相关论文: An analytical comparison of coalescent-based multi…
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…
Large Language Models (LLMs) have been widely adopted across various domains, yet their application in the medical field poses unique challenges, particularly concerning the generation of hallucinations. Hallucinations in open-ended long…
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…
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…
A rigorous methodology is proposed to study cell division data consisting in several observed genealogical trees of possibly different shapes. The procedure takes into account missing observations, data from different trees, as well as the…
Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…
We apply recently developed inference methods based on general coalescent processes to DNA sequence data obtained from various marine species. Several of these species are believed to exhibit so-called shallow gene genealogies, potentially…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
Consensus methods provide a useful strategy for combining information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species tree. To investigate the theoretical…
Bayesian phylogenetics is vital for understanding evolutionary dynamics, and requires accurate and efficient approximation of posterior distributions over trees. In this work, we develop a variational Bayesian approach for ultrametric…
Coalescent models of bifurcating genealogies are used to infer evolutionary parameters from molecular data. However, there are many situations where bifurcating genealogies do not accurately reflect the true underlying ancestral history of…
While Vision-Language Models (VLMs) excel at visual understanding, they often fail to grasp hierarchical knowledge. This leads to common errors where VLMs misclassify coarser taxonomic levels even when correctly identifying the most…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Long-tailed (LT) classification is an unavoidable and challenging problem in the real world. Most existing long-tailed classification methods focus only on solving the class-wise imbalance while ignoring the attribute-wise imbalance. The…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Realizing when a model is right for a wrong reason is not trivial and requires a significant effort by model developers. In some cases an input salience method, which highlights the most important parts of the input, may reveal problematic…
The Colless index is one of the most popular and natural balance indices for bifurcating phylogenetic trees, but it makes no sense for multifurcating trees. In this paper we propose a family of Colless-like balance indices…
A well-established model for the genealogy of a large population in equilibrium is Kingman's coalescent. For the population together with its genealogy evolving in time, this gives rise to a time-stationary tree-valued process. We study the…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
Searching for local sequence patterns is one of the basic tasks in bioinformatics. Sequence patterns might have structural, functional or some other relevance, and numerous methods have been developed to detect and analyze them. These…