Related papers: scCDCG: Efficient Deep Structural Clustering for s…

Single-cell multi-view clustering enables the exploration of cellular heterogeneity within the same cell from different views. Despite the development of several multi-view clustering methods, two primary challenges persist. Firstly, most…

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 provides tremendous insights to understand biological systems. However, the noise from dropout can corrupt the downstream biological analysis. Hence, it is desirable to impute the dropouts accurately. In this…

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…

Motivation: Single-cell RNA sequencing (scRNA-seq) is a groundbreaking technology extensively utilized in biological research, facilitating the examination of gene expression at the individual cell level within a given tissue sample. While…

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) data are important for studying the laws of life at single-cell level. However, it is still challenging to obtain enough high-quality scRNA-seq data. To mitigate the limited availability of data,…

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

Clustering is a fundamental task in data analysis. Recently, deep clustering, which derives inspiration primarily from deep learning approaches, achieves state-of-the-art performance and has attracted considerable attention. Current deep…

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…

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…

Single-cell RNA sequencing (scRNA-seq) has emerged as a transformative technology, offering unparalleled insights into the intricate landscape of cellular diversity and gene expression dynamics. The analysis of scRNA-seq data poses…

Single-cell RNA sequencing (scRNA-seq), especially temporally resolved datasets, enables genome-wide profiling of gene expression dynamics at single-cell resolution across discrete time points. However, current technologies provide only…

scRNA-seq clustering is a critical task for analyzing single-cell RNA sequencing (scRNA-seq) data, as it groups cells with similar gene expression profiles. Transformers, as powerful foundational models, have been applied to scRNA-seq…

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…

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…

A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While recent evidence indicates that batch effects manifest…

Applications of single-cell RNA sequencing in various biomedical research areas have been blooming. This new technology provides unprecedented opportunities to study disease heterogeneity at the cellular level. However, unique…

Rapid advancements in high-throughput single-cell RNA-seq (scRNA-seq) technologies and experimental protocols have led to the generation of vast amounts of genomic data that populates several online databases and repositories. Here, we…

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…