Related papers: Improving Gene Trees without more data

Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…

Analyses of targeted genomic sequencing data from next-generation-sequencing (NGS) technologies typically involves mapping reads to a reference sequence or clustering reads. For a number of species a reference genome is not available so the…

Tree-boosting is a widely used machine learning technique for tabular data. However, its out-of-sample accuracy is critically dependent on multiple hyperparameters. In this article, we empirically compare several popular methods for…

The full strong branching (FSB) rule is well known to produce extremely small branch-and-bound trees. This rule guides branching decisions based exclusively on the information regarding local gains in the linear programming (LP) bounds. We…

Accurate classification of sleep disorders, particularly insomnia and sleep apnea, is important for reducing long term health risks and improving patient quality of life. However, clinical sleep studies are resource intensive and are…

Accurate imputation of race and ethnicity (R&E) is crucial for analyzing disparities and informing policy. Methods like Bayesian Improved Surname Geocoding (BISG) are widely used but exhibit limitations, including systematic…

Summary: GeneSupport implements a genome-scale algorithm: Maximum Gene-Support Tree to estimate species tree from gene trees based on multilocus sequences. It provides a new option for multiple genes to infer species tree. It is…

With the demand for machine learning increasing, so does the demand for tools which make it easier to use. Automated machine learning (AutoML) tools have been developed to address this need, such as the Tree-Based Pipeline Optimization Tool…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

Numerous machine learning (ML) models employed in protein function and structure prediction depend on evolutionary information, which is captured through multiple-sequence alignments (MSA) or position-specific scoring matrices (PSSM) as…

Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…

Under the multispecies coalescent model of molecular evolution, gene trees have independent evolutionary histories within a shared species tree. In comparison, supermatrix concatenation methods assume that gene trees share a single common…

The combinatorial sequential Monte Carlo (CSMC) has been demonstrated to be an efficient complementary method to the standard Markov chain Monte Carlo (MCMC) for Bayesian phylogenetic tree inference using biological sequences. It is…

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,…

Reliable identification of molecular biomarkers is essential for accurate patient stratification. While state-of-the-art machine learning approaches for sample classification continue to push boundaries in terms of performance, most of…

Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…

Most real-world classification problems deal with imbalanced datasets, posing a challenge for Artificial Intelligence (AI), i.e., machine learning algorithms, because the minority class, which is of extreme interest, often proves difficult…

Phylogenetic trees (i.e. evolutionary trees, additive trees or X-trees) play a key role in the processes of modeling and representing species evolution. Genome evolution of a given group of species is usually modeled by a species…

Machine learning (ML) has been used to develop increasingly accurate link quality estimators for wireless networks. However, more in-depth questions regarding the most suitable class of models, most suitable metrics and model performance on…

Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing…