Related papers: BHiCect 2.0: Multi-resolution clustering of Hi-C d…
We develop the hierarchical cluster coherence (HCC) method for brain signals, a procedure for characterizing connectivity in a network by clustering nodes or groups of channels that display high level of coordination as measured by…
Genomic sequence analysis plays a crucial role in various scientific and medical domains. Traditional machine-learning approaches often struggle to capture the complex relationships and hierarchical structures of sequence data when working…
Currently, data-driven discovery in biological sciences resides in finding segmentation strategies in multivariate data that produce sensible descriptions of the data. Clustering is but one of several approaches and sometimes falls short…
We present an unsupervised data processing workflow that is specifically designed to obtain a fast conformational clustering of long molecular dynamics simulation trajectories. In this approach we combine two dimensionality reduction…
Background: Haplotypes, the ordered lists of single nucleotide variations that distinguish chromosomal sequences from their homologous pairs, may reveal an individual's susceptibility to hereditary and complex diseases and affect how our…
Two successful approaches for the segmentation of biomedical images are (1) the selection of segment candidates from a merge-tree, and (2) the clustering of small superpixels by solving a Multi-Cut problem. In this paper, we introduce a…
The Blooming Tree (BT) algorithm, based on the hierarchical clustering method, is designed to identify clusters, groups, and substructures from galaxy redshift surveys. We apply the BT algorithm to a wide-field ($10\times 10$ deg$^2$)…
We present Hecate, a modular lossless genomic compression framework. It is designed around uncommon but practical source-coding choices. Unlike many single-method compressors, Hecate treats compression as a conditional coding problem over…
Significant advances in biotechnology have allowed for simultaneous measurement of molecular data points across multiple genomic and transcriptomic levels from a single tumor/cancer sample. This has motivated systematic approaches to…
Chromatin is a highly compact and dynamic nuclear structure that consists of DNA and associated proteins. The main organizational unit is the nucleosome, which consists of a histone octamer with DNA wrapped around it. Histone proteins are…
Genome assembly using high throughput data with short reads, arguably, remains an unresolvable task in repetitive genomes, since when the length of a repeat exceeds the read length, it becomes difficult to unambiguously connect the flanking…
To understand complex biological systems, the research community has produced huge corpus of gene expression data. A large number of clustering approaches have been proposed for the analysis of gene expression data. However, extracting…
Clustering procedures suitable for the analysis of very high-dimensional data are needed for many modern data sets. In model-based clustering, a method called high-dimensional data clustering (HDDC) uses a family of Gaussian mixture models…
Synthesizing medical images while preserving their structural information is crucial in medical research. In such scenarios, the preservation of anatomical content becomes especially important. Although recent advances have been made by…
In this work, we present an approach for evaluating segmentation strategies and solving the biological problem of creating robust interpretable maps of biological data by employing wards agglomerative hierarchical clustering applied to…
It is well known that the integration among different data-sources is reliable because of its potential of unveiling new functionalities of the genomic expressions which might be dormant in a single source analysis. Moreover, different…
Histo-genomic multi-modal methods have recently emerged as a powerful paradigm, demonstrating significant potential for improving cancer prognosis. However, genome sequencing, unlike histopathology imaging, is still not widely accessible in…
A new method for hierarchical clustering is presented. It combines treelets, a particular multiscale decomposition of data, with a projection on a reproducing kernel Hilbert space. The proposed approach, called kernel treelets (KT),…
Chromatin is a complex of DNA, RNA and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around…
Histopathological images (HI) encrypt resolution dependent heterogeneous textures & diverse color distribution variability, manifesting in micro-structural surface tissue convolutions. Also, inherently high coherency of cancerous cells…