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Since its selection as the method of the year in 2013, single-cell technologies have become mature enough to provide answers to complex research questions. With the growth of single-cell profiling technologies, there has also been a…

Error correction of sequenced reads remains a difficult task, especially in single-cell sequencing projects with extremely non-uniform coverage. While existing error correction tools designed for standard (multi-cell) sequencing data…

The key to the text classification task is language representation and important information extraction, and there are many related studies. In recent years, the research on graph neural network (GNN) in text classification has gradually…

Understanding how stochastic gene expression is regulated in biological systems using snapshots of single-cell transcripts requires state-of-the-art methods of computational analysis and statistical inference. A Bayesian approach to…

Single-cell RNA sequencing allows the quantification of gene expression at the individual cell level, enabling the study of cellular heterogeneity and gene expression dynamics. Dimensionality reduction is a common preprocessing step…

It has been estimated that about 30% of the genes in the human genome are regulated by microRNAs (miRNAs). These are short RNA sequences that can down-regulate the levels of mRNAs or proteins in animals and plants. Genes regulated by miRNAs…

By developing data augmentation methods unique to the negative binomial (NB) distribution, we unite seemingly disjoint count and mixture models under the NB process framework. We develop fundamental properties of the models and derive…

Graph signal recovery (GSR) is a fundamental problem in graph signal processing, where the goal is to reconstruct a complete signal defined over a graph from a subset of noisy or missing observations. A central challenge in GSR is that the…

The detection of rare variants is important for understanding the genetic heterogeneity in mixed samples. Recently, next-generation sequencing (NGS) technologies have enabled the identification of single nucleotide variants (SNVs) in mixed…

High-dimensional variable selection has emerged as one of the prevailing statistical challenges in the big data revolution. Many variable selection methods have been adapted for identifying single nucleotide polymorphisms (SNPs) linked to…

Ultra high-throughput sequencing of transcriptomes (RNA-Seq) is a widely used method for quantifying gene expression levels due to its low cost, high accuracy and wide dynamic range for detection. However, the nature of RNA-Seq makes it…

Heterogeneous graph neural networks (HGNNs) have demonstrated strong capability in modeling complex semantics across multi-type nodes and relations. However, their scalability to large-scale graphs remains challenging due to structural…

Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to…

Single-cell RNA sequencing (scRNA-seq) data simulation is limited by classical methods that rely on linear correlations, failing to capture the intrinsic, nonlinear dependencies. No existing simulator jointly models gene-gene and cell-cell…

Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced…

Heterogeneous Graphs (HGs) effectively model complex relationships in the real world through multi-type nodes and edges. In recent years, inspired by self-supervised learning (SSL), contrastive learning (CL)-based Heterogeneous Graphs…

Single-cell RNA-seq data analysis typically requires representations that capture heterogeneous local structure across multiple scales while remaining stable and interpretable. In this work, we propose a hierarchical sheaf spectral…

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…

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the cellular level. By providing data on gene expression for each individual cell, scRNA-seq generates large datasets with thousands of…

Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…