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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…

Cell type identification from single-cell transcriptomic data is a common goal of single-cell RNA sequencing (scRNAseq) data analysis. Neural networks have been employed to identify cell types from scRNAseq data with high performance.…

We present the use of single-cell entropy (scEntropy) to measure the order of the cellular transcriptome profile from single-cell RNA-seq data, which leads to a method of unsupervised cell type classification through scEntropy followed by…

Single-cell RNA sequencing (scRNA-seq) enables transcriptomic profiling at cellular resolution but suffers from pervasive dropout events that obscure biological signals. We present SCR-MF, a modular two-stage workflow that combines…

Single cell combinatorial indexing RNA sequencing (sci-RNA-seq) is a powerful method for recovering gene expression data from an exponentially scalable number of individual cells or nuclei. However, sci-RNA-seq is a complex protocol that…

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…

Dataset distillation is a newly emerging task that synthesizes a small-size dataset used in training deep neural networks (DNNs) for reducing data storage and model training costs. The synthetic datasets are expected to capture the essence…

The extensive amounts of data required for training deep neural networks pose significant challenges on storage and transmission fronts. Dataset distillation has emerged as a promising technique to condense the information of massive…

Although bulk transcriptomic analyses have significantly contributed to an enhanced comprehension of multifaceted diseases, their exploration capacity is impeded by the heterogeneous compositions of biological samples. Indeed, by averaging…

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) stands as a powerful tool for deciphering cellular heterogeneity and exploring gene expression profiles at high resolution. However, its high cost renders it impractical for extensive sample cohorts…

Diffusion Language Models (DLMs) offer a promising parallel generation paradigm but suffer from slow inference due to numerous refinement steps and the inability to use standard KV caching. We introduce CDLM (Consistency Diffusion Language…

Single-cell transcriptomics techniques, such as scRNA-seq, attempt to characterize gene expression profiles in each cell of a heterogeneous sample individually. Due to growing amounts of data generated and the increasing complexity of the…

Many modern biological assays, including RNA sequencing, yield integer-valued counts that reflect the number of molecules detected. These measurements are often not at the desired resolution: while the unit of interest is typically a single…

Semi-supervised learning utilizes insights from unlabeled data to improve model generalization, thereby reducing reliance on large labeled datasets. Most existing studies focus on limited samples and fail to capture the overall data…

Clustering of single-cell RNA sequencing (scRNA-seq) datasets can give key insights into the biological functions of cells. Therefore, it is not surprising that network-based community detection methods (one of the better clustering…

Dataset distillation aims to compress a training dataset by creating a small number of informative synthetic samples such that neural networks trained on them perform as well as those trained on the original training dataset. Current text…

Single-cell RNA sequencing (scRNA-seq) has transformed our ability to explore biological systems. Nevertheless, proficient expertise is essential for handling and interpreting the data. In this paper, we present scX, an R package built on…

Single-cell RNA sequencing (scRNA-seq) provides a high throughput, quantitative and unbiased framework for scientists in many research fields to identify and characterize cell types within heterogeneous cell populations from various…

Clustering based on vibration responses, such as transmissibility functions (TFs), is promising in structural anomaly detection. However, most existing methods struggle to determine the optimal cluster number, handle high-dimensional…