arXiv subjects

Tomasz Kociumaka

Publications and source records attributed to Tomasz Kociumaka.

At least 19 recordsLinked to original sources

arXiv2026

Metric Weighted Edit Distance: $(3+\varepsilon)$-Approximation in $\widetilde O_\varepsilon(N^{1.6})$ Time

For every $0 < \varepsilon \le 1$, we give a randomized $(3+\varepsilon)$-approximation to weighted edit distance when the costs form a metric on the alphabet augmented with a gap symbol. For strings of total length $N$, the running time is $\widetilde{O}(N^{8/5}/\varepsilon^{16/5})$, where $\widetilde{O}$ suppresses factors polynomial in $\log(N/\varepsilon)$. The dependence on $N$ matches that of the fastest known $(3+\varepsilon)$-approximation for unit-cost edit distance. The algorithm never underestimates the edit distance and achieves the approximation guarantee with inverse-polynomial failure probability in $N$. The running time bound assumes constant-time exact arithmetic operations and metric queries, and it is independent of the numerical range of the edit costs. We build on three tools: the sampling framework of Chakraborty, Das, Goldenberg, Koucký, and Saks (J. ACM, 2020), with subsequent refinements by Andoni (2020); Kuszmaul's removal of inexpensive characters (ICALP 2019); and Klein's data structure for distances in planar graphs (SODA 2005). Our new ingredients include, among others, a decomposition of one string into pieces of bounded length with highly structured total deletion costs. This decomposition lets us compare all pieces against a small family of substrings of the other string.

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arXiv2026

Constant-Time Inverse Suffix Array Queries in Compact Space and Sublinear-Time Construction of Suffix Array Indexes

For a text $T\in[0..σ)^n$ with $2\leqσ\leq n$, its suffix array orders the suffix starting positions lexicographically, while its inverse suffix array maps each position to its suffix's rank. Since compressed suffix arrays and FM-indexes appeared in 2000, a central goal has been to support both queries in $O(n\logσ)$ bits. Thankachan recently reduced inverse suffix array query time to $O(\log\log n/\log\logσ)$, but constant time remained open. We give the first inverse suffix array structure with optimal space and query time: $O(n\logσ)$ bits and $O(1)$ time. For binary texts, this unconditionally separates the two queries for deterministic structures, since every $O(n)$-bit suffix array structure in the cell-probe model with $Θ(\log n)$-bit cells has worst-case query time $Ω(\log\log n/\log\log\log n)$. Construction is a second challenge: linear time can take $Θ(\log_σ n)$ times as long as reading the input or writing a compact index. Previously, sublinear construction was known for only one such index supporting both queries. In the word RAM with $Θ(\log n)$-bit words, we deterministically construct the new structure and two suffix array families from the packed text in $O(n\min(1,\logσ/\sqrt{\log n}))$ time. For $B\geq2$, the first family uses $O(n\logσ(1+\log_B\log_σn))$ bits and has query time $O(B(1+\log_B\log_σn))$, whereas the second uses $O(Bn\logσ(1+\log_B\log_σn))$ bits and has query time $O(1+\log_B\log_σn)$. Each has peak preprocessing space bounded by its index size. For binary texts, the second family matches the deterministic cell-probe time-space lower bound whenever $B\geq(\log\log n)^{Ω(1)}$, and, outside the slowest-query regimes, improving the deterministic construction time to $o(n/\sqrt{\log n})$ would yield an equally fast Dictionary Matching algorithm.

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arXiv2026

Cell-Probe Lower Bounds and Complexity-Preserving Reductions for Suffix Array Queries

For a text $T$ of length $n$ over an alphabet of size $σ$, its suffix array lists the starting positions of the suffixes of $T$ in lexicographic order, and its inverse suffix array gives the lexicographic rank of the suffix starting at each position. Since the introduction of the FM-index and the compressed suffix array in 2000, both queries have been supported in $O((\log_σn)^ε)$ time using $O(n\logσ)$ bits, for any constant $ε>0$. Yet no nontrivial time-space lower bound for suffix-array queries was known. We give the first such lower bound. Specifically, we show that, in the cell-probe model with $Θ(\log n)$-bit words, every $S$-bit data structure answering suffix-array queries on binary strings of length at most $n$ has query time $Ω(\log\log n/\log((S/n)\log\log n))$. Consequently, every structure using $O(n(\log\log n)^{O(1)})$ bits requires $Ω(\log\log n/\log\log\log n)$ query time, while constant query time requires $Ω(n\log^εn)$ bits for some constant $ε>0$. In particular, no $O(n)$-bit suffix-array representation for binary texts supports constant-time queries, answering the 25-year-old question of Grossi and Vitter. We also give exact complexity-preserving equivalences between suffix-array access and simpler prefix queries on short strings. For every $2\leqσ\leq n$, suffix-array queries are equivalent to prefix-select queries, and inverse-suffix-array queries are equivalent to prefix-special-rank queries. The reductions in both directions preserve all four standard measures up to constant factors: space, query time, preprocessing time, and preprocessing space. Unlike previous reductions, they incur no additive $O(\log\log n)$ query-time term. Thus, the corresponding prefix-query problems capture suffix-array and inverse-suffix-array access without asymptotic loss in any of the four measures.

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arXiv2026

Random Access in Grammar-Compressed Strings: Optimal Trade-Offs in Almost All Parameter Regimes

A Random Access query to a string $T\in [0..σ)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\logσ)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the worst case, much research has focused on compressible strings, hoping for smaller data structures that still admit efficient queries. We investigate the grammar-compressed setting, where $T$ is represented by a straight-line grammar. Our main result is a general trade-off that optimizes Random Access time as a function of string length $n$, grammar size (the total length of productions) $g$, alphabet size $σ$, data structure size $M$, and word size $w=Ω(\log n)$ of the word RAM model. For any $M$ with $g\log n 0$ [Belazzougui et al.; ESA'15], [Ganardi, Jeż, Lohrey; J. ACM 2021]. The only tight lower bound [Verbin and Yu; CPM'13] was $Ω(\frac{\log n}{\log\log n})$ for $w=Θ(\log n)$, $n^{Ω(1)}\le g\le n^{1-Ω(1)}$, and $M=g\log^{Θ(1)}n$. In contrast, our result yields tight bounds in all relevant parameters and almost all regimes. Our data structure admits efficient deterministic construction. It relies on novel grammar transformations that generalize contracting grammars [Ganardi; ESA'21]. Beyond Random Access, its variants support substring extraction, rank, and select.

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arXiv2026

The Communication Complexity of Pattern Matching with Edits Revisited

In 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), the task is to list the $k$-error occurrences of $P$ in $T$, that is, all fragments of $T$ whose edit distance to $P$ is at most $k$. The one-way communication complexity of Pattern Matching with Edits is the minimum number of bits that Alice, given an instance $(P, T, k)$ of the problem, must send to Bob so that Bob can reconstruct the answer solely from that message. For the natural parameter regime of $0 < k < m < n/2$, our recent work [STOC'24] yields that $Ω(n/m \cdot k \log(m/k))$ bits are necessary and $O(n/m \cdot k \log^2 m)$ bits are sufficient for Pattern Matching with Edits. More generally, for strings over an alphabet $Σ$, our recent work [STOC'24] gives an $O(n/m \cdot k \log m \log(m|Σ|))$-bit encoding that allows one to recover a shortest sequence of edits for every $k$-error occurrence of $P$ in $T$. In this work, we revisit the original proof and improve the encoding size to $O(n/m \cdot k \log(m|Σ|/k))$, which matches the lower bound for constant-sized alphabets. We further establish a new tight lower bound of $Ω(n/m \cdot k \log(m|Σ|/k))$ for the edit sequence reporting variant that we solve. Our encoding size also matches the communication complexity established for the simpler Pattern Matching with Mismatches problem in the context of streaming algorithms [Clifford, Kociumaka, Porat; SODA'19].

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arXiv2026

Time-Optimal Construction of String Synchronizing Sets

A key principle in string processing is local consistency: using short contexts to handle matching fragments of a string consistently. String synchronizing sets [Kempa, Kociumaka; STOC 2019] are an influential instantiation of this principle. A $τ$-synchronizing set of a length-$n$ string is a set of $O(n/τ)$ positions, chosen via their length-$2τ$ contexts, such that (outside highly periodic regions) at least one position in every length-$τ$ window is selected. Among their applications are faster algorithms for data compression, text indexing, and string similarity in the word RAM model. We show how to preprocess any string $T \in [0..σ)^n$ in $O(n\logσ/\log n)$ time so that, for any $τ\in[1..n]$, a $τ$-synchronizing set of $T$ can be constructed in $O((n\logτ)/(τ\log n))$ time. Both bounds are optimal in the word RAM model with word size $w=Θ(\log n)$. Previously, the construction time was $O(n/τ)$, either after an $O(n)$-time preprocessing [Kociumaka, Radoszewski, Rytter, Waleń; SICOMP 2024], or without preprocessing if $τ<0.2\log_σn$ [Kempa, Kociumaka; STOC 2019]. A simple version of our method outputs the set as a sorted list in $O(n/τ)$ time, or as a bitmask in $O(n/\log n)$ time. Our optimal construction produces a compact fully indexable dictionary, supporting select queries in $O(1)$ time and rank queries in $O(\log(\tfrac{\logτ}{\log\log n}))$ time, matching unconditional cell-probe lower bounds for $τ\le n^{1-Ω(1)}$. We achieve this via a new framework for processing sparse integer sequences in a custom variable-length encoding. For rank and select queries, we augment the optimal variant of van Emde Boas trees [Pătraşcu, Thorup; STOC 2006] with a deterministic linear-time construction. The above query-time guarantees hold after preprocessing time proportional to the encoding size (in words).

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arXiv2025

Faster Algorithms for Longest Common Substring

In the classic longest common substring (LCS) problem, we are given two strings $S$ and $T$, each of length at most $n$, over an alphabet of size $σ$, and we are asked to find a longest string occurring as a fragment of both $S$ and $T$. Weiner, in his seminal paper that introduced the suffix tree, presented an $O(n \log σ)$-time algorithm for this problem [SWAT 1973]. For polynomially-bounded integer alphabets, the linear-time construction of suffix trees by Farach yielded an $O(n)$-time algorithm for the LCS problem [FOCS 1997]. However, for small alphabets, this is not necessarily optimal for the LCS problem in the word RAM model of computation, in which the strings can be stored in $O(n \log σ/\log n )$ space and read in $O(n \log σ/\log n )$ time. We show that, in this model, we can compute an LCS in time $O(n \log σ/ \sqrt{\log n})$, which is sublinear in $n$ if $σ=2^{o(\sqrt{\log n})}$ (in particular, if $σ=O(1)$), using optimal space $O(n \log σ/\log n)$. In fact, it was recently shown that this result is conditionally optimal [Kempa and Kociumaka, STOC 2025]. We then lift our ideas to the problem of computing a $k$-mismatch LCS, which has received considerable attention in recent years. In this problem, the aim is to compute a longest substring of $S$ that occurs in $T$ with at most $k$ mismatches. Thankachan et al.~showed how to compute a $k$-mismatch LCS in $O(n \log^k n)$ time for $k=O(1)$ [J. Comput. Biol. 2016]. We show an $O(n \log^{k-1/2} n)$-time algorithm, for any constant $k>0$ and irrespective of the alphabet size, using $O(n)$ space as the previous approaches. We thus notably break through the well-known $n \log^k n$ barrier, which stems from a recursive heavy-path decomposition technique that was first introduced in the seminal paper of Cole et al. [STOC 2004] for string indexing with $k$ errors.

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arXiv2025

Space-Efficient k-Mismatch Text Indexes

A central task in string processing is text indexing, where the goal is to preprocess a text (a string of length $n$) into an efficient index (a data structure) supporting queries about the text. Cole, Gottlieb, and Lewenstein (STOC 2004) proposed $k$-errata trees, a family of text indexes supporting approximate pattern matching queries of several types. In particular, $k$-errata trees yield an elegant solution to $k$-mismatch queries, where we are to report all substrings of the text with Hamming distance at most $k$ to the query pattern. The resulting $k$-mismatch index uses $O(n\log^k n)$ space and answers a query for a length-$m$ pattern in $O(\log^k n \log \log n + m + occ)$ time, where $occ$ is the number of approximate occurrences. In retrospect, $k$-errata trees appear very well optimized: even though a large body of work has adapted $k$-errata trees to various settings throughout the past two decades, the original time-space trade-off for $k$-mismatch indexing has not been improved in the general case. We present the first such improvement, a $k$-mismatch index with $O(n\log^{k-1} n)$ space and the same query time as $k$-errata trees. Previously, due to a result of Chan, Lam, Sung, Tam, and Wong (Algorithmica 2010), such an $O(n\log^{k-1} n)$-size index has been known only for texts over alphabets of constant size. In this setting, however, we obtain an even smaller $k$-mismatch index of size only $O(n \log^{k-2+\varepsilon+\frac{2}{k+2-(k \bmod 2)}} n)\subseteq O(n\log^{k-1.5+\varepsilon} n)$ for $2\le k\le O(1)$ and any constant $\varepsilon>0$. Along the way, we also develop improved indexes for short patterns, offering better trade-offs in this practically relevant special case.

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arXiv2025

Explaining the Inherent Tradeoffs for Suffix Array Functionality: Equivalences between String Problems and Prefix Range Queries

We study the fundamental question of how efficiently suffix array entries can be accessed when the array cannot be stored explicitly. The suffix array $SA_T[1..n]$ of a text $T$ of length $n$ encodes the lexicographic order of its suffixes and underlies numerous applications in pattern matching, data compression, and bioinformatics. Previous work established one-way reductions showing how suffix array queries can be answered using, for example, rank queries on the Burrows-Wheeler Transform. More recently, a new class of prefix queries was introduced, together with reductions that, among others, transform a simple tradeoff for prefix-select queries into a suffix array tradeoff matching state-of-the-art space and query-time bounds, while achieving sublinear construction time. For binary texts, the resulting data structure achieves space $O(n)$ bits, preprocessing time $O(n / \sqrt{\log n})$, preprocessing space of $O(n)$ bits, and query time $O(\log^ε n)$ for any constant $ε> 0$. However, whether these bounds could be improved using different techniques has remained open. We resolve this question by presenting the first bidirectional reduction showing that suffix array queries are, up to an additive $O(\log\log n)$ term in query time, equivalent to prefix-select queries in all parameters. This result unifies prior approaches and shows that essentially all efficient suffix array representations can be expressed via prefix-select structures. Moreover, we prove analogous equivalences for inverse suffix array queries, pattern ranking, lexicographic range, and SA-interval queries, identifying six core problem pairs that connect string and prefix query models. Our framework thus provides a unified foundation for analyzing and improving the efficiency of fundamental string-processing problems through the lens of prefix queries.

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arXiv2025

Tight Lower Bounds for Central String Queries in Compressed Space

In this work, we study the limits of compressed data structures, i.e., structures that support various queries on an input text $T\inΣ^n$ using space proportional to the size of $T$ in compressed form. Nearly all fundamental queries can currently be efficiently supported in $O(δ(T)\log^{O(1)}n)$ space, where $δ(T)$ is the substring complexity, a strong compressibility measure that lower-bounds the optimal space to represent the text [Kociumaka, Navarro, Prezza, IEEE Trans. Inf. Theory 2023]. However, optimal query time has been characterized only for random access. We address this gap by developing tight lower bounds for nearly all other fundamental queries: (1) We prove that suffix array (SA), inverse suffix array (SA$^{-1}$), longest common prefix (LCP) array, and longest common extension (LCE) queries all require $Ω(\log n/\log\log n)$ time within $O(δ(T)\log^{O(1)}n)$ space, matching known upper bounds. (2) We further show that other common queries, currently supported in $O(\log\log n)$ time and $O(δ(T)\log^{O(1)}n)$ space, including the Burrows-Wheeler Transform (BWT), permuted longest common prefix (PLCP) array, Last-to-First (LF), inverse LF, lexicographic predecessor ($Φ$), and inverse $Φ$ queries, all require $Ω(\log\log n)$ time, yielding another set of tight bounds. Our lower bounds hold even for texts over a binary alphabet. This work establishes a clean dichotomy: the optimal time complexity to support central string queries in compressed space is either $Θ(\log n/\log\log n)$ or $Θ(\log\log n)$. This completes the theoretical foundation of compressed indexing, closing a crucial gap between upper and lower bounds and providing a clear target for future data structures: seeking either the optimal time in the smallest space or the fastest time in the optimal space, both of which are now known for central string queries.

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arXiv2025

Near-Optimal Property Testers for Pattern Matching

The classic exact pattern matching problem, given two strings -- a pattern $P$ of length $m$ and a text $T$ of length $n$ -- asks whether $P$ occurs as a substring of $T$. A property tester for the problem needs to distinguish (with high probability) the following two cases for some threshold $k$: the YES case, where $P$ occurs as a substring of $T$, and the NO case, where $P$ has Hamming distance greater than $k$ from every substring of $T$, that is, $P$ has no $k$-mismatch occurrence in $T$. In this work, we provide adaptive and non-adaptive property testers for the exact pattern matching problem, jointly covering the whole spectrum of parameters. We further establish unconditional lower bounds demonstrating that the time and query complexities of our algorithms are optimal, up to $\mathrm{polylog}\, n$ factors hidden within the $\tilde O(\cdot)$ notation below. In the most studied regime of $n=m+Θ(m)$, our non-adaptive property tester has the time complexity of $\tilde O(n/\sqrt{k})$, and a matching lower bound remains valid for the query complexity of adaptive algorithms. This improves both upon a folklore solution that attains the optimal query complexity but requires $Ω(n)$ time, and upon the only previously known sublinear-time property tester, by Chan, Golan, Kociumaka, Kopelowitz, and Porat [STOC 2020], with time complexity $\tilde O(n/\sqrt[3]{k})$. The aforementioned results remain valid for $n=m+Ω(m)$, where our optimal running time $\tilde O(\sqrt{nm/k}+n/k)$ improves upon the previously best time complexity of $\tilde O(\sqrt[3]{n^2m/k}+n/k)$. In the regime of $n=m+o(m)$, which has not been targeted in any previous work, we establish a surprising separation between adaptive and non-adaptive algorithms, whose optimal time and query complexities are $\tilde O(\sqrt{(n-m+1)m/k}+n/k)$ and $\tilde O(\min(n\sqrt{n-m+1}/k,\sqrt{nm/k}+n/k))$, respectively.

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arXiv2025

Pattern Matching under Weighted Edit Distance

In Pattern Matching with Weighted Edits (PMWED), we are given a pattern $P$ of length $m$, a text $T$ of length $n$, a positive threshold $k$, and oracle access to a weight function that specifies the costs of edits (depending on the involved characters, and normalized so that the cost of each edit is at least $1$). The goal is to compute the starting positions of all fragments of $T$ that can be obtained from $P$ with edits of total cost at most $k$. PMWED captures typical real-world applications more accurately than its unweighted variant (PMED), where all edits have unit costs. We obtain three main results: (a) a conceptually simple $\tilde{O}(nk)$-time algorithm for PMWED, very different from that of Landau and Vishkin for PMED; (b) a significantly more complicated $\tilde{O}(n+k^{3.5} \cdot W^4\cdot n/m)$-time algorithm for PMWED under the assumption that the weight function is a metric with integer values between $0$ and $W$; and (c) an $\tilde{O}(n+k^4 \cdot n/m)$-time algorithm for PMWED for the case of arbitrary weights. In the setting of metrics with small integer values, we nearly match the state of the art for PMED where $W=1$.

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arXiv2025

Dynamic Dyck and Tree Edit Distance: Decompositions and Reductions to String Edit Distance

We present the first dynamic algorithms for Dyck and tree edit distances with subpolynomial update times. Dyck edit distance measures how far a parenthesis string is from a well-parenthesized expression, while tree edit distance quantifies the minimum number of node insertions, deletions, and substitutions required to transform one rooted, ordered, labeled tree into another. Despite extensive study, no prior work has addressed efficient dynamic algorithms for these problems, which naturally arise in evolving structured data such as LaTeX documents, JSON or XML files, and RNA secondary structures. Our main contribution is a set of reductions and decompositions that transform Dyck and tree edit distance instances into efficiently maintainable string edit distance instances, which can be approximated within a $n^{o(1)}$ factor in $n^{o(1)}$ update time. For Dyck edit distance, our reduction incurs only polylogarithmic overheads in approximation and update time, yielding an $n^{o(1)}$-approximation with $n^{o(1)}$ updates. For tree edit distance, we introduce a new static reduction that improves the best-known approximation ratio from $n^{3/4}$ to $\tilde{O}(\sqrt{n})$ and removes the restriction to constant-degree trees. Extending this reduction dynamically achieves $n^{1/2+o(1)}$ approximation with $n^{o(1)}$ update time. A key component is a dynamic maintenance algorithm for history-independent heavy-light decompositions, of independent interest. We also provide a novel static and dynamic decomposition achieving an $O(k \log n)$-approximation when the tree edit distance is at most $k$. Combined with the trivial bound $k \le n$, this yields a dynamic deterministic $O(\sqrt{n \log n})$-approximation. In the static setting, our algorithm runs in near-linear time; dynamically, it requires only polylogarithmic updates, improving on prior linear-time static $O(\sqrt{n})$-approximation.

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arXiv2025

Core-Sparse Monge Matrix Multiplication: Improved Algorithm and Applications

Min-plus matrix multiplication is used in many problems operating on distances in graphs or solvable by dynamic programming. Assuming the APSP hypothesis, there is no subcubic-time algorithm for the min-plus product of two general $n\times n$ matrices, but structured matrices admit faster solutions. Planar graph algorithms often use Monge matrices, which have an $O(n^2)$-time min-plus multiplication procedure. Many results for sequence alignment problems, such as edit distance and longest increasing subsequence, apply simple unit-Monge matrices, whose min-plus product can be computed in $O(n\log n)$ time [Tiskin, SODA'10]. Russo [SPIRE'11] identified the core size $δ$ as the structural parameter behind the underlying matrix representation and showed an $O((n+δ)\log^3 n)$-time min-plus multiplication procedure for arbitrary Monge matrices. In this work, we prove a linear bound on the core size of the product matrix in terms of the core sizes of the input matrices and show how to solve the core-sparse Monge matrix multiplication problem in $O((n+δ)\log n)$ time, matching the complexity for simple unit-Monge matrices, where $δ= O(n)$. As witnessed by the recent work of Gorbachev and Kociumaka [STOC'25] for edit distance with integer weights, our generalization opens up the possibility of speed-ups for weighted sequence alignment problems. Furthermore, our multiplication algorithm can efficiently recover the witness for any entry of the output matrix. This allows us, for example, to preprocess an integer array of size $n$ in $\tilde{O}(n)$ time so that the longest increasing subsequence of any sub-array can be reconstructed in $\tilde{O}(\ell)$ time, where $\ell$ is the length of the reported subsequence. In comparison, Karthik C. S. and Rahul [arXiv, 2024] recently achieved $\tilde{O}(\ell+n^{1/2})$-time reporting after $\tilde{O}(n^{3/2})$-time preprocessing.

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arXiv2025

Bounded Weighted Edit Distance: Dynamic Algorithms and Matching Lower Bounds

The edit distance $ed(X,Y)$ of two strings $X,Y\in Σ^*$ is the minimum number of character edits (insertions, deletions, and substitutions) needed to transform $X$ into $Y$. Its weighted counterpart $ed^w(X,Y)$ minimizes the total cost of edits, which are specified using a function $w$, normalized so that each edit costs at least one. The textbook dynamic-programming procedure, given strings $X,Y\in Σ^{\le n}$ and oracle access to $w$, computes $ed^w(X,Y)$ in $O(n^2)$ time. Nevertheless, one can achieve better running times if the computed distance, denoted $k$, is small: $O(n+k^2)$ for unit weights [Landau and Vishkin; JCSS'88] and $\tilde{O}(n+\sqrt{nk^3})$ for arbitrary weights [Cassis, Kociumaka, Wellnitz; FOCS'23]. In this paper, we study the dynamic version of the weighted edit distance problem, where the goal is to maintain $ed^w(X,Y)$ for strings $X,Y\in Σ^{\le n}$ that change over time, with each update specified as an edit in $X$ or $Y$. Very recently, Gorbachev and Kociumaka [STOC'25] showed that the unweighted distance $ed(X,Y)$ can be maintained in $\tilde{O}(k)$ time per update after $\tilde{O}(n+k^2)$-time preprocessing; here, $k$ denotes the current value of $ed(X,Y)$. Their algorithm generalizes to small integer weights, but the underlying approach is incompatible with large weights. Our main result is a dynamic algorithm that maintains $ed^w(X,Y)$ in $\tilde{O}(k^{3-γ})$ time per update after $\tilde{O}(nk^γ)$-time preprocessing. Here, $γ\in [0,1]$ is a real trade-off parameter and $k\ge 1$ is an integer threshold fixed at preprocessing time, with $\infty$ returned whenever $ed^w(X,Y)>k$. We complement our algorithm with conditional lower bounds showing fine-grained optimality of our trade-off for $γ\in [0.5,1)$ and justifying our choice to fix $k$.

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arXiv2025

Faster Algorithm for Bounded Tree Edit Distance in the Low-Distance Regime

The tree edit distance is a natural dissimilarity measure between rooted ordered trees whose nodes are labeled over an alphabet $Σ$. It is defined as the minimum number of node edits (insertions, deletions, and relabelings) required to transform one tree into the other. In the weighted variant, the edits have associated costs (depending on the involved node labels) normalized so that each cost is at least one, and the goal is to minimize the total cost of edits. The unweighted tree edit distance between two trees of total size $n$ can be computed in $O(n^{2.6857})$ time; in contrast, determining the weighted tree edit distance is fine-grained equivalent to the All-Pairs Shortest Paths problem and requires $n^3/2^{Ω(\sqrt{\log n})}$ time [Nogler et al.; STOC'25]. These super-quadratic running times are unattractive for large but very similar trees, which motivates the bounded version of the problem, where the runtime is parameterized by the computed distance $k$, potentially yielding faster algorithms for $k\ll n$. Previous best algorithms for the bounded unweighted setting run in $O(nk^2\log n)$ time [Akmal & Jin; ICALP'21] and $O(n + k^7\log k)$ time [Das et al.; STOC'23]. For the weighted variant, the only known running time has been $O(n + k^{15})$. We present an $O(n + k^6\log k)$-time algorithm for computing the bounded tree edit distance in both the weighted and unweighted settings. Our approach begins with an alternative $O(nk^2\log n)$-time algorithm that handles weights and is significantly easier to analyze than the existing counterpart. We then introduce a novel optimization that leverages periodic structures within the input trees. To utilize it, we modify the $O(k^5)$-size $O(n)$-time universal kernel, the central component of the prior $O(n + k^{O(1)})$-time algorithms, so that it produces instances containing these periodic structures.

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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.

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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.

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