Related papers: R3F: An R package for evolutionary dates, rates, a…
CRISPR technology has enabled large-scale cell lineage tracing for complex multicellular organisms by mutating synthetic genomic barcodes during organismal development. However, these sophisticated biological tools currently use ad-hoc and…
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…
The goal of this paper is to study the similarity between sequences using a distance between the \emph{context} trees associated to the sequences. These trees are defined in the framework of \emph{Sparse Probabilistic Suffix Trees} (SPST),…
We develop a new Bayesian modelling framework for the class of higher-order, variable-memory Markov chains, and introduce an associated collection of methodological tools for exact inference with discrete time series. We show that a version…
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
This paper introduces an R package ForecastTB that can be used to compare the accuracy of different forecasting methods as related to the characteristics of a time series dataset. The ForecastTB is a plug-and-play structured module, and…
Battery cycle life prediction using early degradation data has many potential applications throughout the battery product life cycle. For that reason, various data-driven methods have been proposed for point prediction of battery cycle life…
In evolutionary studies it is common to use phylogenetic trees to represent the evolutionary history of a set of species. However, in case the transfer of genes or other genetic information between the species or their ancestors has…
Creating accurate 3D models of tree topology is an important task for tree pruning. The 3D model is used to decide which branches to prune and then to execute the pruning cuts. Previous methods for creating 3D tree models have typically…
CVTree is an alignment-free methodology for inferring species phylogeny and taxonomy. This method allows for the efficient and accurate resolution of evolutionary relationships among large numbers of species based on whole-genome sequence…
Canonical distances such as Euclidean distance often fail to capture the appropriate relationships between items, subsequently leading to subpar inference and prediction. Many algorithms have been proposed for automated learning of suitable…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
Random Fourier Features (RFF) is among the most popular and broadly applicable approaches for scaling up kernel methods. In essence, RFF allows the user to avoid costly computations on a large kernel matrix via a fast randomized…
Reliable large-scale data on the state of forests is crucial for monitoring ecosystem health, carbon stock, and the impact of climate change. Current knowledge of tree species distribution relies heavily on manual data collection in the…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
Phylogenetic profiles - presence-absence patterns of genes across taxa - are rich information sources for inferring the evolutionary history of genes and gene families. When aggregated across many genes, these profiles can reveal…
Survival data is encountered in a range of disciplines, most notably health and medical research. Although Bayesian approaches to the analysis of survival data can provide a number of benefits, they are less widely used than classical (e.g.…
A phylogeny describes the evolutionary history of an evolving population. Evolutionary search algorithms can perfectly track the ancestry of candidate solutions, illuminating a population's trajectory through the search space. However,…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…