Algorithms for Discrepancy, Matchings, and Approximations: Fast, Simple, and Practical
Université Paris Cité（巴黎西岱大学）；IRIF（法国信息与自动化研究所（IRIF））；CNRS（法国国家科学研究中心）；DI ENS, Université PSL（巴黎文理研究大学信息学系）；Université Sorbonne Paris Nord（巴黎索邦北大学）；Laboratoire LIPN（LIPN实验室）
We study one of the key tools in data approximation and optimization: low-discrepancy colorings. Formally, given a finite set system $(X,\mathcal S)$, the \emph{discrepancy} of a two-coloring $χ:X\to\{-1,1\}$ is defined as $\max_{S \in \mathcal S}|{χ(S)}|$, where $χ(S)=\sum\limits_{x \in S}χ(x)$.
We propose a randomized algorithm which, for any $d>0$ and $(X,\mathcal S)$ with dual shatter function $π^*(k)=O(k^d)$, returns a coloring with expected discrepancy $O\left({\sqrt{|X|^{1-1/d}\log|\mathcal S|}}\right)$ (this bound is tight) in time $\tilde O\left({|\mathcal S|\cdot|X|^{1/d}+|X|^{2+1/d}}\right)$, improving upon the previous-best time of $O\left(|\mathcal S|\cdot|X|^3\right)$ by at least a factor of $|X|^{2-1/d}$ when $|\mathcal S|\geq|X|$. This setup includes many geometric classes, families of bounded dual VC-dimension, and others. As an immediate consequence, we obtain an improved algorithm to construct $\varepsilon$-approximations of sub-quadratic size.
Our method uses primal-dual reweighing with an improved analysis of randomly updated weights and exploits the structural properties of the set system via matchings with low crossing number -- a fundamental structure in computational geometry. In particular, we get the same $|X|^{2-1/d}$ factor speed-up on the construction time of matchings with crossing number $O\left({|X|^{1-1/d}}\right)$, which is the first improvement since the 1980s.
The proposed algorithms are very simple, which makes it possible, for the first time, to compute colorings with near-optimal discrepancies and near-optimal sized approximations for abstract and geometric set systems in dimensions higher than $2$.
Efficiently computing low discrepancy colorings of various set systems, has been studied extensively since the breakthrough work by Bansal (FOCS 2010), who gave the first polynomial time algorithms for several important settings, including for general set systems, sparse set systems and for set systems with bounded hereditary discrepancy. The hereditary discrepancy of a set system, is the maximum discrepancy over all set systems obtainable by deleting a subset of the ground elements. While being polynomial time, Bansal's algorithms were not practical, with e.g. his algorithm for the hereditary…
We consider the problem of finding a low discrepancy coloring for sparse set systems where each element lies in at most t sets. We give an efficient algorithm that finds a coloring with discrepancy O((t log n)^{1/2}), matching the best known non-constructive bound for the problem due to Banaszczyk. The previous algorithms only achieved an O(t^{1/2} log n) bound. The result also extends to the more general Komlós setting and gives an algorithmic O(log^{1/2} n) bound.
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-…
Given a text $T$ and a pattern $P$, the order-preserving matching problem is to find all substrings in $T$ which have the same relative orders as $P$. Order-preserving matching has been an active research area since it was introduced by Kubica et al. \cite{kubica2013linear} and Kim et al. \cite{kim2014order}. In this paper we present two algorithms for the multiple order-preserving matching problem, one of which runs in sublinear time on average and the other in linear time on average. Both algorithms run much faster than the previous algorithms.
We present a new algorithm which detects the maximal possible number of matched disjoint pairs satisfying a given caliper when a bipartite matching is done with respect to a scalar index (e.g., propensity score), and constructs a corresponding matching. Variable width calipers are compatible with the technique, provided that the width of the caliper is a Lipschitz function of the index. If the observations are ordered with respect to the index then the matching needs $O(N)$ operations, where $N$ is the total number of subjects to be matched. The case of 1-to-$n$ matching is also considered. We…
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 so…
Many modern sequence alignment tools implement fast string matching using the space efficient data structure called FM-index. The succinct nature of this data structure presents unique challenges for the algorithm designers. In this paper, we explore the opportunities for parallelization of the exact and inexact matches and present an efficient SIMD solution for the Occ portion of the algorithm. Our implementation computes all eight Occ values required for the inexact match algorithm step in a single pass. We showcase the algorithm performance in a multi-core genome aligner and discuss effects…
The Permutation Pattern Matching problem asks, given two permutations $σ$ on $n$ elements and $π$, whether $σ$ admits a subsequence with the same relative order as $π$ (or, in the counting version, how many such subsequences are there). This natural problem was shown by Bose, Buss and Lubiw [IPL 1998] to be NP-complete, and hence we should seek exact exponential time solutions. The asymptotically fastest such solution up to date, by Berendsohn, Kozma and Marx [IPEC 2019], works in $\mathcal{O}(1.6181^n)$ time. We design a simple and faster $\mathcal{O}(1.415^{n})$ time algorithm for both the d…
Reconfigurable optical topologies promise to improve the performance in datacenters by dynamically optimizing the physical network in a demand-aware manner. State-of-the-art optical technologies allow to establish and update direct connectivity (in the form of edge-disjoint matchings) between top-of-rack switches within microseconds or less. However, to fully exploit temporal structure in the demand, such fine-grained reconfigurations also require fast algorithms for optimizing the interconnecting matchings. Motivated by the desire to offload a maximum amount of demand to the reconfigurable ne…
Graphs are widely used to model complicated data semantics in many application domains. In this paper, two novel and efficient algorithms Fast-ON and Fast-P are proposed for solving the subgraph isomorphism problem. The two algorithms are based on Ullman algorithm [Ullmann 1976], apply vertex-at-a-time matching manner and path-at-a-time matching manner respectively, and use effective heuristics to cut the search space. Comparing to the well-known algorithms, Fast-ON and Fast-P achieve up to 1-4 orders of magnitude speed-up for both dense and sparse graph data.
Fast Approximation Algorithms for Euclidean Minimum Weight Perfect Matching
Research Institute for Discrete Mathematics and Hausdorff Center for Mathematics, University of Bonn（波恩大学离散数学研究所与豪斯多夫数学中心）；Hamburg University of Technology, Institute for Algorithms and Complexity（汉堡工业大学算法与复杂性研究所）
Exact substring matching is a common task in many software applications. Despite the existence of several algorithms for finding whether or not a pattern string is present in a target string, the most common implementation is a naïve, brute force approach. Alternative approaches either do not provide enough of a benefit for the added complexity, or are impractical for modern character sets, e.g., Unicode. We present a new algorithm, Scout, that is straightforward, quick and appropriate for all applications. We also compare the performance characteristics of the Scout algorithm with several oth…
The degree splitting problem requires coloring the edges of a graph red or blue such that each node has almost the same number of edges in each color, up to a small additive discrepancy. The directed variant of the problem requires orienting the edges such that each node has almost the same number of incoming and outgoing edges, again up to a small additive discrepancy. We present deterministic distributed algorithms for both variants, which improve on their counterparts presented by Ghaffari and Su [SODA'17]: our algorithms are significantly simpler and faster, and have a much smaller discrep…
The Exact Circular Pattern Matching (ECPM) problem consists of reporting every occurrence of a rotation of a pattern $P$ in a text $T$. In many real-world applications, specifically in computational biology, circular rotations are of interest because of their prominence in virus DNA. Thus, given no restrictions on pre-processing time, how quickly all such circular rotation occurrences is of interest to many areas of study. We highlight, to the best of our knowledge, a novel approach to the ECPM problem and present four data structures that accompany this approach, each with their own time-spac…
The $d$-dimensional pattern matching problem is to find an occurrence of a pattern of length $m \times \dots \times m$ within a text of length $n \times \dots \times n$, with $n \ge m$. This task models various problems in text and image processing, among other application areas. This work describes a quantum algorithm which solves the pattern matching problem for random patterns and texts in time $\widetilde{O}((n/m)^{d/2} 2^{O(d^{3/2}\sqrt{\log m})})$. For large $m$ this is super-polynomially faster than the best possible classical algorithm, which requires time $\widetildeΩ( (n/m)^d + n^{d/…
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…
Finding optimal matchings in dense graphs is of general interest and of particular importance in social, transportation and biological networks. While developing optimal solutions for various matching problems is important, the running times of the fastest available optimal matching algorithms are too costly. However, when the vertices of the graphs are point-sets in $R^d$ and edge weights correspond to the euclidean distances, the available optimal matching algorithms are substantially faster. In this paper, we propose a novel network embedding based heuristic algorithm to solve various match…
Given a text $T$ of length $n$ and a pattern $P$ of length $m$, the string matching problem is a task to find all occurrences of $P$ in $T$. In this study, we propose an algorithm that solves this problem in $O((n + m)q)$ time considering the distance between two adjacent occurrences of the same $q$-gram contained in $P$. We also propose a theoretical improvement of it which runs in $O(n + m)$ time, though it is not necessarily faster in practice. We compare the execution times of our and existing algorithms on various kinds of real and artificial datasets such as an English text, a genome seq…
String matching is the problem of finding all the occurrences of a pattern in a text. We propose improved versions of the fast family of string matching algorithms based on hashing $q$-grams. The improvement consists of considering minimal values $q$ such that each $q$-grams of the pattern has a unique hash value. The new algorithms are fastest than algorithm of the HASH family for short patterns on large size alphabets.
A family of comparison-based exact pattern matching algorithms is described. They utilize multi-dimensional arrays in order to process more than one adjacent text window in each iteration of the search cycle. This approach leads to a lower average time complexity by the cost of space. The algorithms of this family perform well for short patterns and middle size alphabets. In such case the shift of the window by several pattern lengths at once is quite probable, which is the main factor of algorithm success. Our algorithms outperform the Boyer-Moore-Horspool algorithm, either in the original ve…
We aim to speed up approximate keyword matching by storing a lightweight, fixed-size block of data for each string, called a fingerprint. These work in a similar way to hash values; however, they can be also used for matching with errors. They store information regarding symbol occurrences using individual bits, and they can be compared against each other with a constant number of bitwise operations. In this way, certain strings can be deduced to be at least within the distance $k$ from each other (using Hamming or Levenshtein distance) without performing an explicit verification. We show expe…
Given a pattern $w$ and a text $t$, the speed of a pattern matching algorithm over $t$ with regard to $w$, is the ratio of the length of $t$ to the number of text accesses performed to search $w$ into $t$. We first propose a general method for computing the limit of the expected speed of pattern matching algorithms, with regard to $w$, over iid texts. Next, we show how to determine the greatest speed which can be achieved among a large class of algorithms, altogether with an algorithm running this speed. Since the complexity of this determination make it impossible to deal with patterns of len…
Institute of Information Science, Academia Sinica（中央研究院信息科学研究所）；National Taiwan University（台湾大学）
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined with pruning strategy. However, the computation cost of those methods is easily dominated by the size of signal N instead of that of template K. This paper proposes a probabilistic and fast matching scheme, which computation costs requires O(N) additions and O(K \log K) multiplications, based on cross-correlation. The nuclear idea is to first downsample signa…
Given a pattern string $P$ of length $n$ and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet of size $Δ$, the {\em exact string matching} problem consists of finding all occurrences of $P$ in $T$. For this problem, we present algorithms that in $O(nΔ^2)$ time pre-process $P$ to essentially identify $sparse(P)$, a rarely occurring substring of $P$, and then use it to find occurrences of $P$ in $T$ efficiently. Our algorithms require a worst case search time of $O(m)$, and expected search time of $O(m/min(|sparse(P)|, Δ))$, where $|sparse(P)|$ is …
We solve the Bin Packing problem in $O^*(2^k)$ time, where $k$ is the number of items less or equal to one third of the bin capacity. This parameter measures the distance from the polynomially solvable case of only large (i.e., greater than one third) items. Our algorithm is actually designed to work for a more general Vector Bin Packing problem, in which items are multidimensional vectors. We improve over the previous fastest $O^*(k! \cdot 4^k)$ time algorithm. Our algorithm works by reducing the problem to finding an exact weight perfect matching in a (multi-)graph with $O^*(2^k)$ edges, who…
Given a pattern string $P$ of length $n$ consisting of $δ$ distinct characters and a query string $T$ of length $m$, where the characters of $P$ and $T$ are drawn from an alphabet $Σ$ of size $Δ$, the {\em exact string matching} problem consists of finding all occurrences of $P$ in $T$. For this problem, we present a randomized heuristic that in $O(nδ)$ time preprocesses $P$ to identify $sparse(P)$, a rarely occurring substring of $P$, and then use it to find all occurrences of $P$ in $T$ efficiently. This heuristic has an expected search time of $O( \frac{m}{min(|sparse(P)|, Δ)})$, where $|sp…
We describe indexes for searching large data sets for variable-length-gapped (VLG) patterns. VLG patterns are composed of two or more subpatterns, between each adjacent pair of which is a gap-constraint specifying upper and lower bounds on the distance allowed between subpatterns. VLG patterns have numerous applications in computational biology (motif search), information retrieval (e.g., for language models, snippet generation, machine translation) and capture a useful subclass of the regular expressions commonly used in practice for searching source code. Our best approach provides search sp…
Gale and Shapley's stable assignment problem has been extensively studied, applied, and extended. In the context of school choice, mechanisms often aim at finding an assignment that is more favorable to students. We investigate two extensions introduced in this framework -- legal assignments and the EADAM algorithm -- through the lens of classical theory of stable matchings. In any instance, the set ${\cal L}$ of legal assignments is known to contain all stable assignments. We prove that ${\cal L}$ is exactly the set of stable assignments in another instance. Moreover, we show that essentially…
Quadratic assignment problems (QAPs) arise in a wide variety of domains, ranging from operations research to graph theory to computer vision to neuroscience. In the age of big data, graph valued data is becoming more prominent, and with it, a desire to run algorithms on ever larger graphs. Because QAP is NP-hard, exact algorithms are intractable. Approximate algorithms necessarily employ an accuracy/efficiency trade-off. We developed a fast approximate quadratic assignment algorithm (FAQ). FAQ finds a local optima in (worst case) time cubic in the number of vertices, similar to other approxima…
