Related papers: Reconstructing pedigrees using probabilistic analy…
Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…
We present a self-training approach to unsupervised dependency parsing that reuses existing supervised and unsupervised parsing algorithms. Our approach, called `iterated reranking' (IR), starts with dependency trees generated by an…
We consider a nonlinear structured population model with a distributed recruitment term. The question of the existence of non-trivial steady states can be treated (at least!) in three different ways. One approach is to study spectral…
Optimal reconstruction of a source sequence from multiple noisy traces corrupted by random insertions, deletions, and substitutions typically requires joint processing of all traces, leading to computational complexity that grows…
There are many instances in genetics in which we wish to determine whether two candidate populations are distinguishable on the basis of their genetic structure. Examples include populations which are geographically separated, case--control…
Genealogical information is the best histories resources for culture study and cultural heritage. The genealogical research generally presents family information and depict tree diagram. This paper presents Parent Bidirectional Breadth…
Researchers are often interested in linking individuals between two datasets that lack a common unique identifier. Matching procedures often struggle to match records with common names, birthplaces or other field values. Computational…
We propose a resampling-based fast variable selection technique for detecting relevant single nucleotide polymorphisms (SNP) in a multi-marker mixed effect model. Due to computational complexity, current practice primarily involves testing…
We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…
For a genetic locus carrying a strongly beneficial allele which has just fixed in a large population, we study the ancestry at a linked neutral locus. During this ``selective sweep'' the linkage between the two loci is broken up by…
In evolutionary biology, the speciation history of living organisms is represented graphically by a phylogeny, that is, a rooted tree whose leaves correspond to current species and branchings indicate past speciation events. Phylogenies are…
Recently, methods have been proposed that exploit the invariance of prediction models with respect to changing environments to infer subsets of the causal parents of a response variable. If the environments influence only few of the…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
The homogeneous reconstructed evolutionary process is a birth-death process without observed extinct lineages. Each species evolves independently with the same diversification rates (speciation rate $\lambda(t)$ and extinction rate…
Mounting evidence suggests that natural populations can harbor extensive fitness diversity with numerous genomic loci under selection. It is also known that genealogical trees for populations under selection are quantifiably different from…
Existing techniques to reconstruct tree models of progression for accumulative processes, such as cancer, seek to estimate causation by combining correlation and a frequentist notion of temporal priority. In this paper, we define a novel…
Species tree reconstruction from genomic data is increasingly performed using methods that account for sources of gene tree discordance such as incomplete lineage sorting. One popular method for reconstructing species trees from unrooted…
The recursive and hierarchical structure of full rooted trees is applicable to represent statistical models in various areas, such as data compression, image processing, and machine learning. In most of these cases, the full rooted tree is…
Imputation using external reference panels is a widely used approach for increasing power in GWAS and meta-analysis. Existing HMM-based imputation approaches require individual-level genotypes. Here, we develop a new method for Gaussian…
The increasing availability of population-level allele frequency data across one or more related populations necessitates the development of methods that can efficiently estimate population genetics parameters, such as the strength of…