arXiv subjects

Dominik Köppl

Publications and source records attributed to Dominik Köppl.

At least 19 recordsLinked to original sources

arXiv2026

MacCorles: Minimum Alignment Cost Computation on Run-Length Encoded Strings

We study a tie-breaking variant of the longest common subsequence problem on run-length encoded strings. Given two strings, the goal is first to maximize the number of equal aligned character pairs, as in the classical longest common subsequence problem, and then, among all such alignments, to minimize the alignment length. Equivalently, after maximizing the number of equal pairs, we minimize the number of insertions and deletions. We show that this problem admits a simple block-boundary dynamic program. If the input strings have lengths $N$ and $M$, and their run-length encodings have $n$ and $m$ runs, respectively, the algorithm runs in $O(mN+nM)$ time using $O(nm)$ space. The algorithm treats every pair of runs as a homogeneous block with an explicit transfer function and stores dynamic-programming values only on run boundaries.

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arXiv2026

Indexing Range Maximum-Sum Segment Queries with Offsets

Given an array of $n$ real numbers, the maximum segment sum (MSS) problem is to find a contiguous subarray that has the largest sum. While the MSS problem can be solved optimally with Kadane's algorithm in $O(n)$ time, the study of its indexing version spawned new extensions such as (a) retrieving the MSS after subtracting a query offset parameter for all array entries or (b) retrieving the MSS for arbitrary query ranges. We here study the combination of both problems (a) and (b), which requires retrieving the MSS for arbitrary query ranges after subtracting a query offset parameter for all array entries. For that, we present an index whose query time is only slower than the best known for (a) by a factor of $O(\log n)$. In detail, our index uses $O(n \log n)$ space, supports queries in $O(\log^2 n)$ time, and can be constructed in $O(n \log^3 n)$ time. More generally, for every integer $d$ with $1\le d\le\lceil\log_2 n\rceil$, we give an $O(dn)$-space index with $O(dn^{1/d}\log n)$ query time; in particular, for every fixed $\varepsilon>0$, we obtain linear space and $O(n^\varepsilon\log n)$ query time. As side results, we obtain the same time-space trade-off in terms of the number of runs of a run-length encoded input, deduce a solution for (a) that works in run-length compressed space and time, and prove a tight $Θ(n^{2/3})$ bound on the number of non-compatible offsets for binary arrays. Finally, we give supportive lower bounds for our query problem, showing that there is only a polylogarithmic gap of improvement left.

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arXiv2026

Relaxation of Square-Freeness

We extend the analysis of nonrepetitive sequences of Entringer et al. [Journal of Combinatorial Theory, 1974] to relaxations of equality testing under nonstandard equivalence relations, in particular parameterized equivalence and order-preserving equivalence. For this setting, we introduce $\ell^+$-squares, defined as squares whose total length is at least $2\ell$. We obtain an infinite $3^+$-parameterized-square-free ternary word and an infinite $3^+$-order-preserving-square-free binary word through an approach based on combinatorics on words. In addition, we report the longest $\ell^+$-square-free words across several equivalence relations.

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arXiv2026

Online Computation of the Longest Repeating Suffix and Smallest Suffixient Sets via Incremental Run-Length BWT-based Indexes

We revisit the online construction of \emph{smallest suffixient sets} and the online computation of the \emph{longest repeating suffix} (LRS). We give the first compressed-space online construction of smallest suffixient sets, and present two space-time trade-offs for both problems: $O(r\log n+n)$ bits of working space and $O(\log^2 n/\log \log n)$ worst-case time per character, and $O(r\log n+n \log \log n)$ bits of working space and $O((\log n/\log \log n)^2)$ worst-case time per character. Here, $r$ is the number of runs in the Burrows-Wheeler transform of the reverse of $T[1..n]$. In particular, for highly repetitive texts satisfying $r=O(n/\log n)$, the first trade-off uses $O(n)$ bits of working space, while the second uses $O(n\log\log n)$ bits. We also prove that any deterministic online algorithm for computing LRS requires $Ω(n)$ bits of peak working space in the worst case, even over a constant-size alphabet. Through reductions from online LRS computation, we extend this lower bound to deterministic online algorithms maintaining either an arbitrary smallest suffixient set augmented with the length of the supermaximal right extension represented by each selected position, or the position-only smallest suffixient set obtained by selecting the rightmost occurrence of every such extension. For constructing smallest suffixient sets, our algorithms are the first online solutions using compressed working space, improving the $O(n)$-word space required by previous online constructions. For compressed-space online LRS computation, compared with the algorithm of Prezza and Rosone~[CiE 2020], our bounds improve their $O(\log^2 n)$ amortized time per character by factors of $Θ(\log\log n)$ and $Θ((\log\log n)^2)$, respectively, while also providing worst-case guarantees.

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arXiv2026

Compact multi-text index for circular Cartesian tree matching

Cartesian tree matching (CTM) is a structural pattern matching approach that identifies sequences with the same Cartesian tree topology, making it suitable for data with natural variability where exact comparisons carry little semantic meaning. While theoretical algorithms for CTM have been studied extensively, systematic empirical evaluations of practical implementations remain rare. This article presents an implementation of the Cartesian Extended Burrows-Wheeler Transform (ceBWT), a BWT-based index structure for CTM. The implementation supports both a dynamically extendable and a statically compressed index variant.

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arXiv2026

Grammar Index By Induced Suffix Sorting

Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new compressed text index built upon a grammar compression based on induced suffix sorting [Nunes et al., DCC'18]. We show that this grammar exhibits a locality sensitive parsing property, which allows us to specify, given a pattern $P$, certain substrings of $P$, called cores, that are similarly parsed in the text grammar whenever these occurrences are extensible to occurrences of $P$. Supported by the cores, given a pattern of length $m$, we can locate all its $occ$ occurrences in a text $T$ of length $n$ within $O(m \lg |\mathcal{S}| + occ_C \lg|\mathcal{S}| \lg n + occ)$ time, where $\mathcal{S}$ is the set of all characters and non-terminals, $occ$ is the number of occurrences, and $occ_C$ is the number of occurrences of a chosen core $C$ of $P$ in the right hand side of all production rules of the grammar of $T$. Our grammar index requires $O(g)$ words of space and can be built in $O(n)$ time using $O(g)$ working space, where $g$ is the sum of the right hand sides of all production rules. We underline the strength of our grammar index with an exhaustive practical evaluation that gives evidence that our proposed solution excels at locating long patterns in highly-repetitive texts.

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arXiv2026

Counting Distinct (Non-)Crossing Substrings in Optimal Time

Let $w$ be a string of length $n$. The problem of counting factors crossing a position -- Problem 64 from the textbook ``125 Problems in Text Algorithms'' [Crochemore, Lecroq, and Rytter, 2021] -- asks to count the number $\mathcal{C}(w,k)$ (resp. $\mathcal{N}(w,k)$) of distinct substrings in $w$ that have occurrences containing (resp. not containing) a position $k$ in $w$. The solutions provided in their textbook compute $\mathcal{C}(w,k)$ and $\mathcal{N}(w,k)$ in $O(n)$ time for a single position $k$ in $w$, and thus a direct application would require $O(n^2)$ time for all positions $k = 1, \ldots, n$ in $w$. Their solution is designed for constant-size alphabets. In this paper, we present new algorithms which compute $\mathcal{C}(w,k)$ in $O(n)$ total time for general ordered alphabets, and $\mathcal{N}(w,k)$ in $O(n)$ total time for linearly sortable alphabets,for all positions $k = 1, \ldots, n$ in $w$. We further derive model-dependent optimal bounds by separating the algorithms into preprocessing and linear-time postprocessing: for $\mathcal{C}$ the preprocessing is run reporting, and for $\mathcal{N}$ it is preprocessing based on longest previous non-overlapping factors (LPnF) and longest next factors (LNF). In particular, all values $\mathcal{C}(w,k)$ can be computed in $O(n\log n)$ time over general unordered alphabets in which direct accesses to alphabet characters are restricted to equality tests, and in $O(n\logσ)$ time in the word RAM model, where $σ$ denotes the number of distinct characters occurring in $w$. For $\mathcal{N}(w,k)$, the equality-testing complexity over general unordered alphabets is $Θ(n^2)$. We also show that our upper bounds are optimal for all of the aforementioned alphabet assumptions and computation models.

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arXiv2026

Smallest suffixient set maintenance in near-real-time

The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to maintain the smallest suffixient set online in near-real-time, that is with small (in our case, polyloglog) worst-case time on processing each letter. Two frameworks are considered: when the text is given letter-by-letter in either a right-to-left or left-to-right direction. Our central algorithmic tool is Weiner's suffix tree algorithm and associated algorithmic primitives for its efficient implementation.

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arXiv2026

The Smallest String Attractors of Fibonacci and Period-Doubling Words

A string attractor of a string $T[1..|T|]$ is a set of positions $Γ$ of $T$ such that any substring $w$ of $T$ has an occurrence that crosses a position in $Γ$, i.e., there is a position $i$ such that $w = T[i..i+|w|-1]$ and the intersection $[i,i+|w|-1]\cap Γ$ is nonempty. The size of the smallest string attractor of Fibonacci words is known to be $2$. We completely characterize the set of all smallest string attractors of Fibonacci words, and show a recursive formula describing the $2^{n-4} + 2^{\lceil n/2 \rceil - 2}$ distinct position pairs that are the smallest string attractors of the $n$th Fibonacci word for $n \geq 7$. Similarly, the size of the smallest string attractor of period-doubling words is known to be $2$. We also completely characterize the set of all smallest string attractors of period-doubling words, and show a formula describing the two distinct position pairs that are the smallest string attractors of the $n$th period-doubling word for $n\geq 2$. Our results show that strings with the same smallest attractor size can have a drastically different number of distinct smallest attractors.

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arXiv2026

Near-real-time Solutions for Online String Problems

Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings, including the computation of the longest repeating suffix array, the (reversed) Lempel-Ziv 77 factorization, and the maintenance of minimal unique substrings, all in an online manner. Our solutions improve over the best known running times for these problems in terms of the worst-case time per letter, for which we achieve a poly-log-logarithmic time complexity, within a linear space. Best known results for these problems require a poly-logarithmic time complexity per letter or only provide amortized complexity bounds. As a result of independent interest, we give conversions between the longest previous factor array and the longest repeating suffix array in space and time bounds based on their irreducible representations, which can have sizes sublinear in the length of the input string.

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arXiv2026

Revisiting the Sparse Matrix Compression Problem

The sparse matrix compression problem asks for a one-dimensional representation of a binary $n \times \ell$ matrix, formed by an integer array of row indices and a shift function for each row, such that accessing a matrix entry is possible in constant time by consulting this representation. It has been shown that the decision problem for finding an integer array of length $\ell+ρ$ or restricting the shift function up to values of $ρ$ is NP-complete (cf. the textbook of Garey and Johnson). As a practical heuristic, a greedy algorithm has been proposed to shift the $i$-th row until it forms a solution with its predecessor rows. Despite that this greedy algorithm is cherished for its good approximation in practice, we show that it actually exhibits an approximation ratio of $Θ(\sqrt{\ell+ρ})$. We give further hardness results for parameterizations such as the number of distinct rows or the maximum number of non-zero entries per row. Finally, we devise a DP-algorithm that solves the problem for double-logarithmic matrix widths or logarithmic widths for further restrictions. We study all these findings also under a new perspective by introducing a variant of the problem, where we wish to minimize the length of the resulting integer array by trimming the non-zero borders, which has not been studied in the literature before but has practical motivations.

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arXiv2025

LZ78 Substring Compression in Compressed Space

The Lempel--Ziv 78 (LZ78) factorization is a well-studied technique for data compression. It and its derivatives are used in compression formats such as "compress" or "gif". Although most research focuses on the factorization of plain data, not much research has been conducted on indexing the data for fast LZ78 factorization. Here, we study the LZ78 factorization and its derivatives in the substring compression model, where we are allowed to index the data and return the factorization of a substring specified at query time. In that model, we propose an algorithm that works in compressed space, computing the factorization with a logarithmic slowdown compared to the optimal time complexity.

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arXiv2025

LZD-style Compression Scheme with Truncation and Repetitions

Lempel-Ziv-Double (LZD) is a variation of the LZ78 compression scheme that achieves better compression on repetitive datasets. Nevertheless, prior research has identified computational inefficiencies and a weakness in its compressibility for certain datasets. In this paper, we introduce LZD+, an enhancement of LZD, which enables expected linear-time online compression by allowing truncated references. To avoid the compressibility weakness exhibited by a lower bound example, we propose LZDR (LZD-runlength compressed), a further enhancement on top of LZD+, which introduces a repetition-based factorization rule while maintaining linear expected time complexity. The both time bounds can be de-randomized by a lookup data structure like a balanced search tree with a logarithmic dependency on the alphabet size. Additionally, we present three flexible parsing variants of LZDR that yield fewer factors in practice. Comprehensive benchmarking on standard corpora reveals that LZD+, LZDR, and its flexible variants outperform existing LZ-based methods in the number of factors while keeping competitive runtime efficiency. However, we note that the difference in the number of factors becomes marginal for large datasets like those of the Pizza&Chili corpus.

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arXiv2024

Extending the Burrows-Wheeler Transform for Cartesian Tree Matching and Constructing It

Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can be of interest for melody matching between musical scores. For the indexing problem, the state-of-the-art data structure is a Burrows-Wheeler transform based solution due to [Kim and Cho, CPM'21], which uses nearly succinct space and can count the number of substrings that Cartesian tree match with a pattern in time linear in the pattern length. The authors address the construction of their data structure with a straight-forward solution that, however, requires pointer-based data structures, which asymptotically need more space than compact solutions [Kim and Cho, CPM'21, Section A.4]. We address this bottleneck by a construction that requires compact space and has a time complexity linear in the product of the text length with some logarithmic terms. Additionally, we can extend this index for indexing multiple circular texts in the spirit of the extended Burrows-Wheeler transform without sacrificing the time and space complexities. We present this index in a dynamic variant, where we pay a logarithmic slowdown and need compact space for the extra functionality that we can incrementally add texts. Our extended setting is of interest for finding repetitive motifs common in the aforementioned applications, independent of offsets and scaling.

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arXiv2024

Hardness Results on Characteristics for Elastic-Degenerated Strings

Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores a character at each of its positions, generalizations consider a set of characters (indeterminate strings), a set of strings of equal length (generalized degenerate strings, or shortly GD strings), or a set of strings of arbitrary lengths (elastic-degenerate strings, or shortly ED strings). These generalizations are of importance to compactly represent such type of data, and find applications in bioinformatics for representing and maintaining a set of genetic sequences of the same taxonomy or a multiple sequence alignment. To be of use, attention has been drawn to answering various query types such as pattern matching or measuring similarity of ED strings by generalizing techniques known to plain strings. However, for some types of queries, it has been shown that a generalization of a polynomial-time solvable query on classic strings becomes NP-hard on ED strings, e.g. [Russo et al.,2022]. In that light, we wonder about other types of queries, which are of particular interest to bioinformatics: the search for the longest repeating factor, unique substrings, absent words, anti-powers, and longest previous factors. While we obtain a polynomial time algorithm for the first problem on ED strings, we show that all others are NP-hard to compute, some of them even under the restriction that the input can be modelled as an indeterminate or GD string.

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arXiv2024

Substring Compression Variations and LZ78-Derivates

We propose algorithms computing the semi-greedy Lempel-Ziv 78 (LZ78), the Lempel-Ziv Double (LZD), and the Lempel-Ziv-Miller-Wegman (LZMW) factorizations in linear time for integer alphabets. For LZD and LZMW, we additionally propose data structures that can be constructed in linear time, which can solve the substring compression problems for these factorizations in time linear in the output size. For substring compression, we give results for lexparse and closed factorizations.

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arXiv2024

Space-time Trade-offs for the LCP Array of Wheeler DFAs

Recently, Conte et al. generalized the longest-common prefix (LCP) array from strings to Wheeler DFAs, and they showed that it can be used to efficiently determine matching statistics on a Wheeler DFA [DCC 2023]. However, storing the LCP array requires $ O(n \log n) $ bits, $ n $ being the number of states, while the compact representation of Wheeler DFAs often requires much less space. In particular, the BOSS representation of a de Bruijn graph only requires a linear number of bits, if the size of alphabet is constant. In this paper, we propose a sampling technique that allows to access an entry of the LCP array in logarithmic time by only storing a linear number of bits. We use our technique to provide a space-time trade-off to compute matching statistics on a Wheeler DFA. In addition, we show that by augmenting the BOSS representation of a $ k $-th order de Bruijn graph with a linear number of bits we can navigate the underlying variable-order de Bruijn graph in time logarithmic in $ k $, thus improving a previous bound by Boucher et al. which was linear in $ k $ [DCC 2015].

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arXiv2024

Bijective BWT based compression schemes

We investigate properties of the bijective Burrows-Wheeler transform (BBWT). We show that for any string $w$, a bidirectional macro scheme of size $O(r_B)$ can be induced from the BBWT of $w$, where $r_B$ is the number of maximal character runs in the BBWT. We also show that $r_B = O(z\log^2 n)$, where $n$ is the length of $w$ and $z$ is the number of Lempel-Ziv 77 factors of $w$. Then, we show a separation between BBWT and BWT by a family of strings with $r_B = Ω(\log n)$ but having only $r=2$ maximal character runs in the standard Burrows--Wheeler transform (BWT). However, we observe that the smallest $r_B$ among all cyclic rotations of $w$ is always at most $r$. While an $o(n^2)$ algorithm for computing an optimal rotation giving the smallest $r_B$ is still open, we show how to compute the Lyndon factorizations -- a component for computing BBWT -- of all cyclic rotations in $O(n)$ time. Furthermore, we conjecture that we can transform two strings having the same Parikh vector to each other by BBWT and rotation operations, and prove this conjecture for the case of binary alphabets and permutations.

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