Related papers: SPAGETI: Stabilizing Phylogenetic Assessment with …

Species tree estimation from multi-locus datasets is statistically challenging for multiple reasons, including gene tree heterogeneity across the genome due to incomplete lineage sorting (ILS). Species tree estimation methods have been…

An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…

Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…

Phylogenetic networks play an important role in evolutionary biology as, other than phylogenetic trees, they can be used to accommodate reticulate evolutionary events such as horizontal gene transfer and hybridization. Recent research has…

Evolution is a process that is influenced by various environmental factors, e.g. the interactions between different species, genes, and biogeographical properties. Hence, it is interesting to study the combined evolutionary history of…

Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…

Decision trees are widely used for non-linear modeling, as they capture interactions between predictors while producing inherently interpretable models. Despite their popularity, performing inference on the non-linear fit remains largely…

Genomes and genes diversify during evolution; however, it is unclear to what extent genes still retain the relationship among species. Model species for molecular phylogenetic studies include yeasts and viruses whose genomes were sequenced…

The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on…

Phylogenomics, even more so than traditional phylogenetics, needs to represent the uncertainty in evolutionary trees due to systematic error. Here we illustrate the analysis of genome-scale alignments of yeast, using robust measures of the…

Decision trees are popular classification models, providing high accuracy and intuitive explanations. However, as the tree size grows the model interpretability deteriorates. Traditional tree-induction algorithms, such as C4.5 and CART,…

I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more…

A common approach to aggregate classification estimates in an ensemble of decision trees is to either use voting or to average the probabilities for each class. The latter takes uncertainty into account, but not the reliability of the…

Models obtained by decision tree induction techniques excel in being interpretable.However, they can be prone to overfitting, which results in a low predictive performance. Ensemble techniques are able to achieve a higher accuracy. However,…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…

If predictions for species extinctions hold, then the `tree of life' today may be quite different to that in (say) 100 years. We describe a technique to quantify how much each species is likely to contribute to future biodiversity, as…

Phylogenomics heavily relies on well-curated sequence data sets that consist, for each gene, exclusively of 1:1-orthologous. Paralogs are treated as a dangerous nuisance that has to be detected and removed. We show here that this severe…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

The prevailing mindset is that a single decision tree underperforms classic random forests in testing accuracy, despite its advantages in interpretability and lightweight structure. This study challenges such a mindset by significantly…

Although the analysis of rooted tree shape has wide-ranging applications, notions of tree balance have developed independently in different domains. In computer science, a balanced tree is one that enables efficient updating and retrieval…