arXiv subjects

Tomasz Kociumaka

Publications and source records attributed to Tomasz Kociumaka.

At least 37 records · Page 2Linked to original sources

arXiv2025

Approximate Circular Pattern Matching

We consider approximate circular pattern matching (CPM, in short) under the Hamming and edit distance, in which we are given a length-$n$ text $T$, a length-$m$ pattern $P$, and a threshold $k>0$, and we are to report all starting positions of fragments of $T$ (called occurrences) that are at distance at most $k$ from some cyclic rotation of $P$. In the decision version of the problem, we are to check if any such occurrence exists. All previous results for approximate CPM were either average-case upper bounds or heuristics, except for the work of Charalampopoulos et al. [CKP$^+$, JCSS'21], who considered only the Hamming distance. For the reporting version of the approximate CPM problem, under the Hamming distance we improve upon the main algorithm of [CKP$^+$, JCSS'21] from ${\cal O}(n+(n/m)\cdot k^4)$ to ${\cal O}(n+(n/m)\cdot k^3)$ time; for the edit distance, we give an ${\cal O}(nk^2)$-time algorithm. We also consider the decision version of the approximate CPM problem. Under the Hamming distance, we obtain an ${\cal O}(n+(n/m)\cdot k^2\log k/\log\log k)$-time algorithm, which nearly matches the algorithm by Chan et al. [CGKKP, STOC'20] for the standard counterpart of the problem. Under the edit distance, the ${\cal O}(nk\log^2 k)$ running time of our algorithm nearly matches the ${\cal O}(nk)$ running time of the Landau-Vishkin algorithm [LV, J. Algorithms'89]. As a stepping stone, we propose an ${\cal O}(nk\log^2 k)$-time algorithm for the Longest Prefix $k'$-Approximate Match problem, proposed by Landau et al. [LMS, SICOMP'98], for all $k'\in \{1,\dots,k\}$. We give a conditional lower bound that suggests a polynomial separation between approximate CPM under the Hamming distance over the binary alphabet and its non-circular counterpart. We also show that a strongly subquadratic-time algorithm for the decision version of approximate CPM under edit distance would refute SETH.

cs.DS↗

arXiv2025

On the Hardness Hierarchy for the $O(n \sqrt{\log n})$ Complexity in the Word RAM

In this work, we study the relative hardness of fundamental problems with state-of-the-art word RAM algorithms that take $O(n\sqrt{\log n})$ time for instances described in $Θ(n)$ machine words ($Θ(n\log n)$ bits). This complexity class, one of six hardness levels identified by Chan and Pătraşcu [SODA 2010], includes diverse problems from several domains: Counting Inversions, string processing problems (BWT Construction, LZ77 Factorization, Longest Common Substring, Batched Longest Previous Factor Queries, Batched Inverse Suffix Array Queries), and computational geometry tasks (Orthogonal Range Counting, Orthogonal Segment Intersection). We offer two main contributions: We establish new links between the above string problems and Dictionary Matching, a classic task solvable using the Aho-Corasick automaton. We restrict Dictionary Matching to instances with $O(n)$ binary patterns of length $m = O(\log n)$ each, and we prove that, unless these instances can be solved in $o(n\sqrt{\log n})$ time, the aforementioned string problems cannot be solved faster either. Via further reductions, we extend this hardness to Counting Inversions (a fundamental component in geometric algorithms) and thus to Orthogonal Range Counting and Orthogonal Segment Intersection. This hinges on String Nesting, a new problem which is equivalent to Dictionary Matching and can be reduced to Counting Inversions in three steps. Together, our results unveil a single problem, with two equivalent formulations, that underlies the hardness of nearly all major problems currently occupying the $O(n\sqrt{\log n})$ level of hardness. These results drastically funnel further efforts to improve the complexity of near-linear problems. As an auxiliary outcome of our framework, we also prove that the alphabet in several central string problems can be efficiently reduced to binary.

cs.DS↗

arXiv2025

Logarithmic-Time Internal Pattern Matching Queries in Compressed and Dynamic Texts

Internal Pattern Matching (IPM) queries on a text $T$, given two fragments $X$ and $Y$ of $T$ such that $|Y|<2|X|$, ask to compute all exact occurrences of $X$ within $Y$. IPM queries have been introduced by Kociumaka, Radoszewski, Rytter, and Waleń [SODA'15 & SICOMP'24], who showed that they can be answered in $O(1)$ time using a data structure of size $O(n)$ and used this result to answer various queries about fragments of $T$. In this work, we study IPM queries on compressed and dynamic strings. Our result is an $O(\log n)$-time query algorithm applicable to any balanced recompression-based run-length straight-line program (RLSLP). In particular, one can use it on top of the RLSLP of Kociumaka, Navarro, and Prezza [IEEE TIT'23], whose size $O\big(δ\log \frac{n\log σ}{δ\log n}\big)$ is optimal (among all text representations) as a function of the text length $n$, the alphabet size $σ$, and the substring complexity $δ$. Our procedure does not rely on any preprocessing of the underlying RLSLP, which makes it readily applicable on top of the dynamic strings data structure of Gawrychowski, Karczmarz, Kociumaka, Łącki and Sankowski [SODA'18], which supports fully persistent updates in logarithmic time with high probability.

cs.DS↗

arXiv2025

Bounded Edit Distance: Optimal Static and Dynamic Algorithms for Small Integer Weights

The edit distance of two strings is the minimum number of insertions, deletions, and substitutions needed to transform one string into the other. The textbook algorithm determines the edit distance of length-$n$ strings in $O(n^2)$ time, which is optimal up to subpolynomial factors under Orthogonal Vectors Hypothesis. In the bounded version of the problem, parameterized by the edit distance $k$, the algorithm of Landau and Vishkin [JCSS'88] achieves $O(n+k^2)$ time, which is optimal as a function of $n$ and $k$. The dynamic version of the problem asks to maintain the edit distance of two strings that change dynamically, with each update modeled as an edit. A folklore approach supports updates in $\tilde O(k^2)$ time, where $\tilde O(\cdot)$ hides polylogarithmic factors. Recently, Charalampopoulos, Kociumaka, and Mozes [CPM'20] showed an algorithm with update time $\tilde O(n)$, which is optimal under OVH in terms of $n$. The update time of $\tilde O(\min\{n,k^2\})$ raised an exciting open question of whether $\tilde O(k)$ is possible; we answer it affirmatively. Our solution relies on tools originating from weighted edit distance, where the weight of each edit depends on the edit type and the characters involved. The textbook algorithm supports weights, but the Landau-Vishkin approach does not, and a simple $O(nk)$-time procedure long remained the fastest for bounded weighted edit distance. Only recently, Das et al. [STOC'23] provided an $O(n+k^5)$-time algorithm, whereas Cassis, Kociumaka, and Wellnitz [FOCS'23] presented an $\tilde O(n+\sqrt{nk^3})$-time solution and a matching conditional lower bound. In this paper, we show that, for integer edit weights between $0$ and $W$, weighted edit distance can be computed in $\tilde O(n+Wk^2)$ time and maintained dynamically in $\tilde O(W^2k)$ time per update. Our static algorithm can also be implemented in $\tilde O(n+k^{2.5})$ time.

cs.DS↗

arXiv2024

Language Edit Distance & Scored Parsing: Faster Algorithms & Connection to Fundamental Graph Problems

Given a context free language $\mathcal{L(G)}$ over alphabet $Σ$ and a string $s \in Σ^*$, {\em the language edit distance} problem seeks the minimum number of edits (insertions, deletions and substitutions) required to convert $s$ into a valid member of $\mathcal{L(G)}$. The well-known dynamic programming algorithm solves this problem in $O(n^3)$ time (ignoring grammar size) where $n$ is the string length [Aho, Peterson 1972, Myers 1985]. Despite its numerous applications, to date there exists no algorithm that computes exact or approximate language edit distance problem in true subcubic time. In this paper we give the first such algorithm that approximates language edit distance in subcubic time. For any arbitrary $ε> 0$, our algorithm runs in $\tilde{O}(\frac{n^{2.491}}{ε^2})$ time and returns an estimate within a multiplicative approximation factor of $(1+ε)$. Moreover, an additive $εn$ approximation can be computed in $O(\frac{n^2}{ε^{0.825}})$ time. To complement our upper bound results, we show that exact computation of language edit distance with insertion-only edits in truly subcubic time will imply a truly subcubic algorithm for all-pairs shortest paths which is a long-standing open question in computer science.

cs.DS↗

arXiv2024

On the Communication Complexity of Approximate Pattern Matching

The decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), asks to list all fragments of $T$ that are at edit distance at most $k$ from $P$. The one-way communication complexity of this problem is the minimum amount of space needed to encode the answer so that it can be retrieved without accessing the input strings $P$ and $T$. The closely related Pattern Matching with Mismatches problem (defined in terms of the Hamming distance instead of the edit distance) is already well understood from the communication complexity perspective: Clifford, Kociumaka, and Porat [SODA 2019] proved that $Ω(n/m \cdot k \log(m/k))$ bits are necessary and $O(n/m \cdot k\log (m|Σ|/k))$ bits are sufficient; the upper bound allows encoding not only the occurrences of $P$ in $T$ with at most $k$ mismatches but also the substitutions needed to make each $k$-mismatch occurrence exact. Despite recent improvements in the running time [Charalampopoulos, Kociumaka, and Wellnitz; FOCS 2020 and 2022], the communication complexity of Pattern Matching with Edits remained unexplored, with a lower bound of $Ω(n/m \cdot k\log(m/k))$ bits and an upper bound of $O(n/m \cdot k^3\log m)$ bits stemming from previous research. In this work, we prove an upper bound of $O(n/m \cdot k \log^2 m)$ bits, thus establishing the optimal communication complexity up to logarithmic factors. We also show that $O(n/m \cdot k \log m \log (m|Σ|))$ bits allow encoding, for each $k$-error occurrence of $P$ in $T$, the shortest sequence of edits needed to make the occurrence exact. We leverage the techniques behind our new result on the communication complexity to obtain quantum algorithms for Pattern Matching with Edits.

cs.DS↗

arXiv2024

Near-Optimal-Time Quantum Algorithms for Approximate Pattern Matching

Approximate Pattern Matching is among the most fundamental string-processing tasks. Given a text $T$ of length $n$, a pattern $P$ of length $m$, and a threshold $k$, the task is to identify the fragments of $T$ that are at distance at most $k$ to $P$. We consider the two most common distances: Hamming distance (the number of character substitutions) in Pattern Matching with Mismatches and edit distance (the minimum number of character insertions, deletions, and substitutions) in Pattern Matching with Edits. We revisit the complexity of these two problems in the quantum setting. Our recent work [STOC'24] shows that $\hat{O}(\sqrt{nk})$ quantum queries are sufficient to solve (the decision version of) Pattern Matching with Edits. However, the quantum time complexity of the underlying solution does not provide any improvement over classical computation. On the other hand, the state-of-the-art algorithm for Pattern Matching with Mismatches [Jin and Nogler; SODA'23] achieves query complexity $\hat{O}(\sqrt{nk^{3/2}})$ and time complexity $\tilde{O}(\sqrt{nk^2})$, falling short of an unconditional lower bound of $Ω(\sqrt{nk})$ queries. In this work, we present quantum algorithms with a time complexity of $\tilde{O}(\sqrt{nk}+\sqrt{n/m}\cdot k^2)$ for Pattern Matching with Mismatches and $\hat{O}(\sqrt{nk}+\sqrt{n/m}\cdot k^{3.5})$ for Pattern Matching with Edits; both solutions use $\hat{O}(\sqrt{nk})$ queries. The running times are near-optimal for $k\ll m^{1/3}$ and $k\ll m^{1/6}$, respectively, and offer advantage over classical algorithms for $k\ll (mn)^{1/4}$ and $k\ll (mn)^{1/7}$, respectively. Our solutions can also report the starting positions of approximate occurrences of $P$ in $T$ (represented as collections of arithmetic progressions); in this case, the unconditional lower bound and the complexities of our algorithms increase by a $Θ(\sqrt{n/m})$ factor.

cs.DS↗

arXiv2024

On the Complexity of Computing the Co-lexicographic Width of a Regular Language

Co-lex partial orders were recently introduced in (Cotumaccio et al., SODA 2021 and JACM 2023) as a powerful tool to index finite state automata, with applications to regular expression matching. They generalize Wheeler orders (Gagie et al., Theoretical Computer Science 2017) and naturally reflect the co-lexicographic order of the strings labeling source-to-node paths in the automaton. Briefly, the co-lex width $p$ of a finite-state automaton measures how sortable its states are with respect to the co-lex order among the strings they accept. Automata of co-lex width $p$ can be compressed to $O(\log p)$ bits per edge and admit regular expression matching algorithms running in time proportional to $p^2$ per matched character. The deterministic co-lex width of a regular language $\mathcal L$ is the smallest width of such a co-lex order, among all DFAs recognizing $\mathcal L$. Since languages of small co-lex width admit efficient solutions to automata compression and pattern matching, computing the co-lex width of a language is relevant in these applications. The paper introducing co-lex orders determined that the deterministic co-lex width $p$ of a language $\mathcal L$ can be computed in time proportional to $m^{O(p)}$, given as input any DFA $\mathcal A$ for $\mathcal L$, of size (number of transitions) $m =|\mathcal A|$. In this paper, using new techniques, we show that it is possible to decide in $O(m^p)$ time if the deterministic co-lex width of the language recognized by a given minimum DFA is strictly smaller than some integer $p\ge 2$. We complement this upper bound with a matching conditional lower bound based on the Strong Exponential Time Hypothesis. The problem is known to be PSPACE-complete when the input is an NFA (D'Agostino et al., Theoretical Computer Science 2023); thus, together with that result, our paper essentially settles the complexity of the problem.

cs.FL↗

arXiv2024

Lempel-Ziv (LZ77) Factorization in Sublinear Time

Lempel-Ziv (LZ77) factorization is a fundamental problem in string processing: Greedily partition a given string $T$ from left to right into blocks (called phrases) so that each phrase is either the leftmost occurrence of a letter or the longest prefix of the unprocessed suffix that has another occurrence earlier in $T$. Due to numerous applications, LZ77 factorization is one of the most studied problems on strings. In the 47 years since its inception, several algorithms were developed for different models of computation, including parallel, GPU, external-memory, and quantum. Remarkably, however, the complexity of the most basic variant is still not settled: All existing algorithms in the RAM model run in $Ω(n)$ time, which is a $Θ(\log n)$ factor away from the lower bound of $Ω(n/\log n)$ (following from the necessity to read the input, which takes $Θ(n/\log n)$ space for $T\in\{0,1\}^{n}$). We present the first $o(n)$-time algorithm for LZ77 factorization, breaking the linear-time barrier present for nearly 50 years. For $T\in\{0,1\}^{n}$, our algorithm runs in $\mathcal{O}(n/\sqrt{\log n})=o(n)$ time and uses the optimal $\mathcal{O}(n/\log n)$ working space. Our algorithm generalizes to $Σ=[0..σ)$, where $σ=n^{\mathcal{O}(1)}$. The runtime and working space then become $\mathcal{O}((n\logσ)/\sqrt{\log n})$ and $\mathcal{O}(n/\log_σ n)$. To obtain our algorithm, we prove a more general result: For any constant $ε\in(0,1)$ and $T\in[0..σ)^{n}$, in $\mathcal{O}((n\logσ)/\sqrt{\log n})$ time and using $\mathcal{O}(n/\log_σn)$ space, we can construct an $\mathcal{O}(n/\log_σn)$-size index that, given any $P=T[j..j+\ell)$ (represented as $(j,\ell)$), computes the leftmost occurrence of $P$ in $T$ in $\mathcal{O}(\log^εn)$ time. In other words, we solve the indexing/online variant of the LZ77 problem.

cs.DS↗

arXiv2024

Small-Space Algorithms for the Online Language Distance Problem for Palindromes and Squares

We study the online variant of the language distance problem for two classical formal languages, the language of palindromes and the language of squares, and for the two most fundamental distances, the Hamming distance and the edit (Levenshtein) distance. In this problem, defined for a fixed formal language $L$, we are given a string $T$ of length $n$, and the task is to compute the minimal distance to $L$ from every prefix of $T$. We focus on the low-distance regime, where one must compute only the distances smaller than a given threshold $k$. In this work, our contribution is twofold: - First, we show streaming algorithms, which access the input string $T$ only through a single left-to-right scan. Both for palindromes and squares, our algorithms use $O(k \cdot\mathrm{poly}~\log n)$ space and time per character in the Hamming-distance case and $O(k^2 \cdot\mathrm{poly}~\log n)$ space and time per character in the edit-distance case. These algorithms are randomised by necessity, and they err with probability inverse-polynomial in $n$. - Second, we show deterministic read-only online algorithms, which are also provided with read-only random access to the already processed characters of $T$. Both for palindromes and squares, our algorithms use $O(k \cdot\mathrm{poly}~\log n)$ space and time per character in the Hamming-distance case and $O(k^4 \cdot\mathrm{poly}~\log n)$ space and amortised time per character in the edit-distance case.

cs.DS↗

arXiv2024

Graph and String Parameters: Connections Between Pathwidth, Cutwidth and the Locality Number

We investigate the locality number, a recently introduced structural parameter for strings (with applications in pattern matching with variables), and its connection to two important graph-parameters, cutwidth and pathwidth. These connections allow us to show that computing the locality number is NP-hard, but fixed-parameter tractable, if parameterised by the locality number or by the alphabet size, which has been formulated as open problems in the literature. Moreover, the locality number can be approximated with ratio O(sqrt(log(opt)) log(n)). An important aspect of our work -- that is relevant in its own right and of independent interest -- is that we identify connections between the string parameter of the locality number on the one hand, and the famous graph parameters of cutwidth and pathwidth, on the other hand. These two parameters have been jointly investigated in the literature and are arguably among the most central graph parameters that are based on "linearisations" of graphs. In this way, we also identify a direct approximation preserving reduction from cutwidth to pathwidth, which shows that any polynomial f(opt,|V|)-approximation algorithm for pathwidth yields a polynomial 2f(2 opt,h)-approximation algorithm for cutwidth on multigraphs (where h is the number of edges). In particular, this translates known approximation ratios for pathwidth into new approximation ratios for cutwidth, namely O(sqrt(log(opt)) log(h)) and O(sqrt(log(opt)) opt) for (multi) graphs with h edges.

cs.DS↗

arXiv2023

Efficient Ranking of Lyndon Words and Decoding Lexicographically Minimal de Bruijn Sequence

We give efficient algorithms for ranking Lyndon words of length $n$ over an alphabet of size $σ$. The rank of a Lyndon word is its position in the sequence of lexicographically ordered Lyndon words of the same length. The outputs are integers of exponential size, and complexity of arithmetic operations on such large integers cannot be ignored. Our model of computations is the word-RAM, in which basic arithmetic operations on (large) numbers of size at most $σ^n$ take $O(n)$ time. Our algorithm for ranking Lyndon words makes $O(n^2)$ arithmetic operations (this would imply directly cubic time on word-RAM). However, using an algebraic approach we are able to reduce the total time complexity on the word-RAM to $O(n^2 \log σ)$. We also present an $O(n^3 \log^2 σ)$-time algorithm that generates the Lyndon word of a given length and rank in lexicographic order. Finally we use the connections between Lyndon words and lexicographically minimal de Bruijn sequences (theorem of Fredricksen and Maiorana) to develop the first polynomial-time algorithm for decoding minimal de Bruijn sequence of any rank $n$ (it determines the position of an arbitrary word of length $n$ within the de Bruijn sequence).

cs.DS↗

arXiv2023

Faster Sublinear-Time Edit Distance

We study the fundamental problem of approximating the edit distance of two strings. After an extensive line of research led to the development of a constant-factor approximation algorithm in almost-linear time, recent years have witnessed a notable shift in focus towards sublinear-time algorithms. Here, the task is typically formalized as the $(k, K)$-gap edit distance problem: Distinguish whether the edit distance of two strings is at most $k$ or more than $K$. Surprisingly, it is still possible to compute meaningful approximations in this challenging regime. Nevertheless, in almost all previous work, truly sublinear running time of $O(n^{1-\varepsilon})$ (for a constant $\varepsilon > 0$) comes at the price of at least polynomial gap $K \ge k \cdot n^{Ω(\varepsilon)}$. Only recently, [Bringmann, Cassis, Fischer, and Nakos; STOC'22] broke through this barrier and solved the sub-polynomial $(k, k^{1+o(1)})$-gap edit distance problem in time $O(n/k + k^{4+o(1)})$, which is truly sublinear if $n^{Ω(1)} \le k \le n^{\frac14-Ω(1)}$.The $n/k$ term is inevitable (already for Hamming distance), but it remains an important task to optimize the $\mathrm{poly}(k)$ term and, in general, solve the $(k, k^{1+o(1)})$-gap edit distance problem in sublinear-time for larger values of $k$. In this work, we design an improved algorithm for the $(k, k^{1+o(1)})$-gap edit distance problem in sublinear time $O(n/k + k^{2+o(1)})$, yielding a significant quadratic speed-up over the previous $O(n/k + k^{4+o(1)})$-time algorithm. Notably, our algorithm is unconditionally almost-optimal (up to subpolynomial factors) in the regime where $k \leq n^{\frac13}$ and improves upon the state of the art for $k \leq n^{\frac12-o(1)}$.

cs.DS↗

arXiv2023

Dynamic Dynamic Time Warping

The Dynamic Time Warping (DTW) distance is a popular similarity measure for polygonal curves (i.e., sequences of points). It finds many theoretical and practical applications, especially for temporal data, and is known to be a robust, outlier-insensitive alternative to the \frechet distance. For static curves of at most $n$ points, the DTW distance can be computed in $O(n^2)$ time in constant dimension. This tightly matches a SETH-based lower bound, even for curves in $\mathbb{R}^1$. In this work, we study \emph{dynamic} algorithms for the DTW distance. Here, the goal is to design a data structure that can be efficiently updated to accommodate local changes to one or both curves, such as inserting or deleting vertices and, after each operation, reports the updated DTW distance. We give such a data structure with update and query time $O(n^{1.5} \log n)$, where $n$ is the maximum length of the curves. As our main result, we prove that our data structure is conditionally \emph{optimal}, up to subpolynomial factors. More precisely, we prove that, already for curves in $\mathbb{R}^1$, there is no dynamic algorithm to maintain the DTW distance with update and query time~\makebox{$O(n^{1.5 - δ})$} for any constant $δ> 0$, unless the Negative-$k$-Clique Hypothesis fails. In fact, we give matching upper and lower bounds for various trade-offs between update and query time, even in cases where the lengths of the curves differ.

cs.CG↗

arXiv2023

Near-Optimal Quantum Algorithms for Bounded Edit Distance and Lempel-Ziv Factorization

Classically, the edit distance of two length-$n$ strings can be computed in $O(n^2)$ time, whereas an $O(n^{2-ε})$-time procedure would falsify the Orthogonal Vectors Hypothesis. If the edit distance does not exceed $k$, the running time can be improved to $O(n+k^2)$, which is near-optimal (conditioned on OVH) as a function of $n$ and $k$. Our first main contribution is a quantum $\tilde{O}(\sqrt{nk}+k^2)$-time algorithm that uses $\tilde{O}(\sqrt{nk})$ queries, where $\tilde{O}(\cdot)$ hides polylogarithmic factors. This query complexity is unconditionally optimal, and any significant improvement in the time complexity would resolve a long-standing open question of whether edit distance admits an $O(n^{2-ε})$-time quantum algorithm. Our divide-and-conquer quantum algorithm reduces the edit distance problem to a case where the strings have small Lempel-Ziv factorizations. Then, it combines a quantum LZ compression algorithm with a classical edit-distance subroutine for compressed strings. The LZ factorization problem can be classically solved in $O(n)$ time, which is unconditionally optimal in the quantum setting. We can, however, hope for a quantum speedup if we parameterize the complexity in terms of the factorization size $z$. Already a generic oracle identification algorithm yields the optimal query complexity of $\tilde{O}(\sqrt{nz})$ at the price of exponential running time. Our second main contribution is a quantum algorithm that achieves the optimal time complexity of $\tilde{O}(\sqrt{nz})$. The key tool is a novel LZ-like factorization of size $O(z\log^2n)$ whose subsequent factors can be efficiently computed through a combination of classical and quantum techniques. We can then obtain the string's run-length encoded Burrows-Wheeler Transform (BWT), construct the $r$-index, and solve many fundamental string processing problems in time $\tilde{O}(\sqrt{nz})$.

cs.DS↗

arXiv2023

Optimal Algorithms for Bounded Weighted Edit Distance

The edit distance of two strings is the minimum number of insertions, deletions, and substitutions of characters needed to transform one string into the other. The textbook dynamic-programming algorithm computes the edit distance of two length-$n$ strings in $O(n^2)$ time, which is optimal up to subpolynomial factors under SETH. An established way of circumventing this hardness is to consider the bounded setting, where the running time is parameterized by the edit distance $k$. A celebrated algorithm by Landau and Vishkin (JCSS '88) achieves time $O(n + k^2)$, which is optimal as a function of $n$ and $k$. Most practical applications rely on a more general weighted edit distance, where each edit has a weight depending on its type and the involved characters from the alphabet $Σ$. This is formalized through a weight function $w : Σ\cup\{\varepsilon\}\timesΣ\cup\{\varepsilon\}\to\mathbb{R}$ normalized so that $w(a,a)=0$ and $w(a,b)\geq 1$ for all $a,b \in Σ\cup\{\varepsilon\}$ with $a \neq b$; the goal is to find an alignment of the two strings minimizing the total weight of edits. The $O(n^2)$-time algorithm supports this setting seamlessly, but only very recently, Das, Gilbert, Hajiaghayi, Kociumaka, and Saha (STOC '23) gave the first non-trivial algorithm for the bounded version, achieving time $O(n + k^5)$. While this running time is linear for $k\le n^{1/5}$, it is still very far from the bound $O(n+k^2)$ achievable in the unweighted setting. In this paper, we essentially close this gap by showing both an improved $\tilde O(n+\sqrt{nk^3})$-time algorithm and, more surprisingly, a matching lower bound: Conditioned on the All-Pairs Shortest Paths (APSP) hypothesis, our running time is optimal for $\sqrt{n}\le k\le n$ (up to subpolynomial factors). This is the first separation between the complexity of the weighted and unweighted edit distance problems.

cs.DS↗

arXiv2023

Near-Optimal Search Time in $δ$-Optimal Space, and Vice Versa

Two recent lower bounds on the compressibility of repetitive sequences, $δ\le γ$, have received much attention. It has been shown that a length-$n$ string $S$ over an alphabet of size $σ$ can be represented within the optimal $O(δ\log\tfrac{n\log σ}{δ\log n})$ space, and further, that within that space one can find all the $occ$ occurrences in $S$ of any length-$m$ pattern in time $O(m\log n + occ \log^εn)$ for any constant $ε>0$. Instead, the near-optimal search time $O(m+({occ+1})\log^εn)$ has been achieved only within $O(γ\log\frac{n}γ)$ space. Both results are based on considerably different locally consistent parsing techniques. The question of whether the better search time could be supported within the $δ$-optimal space remained open. In this paper, we prove that both techniques can indeed be combined to obtain the best of both worlds: $O(m+({occ+1})\log^εn)$ search time within $O(δ\log\tfrac{n\log σ}{δ\log n})$ space. Moreover, the number of occurrences can be computed in $O(m+\log^{2+ε}n)$ time within $O(δ\log\tfrac{n\log σ}{δ\log n})$ space. We also show that an extra sublogarithmic factor on top of this space enables optimal $O(m+occ)$ search time, whereas an extra logarithmic factor enables optimal $O(m)$ counting time.

cs.DS↗

arXiv2023

Collapsing the Hierarchy of Compressed Data Structures: Suffix Arrays in Optimal Compressed Space

In the last decades, the necessity to process massive amounts of textual data fueled the development of compressed text indexes: data structures efficiently answering queries on a given text while occupying space proportional to the compressed representation of the text. A widespread phenomenon in compressed indexing is that more powerful queries require larger indexes. For example, random access, the most basic query, can be supported in $O(δ\log\frac{n\logσ}{δ\log n})$ space (where $n$ is the text length, $σ$ is the alphabet size, and $δ$ is text's substring complexity), which is the asymptotically smallest space to represent a string, for all $n$, $σ$, and $δ$ (Kociumaka, Navarro, Prezza; IEEE Trans. Inf. Theory 2023). The other end of the hierarchy is occupied by indexes supporting the powerful suffix array (SA) queries. The currently smallest one takes $O(r\log\frac{n}{r})$ space, where $r\geqδ$ is the number of runs in the BWT of the text (Gagie, Navarro, Prezza; J. ACM 2020). We present a new compressed index that needs only $O(δ\log\frac{n\logσ}{δ\log n})$ space to support SA functionality in $O(\log^{4+ε} n)$ time. This collapses the hierarchy of compressed data structures into a single point: The space required to represent the text is simultaneously sufficient for efficient SA queries. Our result immediately improves the space complexity of dozens of algorithms, which can now be executed in optimal compressed space. In addition, we show how to construct our index in $O(δ\text{ polylog } n)$ time from the LZ77 parsing of the text. For highly repetitive texts, this is up to exponentially faster than the previously best algorithm. To obtain our results, we develop numerous techniques of independent interest, including the first $O(δ\log\frac{n\logσ}{δ\log n})$-size index for LCE queries.

cs.DS↗