Related papers: On Two Measures of Distance between Fully-Labelled…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
In the infinite regular tree $\mathbb{T}_{q+1}$ with $q \in \mathbb{Z}_{\ge 2}$, we consider families $\{\mu_u^n\}$, indexed by vertices $u$ and nonnegative integers ("discrete time steps") $n$, of probability measures such that $\mu_u^n(v)…
The set of all permutations with $n$ symbols is a symmetric group denoted by $S_n$. A transposition tree, $T$, is a spanning tree over its $n$ vertices $V_T=${$1, 2, 3, \ldots n$} where the vertices are the positions of a permutation $\pi$…
We propose a new exact method for shortest-path distance queries on large-scale networks. Our method precomputes distance labels for vertices by performing a breadth-first search from every vertex. Seemingly too obvious and too inefficient…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
The emergence of massive graph data sets requires fast mining algorithms. Centrality measures to identify important vertices belong to the most popular analysis methods in graph mining. A measure that is gaining attention is forest…
Rotation distances measure the differences in structure between rooted ordered binary trees. The one-dimensional skeleta of associahedra are rotation graphs, where two vertices representing trees are connected by an edge if they differ by a…
Genome rearrangement is a common model for molecular evolution. In this paper, we consider the Pairwise Rearrangement problem, which takes as input two genomes and asks for the number of minimum-length sequences of permissible operations…
During cancer progression, malignant cells accumulate somatic mutations that can lead to genetic aberrations. In particular, evolutionary events akin to segmental duplications or deletions can alter the copy-number profile (CNP) of a set of…
A routing labeling scheme assigns a binary string, called a label, to each node in a network, and chooses a distinct port number from $\{1,\ldots,d\}$ for every edge outgoing from a node of degree $d$. Then, given the labels of $u$ and $w$…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
Short spanning trees subject to additional constraints are important building blocks in various approximation algorithms. Especially in the context of the Traveling Salesman Problem (TSP), new techniques for finding spanning trees with…
Edit distance between trees is a natural generalization of the classical edit distance between strings, in which the allowed elementary operations are contraction, uncontraction and relabeling of an edge. Demaine et al. [ACM Trans. on…
Full binary trees naturally represent commutative non-associative products. There are many important examples of these products: finite-precision floating-point addition and NAND gates, among others. Balance in such a tree is highly…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
Distances on merge trees facilitate visual comparison of collections of scalar fields. Two desirable properties for these distances to exhibit are 1) the ability to discern between scalar fields which other, less complex topological…
Metrics for merge trees that are simultaneously stable, informative, and efficiently computable have so far eluded researchers. We show in this work that it is possible to devise such a metric when restricting merge trees to ordered domains…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Suppose we label the vertices of a tree by positive integers. The weight of an edge is defined by a monotonically increasing function of the absolute value of the difference of the labels of its endpoints. We define the total cost of the…