Related papers: Approximate Cartesian Tree Matching: an Approach U…
The algorithmic tasks of computing the Hamming distance between a given pattern of length $m$ and each location in a text of length $n$ is one of the most fundamental algorithmic tasks in string algorithms. Unfortunately, there is evidence…
Given two rooted phylogenetic trees on the same set of taxa X, the Maximum Agreement Forest problem (MAF) asks to find a forest that is, in a certain sense, common to both trees and has a minimum number of components. The Maximum Acyclic…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…
We consider here the problem of chaining seeds in ordered trees. Seeds are mappings between two trees Q and T and a chain is a subset of non overlapping seeds that is consistent with respect to postfix order and ancestrality. This problem…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
Let $T=t_0 ... t_{n-1}$ be a text and $P = p_0 ... p_{m-1}$ a pattern taken from some finite alphabet set $\Sigma$, and let $\dist$ be a metric on $\Sigma$. We consider the problem of calculating the sum of distances between the symbols of…
Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Uniform cost-distance Steiner trees minimize the sum of the total length and weighted path lengths from a dedicated root to the other terminals. They are applied when the tree is intended for signal transmission, e.g. in chip design or…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
Let $t$ be a permutation (that shall play the role of the {\em text}) on $[n]$ and a pattern $p$ be a sequence of $m$ distinct integer(s) of $[n]$, $m\leq n$. The pattern $p$ occurs in $t$ in position $i$ if and only if $p_1... p_m$ is…
A matching complex of a simple graph $G$ is a simplicial complex with faces given by the matchings of $G$. The topology of matching complexes is mysterious; there are few graphs for which the homotopy type is known. Marietti and Testa…
This paper investigates the execution of tree-shaped task graphs using multiple processors. Each edge of such a tree represents a large IO file. A task can only be executed if all input and output files fit into memory, and a file can only…
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…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the approximate pattern matching problem asks for computation of a particular \emph{distance} function between $P$ and every $m$-substring of $T$. We consider a…
As online dating has become more popular in the past few years, an efficient and effective algorithm to match users is needed. In this project, we proposed a new dating matching algorithm that uses Kendall-Tau distance to measure the…
For a graph $G = (V, E)$, the $\gamma$-graph of $G$, denoted $G(\gamma) = (V(\gamma), E(\gamma))$, is the graph whose vertex set is the collection of minimum dominating sets, or $\gamma$-sets of $G$, and two $\gamma$-sets are adjacent in…