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Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
A bipartite graph $G=(A, B, E)$ is said to be a biconvex bipartite graph if there exist orderings $<_A$ in $A$ and $<_B$ in $B$ such that the neighbors of every vertex in $A$ are consecutive with respect to $<_B$ and the neighbors of every…
A characterization is provided for each natural number except one (1) by means of an ordered pair of elements. The first element is a natural number called the type of the natural number characterized, and the second is a natural number…
A transversal in a rooted tree is any set of nodes that meets every path from the root to a leaf. We let c(T,k) denote the number of transversals of size k in a rooted tree T. We define a partial order on the set of all rooted trees with n…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Self-explaining text categorization requires a classifier to make a prediction along with supporting evidence. A popular type of evidence is sub-sequences extracted from the input text which are sufficient for the classifier to make the…
We apply the theory of markov random fields on trees to derive a phase transition in the number of samples needed in order to reconstruct phylogenies. We consider the Cavender-Farris-Neyman model of evolution on trees, where all the inner…
A composition of a nonnegative integer (n) is a sequence of positive integers whose sum is (n). A composition is palindromic if it is unchanged when its terms are read in reverse order. We provide a generating function for the number of…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…
A semiregular tree is a tree where all non-pendant vertices have the same degree. Belardo et al. (MATCH Commun. Math. Chem. 61(2), pp. 503-515, 2009) have shown that among all semiregular trees with a fixed order and degree, a graph with…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
A tree $T$ on $2^n$ vertices is called set-sequential if the elements in $V(T)\cup E(T)$ can be labeled with distinct nonzero $(n+1)$-dimensional $01$-vectors such that the vector labeling each edge is the component-wise sum modulo $2$ of…
We present a new formulation of the loop-tree duality theorem for higher loop diagrams valid both for massless and massive cases. $l$-loop integrals are expressed as weighted sum of trees obtained from cutting $l$ internal propagators of…
In agglomerative hierarchical clustering, pair-group methods suffer from a problem of non-uniqueness when two or more distances between different clusters coincide during the amalgamation process. The traditional approach for solving this…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
Motivated by the bijection between Schnyder labelings of a plane triangulation and partitions of its inner edges into three trees, we look for binary labelings for quadrangulations (whose edges can be partitioned into two trees). Our…
An m-extracting procedure produces unbiased random bits from a loaded dice with m faces. A binarization takes inputs from an m-faced dice and produce bit sequences to be fed into a (binary) extracting procedure to obtain random bits. Thus,…