Related papers: Split scores: a tool to quantify phylogenetic sign…

The algebraic properties of flattenings and subflattenings provide direct methods for identifying edges in the true phylogeny -- and by extension the complete tree -- using pattern counts from a sequence alignment. The relatively small…

Polyploidization is an important evolutionary process which affects organisms ranging from plants to fish and fungi. The signal left behind by it is in the form of a species' ploidy level (number of complete chromosome sets found in a cell)…

In this article we are describing a new algorithm for detecting and validating partial horizontal gene transfers (HGT). The presented algorithm is based on a sliding window procedure which analyzes fragments of the given multiple sequence…

We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…

A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…

Clustering is a difficult and widely-studied data mining task, with many varieties of clustering algorithms proposed in the literature. Nearly all algorithms use a similarity measure such as a distance metric (e.g. Euclidean distance) to…

In this article we propose an optimal method referred to as SPlit for splitting a dataset into training and testing sets. SPlit is based on the method of Support Points (SP), which was initially developed for finding the optimal…

Analysis of multi-source dataset, where data on the same objects are collected from multiple sources, is of rising importance in many fields, most notably in multi-omics biology. A novel framework and algorithms for integrative…

Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…

Variation in the evolutionary process across the sites of nucleotide sequence alignments is well established, and is an increasingly pervasive feature of datasets composed of gene regions sampled from multiple loci and/or different genomes.…

A standard approach for assessing the performance of partition models is to create synthetic data sets with a prespecified clustering structure, and assess how well the model reveals this structure. A common format is that subjects are…

As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…

Understanding the population structure and patterns of gene flow within species is of fundamental importance to the study of evolution. In the fields of population and evolutionary genetics, measures of genetic differentiation are commonly…

Biomarker discovery and gene ranking is a standard task in genomic high throughput analysis. Typically, the ordering of markers is based on a stabilized variant of the t-score, such as the moderated t or the SAM statistic. However, these…

Using topological summaries of gene trees as a basis for species tree inference is a promising approach to obtain acceptable speed on genomic-scale datasets, and to avoid some undesirable modeling assumptions. Here we study the…

Due to the increasing complexity and interconnectedness of different components in modern automotive software systems there is a great number of interactions between these system components and their environment. These interactions result…

We propose a novel methodology for feature screening in clustering massive datasets, in which both the number of features and the number of observations can potentially be very large. Taking advantage of a fusion penalization based convex…

Score matching is a vital tool for learning the distribution of data with applications across many areas including diffusion processes, energy based modelling, and graphical model estimation. Despite all these applications, little work…

Survival analysis concerns the task of predicting the time until an event occurs. Often used in the medical field, survival analysis deals with incomplete (i.e., censored) data, for instance, from patients who did not experience the event…

Identification of functional elements of a genome often requires dividing a sequence of measurements along a genome into segments differing from adjacent segments. In many applications, the mean of the measured values at multiple genomic…