Graph Neural Network(GNN), is proven to be an effective KG embedding technique that…

Many real-world graphs (networks) are heterogeneous with different types of nodes and edges. Heterogeneous graph embedding, aiming at learning the low-dimensional node representations of a heterogeneous graph, is vital for various…

Graph transformer networks (GTN) are a variant of graph convolutional networks (GCN) that are targeted to heterogeneous graphs in which nodes and edges have associated type information that can be exploited to improve inference accuracy.…

Predictions over graphs play a crucial role in various domains, including social networks and medicine. Graph Neural Networks (GNNs) have emerged as the dominant approach for learning on graph data. Although a graph-structure is provided as…

Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes…

Graph or network data is ubiquitous in the real world, including social networks, information networks, traffic networks, biological networks and various technical networks. The non-Euclidean nature of graph data poses the challenge for…

Recent studies have indicated that Graph Convolutional Networks (GCNs) act as a \emph{low pass} filter in spectral domain and encode smoothed node representations. In this paper, we consider their opposite, namely Graph Deconvolutional…

Graph neural networks (GNNs) have drawn significant research attention recently, mostly under the setting of semi-supervised learning. When task-agnostic representations are preferred or supervision is simply unavailable, the auto-encoder…

Geometric deep learning provides a principled and versatile manner for the integration of imaging and non-imaging modalities in the medical domain. Graph Convolutional Networks (GCNs) in particular have been explored on a wide variety of…

Network topology inference is a prominent problem in Network Science. Most graph signal processing (GSP) efforts to date assume that the underlying network is known, and then analyze how the graph's algebraic and spectral characteristics…

How to properly model graphs is a long-existing and important problem in NLP area, where several popular types of graphs are knowledge graphs, semantic graphs and dependency graphs. Comparing with other data structures, such as sequences…

Recently, the pretrain-finetuning paradigm has attracted tons of attention in graph learning community due to its power of alleviating the lack of labels problem in many real-world applications. Current studies use existing techniques, such…

Over the past twenty years, artificial Gene Regulatory Networks (GRNs) have shown their capacity to solve real-world problems in various domains such as agent control, signal processing and artificial life experiments. They have also…

The inductive bias of a graph neural network (GNN) is largely encoded in its specified graph. Latent graph inference relies on latent geometric representations to dynamically rewire or infer a GNN's graph to maximize the GNN's predictive…

Inferring synaptic connectivity from neural population activity is a fundamental challenge in computational neuroscience, complicated by partial observability and mismatches between inference models and true circuit dynamics. In this study,…

Recently, text classification model based on graph neural network (GNN) has attracted more and more attention. Most of these models adopt a similar network paradigm, that is, using pre-training node embedding initialization and two-layer…

Recently a variety of methods have been developed to encode graphs into low-dimensional vectors that can be easily exploited by machine learning algorithms. The majority of these methods start by embedding the graph nodes into a…

Unraveling the co-expression of genes across studies enhances the understanding of cellular processes. Inferring gene co-expression networks from transcriptome data presents many challenges, including spurious gene correlations, sample…

Despite the enormous success of graph neural networks (GNNs), most existing GNNs can only be applicable to undirected graphs where relationships among connected nodes are two-way symmetric (i.e., information can be passed back and forth).…