相关论文: Individual-Level SNP Diversity and Similarity Prof…
Background: Several sources of noise obfuscate the identification of single nucleotide variation (SNV) in next generation sequencing data. For instance, errors may be introduced during library construction and sequencing steps. In addition,…
Given an observed sample from a population of individuals belonging to species, "species-sampling" problems (SSPs) call for estimating some features of the unknown species composition of additional unobservable samples from the same…
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in…
Genome-wide association studies (GWAS) are commonly employed to study the genetic basis of complex traits and diseases, and a key question is how much heritability could be explained by all variants in GWAS. One widely used approach that…
In biodiversity conservation it is often necessary to prioritize the species to conserve. Existing approaches to prioritization, e.g. the Fair Proportion Index and the Shapley Value, are based on phylogenetic trees and rank species…
The participation coefficient is a widely used metric of the diversity of a node's connections with respect to a modular partition of a network. An information-theoretic formulation of this concept of connection diversity, referred to here…
Haplotypes, the global patterns of DNA sequence variation, have important implications for identifying complex traits. Recently, blocks of limited haplotype diversity have been discovered in human chromosomes, intensifying the research on…
Diagnosis and risk stratification of cancer and many other diseases require the detection of genomic breakpoints as a prerequisite of calling copy number alterations (CNA). This, however, is still challenging and requires time-consuming…
This paper studies the complexity of estimating Renyi divergences of discrete distributions: $p$ observed from samples and the baseline distribution $q$ known \emph{a priori}. Extending the results of Acharya et al. (SODA'15) on estimating…
Identifying drivers of complex traits from the noisy signals of genetic variation obtained from high throughput genome sequencing technologies is a central challenge faced by human geneticists today. We hypothesize that the variants…
In this paper we propose a method and discuss its computational implementation as an integrated tool for the analysis of viral genetic diversity on data generated by high-throughput sequencing. Most methods for viral diversity estimation…
The profile of a sample is the multiset of its symbol frequencies. We show that for samples of discrete distributions, profile entropy is a fundamental measure unifying the concepts of estimation, inference, and compression. Specifically,…
Motivation: Researchers need a rich trove of genomic datasets that they can leverage to gain a better understanding of the genetic basis of the human genome and identify associations between phenotypes and specific parts of DNA. However,…
Demographic models built from genetic data play important roles in illuminating prehistorical events and serving as null models in genome scans for selection. We introduce an inference method based on the joint frequency spectrum of genetic…
Semantic similarity measures (SSMs) refer to a set of algorithms used to quantify the similarity of two or more terms belonging to the same ontology. Ontology terms may be associated to concepts, for instance in computational biology gene…
Entropy is a measure of heterogeneity widely used in applied sciences, often when data are collected over space. Recently, a number of approaches has been proposed to include spatial information in entropy. The aim of entropy is to…
The person re-identification task requires to robustly estimate visual similarities between person images. However, existing person re-identification models mostly estimate the similarities of different image pairs of probe and gallery…
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms…
The human genotope is the convex hull of all allele frequency vectors that can be obtained from the genotypes present in the human population. In this paper we take a few initial steps towards a description of this object, which may be…
A system's heterogeneity (\textit{diversity}) is the effective size of its event space, and can be quantified using the R\'enyi family of indices (also known as Hill numbers in ecology or Hannah-Kay indices in economics), which are indexed…