相关论文: Constraints on the perfect phylogeny mixture model…

Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…

Phylogenetic mixture models, in which the sites in sequences undergo different substitution processes along the same or different trees, allow the description of heterogeneous evolutionary processes. As data sets consisting of longer…

We analyse a maximum-likelihood approach for combining phylogenetic trees into a larger `supertree'. This is based on a simple exponential model of phylogenetic error, which ensures that ML supertrees have a simple combinatorial description…

The perfect phylogeny is one of the most used models in different areas of computational biology. In this paper we consider the problem of the Persistent Perfect Phylogeny (referred as P-PP) recently introduced to extend the perfect…

Phylogenetic comparative methods (PCMs) are widely used to study trait evolution. However, many evolutionary histories involve reticulate evolutionary scenarios, such as hybridization, that violate core assumptions of these methods. In this…

Precision medicine is accelerating rapidly in the field of health research. This includes fitting predictive models for individual patients based on patient similarity in an attempt to improve model performance. We propose an algorithm…

Linear Mixed Models (LMMs) are important tools in statistical genetics. When used for feature selection, they allow to find a sparse set of genetic traits that best predict a continuous phenotype of interest, while simultaneously correcting…

We propose a novel approach for modeling multivariate longitudinal data in the presence of unobserved heterogeneity for the analysis of the Health and Retirement Study (HRS) data. Our proposal can be cast within the framework of linear…

The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…

Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…

A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…

Linear mixed models (LMMs) are a powerful and established tool for studying genotype-phenotype relationships. A limiting assumption of LMMs is that the residuals are Gaussian distributed, a requirement that rarely holds in practice.…

Phylogenetic Diversity (PD) is a measure of the overall biodiversity of a set of present-day species (taxa) within a phylogenetic tree. In Maximize Phylogenetic Diversity (MPD) one is asked to find a set of taxa (of bounded size/cost) for…

Advances in precision medicine increasingly drive methodological innovation in health research. A key development is the use of personalized prediction models (PPMs), which are fit using a similar subpopulation tailored to a specific index…

We consider scenarios where a very accurate (often small) predictive model using restricted features is available when training a full-featured (often larger) model. This restricted model may be thought of as side-information'', and can…

Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…

Clinical machine learning applications are often plagued with confounders that are clinically irrelevant, but can still artificially boost the predictive performance of the algorithms. Confounding is especially problematic in mobile health…

The software program BAMM has been widely used to study the dynamics of speciation, extinction, and phenotypic evolution on phylogenetic trees. The program implements a model-based clustering algorithm to identify clades that share common…

Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…

Model pruning is a popular approach to enable the deployment of large deep learning models on edge devices with restricted computational or storage capacities. Although sparse models achieve performance comparable to that of their dense…