Shay Mozes

• Reichman University

We present efficient data structures for submatrix maximum queries in Monge matrices and Monge partial matrices. For n×n Monge matrices, we give a data structure that requires O(n) space and answers submatrix maximum queries in O(logn) time. The best previous data structure [Kaplan et al., SODA‘12] required O(n logn) space and O(log2n) query time....

Given a triangulated planar graph G on n vertices and an integer r<n, an r--division of G with few holes is a decomposition of G into O(n/r) regions of size at most r such that each region contains at most a constant number of faces that are not faces of G (also called holes), and such that, for each region, the total number of vertices on these fa...

We give an O(n log^3 n) algorithm that, given an n-node directed planar graph with arc capacities, a set of source nodes, and a set of sink nodes, finds a maximum flow from the sources to the sinks. Previously, the fastest algorithms known for this problem were those for general graphs.

We give a randomized algorithm that finds a minimum cut in an undirected weighted m-edge n-vertex graph G with high probability in O(mlog2n)\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt...

We show how to assign labels of size $\tilde O(1)$ to the vertices of a directed planar graph $G$, such that from the labels of any three vertices $s,t,f$ we can deduce in $\tilde O(1)$ time whether $t$ is reachable from $s$ in the graph $G\setminus \{f\}$. Previously it was only known how to achieve $\tilde O(1)$ queries using a centralized $\tild...

The Voronoi diagrams technique was introduced by Cabello to compute the diameter of planar graphs in subquadratic time. We present novel applications of this technique in static, fault-tolerant, and partially-dynamic undirected unweighted planar graphs, as well as some new limitations. 1. In the static case, we give $n^{3+o(1)}/D^2$ and $\tilde{O}(...

We consider the problem of preprocessing a weighted directed planar graph in order to quickly answer exact distance queries. The main tension in this problem is between space S and query time Q , and since the mid-1990s all results had polynomial time-space tradeoffs, e.g., Q = ~ Θ( n/√ S ) or Q = ~Θ( n 5/2 /S 3/2 ). In this article we show that th...

We give an $\tilde O(n^2)$ time algorithm for computing the exact Dynamic Time Warping distance between two strings whose run-length encoding is of size at most $n$. This matches (up to log factors) the known (conditional) lower bound, and should be compared with the previous fastest $O(n^3)$ time exact algorithm and the $\tilde O(n^2)$ time approx...

We consider the edit distance problem on rooted ordered trees parameterized by the trees’ depth. For two trees of size at most n and depth at most d, the state-of-the-art solutions of Zhang and Shasha [SICOMP 1989] and Demaine et al. [TALG 2009] have runtimes O(n2d2) and O(n3), respectively, and are based on so-called decomposition algorithms. It h...

In fault-tolerant distance labeling we wish to assign short labels to the vertices of a graph G such that from the labels of any three vertices u,v,f we can infer the u-to-v distance in the graph G∖{f}. We show that any directed weighted planar graph (and in fact any graph in a graph family with O(n)-size separators, such as minor-free graphs) admi...

Let $G=(V,E)$ be an undirected unweighted planar graph. Consider a vector storing the distances from an arbitrary vertex $v$ to all vertices $S = \{ s_1 , s_2 , \ldots , s_k \}$ of a single face in their cyclic order. The pattern of $v$ is obtained by taking the difference between every pair of consecutive values of this vector. In STOC'19, Li and...

We consider exact distance oracles for directed weighted planar graphs in the presence of failing vertices. Given a source vertex u , a target vertex v and a set X of k failed vertices, such an oracle returns the length of a shortest u -to- v path that avoids all vertices in X . We propose oracles that can handle any number k of failures. We show s...

Given two strings $S$ and $P$, the Episode Matching problem is to compute the length of the shortest substring of $S$ that contains $P$ as a subsequence. The best known upper bound for this problem is $\tilde O(nm)$ by Das et al. (1997), where $n,m$ are the lengths of $S$ and $P$, respectively. Although the problem is well studied and has many appl...

In fault-tolerant distance labeling we wish to assign short labels to the vertices of a graph G such that from the labels of any three vertices u, v, f we can infer the u-to-v distance in the graph \(G\setminus \{f\}\). We show that any directed weighted planar graph (and in fact any graph in a graph family with \(O(\sqrt{n})\)-size separators, suc...

We consider the problem of preprocessing two strings $S$ and $T$, of lengths $m$ and $n$, respectively, in order to be able to efficiently answer the following queries: Given positions $i,j$ in $S$ and positions $a,b$ in $T$, return the optimal alignment of $S[i \mathinner{.\,.} j]$ and $T[a \mathinner{.\,.} b]$. Let $N=mn$. We present an oracle wi...

In fault-tolerant distance labeling we wish to assign short labels to the vertices of a graph $G$ such that from the labels of any three vertices $u,v,f$ we can infer the $u$-to-$v$ distance in the graph $G\setminus \{f\}$. We show that any directed weighted planar graph (and in fact any graph in a graph family with $O(\sqrt{n})$-size separators, s...

Given an undirected, unweighted planar graph $G$ with $n$ vertices, we present a truly subquadratic size distance oracle for reporting exact shortest-path distances between any pair of vertices of $G$ in constant time. For any $\varepsilon > 0$, our distance oracle takes up $O(n^{5/3+\varepsilon})$ space and is capable of answering shortest-path di...

Given an undirected edge-weighted graph $G=(V,E)$ with $m$ edges and $n$ vertices, the minimum cut problem asks to find a subset of vertices $S$ such that the total weight of all edges between $S$ and $V \setminus S$ is minimized. Karger's longstanding $O(m \log^3 n)$ time randomized algorithm for this problem was very recently improved in two inde...

We present an optimal data structure for submatrix maximum queries in n × n Monge matrices. Our result is a two-way reduction showing that the problem is equivalent to the classical predecessor problem in a universe of polynomial size. This gives a data structure of O ( n ) space that answers submatrix maximum queries in O (log log n ) time, as wel...

We give a randomized algorithm that finds a minimum cut in an undirected weighted $m$-edge $n$-vertex graph $G$ with high probability in $O(m \log^2 n)$ time. This is the first improvement to Karger's celebrated $O(m \log^3 n)$ time algorithm from 1996. Our main technical contribution is an $O(m \log n)$ time algorithm that, given a spanning tree $...

Let G be a graph where each vertex is associated with a label. A vertex-labeled approximate distance oracle is a data structure that, given a vertex v and a label λ, returns a (1 + ε)-approximation of the distance from v to the closest vertex with label λ in G. Such an oracle is dynamic if it also supports label changes. In this paper we present th...

Given a string S of n integers in [0,σ), a range minimum query RMQ(i,j) asks for the index of the smallest integer in S[i…j]. It is well known that the problem can be solved with a succinct data structure of size 2n+o(n) and constant query-time. In this paper we show how to preprocess S into a compressed representation that allows fast range minimu...

We present new tradeoffs between space and query-time for exact distance oracles in directed weighted planar graphs. These tradeoffs are almost optimal in the sense that they are within polylogarithmic, subpolynomial or arbitrarily small polynomial factors from the naïve linear space, constant query-time lower bound. These tradeoffs include: (i) an...

Given a string $S$ of $n$ integers in $[0,\sigma)$, a range minimum query $\textsf{RMQ}(i, j)$ asks for the index of the smallest integer in $S[i \dots j]$. It is well known that the problem can be solved with a succinct data structure of size $2n + o(n)$ and constant query-time. In this paper we show how to preprocess $S$ into a {\em compressed re...

We present new tradeoffs between space and query-time for exact distance oracles in directed weighted planar graphs. These tradeoffs are almost optimal in the sense that they are within polylogarithmic, sub-polynomial or arbitrarily small polynomial factors from the na\"{\i}ve linear space, constant query-time lower bound. These tradeoffs include:...

Given a string S of n integers in , a range minimum query asks for the index of the smallest integer in . It is well known that the problem can be solved with a succinct data structure of size and constant query-time. In this paper we show how to preprocess S into a compressed representation that allows fast range minimum queries. This allows for s...

We consider exact distance oracles for directed weighted planar graphs in the presence of failing vertices. Given a source vertex $u$, a target vertex $v$ and a set $X$ of $k$ failed vertices, such an oracle returns the length of a shortest $u$-to-$v$ path that avoids all vertices in $X$. We propose oracles that can handle any number $k$ of failure...

Given a graph $G$ and a set of terminals $T$, a \emph{distance emulator} of $G$ is another graph $H$ (not necessarily a subgraph of $G$) containing $T$, such that all the pairwise distances in $G$ between vertices of $T$ are preserved in $H$. An important open question is to find the smallest possible distance emulator. We prove that, given any sub...

Let G be a graph where each vertex is associated with a label. A Vertex-Labeled Approximate Distance Oracle is a data structure that, given a vertex v and a label , returns a -approximation of the distance from v to the closest vertex with label in G. Such an oracle is dynamic if it also supports label changes. In this paper we present three differ...

We consider distance queries in vertex labeled planar graphs. For any fixed $0 < \epsilon \leq 1/2$ we show how to preprocess a planar graph with vertex labels and edge lengths into a data structure that answers queries of the following form. Given a vertex $u$ and a label $\lambda$ return a $(1+O(\epsilon))$-approximation of the distance between $...

We start a systematic study of data structures for the nearest colored node problem on trees. Given a tree with colored nodes and weighted edges, we want to answer queries (v,c) asking for the nearest node to node v that has color c. This is a natural generalization of the well-known nearest marked ancestor problem. We give an O(n)-space O(log log...

We present an $O(n^{1.5})$-space distance oracle for directed planar graphs that answers distance queries in $O(\log n)$ time. Our oracle both significantly simplifies and significantly improves the recent oracle of Cohen-Addad, Dahlgaard and Wulff-Nilsen [FOCS 2017], which uses $O(n^{5/3})$-space and answers queries in $O(\log n)$ time. We achieve...

Let $G$ be a graph where each vertex is associated with a label. A Vertex-Labeled Approximate Distance Oracle is a data structure that, given a vertex $v$ and a label $\lambda$, returns a $(1+\varepsilon)$-approximation of the distance from $v$ to the closest vertex with label $\lambda$ in $G$. Such an oracle is dynamic if it also supports label ch...

In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to select nodes so that the minimum distance is larger than 1. We design an optimal $O(n)$ time algorithm for the disp...

We present a deterministic algorithm that computes the diameter of a directed planar graph with real arc lengths in $\tilde{O}(n^{5/3})$ time. This improves the recent breakthrough result of Cabello (SODA'17), both by improving the running time (from $\tilde{O}(n^{11/6})$), and by using a deterministic algorithm. It is in fact the first truly subqu...

We present an explicit and efficient construction of additively weighted Voronoi diagrams on planar graphs. Let $G$ be a planar graph with $n$ vertices and $b$ sites that lie on a constant number of faces. We show how to preprocess $G$ in $\tilde O(nb^2)$ time (footnote: The $\tilde O$ notation hides polylogarithmic factors.) so that one can comput...

The edit distance between two rooted ordered trees with n nodes labeled from an alphabet Ʃ is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. Tree edit distance is a well-known generalization of string edit distance....

The edit distance 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 elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. Tree edit distance is a well known generalization of string edit...

The Planar Graph Metric Compression Problem is to compactly encode the distances among $k$ nodes in a planar graph of size $n$. Two na\"ive solutions are to store the graph using $O(n)$ bits, or to explicitly store the distance matrix with $O(k^2 \log{n})$ bits. The only lower bounds are from the seminal work of Gavoille, Peleg, Prennes, and Raz [S...

We describe a data structure for submatrix maximum queries in Monge matrices or partial Monge matrices, where a query seeks the maximum element in a contiguous submatrix of the given matrix. The structure, for an n × n Monge matrix, takes O(nlog n) space and O(nlogn) preprocessing time, and answers queries in O(log²n) time. For partial Monge matric...

We give an O(n log³ n) algorithm that, given an n-node directed planar graph with arc capacities, a set of source nodes, and a set of sink nodes finds a maximum flow from the sources to the sinks. Previously, the fastest algorithms known for this problem were those for general graphs.

We provide an implementation of an algorithm that, given a triangulated planar graph with m edges, returns a simple cycle that is a 3/4-balanced separator consisting of at most &sqrt;8m edges. An efficient construction of a short and balanced separator that forms a simple cycle is essential in numerous planar graph algorithms, for example, for comp...

We give an $O(n \log \log n)$ time algorithm for computing the minimum cut (or equivalently, the shortest cycle) of a weighted directed planar graph. This improves the previous fastest $O(n\log^2 n)$ solution [SODA'04]. Interestingly, while in undirected planar graphs both min-cut and min $st$-cut have $O(n \log \log n)$ solutions [ESA'11, STOC'11]...

We consider distance queries in vertex labeled planar graphs. For any fixed \(0 < \epsilon \le 1/2\) we show how to preprocess an undirected planar graph with vertex labels and edge lengths to answer queries of the following form. Given a vertex u and a label \(\lambda \) return a \((1+\epsilon )\)-approximation of the distance between u and its cl...

Given an undirected graph with edge costs and node weights, the minimum bisection problem asks for a partition of the nodes into two parts of equal weight such that the sum of edge costs between the parts is minimized. We give a polynomial time bicriteria approximation scheme for bisection on planar graphs. Specifically, let $W$ be the total weight...

We consider distance queries in vertex-labeled planar graphs. For any fixed $0 < \epsilon \leq 1/2$ we show how to preprocess a directed planar graph with vertex labels and arc lengths into a data structure that answers queries of the following form. Given a vertex $u$ and a label $\lambda$ return a $(1+\epsilon)$-approximation of the distance from...

We present an optimal data structure for submatrix maximum queries in n x n Monge matrices. Our result is a two-way reduction showing that the problem is equivalent to the classical predecessor problem. This gives a data structure of O(n) space that answers submatrix maximum queries in O(loglogn) time. It also gives a matching lower bound, showing...

We show how to combine two techniques for efficiently computing shortest paths in directed planar graphs. The first is the linear-time shortest-path algorithm of Henzinger, Klein, Subramanian, and Rao [STOC'94]. The second is Fakcharoenphol and Rao's algorithm [FOCS'01] for emulating Dijkstra's algorithm on the dense distance graph (DDG). A DDG is...

We provide an implementation of an algorithm that, given a triangulated planar graph with m edges, returns a simple cycle that is a 2/3-balanced separator consisting of at most √8m edges. An efficient construction of a short and balanced separator that forms a simple cycle is essential in numerous planar graph algorithms, e.g., for computing shorte...

We describe a data structure for submatrix maximum queries in Monge matrices or Monge partial matrices, where a query specifies a contiguous submatrix of the given matrix, and its output is the maximum element of that submatrix. Our data structure for an n x n Monge matrix takes O(n log n) space, O(n log2n) preprocessing time, and can answer querie...

We develop a new technique for computing maximum flow in directed planar graphs with multiple sources and a single sink that significantly deviates from previously known techniques for flow problems. This gives rise to an O(diameter*n*log(n)) algorithm for the problem.

We give an $O(n^{1.5} \log n)$ algorithm that, given a directed planar graph with arc capacities, a set of source nodes and a set of sink nodes, finds a maximum flow from the sources to the sinks. Comment: to be merged with 1) Yahav Nussbaum 1012.4767 2) Philip N. Klein and Shay Mozes 1008.5332 3) Glencora Borradaile and Christian Wulff-Nilsen 1008...

We present new and improved data structures that answer exact node-to-node distance queries in planar graphs. Such data structures are also known as distance oracles. For any directed planar graph on n nodes with non-negative lengths we obtain the following: * Given a desired space allocation $S\in[n\lg\lg n,n^2]$, we show how to construct in $\til...

We consider the train delivery problem which is a generalization of the bin packing problem and is equivalent to a one dimensional version of the vehicle routing problem with unsplittable demands. The problem is also equivalent to the problem of minimizing the makespan on a single batch machine with non-identical job sizes. The train delivery probl...

Given an n-vertex planar directed graph with real edge lengths and with no negative cycles, we show how to compute single-source shortest path distances in the graph in O(nlog 2 n/loglogn) time with O(n) space. This improves on a recent O(nlog 2 n) time bound by P. N. Klein et al. [“Shortest paths in directed planar graphs with negative lengths: a...

We give an $O(n^{1.5} \log n)$ algorithm that, given a directed planar graph with arc capacities, a set of source nodes and a single sink node, finds a maximum flow from the sources to the sink . This is the first subquadratic-time strongly polynomial algorithm for the problem. Comment: 13 pages, 2 figures. Corrected spelling in one citation

Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics comprised of multiple duplicated fragments. This complex genomic organization complicates analysis of the evolutionary history of these sequences. One model proposed to explain this mosaic patterns is a model of...

Given an $n$-vertex planar directed graph with real edge lengths and with no negative cycles, we show how to compute single-source shortest path distances in the graph in $O(n\log^2n/\log\log n)$ time with O(n) space. This is an improvement of a recent time bound of $O(n\log^2n)$ by Klein et al.

The LCS of two rooted, ordered, and labeled trees F and G is the largest forest that can be obtained from both trees by deleting nodes. We present algorithms for computing tree LCS which exploit the sparsity inherent to the tree LCS problem. Assuming G is smaller than F, our first algorithm runs in time , where r is the number of pairs (v∈F,w∈G) su...

Segmental duplications, or low-copy repeats, are common in mammalian genomes. In the human genome, most segmental duplications are mosaics consisting of pieces of multiple other segmental duplications. This complex genomic organization complicates analysis of the evolutionary history of these sequences. Earlier, we introduced a genomic distance, ca...

We present a method to speed up the dynamic program algorithms used for solving the HMM decoding and training problems for discrete time-independent HMMs. We discuss the application of our method to Viterbi’s decoding and training algorithms (IEEE Trans. Inform. Theory IT-13:260–269, 1967), as well as to the forward-backward and Baum-Welch (Inequal...

We give an O(n log2 n)-time, linear-space algorithm that, given a directed planar graph with positive and negative arc-lengths, and given a node s, finds the distances from s to all nodes.

The edit distance between two ordered rooted trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this paper, we present a worst-case O(n 3)-time algorithm for this problem, improving the pr...

We give an O(n log2 n)-time, linear-space algorithm that, given a directed planar graph with positive and negative arc-lengths, and given a node s, finds the distances from s to all nodes. The best previ- ously known algorithm requires O(n log3 n )t ime and

The LCS of two rooted, ordered, and labeled trees F and G is the largest forest that can be obtained from both trees by deleting nodes. We present algorithms for computing tree LCS which exploit the sparsity inherent to the tree LCS problem. Assuming G is smaller than F, our first algorithm runs in time O(rheight(F) height(G)lglg|G|)O(r\cdot {\rm...

We address the extension of the binary search technique from sorted arrays and totally ordered sets to trees and tree-like partially ordered sets. As in the sorted array case, the goal is to minimize the number of queries required to flnd a target element in the worst case. However, while the optimal strategy for searching an array is straightforwa...

The edit distance between two ordered rooted trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this article, we present a worst-case O(n3)-time algorithm for the problem when the two tree...

We present a new way of encoding a quantum computation into a 3-local Hamiltonian. Our construction is novel in that it does not include any terms that induce legal-illegal clock transitions. Therefore, the weights of the terms in the Hamiltonian do not scale with the size of the problem as in previous constructions. This improves the construction...

The {\em edit distance} between two ordered trees with vertex labels is the minimum cost of transforming one tree into the other by a sequence of elementary operations consisting of deleting and relabeling existing nodes, as well as inserting new nodes. In this paper, we present a worst-case $O(n^3)$-time algorithm for this problem, improving the p...

The utilization of a d-level partially entangled state, shared by two parties wishing to communicate classical information without errors over a noiseless quantum channel, is discussed. We analytically construct deterministic dense coding schemes for certain classes of nonmaximally entangled states, and numerically obtain schemes in the general cas...

The utilization of a $d$-level partially entangled state, shared by two parties wishing to communicate classical information without errors over a noiseless quantum channel, is discussed. We analytically construct deterministic dense coding schemes for certain classes of non-maximally entangled states, and numerically obtain schemes in the general...

The effect of unitary noise on the performance of Grover’s quantum search algorithm is studied. This type of noise may result from tiny fluctuations and drift in the parameters of the (quantum) components performing the computation. The resulting operations are still unitary, but not precisely those assumed in the design of the algorithm. Here we f...

This report describes parallel Java implementations of several variants of Viterbi's algorithm, discussed in my recent paper [1]. The aim of this project is to study the issues that arise when trying to implement the approach of [1] in parallel using Java. I compare and discuss the performance of several variants under various circumstances.

Abstract In this report I describe my results on the Tree Edit Distance problem [13, 27]. The edit distance between two ordered rooted trees with vertex labels is the minimum,cost of trans- forming one tree into the other by a sequence of elementary operations consisting of delet- ing and relabeling existing nodes, as well as inserting new nodes. T...