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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…
This article provides a new type of analysis of a compressed-sensing based technique for recovering column-sparse matrices, namely minimization of the $\ell_{1,2}$-norm. Rather than providing conditions on the measurement matrix which…
Given a linear system in a real or complex domain, linear regression aims to recover the model parameters from a set of observations. Recent studies in compressive sensing have successfully shown that under certain conditions, a linear…
In the analysis of single-cell RNA sequencing data, researchers often characterize the variation between cells by estimating a latent variable, such as cell type or pseudotime, representing some aspect of the individual cell's state. They…
Reliability in cell type annotation is challenging in single-cell RNA-sequencing data analysis because both expert-driven and automated methods can be biased or constrained by their training data, especially for novel or rare cell types.…
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…
Sequencing costs currently prohibit the application of single-cell mRNA-seq to many biological and clinical analyses. Targeted single-cell mRNA-sequencing reduces sequencing costs by profiling reduced gene sets that capture biological…
Single-cell sequencing technologies have significantly advanced molecular and cellular biology, offering unprecedented insights into cellular heterogeneity by allowing for the measurement of gene expression at an individual cell level.…
RNA-seq has rapidly become the de facto technique to measure gene expression. However, the time required for analysis has not kept up with the pace of data generation. Here we introduce Sailfish, a novel computational method for quantifying…
Recent research has generated hope that inference scaling, such as resampling solutions until they pass verifiers like unit tests, could allow weaker models to match stronger ones. Beyond inference, this approach also enables training…
Single-cell RNA sequencing (scRNA-seq) provides unprecedented insights into cellular heterogeneity, enabling detailed analysis of complex biological systems at single-cell resolution. However, the high dimensionality and technical noise…
Speech emotion recognition (SER) models typically rely on costly human-labeled data for training, making scaling methods to large speech datasets and nuanced emotion taxonomies difficult. We present LanSER, a method that enables the use of…
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…
Computational capability often falls short when confronted with massive data, posing a common challenge in establishing a statistical model or statistical inference method dealing with big data. While subsampling techniques have been…
While single-cell RNA sequencing provides an understanding of the transcriptome of individual cells, its high sparsity, often termed dropout, hampers the capture of significant cell-cell relationships. Here, we propose scFP (single-cell…
Small-angle neutron scattering (SANS) is a powerful technique for probing the nanoscale structure of materials. However, the fundamental limitations of neutron flux pose significant challenges for rapid, high-fidelity data acquisition…
In this paper we consider the problem of recovering a high dimensional data matrix from a set of incomplete and noisy linear measurements. We introduce a new model that can efficiently restrict the degrees of freedom of the problem and is…
Clustering with variable selection is a challenging yet critical task for modern small-n-large-p data. Existing methods based on sparse Gaussian mixture models or sparse K-means provide solutions to continuous data. With the prevalence of…
Motivation: Computational methods are essential to extract actionable information from raw sequencing data, and to thus fulfill the promise of next-generation sequencing technology. Unfortunately, computational tools developed to call…
Deep sequencing has become one of the most popular tools for transcriptome profiling in biomedical studies. While an abundance of computational methods exists for "normalizing" sequencing data to remove unwanted between-sample variations…