Related papers: Correlation Between GC-content and Palindromes in …
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
Analyzing the relation between intelligence and neural activity is of the utmost importance in understanding the working principles of the human brain in health and disease. In existing literature, functional brain connectomes have been…
The main statistical distributions applicable to the analysis of genome architecture and genome tracks are briefly discussed and critically assessed. Although the observed features in distributions of element lengths can be equally well…
This paper investigates Frequentist consistency properties of the posterior distributions constructed via Generalized Variational Inference (GVI). A number of generic and novel strategies are given for proving consistency, relying on the…
Many common diseases are highly polygenic, modulated by a large number genetic factors with small effects on susceptibility to disease. These small effects are difficult to map reliably in genetic association studies. To address this…
Following the recent work of Sznitman (arXiv:0805.4516), we investigate the microscopic picture induced by a random walk trajectory on a cylinder of the form G_N x Z, where G_N is a large finite connected weighted graph, and relate it to…
Message passing is a core mechanism in Graph Neural Networks (GNNs), enabling the iterative update of node embeddings by aggregating information from neighboring nodes. Graph Convolutional Networks (GCNs) exemplify this approach by adapting…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
Graph Generating Dependencies (GGDs) informally express constraints between two (possibly different) graph patterns which enforce relationships on both graph's data (via property value constraints) and its structure (via topological…
The rapid growth of graph data poses significant challenges in storage, transmission, and particularly the training of graph neural networks (GNNs). To address these challenges, graph condensation (GC) has emerged as an innovative solution.…
A fundamental problem on graph-structured data is that of quantifying similarity between graphs. Graph kernels are an established technique for such tasks; in particular, those based on random walks and return probabilities have proven to…
Background: Representing biological networks as graphs is a powerful approach to reveal underlying patterns, signatures, and critical components from high-throughput biomolecular data. However, graphs do not natively capture the multi-way…
Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits, and some variants are shown to be associated with multiple complex traits. Genetic covariance between two traits is defined…
Granger-Geweke causality (GGC) is a powerful and popular method for identifying directed functional (`causal') connectivity in neuroscience. In a recent paper, Stokes and Purdon [1] raise several concerns about its use. They make two…
Genome-wide epistasis analysis is a powerful tool to infer gene interactions, which can guide drug and vaccine development and lead to a deeper understanding of microbial pathogenesis. We have considered all complete SARS-CoV-2 genomes…
Uniform random intersection graphs have received much interest and been used in diverse applications. A uniform random intersection graph with $n$ nodes is constructed as follows: each node selects a set of $K_n$ different items uniformly…
The burgeoning volume of graph data presents significant computational challenges in training graph neural networks (GNNs), critically impeding their efficiency in various applications. To tackle this challenge, graph condensation (GC) has…
In settings requiring synthetic data generation based on a clinical cohort, e.g., due to data protection regulations, heterogeneity across individuals might be a nuisance that we need to control or faithfully preserve. The sources of such…
The ICTV develops, refines and maintains a universal virus taxonomy; Order is the highest taxon in the branching hierarchy of recognised viral taxa. Historically, ICTV (sub)committees have classified viruses on the basis of morphological…
We study global fluctuations of the guanine and cytosine base content (GC%) in mouse genomic DNA using spectral analyses. Power spectra S(f) of GC% fluctuations in all nineteen autosomal and two sex chromosomes are observed to have the…