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Single-cell RNA sequencing (scRNA-seq) has revolutionized our understanding of cellular processes by enabling gene expression analysis at the individual cell level. Clustering allows for the identification of cell types and the further…

We propose a novel method, scTree, for single-cell Tree Variational Autoencoders, extending a hierarchical clustering approach to single-cell RNA sequencing data. scTree corrects for batch effects while simultaneously learning a…

Single-cell RNA sequencing technologies have revolutionized our understanding of cellular heterogeneity, yet computational methods often struggle to balance performance with biological interpretability. Embedded topic models have been…

Single-cell sequencing has a significant role to explore biological processes such as embryonic development, cancer evolution, and cell differentiation. These biological properties can be presented by a two-dimensional scatter plot.…

With ongoing developments and innovations in single-cell RNA sequencing methods, advancements in sequencing performance could empower significant discoveries as well as new emerging possibilities to address biological and medical…

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…

Single-cell RNA sequencing (scRNA-seq) enables dissecting cellular heterogeneity in tissues, resulting in numerous biological discoveries. Various computational methods have been devised to delineate cell types by clustering scRNA-seq data…

Single-cell RNA sequencing (scRNA-seq) is widely used to reveal heterogeneity in cells, which has given us insights into cell-cell communication, cell differentiation, and differential gene expression. However, analyzing scRNA-seq data is a…

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…

Graph representation learning (GRL) has emerged as a powerful technique for solving graph analytics tasks. It can effectively convert discrete graph data into a low-dimensional space where the graph structural information and graph…

Self-supervised learning (SSL) has proven to be a powerful approach for extracting biologically meaningful representations from single-cell data. To advance our understanding of SSL methods applied to single-cell data, we present…

Gene regulatory network (GRN) refers to the complex network formed by regulatory interactions between genes in living cells. In this paper, we consider inferring GRNs in single cells based on single cell RNA sequencing (scRNA-seq) data. In…

Graph clustering aims to divide the graph into different clusters. The recently emerging deep graph clustering approaches are largely built on graph neural networks (GNN). However, GNN is designed for general graph encoding and there is a…

Inferring gene regulatory networks (GRNs) from single-cell RNA sequencing (scRNA-seq) data is a complex challenge that requires capturing the intricate relationships between genes and their regulatory interactions. In this study, we tackle…

Contrastive learning has recently attracted plenty of attention in deep graph clustering for its promising performance. However, complicated data augmentations and time-consuming graph convolutional operation undermine the efficiency of…

Attempting to fully exploit the rich information of topological structure and node features for attributed graph, we introduce self-supervised learning mechanism to graph representation learning and propose a novel Self-supervised Consensus…

Graph Neural Networks (GNN) are reshaping our understanding of biomedicine and diseases by revealing the deep connections among genes and cells. As both algorithmic and biomedical technologies have advanced significantly, we're entering a…

Background: Single-cell RNA sequencing (scRNA-seq) yields valuable insights about gene expression and gives critical information about complex tissue cellular composition. In the analysis of single-cell RNA sequencing, the annotations of…

Single-cell RNA sequencing (scRNA-seq) has revealed complex cellular heterogeneity, but recent studies emphasize that understanding biological function also requires modeling cell-cell communication (CCC), the signaling interactions…

Classifying nodes in a graph is a common problem. The ideal classifier must adapt to any imbalances in the class distribution. It must also use information in the clustering structure of real-world graphs. Existing Graph Neural Networks…