Cartesian tree matching is the problem of finding all substrings of a given text which have the same Cartesian trees as that of a given pattern. So far there is one linear-time solution for Cartesian tree matching, which is based on the KMP algorithm. We improve the running time of the previous solution by introducing new representations. We present the framework of a binary filtration method and an efficient verification technique for Cartesian tree matching. Any exact string matching algorithm can be used as a filtration for Cartesian tree matching on our framework. We also present a SIMD solution for Cartesian tree matching suitable for short patterns. By experiments we show that known string matching algorithms combined on our framework of binary filtration and efficient verification produce algorithms of good performances for Cartesian tree matching.
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a pattern of length m, and multiple pattern matching for a text of length n and k patterns of total length m. We present an O(n+m) time algorithm for single pattern matching, and an O((n+m) log k) deterministic time or O(n+m) randomized time algorithm for multiple pattern matching. We also define an index data structure called Cartesian suffix tree, and present…
Cartesian tree matching is the problem of finding all substrings in a given text which have the same Cartesian trees as that of a given pattern. In this paper, we deal with Cartesian tree matching for the case of multiple patterns. We present two fingerprinting methods, i.e., the parent-distance encoding and the binary encoding. By combining an efficient fingerprinting method and a conventional multiple string matching algorithm, we can efficiently solve multiple pattern Cartesian tree matching. We propose three practical algorithms for multiple pattern Cartesian tree matching based on the Wu-…
Park et al. [TCS 2020] observed that the similarity between two (numerical) strings can be captured by the Cartesian trees: The Cartesian tree of a string is a binary tree recursively constructed by picking up the smallest value of the string as the root of the tree. Two strings of equal length are said to Cartesian-tree match if their Cartesian trees are isomorphic. Park et al. [TCS 2020] introduced the following Cartesian tree substring matching (CTMStr) problem: Given a text string $T$ of length $n$ and a pattern string of length $m$, find every consecutive substring $S = T[i..j]$ of a text…
The Cartesian-tree pattern matching is a recently introduced scheme of pattern matching that detects fragments in a sequential data stream which have a similar structure as a query pattern. Formally, Cartesian-tree pattern matching seeks all substrings $S'$ of the text string $S$ such that the Cartesian tree of $S'$ and that of a query pattern $P$ coincide. In this paper, we present a new indexing structure for this problem called the Cartesian-tree Position Heap (CPH). Let $n$ be the length of the input text string $S$, $m$ the length of a query pattern $P$, and $σ$ the alphabet size. We show…
The article describes the structural and algorithmic relations between Cartesian trees and Lyndon Trees. This leads to a uniform presentation of the Lyndon table of a word corresponding to the Next Nearest Smaller table of a sequence of numbers. It shows how to efficiently compute runs, that is, maximal periodicities occurring in a word.
Selection on the Cartesian product is a classic problem in computer science. Recently, an optimal algorithm for selection on $X+Y$, based on soft heaps, was introduced. By combining this approach with layer-ordered heaps (LOHs), an algorithm using a balanced binary tree of $X+Y$ selections was proposed to perform $k$-selection on $X_1+X_2+\cdots+X_m$ in $o(n\cdot m + k\cdot m)$, where $X_i$ have length $n$. Here, that $o(n\cdot m + k\cdot m)$ algorithm is combined with a novel, optimal LOH-based algorithm for selection on $X+Y$ (without a soft heap). Performance of algorithms for selection on …
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
In this paper, we have developed a fully-dynamic algorithm for maintaining cardinality of maximum-matching in a tree using the construction of top-trees. The time complexities are as follows: 1. Initialization Time: $O(n(log(n)))$ to build the Top-tree. 2. Update Time: $O(log(n))$ 3. Query Time: O(1) to query the cardinality of maximum-matching and $O(log(n))$ to find if a particular edge is matched.
We show that there exist linear-time algorithms that compute the strong chromatic index and a maximum induced matching of tree-cographs when the decomposition tree is a part of the input. We also show that there exists an efficient algorithm for the strong chromatic index of permutation graphs.
Error Tree is a novel tree structure that is mainly oriented to solve the approximate pattern matching problems, Hamming and edit distances, as well as the wildcards matching problem. The input is a text of length $n$ over a fixed alphabet of length $Σ$, a pattern of length $m$, and $k$. The output is to find all positions that have $\leq$ $k$ Hamming distance, edit distance, or wildcards matching with $P$. The algorithm proposes for Hamming distance and wildcards matching a tree structure that needs $O(n\frac{log_Σ^{k}n}{k!})$ words and takes $O(\frac {m^k}{k!} + occ$)($O(m + \frac {log_Σ^kn}…
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 vertex-labeled trees and graphs by replacing "substring" with "connected subgraph". In this paper, we give an $O(n^2 / \log^2 n)$-time solution for trees, matching the currently best bound for (the simpler problem of) strings. We also give an $\Oh{g^{2 / 3} n^{4 / 3}/(\log n)^{4/3}}$-time solution for strings that are compressed by a grammar of size $g$. This solution im…
We consider how to index strings, trees and graphs for jumbled pattern matching when we are asked to return a match if one exists. For example, we show how, given a tree containing two colours, we can build a quadratic-space index with which we can find a match in time proportional to the size of the match. We also show how we need only linear space if we are content with approximate matches.
Given two rooted, labeled trees $P$ and $T$ the tree path subsequence problem is to determine which paths in $P$ are subsequences of which paths in $T$. Here a path begins at the root and ends at a leaf. In this paper we propose this problem as a useful query primitive for XML data, and provide new algorithms improving the previously best known time and space bounds.
We prove that given a discrete space with $n$ points which is either embedded in a system of $k$ trees, or the Cartesian product of $k$ trees, we can compute all eccentricities in ${\cal O}(2^{{\cal O}(k\log{k})}(N+n)^{1+o(1)})$ time, where $N$ is the cumulative total order over all these $k$ trees. This is near optimal under the Strong Exponential-Time Hypothesis, even in the very special case of an $n$-vertex graph embedded in a system of $ω(\log{n})$ spanning trees. However, given such an embedding in the strong product of $k$ trees, there is a much faster ${\cal O}(N + kn)$-time algorithm …
On-demand peer-to-peer ride-sharing services provide flexible mobility options, and are expected to alleviate congestion by sharing empty car seats. An efficient matching algorithm is essential to the success of a ride-sharing system. The matching problem is related to the well-known dial-a-ride problem, which also tries to find the optimal pickup and delivery sequence for a given set of passengers. In this paper, we propose an efficient dynamic tree algorithm to solve the on-demand peer-to-peer ride-sharing matching problem. The dynamic tree algorithm benefits from given ride-sharing driver s…
The order preserving pattern matching (OPPM) problem is, given a pattern string $p$ and a text string $t$, find all substrings of $t$ which have the same relative orders as $p$. In this paper, we consider two variants of the OPPM problem where a set of text strings is given as a tree or a DAG. We show that the OPPM problem for a single pattern $p$ of length $m$ and a text tree $T$ of size $N$ can be solved in $O(m+N)$ time if the characters of $p$ are drawn from an integer alphabet of polynomial size. The time complexity becomes $O(m \log m + N)$ if the pattern $p$ is over a general ordered al…
Packing several characters into one computer word is a simple and natural way to compress the representation of a string and to speed up its processing. Exploiting this idea, we propose an index for a packed string, based on a {\em sparse suffix tree} \cite{KU-96} with appropriately defined suffix links. Assuming, under the standard unit-cost RAM model, that a word can store up to $\log_σn$ characters ($σ$ the alphabet size), our index takes $O(n/\log_σn)$ space, i.e. the same space as the packed string itself. The resulting pattern matching algorithm runs in time $O(m+r^2+r\cdot occ)$, where …
We study the Maximum Cardinality Matching (MCM) and the Maximum Weight Matching (MWM) problems, on trees and on some special classes of graphs, in the Online Preemptive and the Incremental Dynamic Graph models. In the {\em Online Preemptive} model, the edges of a graph are revealed one by one and the algorithm is required to always maintain a valid matching. On seeing an edge, the algorithm has to either accept or reject the edge. If accepted, then the adjacent edges are discarded, and all rejections are permanent. In this model, the complexity of the problems is settled for deterministic algo…
We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $σ$, our algorithm uses $O(n+\frac{nσ}{w})$ space and $O(n+\frac{nσ}{w}+m\log N\log w\cdot occ)$ or $O(n+\frac{nσ}{w}\log w+m\log N\cdot occ)$ time. Here $w$ is the word size and $occ$ is the number of occurrences of the pattern. Our algorithm uses less space than previous algorithms and is also faster for $occ=o(\frac{n}{\log N})$ occurrences. The algorithm uses a new data structure that allows…
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 algorithm allows the input trees to be mixed trees, i.e., trees that may contain directed and undirected edges at the same time. Our algorithm adopts a recursive strategy exploiting a technique called label compression. The backbone of this technique is an algorithm that computes the maximum weight matchings over many subgraphs of a bipartite graph as fast as it tak…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two special kinds, namely, uniformly labeled trees (i.e., trees with all their nodes labeled by the same symbol) and evolutionary trees (i.e., leaf-labeled trees with distinct symbols for distinct leaves). This paper presents an algorithm for comparing trees that are labeled in an arbitrary manner. In addition to this generality, this algorithm is faster than the pr…
Motivated by recent developments in optical switching and reconfigurable network design, we study dynamic binary search trees (BSTs) in the matching model. In the classical dynamic BST model, the cost of both link traversal and basic reconfiguration (rotation) is $O(1)$. However, in the matching model, the BST is defined by two optical switches (that represent two matchings in an abstract way), and each switch (or matching) reconfiguration cost is $α$ while a link traversal cost is still $O(1)$. In this work, we propose Arithmetic BST (A-BST), a simple dynamic BST algorithm that is based on dy…
We present $O(\log\log n)$ round scalable Massively Parallel Computation algorithms for maximal independent set and maximal matching, in trees and more generally graphs of bounded arboricity, as well as for constant coloring trees. Following the standards, by a scalable MPC algorithm, we mean that these algorithms can work on machines that have capacity/memory as small as $n^δ$ for any positive constant $δ<1$. Our results improve over the $O(\log^2\log n)$ round algorithms of Behnezhad et al. [PODC'19]. Moreover, our matching algorithm is presumably optimal as its bound matches an $Ω(\log\log …
In this paper we consider alignment of sparse graphs, for which we introduce the Neighborhood Tree Matching Algorithm (NTMA). For correlated Erdős-Rényi random graphs, we prove that the algorithm returns -- in polynomial time -- a positive fraction of correctly matched vertices, and a vanishing fraction of mismatches. This result holds with average degree of the graphs in $O(1)$ and correlation parameter $s$ that can be bounded away from 1, conditions under which random graph alignment is particularly challenging. As a byproduct of the analysis we introduce a matching metric between trees and …
Bytewise approximate matching algorithms have in recent years shown significant promise in de- tecting files that are similar at the byte level. This is very useful for digital forensic investigators, who are regularly faced with the problem of searching through a seized device for pertinent data. A common scenario is where an investigator is in possession of a collection of "known-illegal" files (e.g. a collection of child abuse material) and wishes to find whether copies of these are stored on the seized device. Approximate matching addresses shortcomings in traditional hashing, which can on…
In this paper, a contrastive evaluation of massively parallel implementations of suffix tree and suffix array to accelerate genome sequence matching are proposed based on Intel Core i7 3770K quad-core and NVIDIA GeForce GTX680 GPU. Besides suffix array only held approximately 20%~30% of the space relative to suffix tree, the coalesced binary search and tile optimization make suffix array clearly outperform suffix tree using GPU. Consequently, the experimental results show that multiple genome sequence matching based on suffix array is more than 99 times speedup than that of CPU serial implemen…
String matching is one of the most fundamental problems in computer science. A natural problem is to determine the number of characters that need to be queried (i.e. the decision tree complexity) in a string in order to decide whether this string contains a certain pattern. Rivest showed that for every pattern $p$, in the worst case any deterministic algorithm needs to query at least $n-|p|+1$ characters, where $n$ is the length of the string and $|p|$ is the length of the pattern. He further conjectured that this bound is tight. By using the adversary method, Tuza disproved this conjecture an…
We propose an efficient algorithm for graph matching based on similarity scores constructed from counting a certain family of weighted trees rooted at each vertex. For two Erdős-Rényi graphs $\mathcal{G}(n,q)$ whose edges are correlated through a latent vertex correspondence, we show that this algorithm correctly matches all but a vanishing fraction of the vertices with high probability, provided that $nq\to\infty$ and the edge correlation coefficient $ρ$ satisfies $ρ^2>α\approx 0.338$, where $α$ is Otter's tree-counting constant. Moreover, this almost exact matching can be made exact under an…
