Related papers: Analyzing scRNA-seq data by CCP-assisted UMAP and …

This paper focuses on scalability and robustness of spectral clustering for extremely large-scale datasets with limited resources. Two novel algorithms are proposed, namely, ultra-scalable spectral clustering (U-SPEC) and ultra-scalable…

Nonlinear data visualization using t-distributed stochastic neighbor embedding (t-SNE) enables the representation of complex single-cell transcriptomic landscapes in two or three dimensions to depict biological populations accurately.…

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of cellular heterogeneity, enabling detailed molecular profiling at the individual cell level. However, integrating high-dimensional single-cell data into causal mediation…

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…

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…

It has been shown that for automated PAP-smear image classification, nucleus features can be very informative. Therefore, the primary step for automated screening can be cell-nuclei detection followed by segmentation of nuclei in the…

Accurate land cover segmentation of spectral images is challenging and has drawn widespread attention in remote sensing due to its inherent complexity. Although significant efforts have been made for developing a variety of methods, most of…

Unsupervised clustering algorithms for vectors has been widely used in the area of machine learning. Many applications, including the biological data we studied in this paper, contain some boundary datapoints which show combination…

It is a challenging task to accurately perform semantic segmentation due to the complexity of real picture scenes. Many semantic segmentation methods based on traditional deep learning insufficiently captured the semantic and appearance…

Modeling cellular dynamics from single-cell RNA sequencing (scRNA-seq) data is critical for understanding cell development and underlying gene regulatory relationships. Many current methods rely on single-cell velocity to obtain pseudotime,…

Motivation: How do we integratively analyze large-scale multi-platform genomic data that are high dimensional and sparse? Furthermore, how can we incorporate prior knowledge, such as the association between genes, in the analysis…

Single-cell RNA sequencing (scRNA-seq) provides high-dimensional profiles of cellular states, enabling data-driven modeling of cellular dynamics over time. In practice, time-resolved scRNA-seq is collected at only a few discrete time points…

Single-cell RNA-seq data allow the quantification of cell type differences across a growing set of biological contexts. However, pinpointing a small subset of genomic features explaining this variability can be ill-defined and…

Dimensionality reduction techniques are essential for visualizing and analyzing high-dimensional biological sequencing data. t-distributed Stochastic Neighbor Embedding (t-SNE) is widely used for this purpose, traditionally employing the…

The availability of large-scale annotated image datasets and recent advances in supervised deep learning methods enable the end-to-end derivation of representative image features that can impact a variety of image analysis problems. Such…

Spectral clustering has found extensive use in many areas. Most traditional spectral clustering algorithms work in three separate steps: similarity graph construction; continuous labels learning; discretizing the learned labels by k-means…

Dimensionality reduction, cluster analysis, and sparse representation are basic components in machine learning. However, their relationships have not yet been fully investigated. In this paper, we find that the spectral graph theory…

Many approaches to transform classification problems from non-linear to linear by feature transformation have been recently presented in the literature. These notably include sparse coding methods and deep neural networks. However, many of…

Single-cell RNA-Sequencing (scRNA-Seq) is a revolutionary technique for discovering and describing cell types in heterogeneous tissues, yet its measurement of expression often suffers from large systematic bias. A major source of this bias…

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…