Related papers: Phylogenetic estimation with partial likelihood te…
Loss tomography has received considerable attention in recent years and a number of estimators based on maximum likelihood (ML) or Bayesian principles have been proposed. Almost all of the estimators are devoted to the tree topology despite…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
Probabilistic Latent Tensor Factorization (PLTF) is a recently proposed probabilistic framework for modelling multi-way data. Not only the common tensor factorization models but also any arbitrary tensor factorization structure can be…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
This paper concerns the use of the expectation-maximisation (EM) algorithm for inference in partially observed diffusion processes. In this context, a well known problem is that all except a few diffusion processes lack closed-form…
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.…
Probabilistic inference is a fundamental task in modern machine learning. Recent advances in tensor network (TN) contraction algorithms have enabled the development of better exact inference methods. However, many common inference tasks in…
We study the problem of model selection type aggregation with respect to the Kullback-Leibler divergence for various probabilistic models. Rather than considering a convex combination of the initial estimators $f_1, \ldots, f_N$, our…
The quality of the inferences we make from pathogen sequence data is determined by the number and composition of pathogen sequences that make up the sample used to drive that inference. However, there remains limited guidance on how to best…
Boolean tensor decomposition approximates data of multi-way binary relationships as product of interpretable low-rank binary factors, following the rules of Boolean algebra. Here, we present its first probabilistic treatment. We facilitate…
Many fundamental questions concerning the emergence and subsequent evolution of eukaryotic exon-intron organization are still unsettled. Genome-scale comparative studies, which can shed light on crucial aspects of eukaryotic evolution,…
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…
Modern population genetics studies typically involve genome-wide genotyping of individuals from a diverse network of ancestries. An important, unsolved problem is how to formulate and estimate probabilistic models of observed genotypes that…
This paper focuses on the estimation of partially observed branching processes. First, the estimators from a frequentist perspective proposed in the literature are reviewed. The main objective of this paper is to present computational tools…
Biological data objects often have both of the following features: (i) they are functions rather than single numbers or vectors, and (ii) they are correlated due to phylogenetic relationships. In this paper we give a flexible statistical…
As a technique to investigate link-level loss rates of a computer network with low operational cost, loss tomography has received considerable attentions in recent years. A number of parameter estimation methods have been proposed for loss…
Phylogenetically informed k-mers, or phylo-k-mers for short, are k-mers that are predicted to appear within a given genomic region at predefined locations of a fixed phylogeny. Given a reference alignment for this genomic region and…
In this article, a Probability Mass Function (PMF) estimation method which tames the curse of dimensionality is proposed. This method, called Partial Coupled Tensor Factorization of 3D marginals or PCTF3D, has for principle to partially…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
The evolution of molecular and phenotypic traits is commonly modelled using Markov processes along a phylogeny. This phylogeny can be a tree, or a network if it includes reticulations, representing events such as hybridization or admixture.…