Related papers: An empirical guide for producing a dated phylogeny…

Tree search is a fundamental tool for planning, as many sequential decision-making problems can be framed as searching over tree-structured spaces. We propose an uncertainty-guided tree search algorithm for settings where the reward…

Various time series in natural and social processes have been found to be bursty. Events in the time series rapidly occur within short time periods, forming bursts, which are alternated with long inactive periods. As the timescale defining…

The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…

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…

Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…

The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…

We have developed a unified format for phylogenetic placements, that is, mappings of environmental sequence data (e.g. short reads) into a phylogenetic tree. We are motivated to do so by the growing number of tools for computing and…

Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees. Many of these measures are NP-hard to compute and this has stimulated a…

We introduce PPL Bench, a new benchmark for evaluating Probabilistic Programming Languages (PPLs) on a variety of statistical models. The benchmark includes data generation and evaluation code for a number of models as well as…

Temporal logics like Computation Tree Logic (CTL) have been widely used as expressive formalisms to capture rich behavioral specifications. CTL can express properties such as reachability, termination, invariants and responsiveness, which…

We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…

When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…

We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…

The history of gene families - which are equivalent to \emph{event-labeled} gene trees - can be reconstructed from empirically estimated evolutionary event-relations containing pairs of orthologous, paralogous or xenologous genes. The…

Constructing taxonomies from citation graphs is essential for organizing scientific knowledge, facilitating literature reviews, and identifying emerging research trends. However, manual taxonomy construction is labor-intensive,…

In this work, we propose a novel tree-based explanation technique, PEACH (Pretrained-embedding Explanation Across Contextual and Hierarchical Structure), that can explain how text-based documents are classified by using any pretrained…

We propose a novel tree classification system called Treelogy, that fuses deep representations with hand-crafted features obtained from leaf images to perform leaf-based plant classification. Key to this system are segmentation of the leaf…

Code generation is one of the tasks for which the use of Large Language Models is widely adopted and highly successful. Given this popularity, there are many benchmarks dedicated to code generation that can help select the best model.…

In mathematical phylogenetics, labeled histories describe the sequences by which sets of labeled lineages coalesce to a shared ancestral lineage. We study labeled histories for at-most-$r$-furcating trees. Consider a rooted leaf-labeled…

This report explores how (potentially constrained) natural language can be used to enable non-experts to develop process models by simply describing scenarios in plain text. To this end, a framework, called BeePath, is proposed. It allows…