Related papers: Analyzing Single Cell RNA Sequencing with Topologi…

Nonnegative Matrix Factorization (NMF) is an important unsupervised learning method to extract meaningful features from data. To address the NMF problem within a polynomial time framework, researchers have introduced a separability…

Nonnegative Matrix Factorization (NMF) is the problem of approximating a nonnegative matrix with the product of two low-rank nonnegative matrices and has been shown to be particularly useful in many applications, e.g., in text mining, image…

Nonnegative matrix factorization (NMF) is a linear dimensionality reduction technique for nonnegative data, with applications such as hyperspectral unmixing and topic modeling. NMF is a difficult problem in general (NP-hard), and its…

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…

Nonnegative matrix factorization (NMF) is a powerful class of feature extraction techniques that has been successfully applied in many fields, namely in signal and image processing. Current NMF techniques have been limited to a…

Neuronal circuits formed in the brain are complex with intricate connection patterns. Such complexity is also observed in the retina as a relatively simple neuronal circuit. A retinal ganglion cell receives excitatory inputs from neurons in…

According to the National Cancer Institute, there were 9.5 million cancer-related deaths in 2018. A challenge in improving treatment is resistance in genetically unstable cells. The purpose of this study is to evaluate unsupervised machine…

Referring back to the original text in the course of hierarchical learning is a common human trait that ensures the right direction of learning. The models developed based on the concept of Non-negative Matrix Factorization (NMF), in this…

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…

Extracting genetic information from a full range of sequencing data is important for understanding diseases. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. We…

Nonnegative Matrix Factorization (NMF) is a widely used technique for data representation. Inspired by the expressive power of deep learning, several NMF variants equipped with deep architectures have been proposed. However, these methods…

The development of high throughput single-cell sequencing technologies now allows the investigation of the population level diversity of cellular transcriptomes. This diversity has shown two faces. First, the expression dynamics (gene to…

In this paper, we propose a new Semi-Nonnegative Matrix Factorization method for 2-dimensional (2D) data, named TS-NMF. It overcomes the drawback of existing methods that seriously damage the spatial information of the data by converting 2D…

Non-negative Matrix Factorization (NMF) is an intensively used technique for obtaining parts-based, lower dimensional and non-negative representation. Researchers in biology, medicine, pharmacy and other fields often prefer NMF over other…

Nonnegative Matrix Factorization (NMF) was first introduced as a low-rank matrix approximation technique, and has enjoyed a wide area of applications. Although NMF does not seem related to the clustering problem at first, it was shown that…

Background: Mining gene modules from genomic data is an important step to detect gene members of pathways or other relations such as protein-protein interactions. In this work, we explore the plausibility of detecting gene modules by…

Single-cell RNA-sequencing (scRNA-seq) has become a routinely used technique to quantify the gene expression profile of thousands of single cells simultaneously. Analysis of scRNA-seq data plays an important role in the study of cell states…

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) reveals cell heterogeneity, with cell clustering playing a key role in identifying cell types and marker genes. Recent advances, especially graph neural networks (GNNs)-based methods, have…

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…