Related papers: Fitting Distances by Tree Metrics Minimizing the T…
Imagine that unlabelled tokens are placed on the edges of a graph, such that no two tokens are placed on incident edges. A token can jump to another edge if the edges having tokens remain independent. We study the problem of determining the…
The tree edit distance (TED) between two rooted ordered trees with $n$ nodes labeled from an alphabet $\Sigma$ is the minimum cost of transforming one tree into the other by a sequence of valid operations consisting of insertions, deletions…
Recent years have witnessed a surge of biological interest in the minimum spanning tree (MST) problem for its relevance to automatic model construction using the distances between data points. Despite the increasing use of MST algorithms…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
The cost-distance Steiner tree problem seeks a Steiner tree that minimizes the total congestion cost plus the weighted sum of source-sink delays. This problem arises as a subroutine in timing-constrained global routing with a linear delay…
Given a set of n points in the plane, each point having a positive weight, and an integer k>0, we present an optimal O(n \log n)-time deterministic algorithm to compute a step function with k steps that minimizes the maximum weighted…
We present a deterministic algorithm for solving a wide range of dynamic programming problems in trees in $O(\log D)$ rounds in the massively parallel computation model (MPC), with $O(n^\delta)$ words of local memory per machine, for any…
A variety of algorithms have been proposed for reconstructing trees that show the evolutionary relationships between species by comparing differences in genetic data across present-day taxa. If the leaf-to-leaf distances in a tree can be…
The automaton constrained tree knapsack problem is a variant of the knapsack problem in which the items are associated with the vertices of the tree, and we can select a subset of items that is accepted by a top-down tree automaton. If the…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Matrix Factorization plays an important role in machine learning such as Non-negative Matrix Factorization, Principal Component Analysis, Dictionary Learning, etc. However, most of the studies aim to minimize the loss by measuring the…
We study the problem of estimating the Earth Mover's Distance (EMD) between probability distributions when given access only to samples. We give closeness testers and additive-error estimators over domains in $[0, \Delta]^d$, with sample…
We consider the approximate pattern matching problem under edit distance. In this problem we are given a pattern $P$ of length $w$ and a text $T$ of length $n$ over some alphabet $\Sigma$, and a positive integer $k$. The goal is to find all…
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…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
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…
Considering the worst-case scenario, junction tree algorithm remains the most general solution for exact MAP inference with polynomial run-time guarantees. Unfortunately, its main tractability assumption requires the treewidth of a…
In the Tree Deletion Set problem the input is a graph G together with an integer k. The objective is to determine whether there exists a set S of at most k vertices such that G-S is a tree. The problem is NP-complete and even NP-hard to…
For the General Factor problem we are given an undirected graph $G$ and for each vertex $v\in V(G)$ a finite set $B_v$ of non-negative integers. The task is to decide if there is a subset $S\subseteq E(G)$ such that $deg_S(v)\in B_v$ for…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…