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RNA-Seq technology allows for studying the transcriptional state of the cell at an unprecedented level of detail. Beyond quantification of whole-gene expression, it is now possible to disentangle the abundance of individual alternatively…

The advancement of single-cell RNA-sequencing (scRNA-seq) technologies allow us to study the individual level cell-type-specific gene expression networks by direct inference of genes' conditional independence structures. scRNA-seq data…

Acquiring genomes at single-cell resolution has many applications such as in the study of microbiota. However, deep sequencing and assembly of all of millions of cells in a sample is prohibitively costly. A property that can come to rescue…

Single-cell RNA sequencing (scRNA-seq) has revolutionized our ability to analyze gene expression at the resolution of individual cells, providing unprecedented insights into cellular heterogeneity and complex biological systems. This paper…

Four-dimensional scanning transmission electron microscopy (4D-STEM) enables mapping of diffraction information with nanometer-scale spatial resolution, offering detailed insight into local structure, orientation, and strain. However, as…

Clustering analysis is fundamental in single-cell RNA sequencing (scRNA-seq) data analysis for elucidating cellular heterogeneity and diversity. Recent graph-based scRNA-seq clustering methods, particularly graph neural networks (GNNs),…

The Regression Discontinuity Design (RDD) is a quasi-experimental design that estimates the causal effect of a treatment when its assignment is defined by a threshold value for a continuous assignment variable. The RDD assumes that subjects…

Image diffusion distillation achieves high-fidelity generation with very few sampling steps. However, applying these techniques directly to video diffusion often results in unsatisfactory frame quality due to the limited visual quality in…

Sequential change-point detection seeks to rapidly identify distributional changes in streaming data while controlling false alarms. Existing multi-stream detection methods typically rely on non-private access to raw observations or…

In this paper, we propose Discriminative Neural Clustering (DNC) that formulates data clustering with a maximum number of clusters as a supervised sequence-to-sequence learning problem. Compared to traditional unsupervised clustering…

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across…

In recent years, the field of single-cell data analysis has seen a marked advancement in the development of clustering methods. Despite advancements, most of these algorithms still concentrate on analyzing the provided single-cell matrix…

In this paper, we study different discrete data clustering methods, which use the Model-Based Clustering (MBC) framework with the Multinomial distribution. Our study comprises several relevant issues, such as initialization, model…

Dirichlet Process Mixture Models (DPMMs) are widely used to address clustering problems. Their main advantage lies in their ability to automatically estimate the number of clusters during the inference process through the Bayesian…

The Dirichlet Process Gaussian Mixture Model (DPGMM) is often used to cluster data when the number of clusters is unknown. One main DPGMM inference paradigm relies on sampling. Here we consider a known state-of-art sampler (proposed by…

Discrete diffusion or flow models could enable faster and more controllable sequence generation than autoregressive models. We show that na\"ive linear flow matching on the simplex is insufficient toward this goal since it suffers from…

Diffusion models (DMs) have emerged as powerful foundation models for a variety of tasks, with a large focus in synthetic image generation. However, their requirement of large annotated datasets for training limits their applicability in…

Direct cDNA preamplification protocols developed for single-cell RNA-seq have enabled transcriptome profiling of precious clinical samples and rare cells without sample pooling or RNA extraction. Currently, there is no algorithm optimized…

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…

High-dimensional point cloud data arise across many scientific domains, especially single-cell biology. The shapes or topologies of these datasets determine the types of information that can be extracted. For example, clustered data…