We revisit the task of computing the edit distance in sublinear time. In the $(k,K)$-gap edit distance problem the task is to distinguish whether the edit distance of two strings is at most $k$ or at least $K$. It has been established by Goldenberg, Krauthgamer and Saha (FOCS '19), with improvements by Kociumaka and Saha (FOCS '20), that the $(k,k^2)$-gap problem can be solved in time $\widetilde O(n/k+\operatorname{poly}(k))$. One of the most natural questions in this line of research is whether the $(k,k^2)$-gap is best-possible for the running time $\widetilde O(n/k+\operatorname{poly}(k))$.
In this work we answer this question by significantly improving the gap. Specifically, we show that in time $O(n/k+\operatorname{poly}(k))$ we can even solve the $(k,k^{1+o(1)})$-gap problem. This is the first algorithm that breaks the $(k,k^2)$-gap in this running time. Our algorithm is almost optimal in the following sense: In the low distance regime ($k\le n^{0.19}$) our running time becomes $O(n/k)$, which matches a known $n/k^{1+o(1)}$ lower bound for the $(k,k^{1+o(1)})$-gap problem up to lower order factors.
Our result also reveals a surprising similarity of Hamming distance and edit distance in the low distance regime: For both, the $(k,k^{1+o(1)})$-gap problem has time complexity $n/k^{1\pm o(1)}$ for small $k$.
In contrast to previous work, which employed a subsampled variant of the Landau-Vishkin algorithm, we instead build upon the algorithm of Andoni, Krauthgamer and Onak (FOCS '10). We first simplify their approach and then show how to to effectively prune their computation tree in order to obtain a sublinear-time algorithm in the given time bound. Towards that, we use a variety of structural insights on the (local and global) patterns that can emerge during this process and design appropriate property testers to effectively detect these patterns.
We study the problem of approximating the edit distance of two strings in sublinear time, in a setting where one or both string(s) are preprocessed, as initiated by Goldenberg, Rubinstein, Saha (STOC '20). Specifically, in the $(k, K)$-gap edit distance problem, the goal is to distinguish whether the edit distance of two strings is at most $k$ or at least $K$. We obtain the following results: * After preprocessing one string in time $n^{1+o(1)}$, we can solve $(k, k \cdot n^{o(1)})$-gap edit distance in time $(n/k + k) \cdot n^{o(1)}$. * After preprocessing both strings separately in time $n^{…
In this paper, we design new sublinear-time algorithms for solving the gap edit distance problem and for embedding edit distance to Hamming distance. For the gap edit distance problem, we give an $\tilde{O}(\frac{n}{k}+k^2)$-time greedy algorithm that distinguishes between length-$n$ input strings with edit distance at most $k$ and those with edit distance exceeding $(3k+5)k$. This is an improvement and a simplification upon the result of Goldenberg, Krauthgamer, and Saha [FOCS 2019], where the $k$ vs $Θ(k^2)$ gap edit distance problem is solved in $\tilde{O}(\frac{n}{k}+k^3)$ time. We further…
We study the problem of estimating the edit distance between two $n$-character strings. While exact computation in the worst case is believed to require near-quadratic time, previous work showed that in certain regimes it is possible to solve the following {\em gap edit distance} problem in sub-linear time: distinguish between inputs of distance $\le k$ and $>k^2$. Our main result is a very simple algorithm for this benchmark that runs in time $\tilde O(n/\sqrt{k})$, and in particular settles the open problem of obtaining a truly sublinear time for the entire range of relevant $k$. Building on…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. A simple dynamic programming computes the edit distance between two strings of length $n$ in $O(n^2)$ time, and a more sophisticated algorithm runs in time $O(n+t^2)$ when the edit distance is $t$ [Landau, Myers and Schmidt, SICOMP 1998]. In pursuit of obtaining faster running time, the last couple of decades have seen a flurry of research on approximating edit distance, includi…
We present an algorithm for approximating semidefinite programs with running time that is sublinear in the number of entries in the semidefinite instance. We also present lower bounds that show our algorithm to have a nearly optimal running time.
We study the problem of approximating edit distance in sublinear time. This is formalized as the $(k,k^c)$-Gap Edit Distance problem, where the input is a pair of strings $X,Y$ and parameters $k,c>1$, and the goal is to return YES if $ED(X,Y)\leq k$, NO if $ED(X,Y)> k^c$, and an arbitrary answer when $k < ED(X,Y) \le k^c$. Recent years have witnessed significant interest in designing sublinear-time algorithms for Gap Edit Distance. In this work, we resolve the non-adaptive query complexity of Gap Edit Distance for the entire range of parameters, improving over a sequence of previous results. S…
In this work, we consider the problem of sampling a $k$-clique in a graph from an almost uniform distribution in sublinear time in the general graph query model. Specifically the algorithm should output each $k$-clique with probability $(1\pm ε)/n_k$, where $n_k$ denotes the number of $k$-cliques in the graph and $ε$ is a given approximation parameter. We prove that the query complexity of this problem is \[ Θ^*\left(\max\left\{ \left(\frac{(nα)^{k/2}}{ n_k}\right)^{\frac{1}{k-1}} ,\; \min\left\{nα,\frac{nα^{k-1}}{n_k} \right\}\right\}\right). \] where $n$ is the number of vertices in the grap…
The edit distance between two strings is defined as the smallest number of insertions, deletions, and substitutions that need to be made to transform one of the strings to another one. Approximating edit distance in subquadratic time is "one of the biggest unsolved problems in the field of combinatorial pattern matching". Our main result is a quantum constant approximation algorithm for computing the edit distance in truly subquadratic time. More precisely, we give an $O(n^{1.858})$ quantum algorithm that approximates the edit distance within a factor of $7$. We further extend this result to a…
We investigate the approximation for computing the sum $a_1+...+a_n$ with an input of a list of nonnegative elements $a_1,..., a_n$. If all elements are in the range $[0,1]$, there is a randomized algorithm that can compute an $(1+ε)$-approximation for the sum problem in time ${O({n(\log\log n)\over\sum_{i=1}^n a_i})}$, where $ε$ is a constant in $(0,1)$. Our randomized algorithm is based on the uniform random sampling, which selects one element with equal probability from the input list each time. We also prove a lower bound $Ω({n\over \sum_{i=1}^n a_i})$, which almost matches the upper bound…
Analyzing patterns in data streams generated by network traffic, sensor networks, or satellite feeds is a challenge for systems in which the available storage is limited. In addition, real data is noisy, which makes designing data stream algorithms even more challenging. Motivated by such challenges, we study algorithms for detecting the similarity of two data streams that can be read in sync. Two strings $S, T\in Σ^n$ form a $d$-near-alignment if the distance between them in some given metric is at most $d$. We study the problem of identifying a longest substring of $S$ and $T$ that forms a $…
In the longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. This is a classical and well-studied problem in computer science with a known $\mathcal{O}(n)$-time solution. In the fully dynamic version of the problem, edit operations are allowed in either of the two strings, and we are asked to report an LCS after each such operation. We present the first solution to this problem that requires sublinear time per edit operation. In particular, we show how to r…
The longest common extension problem (LCE problem) is to construct a data structure for an input string $T$ of length $n$ that supports LCE$(i,j)$ queries. Such a query returns the length of the longest common prefix of the suffixes starting at positions $i$ and $j$ in $T$. This classic problem has a well-known solution that uses $O(n)$ space and $O(1)$ query time. In this paper we show that for any trade-off parameter $1 \leq τ\leq n$, the problem can be solved in $O(\frac{n}τ)$ space and $O(τ)$ query time. This significantly improves the previously best known time-space trade-offs, and almos…
Recently, studying fundamental graph problems in the \emph{Massively Parallel Computation (MPC) framework, inspired by the MapReduce paradigm, has gained a lot of attention. An assumption common to a vast majority of approaches is to allow $\widetildeΩ(n)$ memory per machine, where $n$ is the number of nodes in the graph and $\widetildeΩ$ hides polylogarithmic factors. However, as pointed out by Karloff et al. [SODA'10] and Czumaj et al. [STOC'18], it might be unrealistic for a single machine to have linear or only slightly sublinear memory. In this paper, we thus study a more practical varian…
We present a simple sublinear-time algorithm for sampling an arbitrary subgraph $H$ \emph{exactly uniformly} from a graph $G$ with $m$ edges, to which the algorithm has access by performing the following types of queries: (1) degree queries, (2) neighbor queries, (3) pair queries and (4) edge sampling queries. The query complexity and running time of our algorithm are $\tilde{O}(\min\{m, \frac{m^{ρ(H)}}{\# H}\})$ and $\tilde{O}(\frac{m^{ρ(H)}}{\# H})$, respectively, where $ρ(H)$ is the fractional edge-cover of $H$ and $\# H$ is the number of copies of $H$ in $G$. For any clique on $r$ vertices…
Edit distance is a measurement of similarity between two sequences such as strings, point sequences, or polygonal curves. Many matching problems from a variety of areas, such as signal analysis, bioinformatics, etc., need to be solved in a geometric space. Therefore, the geometric edit distance (GED) has been studied. In this paper, we describe the first strictly sublinear approximate near-linear time algorithm for computing the GED of two point sequences in constant dimensional Euclidean space. Specifically, we present a randomized (O(n\log^2n)) time (O(\sqrt n))-approximation algorithm. Then…
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 with preprocessing time $N^{1+o(1)}$ and space $N^{1+o(1)}$ that answers queries in $\log^{2+o(1)}N$ time. In other words, we show that we can query the alignment of every two substrings in almost the same time it takes to compute just the alignment of…
We present a new approach for solving (minimum disagreement) correlation clustering that results in sublinear algorithms with highly efficient time and space complexity for this problem. In particular, we obtain the following algorithms for $n$-vertex $(+/-)$-labeled graphs $G$: -- A sublinear-time algorithm that with high probability returns a constant approximation clustering of $G$ in $O(n\log^2{n})$ time assuming access to the adjacency list of the $(+)$-labeled edges of $G$ (this is almost quadratically faster than even reading the input once). Previously, no sublinear-time algorithm was …
We study two basic problems regarding edit error, i.e. document exchange and error correcting codes for edit errors (insdel codes). For message length $n$ and edit error upper bound $k$, it is known that in both problems the optimal sketch size or the optimal number of redundant bits is $Θ(k \log \frac{n}{k})$. However, known constructions are far from achieving these bounds. We significantly improve previous results on both problems. For document exchange, we give an efficient deterministic protocol with sketch size $O(k\log^2 \frac{n}{k})$. This significantly improves the previous best known…
We revisit the complexity of the classical Interval Scheduling in the dynamic setting. In this problem, the goal is to maintain a set of intervals under insertions and deletions and report the size of the maximum size subset of pairwise disjoint intervals after each update. Nontrivial approximation algorithms are known for this problem, for both the unweighted and weighted versions [Henzinger, Neumann, Wiese, SoCG 2020]. Surprisingly, it was not known if the general exact version admits an exact solution working in sublinear time, that is, without recomputing the answer after each update. Our …
Document exchange and error correcting codes are two fundamental problems regarding communications. In the first problem, Alice and Bob each holds a string, and the goal is for Alice to send a short sketch to Bob, so that Bob can recover Alice's string. In the second problem, Alice sends a message with some redundant information to Bob through a channel that can add adversarial errors, and the goal is for Bob to correctly recover the message despite the errors. In a recent work \cite{CJLW18}, the authors constructed explicit deterministic document exchange protocols and binary error correcting…
Given two strings of length $n$ over alphabet $Σ$, and an upper bound $k$ on their edit distance, the algorithm of Myers (Algorithmica'86) and Landau and Vishkin (JCSS'88) computes the unweighted string edit distance in $\mathcal{O}(n+k^2)$ time. Till date, it remains the fastest algorithm for exact edit distance computation, and it is optimal under the Strong Exponential Hypothesis (STOC'15). Over the years, this result has inspired many developments, including fast approximation algorithms for string edit distance as well as similar $\tilde{\mathcal{O}}(n+$poly$(k))$-time algorithms for gene…
Given a pair of strings, the problems of computing their Longest Common Subsequence and Edit Distance have been extensively studied for decades. For exact algorithms, LCS and Edit Distance (with character insertions and deletions) are equivalent; the state of the art running time is (almost) quadratic and this is tight under plausible fine-grained complexity assumptions. But for approximation algorithms the picture is different: there is a long line of works with improved approximation factors for Edit Distance, but for LCS (with binary strings) only a trivial $1/2$-approximation was known. In…
We study the problem of parameterized matching in a stream where we want to output matches between a pattern of length m and the last m symbols of the stream before the next symbol arrives. Parameterized matching is a natural generalisation of exact matching where an arbitrary one-to-one relabelling of pattern symbols is allowed. We show how this problem can be solved in constant time per arriving stream symbol and sublinear, near optimal space with high probability. Our results are surprising and important: it has been shown that almost no streaming pattern matching problems can be solved (no…
Almost 30 years ago, Zhang and Shasha (1989) published a seminal paper describing an efficient dynamic programming algorithm computing the tree edit distance, that is, the minimum number of node deletions, insertions, and replacements that are necessary to transform one tree into another. Since then, the tree edit distance has been widely applied, for example in biology and intelligent tutoring systems. However, the original paper of Zhang and Shasha can be challenging to read for newcomers and it does not describe how to efficiently infer the optimal edit script. In this contribution, we prov…
A distance labeling scheme is an assignment of bit-labels to the vertices of an undirected, unweighted graph such that the distance between any pair of vertices can be decoded solely from their labels. We propose a series of new labeling schemes within the framework of so-called hub labeling (HL, also known as landmark labeling or 2-hop-cover labeling), in which each node $u$ stores its distance to all nodes from an appropriately chosen set of hubs $S(u) \subseteq V$. For a queried pair of nodes $(u,v)$, the length of a shortest $u-v$-path passing through a hub node from $S(u)\cap S(v)$ is the…
The distributed single-source shortest paths problem is one of the most fundamental and central problems in the message-passing distributed computing. Classical Bellman-Ford algorithm solves it in $O(n)$ time, where $n$ is the number of vertices in the input graph $G$. Peleg and Rubinovich (FOCS'99) showed a lower bound of $\tildeΩ(D + \sqrt{n})$ for this problem, where $D$ is the hop-diameter of $G$. Whether or not this problem can be solved in $o(n)$ time when $D$ is relatively small is a major notorious open question. Despite intensive research \cite{LP13,N14,HKN15,EN16,BKKL16} that yielded…
Tree edit distance is a well-studied measure of dissimilarity between rooted trees with node labels. It can be computed in $O(n^3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007], and fine-grained hardness results suggest that the weighted version of this problem cannot be solved in truly subcubic time unless the APSP conjecture is false [Bringmann, Gawrychowski, Mozes, and Weimann, SODA 2018]. We consider the unweighted version of tree edit distance, where every insertion, deletion, or relabeling operation has unit cost. Given a parameter $k$ as an upper bound on the distance, the pr…
Longest common subsequence ($\mathsf{LCS}$) is a classic and central problem in combinatorial optimization. While $\mathsf{LCS}$ admits a quadratic time solution, recent evidence suggests that solving the problem may be impossible in truly subquadratic time. A special case of $\mathsf{LCS}$ wherein each character appears at most once in every string is equivalent to the longest increasing subsequence problem ($\mathsf{LIS}$) which can be solved in quasilinear time. In this work, we present novel algorithms for approximating $\mathsf{LCS}$ in truly subquadratic time and $\mathsf{LIS}$ in truly …
The (unweighted) tree edit distance problem for $n$ node trees asks to compute a measure of dissimilarity between two rooted trees with node labels. The current best algorithm from more than a decade ago runs in $O(n ^ 3)$ time [Demaine, Mozes, Rossman, and Weimann, ICALP 2007]. The same paper also showed that $O(n ^ 3)$ is the best possible running time for any algorithm using the so-called decomposition strategy, which underlies almost all the known algorithms for this problem. These algorithms would also work for the weighted tree edit distance problem, which cannot be solved in truly sub-c…
Quasi-threshold graphs are $\{C_4, P_4\}$-free graphs, i.e., they do not contain any cycle or path of four nodes as an induced subgraph. We study the $\{C_4, P_4\}$-free editing problem, which is the problem of finding a minimum number of edge insertions or deletions to transform an input graph into a quasi-threshold graph. This problem is NP-hard but fixed-parameter tractable (FPT) in the number of edits by using a branch-and-bound algorithm and admits a simple integer linear programming formulation (ILP). Both methods are also applicable to the general $F$-free editing problem for any finite…
A distance labeling scheme labels the $n$ nodes of a graph with binary strings such that, given the labels of any two nodes, one can determine the distance in the graph between the two nodes by looking only at the labels. A $D$-preserving distance labeling scheme only returns precise distances between pairs of nodes that are at distance at least $D$ from each other. In this paper we consider distance labeling schemes for the classical case of unweighted graphs with both directed and undirected edges. We present a $O(\frac{n}{D}\log^2 D)$ bit $D$-preserving distance labeling scheme, improving t…
An Algorithmic Bridge Between Hamming and Levenshtein Distances
Academic College of Tel Aviv-Yafo（特拉维夫雅法学术学院）；Max Planck Institute for Informatics（马克斯·普朗克计算机科学研究所）；Weizmann Institute of Science（魏茨曼科学研究所）；University of California, San Diego（加利福尼亚大学圣地亚哥分校）
This paper concerns {\em randomized} leader election in synchronous distributed networks. A distributed leader election algorithm is presented for complete $n$-node networks that runs in O(1) rounds and (with high probability) uses only $O(\sqrt{n}\log^{3/2} n)$ messages to elect a unique leader (with high probability). When considering the "explicit" variant of leader election where eventually every node knows the identity of the leader, our algorithm yields the asymptotically optimal bounds of O(1) rounds and O(n) messages. This algorithm is then extended to one solving leader election on an…
We study the problem of estimating the value of sums of the form $S_p \triangleq \sum \binom{x_i}{p}$ when one has the ability to sample $x_i \geq 0$ with probability proportional to its magnitude. When $p=2$, this problem is equivalent to estimating the selectivity of a self-join query in database systems when one can sample rows randomly. We also study the special case when $\{x_i\}$ is the degree sequence of a graph, which corresponds to counting the number of $p$-stars in a graph when one has the ability to sample edges randomly. Our algorithm for a $(1 \pm \varepsilon)$-multiplicative app…
A distributed network is modeled by a graph having $n$ nodes (processors) and diameter $D$. We study the time complexity of approximating {\em weighted} (undirected) shortest paths on distributed networks with a $O(\log n)$ {\em bandwidth restriction} on edges (the standard synchronous \congest model). The question whether approximation algorithms help speed up the shortest paths (more precisely distance computation) was raised since at least 2004 by Elkin (SIGACT News 2004). The unweighted case of this problem is well-understood while its weighted counterpart is fundamental problem in the are…
A singularly (near) optimal distributed algorithm is one that is (near) optimal in \emph{two} criteria, namely, its time and message complexities. For \emph{synchronous} CONGEST networks, such algorithms are known for fundamental distributed computing problems such as leader election [Kutten et al., JACM 2015] and Minimum Spanning Tree (MST) construction [Pandurangan et al., STOC 2017, Elkin, PODC 2017]. However, it is open whether a singularly (near) optimal bound can be obtained for the MST construction problem in general \emph{asynchronous} CONGEST networks. We present a randomized distribu…
In this paper, we study edit distance (ED) and longest common subsequence (LCS) in the asymmetric streaming model, introduced by Saks and Seshadhri [SS13]. As an intermediate model between the random access model and the streaming model, this model allows one to have streaming access to one string and random access to the other string. Our first main contribution is a systematic study of space lower bounds for ED and LCS in the asymmetric streaming model. Previously, there are no explicitly stated results in this context, although some lower bounds about LCS can be inferred from the lower boun…
Quasiperiodicity in strings was introduced almost 30 years ago as an extension of string periodicity. The basic notions of quasiperiodicity are cover and seed. A cover of a text $T$ is a string whose occurrences in $T$ cover all positions of $T$. A seed of text $T$ is a cover of a superstring of $T$. In various applications exact quasiperiodicity is still not sufficient due to the presence of errors. We consider approximate notions of quasiperiodicity, for which we allow approximate occurrences in $T$ with a small Hamming, Levenshtein or weighted edit distance. In previous work Sip et al. (200…
We give the first almost optimal polynomial-time proper learning algorithm of Boolean sparse multivariate polynomial under the uniform distribution. For $s$-sparse polynomial over $n$ variables and $ε=1/s^β$, $β>1$, our algorithm makes $$q_U=\left(\frac{s}ε\right)^{\frac{\log β}β+O(\frac{1}β)}+ \tilde O\left(s\right)\left(\log\frac{1}ε\right)\log n$$ queries. Notice that our query complexity is sublinear in $1/ε$ and almost linear in $s$. All previous algorithms have query complexity at least quadratic in $s$ and linear in $1/ε$. We then prove the almost tight lower bound $$q_L=\left(\frac{s}ε…
We consider the approximate pattern matching problem under the edit distance. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to find the starting positions of all substrings of $T$ that can be transformed to $P$ with at most $k$ edits. More than 20 years ago, Cole and Hariharan [SODA'98, J. Comput.'02] gave an $\mathcal{O}(n+k^4 \cdot n/ m)$-time algorithm for this classic problem, and this runtime has not been improved since. Here, we present an algorithm that runs in time $\mathcal{O}(n+k^{3.5} \sqrt{\log m \log k} \cdot n/m)$, thus breaking thr…
We study parallel algorithms for correlation clustering. Each pair among $n$ objects is labeled as either "similar" or "dissimilar". The goal is to partition the objects into arbitrarily many clusters while minimizing the number of disagreements with the labels. Our main result is an algorithm that for any $ε> 0$ obtains a $(3+ε)$-approximation in $O(1/ε)$ rounds (of models such as massively parallel computation, local, and semi-streaming). This is a culminating point for the rich literature on parallel correlation clustering. On the one hand, the approximation (almost) matches a natural barri…
Spectral partitioning is a simple, nearly-linear time, algorithm to find sparse cuts, and the Cheeger inequalities provide a worst-case guarantee for the quality of the approximation found by the algorithm. Local graph partitioning algorithms [ST08,ACL06,AP09] run in time that is nearly linear in the size of the output set, and their approximation guarantee is worse than the guarantee provided by the Cheeger inequalities by a polylogarithmic $\log^{Ω(1)} n$ factor. It has been a long standing open problem to design a local graph clustering algorithm with an approximation guarantee close to the…
We study distributed algorithms built around minor-based vertex sparsifiers, and give the first algorithm in the CONGEST model for solving linear systems in graph Laplacian matrices to high accuracy. Our Laplacian solver has a round complexity of $O(n^{o(1)}(\sqrt{n}+D))$, and thus almost matches the lower bound of $\widetildeΩ(\sqrt{n}+D)$, where $n$ is the number of nodes in the network and $D$ is its diameter. We show that our distributed solver yields new sublinear round algorithms for several cornerstone problems in combinatorial optimization. This is achieved by leveraging the powerful a…
The minimum-cost $k$-edge-connected spanning subgraph ($k$-ECSS) problem is a generalization and strengthening of the well-studied minimum-cost spanning tree (MST) problem. While the round complexity of distributedly computing the latter has been well-understood, the former remains mostly open, especially as soon as $k\geq 3$. In this paper, we present the first distributed algorithm that computes an approximation of $k$-ECSS in sublinear time for general $k$. Concretely, we describe a randomized distributed algorithm that, in $\tilde{O}(k(D+k\sqrt{n}))$ rounds, computes a $k$-edge-connected s…
