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Single-cell RNA sequencing (scRNA-seq) technology provides high-throughput gene expression data to study the cellular heterogeneity and dynamics of complex organisms. Graph neural networks (GNNs) have been widely used for automatic cell…

Single-cell RNA sequencing (scRNA-seq) data analysis is pivotal for understanding cellular heterogeneity. However, the high sparsity and complex noise patterns inherent in scRNA-seq data present significant challenges for traditional…

Identifying cell clusters is a critical step for single-cell transcriptomics study. Despite the numerous clustering tools developed recently, the rapid growth of scRNA-seq volumes prompts for a more (computationally) efficient clustering…

Exploring sample relationships within each mini-batch has shown great potential for learning image representations. Existing works generally adopt the regular Transformer to model the visual content relationships, ignoring the cues of…

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs),…

Learning representations on large-sized graphs is a long-standing challenge due to the inter-dependence nature involved in massive data points. Transformers, as an emerging class of foundation encoders for graph-structured data, have shown…

Transformer has become ubiquitous in the deep learning field. One of the key ingredients that destined its success is the self-attention mechanism, which allows fully-connected contextual encoding over input tokens. However, despite its…

Graph Representation Learning (GRL) is an influential methodology, enabling a more profound understanding of graph-structured data and aiding graph clustering, a critical task across various domains. The recent incursion of attention…

Single-cell RNA sequencing (scRNA-seq) is essential for unraveling cellular heterogeneity and diversity, offering invaluable insights for bioinformatics advancements. Despite its potential, traditional clustering methods in scRNA-seq data…

Graph-based subspace clustering methods have exhibited promising performance. However, they still suffer some of these drawbacks: encounter the expensive time overhead, fail in exploring the explicit clusters, and cannot generalize to…

Single-cell RNA sequencing (scRNA-seq) enables researchers to analyze gene expression at single-cell level. One important task in scRNA-seq data analysis is unsupervised clustering, which helps identify distinct cell types, laying down the…

The swift advancement of single-cell RNA sequencing (scRNA-seq) technologies enables the investigation of cellular-level tissue heterogeneity. Cell annotation significantly contributes to the extensive downstream analysis of scRNA-seq data.…

Dynamic graph learning plays a pivotal role in modeling evolving relationships over time, especially for temporal link prediction tasks in domains such as traffic systems, social networks, and recommendation platforms. While…

Single-cell RNA sequencing (scRNA-seq) enables single-cell transcriptomic profiling, revealing cellular heterogeneity and rare populations. Recent deep learning models like Geneformer and Mouse-Geneformer perform well on tasks such as…

In recent years, the advances in single-cell RNA-seq techniques have enabled us to perform large-scale transcriptomic profiling at single-cell resolution in a high-throughput manner. Unsupervised learning such as data clustering has become…

Node classification has gained significant importance in graph deep learning with real-world applications such as recommendation systems, drug discovery, and citation networks. Graph Convolutional Networks and Graph Transformers have…

The Transformer architecture has gained growing attention in graph representation learning recently, as it naturally overcomes several limitations of graph neural networks (GNNs) by avoiding their strict structural inductive biases and…

Single-cell RNA sequencing (scRNA-seq) is powerful technology that allows researchers to understand gene expression patterns at the single-cell level. However, analysing scRNA-seq data is challenging due to issues and biases in data…

Learning representations on large graphs is a long-standing challenge due to the inter-dependence nature. Transformers recently have shown promising performance on small graphs thanks to its global attention for capturing all-pair…

Graph Transformer (GT), as a special type of Graph Neural Networks (GNNs), utilizes multi-head attention to facilitate high-order message passing. However, this also imposes several limitations in node classification applications: 1) nodes…