Related papers: Reconstructing pedigrees using probabilistic analy…
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
Recent theoretical work has demonstrated that Neighbor Joining applied to concatenated DNA sequences is a statistically consistent method of species tree reconstruction. This brief note compares the accuracy of this approach to other…
Probabilistic modeling is fundamental to the statistical analysis of complex data. In addition to forming a coherent description of the data-generating process, probabilistic models enable parameter inference about given data sets. This…
We use Bayesian inference and nested sampling to develop a non-parametric method to reconstruct the primordial power spectrum $P_{\mathcal{R}}(k)$ from Large Scale Structure (LSS) data. The performance of the method is studied by applying…
We analyse a model consisting of a population of individuals which is subdivided into a finite set of demes, each of which has a fixed but differing number of individuals. The individuals can reproduce, die and migrate between the demes…
Genetic risk prediction is an important component of individualized medicine, but prediction accuracies remain low for many complex diseases. A fundamental limitation is the sample sizes of the studies on which the prediction algorithms are…
There is little debate about the importance of the ancestral recombination graph in population genetics. An important theoretical tool, the main obstacle to its widespread usage is the computational cost required to match the…
In this report a systematic approach is used to determine the approximate genetic network and robust dependencies underlying differentiation. The data considered is in the form of a binary matrix and represent the expression of the nine…
We consider a continuous-time Markov chain model of SIR disease dynamics with two levels of mixing. For this so-called stochastic households model, we provide two methods for inferring the model parameters---governing within-household…
We propose a method for estimating the posterior distribution of a standard geostatistical model. After choosing the model formulation and specifying a prior, we use normal mixture densities to approximate the posterior distribution. The…
This work presents a new classifier that is specifically designed to be fully interpretable. This technique determines the probability of a class outcome, based directly on probability assignments measured from the training data. The…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Data augmentation is a widely used technique in many machine learning tasks, such as image classification, to virtually enlarge the training dataset size and avoid overfitting. Traditional data augmentation techniques for image…
We describe a new and computationally efficient Bayesian methodology for inferring species trees and demographics from unlinked binary markers. Likelihood calculations are carried out using diffusion models of allele frequency dynamics…
The rapid development of sequencing technologies represents new opportunities for population genetics research. It is expected that genomic data will increase our ability to reconstruct the history of populations. While this increase in…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Speech enhancement in hearing aids remains a difficult task in nonstationary acoustic environments, mainly because current signal processing algorithms rely on fixed, manually tuned parameters that cannot adapt in situ to different users or…
This paper studies the mutation-selection balance in three simplified replication models. The first model considers a population of organisms replicating via the production of asexual spores. The second model considers a sexually…
Sweepstakes reproduction may be generated by chance matching of reproduction with favorable environmental conditions. Gene genealogies generated by sweepstakes reproduction are in the domain of attraction of multiple-merger coalescents…
We present a computational model to reconstruct trees of ancestors for animals with sexual reproduction. Through a recursive algorithm combined with a random number generator, it is possible to reproduce the number of ancestors for each…