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Tree congruence metrics are typically global indices that describe the similarity or dissimilarity between dendrograms. This study principally focuses on topological congruence metrics that quantify similarity between two dendrograms and…
Nonlinear metrics, such as the F1-score, Matthews correlation coefficient, and Fowlkes-Mallows index, are often used to evaluate the performance of machine learning models, in particular, when facing imbalanced datasets that contain more…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
This work introduces a novel nonparametric density index defined on graphs, the Sum-over-Forests (SoF) density index. It is based on a clear and intuitive idea: high-density regions in a graph are characterized by the fact that they contain…
We identify a structural pattern in the construction of known infinite families of trees whose independence polynomials are not log-concave. Using this pattern and properties of polynomial ring ideals, we derive linear recurrences for these…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
We introduce generalizations of Aldous' Brownian Continuous Random Tree as scaling limits for multicritical models of discrete trees. These discrete models involve trees with fine-tuned vertex-dependent weights ensuring a k-th root…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Let $f:T^2\to \mathbb{R}$ be Morse function on $2$-torus $T^2,$ and $\mathcal{O}(f)$ be the orbit of $f$ with respect to the right action of the group of diffeomorphisms $\mathcal{D}(T^2)$ on $C^{\infty}(T^2)$. Let also $\mathcal{O}_f(f,X)$…
This paper presents a new approach for trees-based regression, such as simple regression tree, random forest and gradient boosting, in settings involving correlated data. We show the problems that arise when implementing standard…
A multi-labeled tree, or MUL-tree, is a phylogenetic tree where two or more leaves share a label, e.g., a species name. A MUL-tree can imply multiple conflicting phylogenetic relationships for the same set of taxa, but can also contain…
A closed-form formula is derived for the number of occurrences of matches of a multiset of patterns among all ordered (plane-planted) trees with a given number of edges. A pattern looks like a tree, with internal nodes and leaves, but also…
In this paper we investigate an extremal problem on binary phylogenetic trees. Given two such trees $T_1$ and $T_2$, both with leaf-set ${1,2,...,n}$, we are interested in the size of the largest subset $S \subseteq {1,2,...,n}$ of leaves…
A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…
We present a new method for inferring species trees from multi-copy gene trees. Our method is based on a generalization of the Robinson-Foulds (RF) distance to multi-labeled trees (mul-trees), i.e., gene trees in which multiple leaves can…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
Rooted and ranked binary trees are mathematical objects of great importance used to model hierarchical data and evolutionary relationships with applications in many fields including evolutionary biology and genetic epidemiology. Bayesian…
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…
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…
The paper attempts to validate the effectiveness of tree classifiers to classify tabla strokes especially the ones which are overlapping in nature. It uses decision tree, ID3 and random forest as classifiers. A custom made data sets of 650…