Related papers: scBiGNN: Bilevel Graph Representation Learning for…

Graph similarity computation (GSC) aims to quantify the similarity score between two graphs. Although recent GSC methods based on graph neural networks (GNNs) take advantage of intra-graph structures in message passing, few of them fully…

Graphs are naturally used to describe the structures of various real-world systems in biology, society, computer science etc., where subgraphs or motifs as basic blocks play an important role in function expression and information…

Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect…

Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…

This study aims to build a pre-trained Graph Neural Network (GNN) model on molecules without human annotations or prior knowledge. Although various attempts have been proposed to overcome limitations in acquiring labeled molecules, the…

Single-cell RNA sequencing (scRNA-seq) enables high-resolution analysis of cellular heterogeneity, but its complexity, which is marked by high dimensionality, sparsity, and batch effects, which poses major computational challenges.…

Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have…

Graph Neural Networks (GNNs) have become the state-of-the-art method for many applications on graph structured data. GNNs are a model for graph representation learning, which aims at learning to generate low dimensional node embeddings that…

Graph neural networks (GNNs) have received massive attention in the field of machine learning on graphs. Inspired by the success of neural networks, a line of research has been conducted to train GNNs to deal with various tasks, such as…

Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to…

Graph similarity search is among the most important graph-based applications, e.g. finding the chemical compounds that are most similar to a query compound. Graph similarity computation, such as Graph Edit Distance (GED) and Maximum Common…

Representing a graph as a vector is a challenging task; ideally, the representation should be easily computable and conducive to efficient comparisons among graphs, tailored to the particular data and analytical task at hand. Unfortunately,…

Graph-based semi-supervised node classification has been shown to become a state-of-the-art approach in many applications with high research value and significance. Most existing methods are only based on the original intrinsic or…

Analysis of single-cell RNA sequencing data is often conducted through network projections such as coexpression networks, primarily due to the abundant availability of network analysis tools for downstream tasks. However, this approach has…

Single-cell RNA sequencing (scRNA-seq) has revolutionized biological discovery, providing an unbiased picture of cellular heterogeneity in tissues. While scRNA-seq has been used extensively to provide insight into both healthy systems and…

Sequential recommendation effectively addresses information overload by modeling users' temporal and sequential interaction patterns. To overcome the limitations of supervision signals, recent approaches have adopted self-supervised…

The single-cell RNA sequencing (scRNA-seq) technology enables researchers to study complex biological systems and diseases with high resolution. The central challenge is synthesizing enough scRNA-seq samples; insufficient samples can impede…

Unsupervised cell type identification is crucial for uncovering and characterizing heterogeneous populations in single cell omics studies. Although a range of clustering methods have been developed, most focus exclusively on intrinsic…

This paper studies semi-supervised graph classification, which is an important problem with various applications in social network analysis and bioinformatics. This problem is typically solved by using graph neural networks (GNNs), which…

Recent graph neural networks (GNNs) with the attention mechanism have historically been limited to small-scale homogeneous graphs (HoGs). However, GNNs handling heterogeneous graphs (HeGs), which contain several entity and relation types,…