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Nervous systems are characterized by neurons displaying a diversity of morphological shapes. Traditionally, different shapes have been qualitatively described based on visual inspection and quantitatively described based on morphometric…
Phylogenetic trees are important tools in the study of evolutionary relationships between species. Measures such as the index of Sackin, Colless, and Total Cophenetic have been extensively used to quantify tree balance, one key property of…
Working with tree graphs is always easier than with loopy ones and spanning trees are the closest tree-like structures to a given graph. We find a correspondence between the solutions of random K-satisfiability problem and those of spanning…
The method of flexi-Weighted Least Squares on evolutionary trees uses simple polynomial or exponential functions of the evolutionary distance in place of model-based variances. This has the advantage that unexpected deviations from…
The concept of $k$-compatibility measures how many phylogenetic trees it would take to display all splits in a given set. A set of trees that display every single possible split is termed a \textit{universal tree set}. In this note, we find…
We give the asymptotic distribution of the length of partial coalescent trees for Beta and related coalescents. This allows us to give the asymptotic distribution of the number of (neutral) mutations in the partial tree. This is a first…
We define a statistical ensemble of non-degenerate graphs, i.e. graphs without multiple- and self-connections between nodes. The node degree distribution is arbitrary, but the nodes are assumed to be uncorrelated. This completes our earlier…
Tree-cut width is a parameter that has been introduced as an attempt to obtain an analogue of treewidth for edge cuts. Unfortunately, in spite of its desirable structural properties, it turned out that tree-cut width falls short as an…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic inference, the task of reconstructing how related sequences evolved from common ancestors, is a central objective in evolutionary genomics. The current state-of-the-art methods exploit probabilistic models of sequence evolution…
High-dimensional data often exhibit hierarchical structures in both modes: samples and features. Yet, most existing approaches for hierarchical representation learning consider only one mode at a time. In this work, we propose an…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Here, based on an idea of Bruen and Bryant, we propose and analyze a new distance measure: the Maximum Parsimony (MP)…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Phylogeny is the study of the relations between biological entities. From it, the need to compare tree-like graphs has risen and several metrics were established and researched, but since there is no definitive way to compare them, its…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In a recent series of papers devoted to the…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
The Nested Dirichlet Distribution (NDD) provides a flexible alternative to the Dirichlet distribution for modeling compositional data, relaxing constraints on component variances and correlations through a hierarchical tree structure. While…
We consider two parametrized random digraph families, namely, proportional-edge and central similarity proximity catch digraphs (PCDs) and compare the performance of these two PCD families in testing spatial point patterns. These PCD…