Related papers: Analyzing Chromatin Using Tiled Binned Scatterplot…

Binned scatter plots are a powerful statistical tool for empirical work in the social, behavioral, and biomedical sciences. Available methods rely on a quantile-based partitioning estimator of the conditional mean regression function to…

Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation…

In the present work we have selected a collection of statistical and mathematical tools useful for the exploration of multivariate data and we present them in a form that is meant to be particularly accessible to a classically trained…

Clustering algorithms became an essential part of the neurophysiological data analysis toolbox in the last twenty five years. Many problems, from the definition of cell types/groups based on morphological, molecular and physiological data…

Visualization of data is an important step in the understanding of data and the evaluation of statistical models. Topological Data Analysis Ball Mapper (TDABM) after Dlotko (2019), provides a model free means to visualize multivariate…

Biclustering is an unsupervised machine-learning approach aiming to cluster rows and columns simultaneously in a data matrix. Several biclustering algorithms have been proposed for handling numeric datasets. However, real-world data mining…

The huge amount of data acquired by high-throughput sequencing requires data reduction for effective analysis. Here we give a clustering algorithm for genome-wide open chromatin data using a new data reduction method. This method regards…

The amount of image datasets collected for environmental monitoring purposes has increased in the past years as computer vision assisted methods have gained interest. Computer vision applications rely on high-quality datasets, making data…

Rapidly growing data sizes of scientific simulations pose significant challenges for interactive visualization and analysis techniques. In this work, we propose a compact probabilistic representation to interactively visualize large…

Binscatter is a popular method for visualizing bivariate relationships and conducting informal specification testing. We study the properties of this method formally and develop enhanced visualization and econometric binscatter tools. These…

Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play critical roles in a wide range of cellular processes by regulating gene…

For the Bio+Med-Vis Challenge 2024, we propose a visual analytics system as a redesign for the scatter pie chart visualization of cell type proportions of spatial transcriptomics data. Our design uses three linked views: a view of the…

There is an ongoing need for scalable tools to aid researchers in both retrospective and prospective standardization of discrete entity types -- such as disease names, cell types or chemicals -- that are used in metadata associated with…

Traditional clustering methods are limited when dealing with huge and heterogeneous groups of gene expression data, which motivates the development of bi-clustering methods. Bi-clustering methods are used to mine bi-clusters whose subsets…

Dimension reduction is increasingly applied to high-dimensional biomedical data to improve its interpretability. When datasets are reduced to two dimensions, each observation is assigned an x and y coordinates and is represented as a point…

Rapid technological advances have allowed for molecular profiling across multiple omics domains from a single sample for clinical decision making in many diseases, especially cancer. As tumor development and progression are dynamic…

In this study, we present a comprehensive evaluation of the Two-Block Gibbs (2BG) sampler as a robust alternative to the traditional Three-Block Gibbs (3BG) sampler in Bayesian shrinkage models. Through extensive simulation studies, we…

The past decade has seen rapid growth in the number of experimentally realized two-dimensional (2D) materials with diverse chemical and physical properties. However, information on their crystal structure, synthesis routes, and measured or…

In recent years, data have become increasingly higher dimensional and, therefore, an increased need has arisen for dimension reduction techniques for clustering. Although such techniques are firmly established in the literature for…

The development of multicellular organisms relies on the precise coordination of molecular events across multiple spatial and temporal scales. Understanding how information flows from molecular interactions to cellular processes and tissue…