Related papers: Alignment-free phylogenetic reconstruction: Sample…
Bayesian inference methods rely on numerical algorithms for both model selection and parameter inference. In general, these algorithms require a high computational effort to yield reliable estimates. One of the major challenges in…
As whole genomes become widely available, maximum likelihood and Bayesian phylogenetic methods are demonstrating their limits in meeting the escalating computational demands. Conversely, distance-based phylogenetic methods are efficient,…
Gene gain-loss-duplication models are commonly based on continuous-time birth-death processes. Employed in a phylogenetic context, such models have been increasingly popular in studies of gene content evolution across multiple genomes.…
Sampling is a fundamental technique, and sampling without replacement is often desirable when duplicate samples are not beneficial. Within machine learning, sampling is useful for generating diverse outputs from a trained model. We present…
We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…
In recent years the importance of finding a meaningful pattern from huge datasets has become more challenging. Data miners try to adopt innovative methods to face this problem by applying feature selection methods. In this paper we propose…
Stem cells, through their ability to produce daughter stem cells and differentiate into specialized cells, are essential in the growth, maintenance, and repair of biological tissues. Understanding the dynamics of cell populations in the…
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…
It is known that evolution strategies in continuous domains might not converge in the presence of noise. It is also known that, under mild assumptions, and using an increasing number of resamplings, one can mitigate the effect of additive…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…
Agent-based simulation platforms play a key role in enabling fast-to-run evolution experiments that can be precisely controlled and observed in detail. Availability of high-resolution snapshots of lineage ancestries from digital…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
We consider the reconstruction of a phylogeny from multiple genes under the multispecies coalescent. We establish a connection with the sparse signal detection problem, where one seeks to distinguish between a distribution and a mixture of…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
We study the problem of complexity estimation in the context of parallelizing an advanced Branch and Bound-type algorithm over graphical models. The algorithm's pruning power makes load balancing, one crucial element of every distributed…