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Dominik Köppl

Publications and source records attributed to Dominik Köppl.

54 records · Page 3Linked to original sources
arXiv2021

PHONI: Streamed Matching Statistics with Multi-Genome References

Computing the matching statistics of patterns with respect to a text is a fundamental task in bioinformatics, but a formidable one when the text is a highly compressed genomic database. Bannai et al. gave an efficient solution for this case, which Rossi et al. recently implemented, but it uses two passes over the patterns and buffers a pointer for each character during the first pass. In this paper, we simplify their solution and make it streaming, at the cost of slowing it down slightly. This means that, first, we can compute the matching statistics of several long patterns (such as whole human chromosomes) in parallel while still using a reasonable amount of RAM; second, we can compute matching statistics online with low latency and thus quickly recognize when a pattern becomes incompressible relative to the database.

cs.DS↗
arXiv2020

c-trie++: A Dynamic Trie Tailored for Fast Prefix Searches

Given a dynamic set $K$ of $k$ strings of total length $n$ whose characters are drawn from an alphabet of size $σ$, a keyword dictionary is a data structure built on $K$ that provides locate, prefix search, and update operations on $K$. Under the assumption that $α= w / \lg σ$ characters fit into a single machine word $w$, we propose a keyword dictionary that represents $K$ in $n \lg σ+ Θ(k \lg n)$ bits of space, supporting all operations in $O(m / α+ \lg α)$ expected time on an input string of length $m$ in the word RAM model. This data structure is underlined with an exhaustive practical evaluation, highlighting the practical usefulness of the proposed data structure, especially for prefix searches - one of the most elementary keyword dictionary operations.

cs.DS↗
arXiv2020

Space-Efficient Algorithms for Computing Minimal/Shortest Unique Substrings

Given a string $T$ of length $n$, a substring $u = T[i..j]$ of $T$ is called a shortest unique substring (SUS) for an interval $[s,t]$ if (a) $u$ occurs exactly once in $T$, (b) $u$ contains the interval $[s,t]$ (i.e. $i \leq s \leq t \leq j$), and (c) every substring $v$ of $T$ with $|v| < |u|$ containing $[s,t]$ occurs at least twice in $T$. Given a query interval $[s, t] \subset [1, n]$, the interval SUS problem is to output all the SUSs for the interval $[s,t]$. In this article, we propose a $4n + o(n)$ bits data structure answering an interval SUS query in output-sensitive $O(\mathit{occ})$ time, where $\mathit{occ}$ is the number of returned SUSs. Additionally, we focus on the point SUS problem, which is the interval SUS problem for $s = t$. Here, we propose a $\lceil (\log_2{3} + 1)n \rceil + o(n)$ bits data structure answering a point SUS query in the same output-sensitive time. We also propose space-efficient algorithms for computing the minimal unique substrings of $T$.

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arXiv2020

Dynamic Path-Decomposed Tries

A keyword dictionary is an associative array whose keys are strings. Recent applications handling massive keyword dictionaries in main memory have a need for a space-efficient implementation. When limited to static applications, there are a number of highly-compressed keyword dictionaries based on the advancements of practical succinct data structures. However, as most succinct data structures are only efficient in the static case, it is still difficult to implement a keyword dictionary that is space efficient and dynamic. In this article, we propose such a keyword dictionary. Our main idea is to embrace the path decomposition technique, which was proposed for constructing cache-friendly tries. To store the path-decomposed trie in small memory, we design data structures based on recent compact hash trie representations. Experiments on real-world datasets reveal that our dynamic keyword dictionary needs up to 68% less space than the existing smallest ones, while achieving a relevant space-time tradeoff.

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arXiv2020

Grammar-compressed Self-index with Lyndon Words

We introduce a new class of straight-line programs (SLPs), named the Lyndon SLP, inspired by the Lyndon trees (Barcelo, 1990). Based on this SLP, we propose a self-index data structure of $O(g)$ words of space that can be built from a string $T$ in $O(n \lg n)$ expected time, retrieving the starting positions of all occurrences of a pattern $P$ of length $m$ in $O(m + \lg m \lg n + occ \lg g)$ time, where $n$ is the length of $T$, $g$ is the size of the Lyndon SLP for $T$, and $occ$ is the number of occurrences of $P$ in $T$.

cs.DS↗
arXiv2020

In-Place Bijective Burrows-Wheeler Transforms

One of the most well-known variants of the Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994] is the bijective BWT (BBWT) [Gil and Scott, arXiv 2012], which applies the extended BWT (EBWT) [Mantaci et al., TCS 2007] to the multiset of Lyndon factors of a given text. Since the EBWT is invertible, the BBWT is a bijective transform in the sense that the inverse image of the EBWT restores this multiset of Lyndon factors such that the original text can be obtained by sorting these factors in non-increasing order. In this paper, we present algorithms constructing or inverting the BBWT in-place using quadratic time. We also present conversions from the BBWT to the BWT, or vice versa, either (a) in-place using quadratic time, or (b) in the run-length compressed setting using $O(n \lg r / \lg \lg r)$ time with $O(r \lg n)$ bits of words, where $r$ is the sum of character runs in the BWT and the BBWT.

cs.DS↗
arXiv2019

Bidirectional Text Compression in External Memory

Bidirectional compression algorithms work by substituting repeated substrings by references that, unlike in the famous LZ77-scheme, can point to either direction. We present such an algorithm that is particularly suited for an external memory implementation. We evaluate it experimentally on large data sets of size up to 128 GiB (using only 16 GiB of RAM) and show that it is significantly faster than all known LZ77 compressors, while producing a roughly similar number of factors. We also introduce an external memory decompressor for texts compressed with any uni- or bidirectional compression scheme.

cs.DS↗
arXiv2019

Re-Pair In Small Space

Re-Pair is a grammar compression scheme with favorably good compression rates. The computation of Re-Pair comes with the cost of maintaining large frequency tables, which makes it hard to compute Re-Pair on large scale data sets. As a solution for this problem we present, given a text of length $n$ whose characters are drawn from an integer alphabet, an $O(n^2) \cap O(n^2 \lg \log_τn \lg \lg \lg n / \log_τn)$ time algorithm computing Re-Pair in $n \lg \max(n,τ)$ bits of space including the text space, where $τ$ is the number of terminals and non-terminals. The algorithm works in the restore model, supporting the recovery of the original input in the time for the Re-Pair computation with $O(\lg n)$ additional bits of working space. We give variants of our solution working in parallel or in the external memory model.

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arXiv2019

Separate Chaining Meets Compact Hashing

While separate chaining is a common strategy for resolving collisions in a hash table taught in most textbooks, compact hashing is a less common technique for saving space when hashing integers whose domain is relatively small with respect to the problem size. It is widely believed that hash tables waste a considerable amount of memory, as they either leave allocated space untouched (open addressing) or store additional pointers (separate chaining). For the former, Cleary introduced the compact hashing technique that stores only a part of a key to save space. However, as can be seen by the line of research focusing on compact hash tables with open addressing, there is additional information, called displacement, required for restoring a key. There are several representations of this displacement information with different space and time trade-offs. In this article, we introduce a separate chaining hash table that applies the compact hashing technique without the need for the displacement information. Practical evaluations reveal that insertions in this hash table are faster or use less space than all previously known compact hash tables on modern computer architectures when storing sufficiently large satellite data.

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arXiv2018

Deterministic Sparse Suffix Sorting in the Restore Model

Given a text $T$ of length $n$, we propose a deterministic online algorithm computing the sparse suffix array and the sparse longest common prefix array of $T$ in $O(c \sqrt{\lg n} + m \lg m \lg n \lg^* n)$ time with $O(m)$ words of space under the premise that the space of $T$ is rewritable, where $m \le n$ is the number of suffixes to be sorted (provided online and arbitrarily), and $c$ is the number of characters with $m \le c \le n$ that must be compared for distinguishing the designated suffixes.

cs.DS↗
arXiv2017

Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries

We present the first thorough practical study of the Lempel-Ziv-78 and the Lempel-Ziv-Welch computation based on trie data structures. With a careful selection of trie representations we can beat well-tuned popular trie data structures like Judy, m-Bonsai or Cedar.

cs.DS↗
arXiv2017

Computing All Distinct Squares in Linear Time for Integer Alphabets

Given a string on an integer alphabet, we present an algorithm that computes the set of all distinct squares belonging to this string in time linear to the string length. As an application, we show how to compute the tree topology of the minimal augmented suffix tree in linear time. Asides from that, we elaborate an algorithm computing the longest previous table in a succinct representation using compressed working space.

cs.DS↗
arXiv2016

On the Benefit of Merging Suffix Array Intervals for Parallel Pattern Matching

We present parallel algorithms for exact and approximate pattern matching with suffix arrays, using a CREW-PRAM with $p$ processors. Given a static text of length $n$, we first show how to compute the suffix array interval of a given pattern of length $m$ in $O(\frac{m}{p}+ \lg p + \lg\lg p\cdot\lg\lg n)$ time for $p \le m$. For approximate pattern matching with $k$ differences or mismatches, we show how to compute all occurrences of a given pattern in $O(\frac{m^kσ^k}{p}\max\left(k,\lg\lg n\right)\!+\!(1+\frac{m}{p}) \lg p\cdot \lg\lg n + \text{occ})$ time, where $σ$ is the size of the alphabet and $p \le σ^k m^k$. The workhorse of our algorithms is a data structure for merging suffix array intervals quickly: Given the suffix array intervals for two patterns $P$ and $P'$, we present a data structure for computing the interval of $PP'$ in $O(\lg\lg n)$ sequential time, or in $O(1+\lg_p\lg n)$ parallel time. All our data structures are of size $O(n)$ bits (in addition to the suffix array).

cs.DS↗
arXiv2016

Lempel-Ziv Computation In Compressed Space (LZ-CICS)

We show that both the Lempel Ziv 77- and the 78-factorization of a text of length $n$ on an integer alphabet of size $σ$ can be computed in $O(n \lg \lg σ)$ time (linear time if we allow randomization) using $O(n \lg σ)$ bits of working space. Given that a compressed representation of the suffix tree is loaded into RAM, we can compute both factorizations in $O(n)$ time using $z \lg n + O(n)$ bits of space, where $z$ is the number of factors.

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arXiv2015

Efficiently Finding All Maximal $α$-gapped Repeats

For $α\geq 1$, an $α$-gapped repeat in a word $w$ is a factor $uvu$ of $w$ such that $|uv|\leq α|u|$; the two factors $u$ in such a repeat are called arms, while the factor $v$ is called gap. Such a repeat is called maximal if its arms cannot be extended simultaneously with the same symbol to the right or, respectively, to the left. In this paper we show that the number of maximal $α$-gapped repeats that may occur in a word is upper bounded by $18αn$. This allows us to construct an algorithm finding all the maximal $α$-gapped repeats of a word in $O(αn)$; this is optimal, in the worst case, as there are words that have $Θ(αn)$ maximal $α$-gapped repeats. Our techniques can be extended to get comparable results in the case of $α$-gapped palindromes, i.e., factors $uvu^\mathrm{T}$ with $|uv|\leq α|u|$.

cs.DS↗
arXiv2015

Lempel Ziv Computation In Small Space (LZ-CISS)

For both the Lempel Ziv 77- and 78-factorization we propose algorithms generating the respective factorization using $(1+ε) n \lg n + O(n)$ bits (for any positive constant $ε\le 1$) working space (including the space for the output) for any text of size \$n\$ over an integer alphabet in $O(n / ε^{2})$ time.

cs.DS↗
arXiv2013

Pseudodifferentialoperatoren mit nichtglatten Koeffizienten auf Mannigfaltigkeiten

A generalization of differential operators are pseudodifferential operators which are used for reasoning about partial differential equations with variable coefficients. A lot of useful properties about classical pseudodifferential operators are already discovered by the works of H. Kumano-Go and L. Hörmander. In this work, we like to transfer their ideas on those operators which symbols are merely Hölder-continous. We focus on the composition of operators, symbol smoothing and operators on manifolds.

math.AP↗