arXiv subjects

Nicola Prezza

Publications and source records attributed to Nicola Prezza.

At least 37 records · Page 2Linked to original sources

arXiv2023

Optimal Wheeler Language Recognition

A Wheeler automaton is a finite state automaton whose states admit a total Wheeler order, reflecting the co-lexicographic order of the strings labeling source-to-node paths. A Wheeler language is a regular language admitting an accepting Wheeler automaton. Wheeler languages admit efficient and elegant solutions to hard problems such as automata compression and regular expression matching, therefore deciding whether a regular language is Wheeler is relevant in applications requiring efficient solutions to those problems. In this paper, we show that it is possible to decide whether a DFA with n states and m transitions recognizes a Wheeler language in $O(mn)$ time. This is a significant improvement over the running time $O(n^{13} + m\log n)$ of the previous polynomial-time algorithm (Alanko et al., Information and Computation 2021). A proof-of-concept implementation of this algorithm is available in a public repository. We complement this upper bound with a conditional matching lower bound stating that, unless the strong exponential time hypothesis (SETH) fails, the problem cannot be solved in strongly subquadratic time. The same problem is known to be PSPACE-complete when the input is an NFA (D'Agostino et al., Theoretical Computer Science 2023). Together with that result, our paper essentially closes the algorithmic problem of Wheeler language recognition.

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arXiv2023

Verifiable Learning for Robust Tree Ensembles

Verifying the robustness of machine learning models against evasion attacks at test time is an important research problem. Unfortunately, prior work established that this problem is NP-hard for decision tree ensembles, hence bound to be intractable for specific inputs. In this paper, we identify a restricted class of decision tree ensembles, called large-spread ensembles, which admit a security verification algorithm running in polynomial time. We then propose a new approach called verifiable learning, which advocates the training of such restricted model classes which are amenable for efficient verification. We show the benefits of this idea by designing a new training algorithm that automatically learns a large-spread decision tree ensemble from labelled data, thus enabling its security verification in polynomial time. Experimental results on public datasets confirm that large-spread ensembles trained using our algorithm can be verified in a matter of seconds, using standard commercial hardware. Moreover, large-spread ensembles are more robust than traditional ensembles against evasion attacks, at the cost of an acceptable loss of accuracy in the non-adversarial setting.

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arXiv2023

Co-lexicographically Ordering Automata and Regular Languages -- Part I

In the present work, we lay out a new theory showing that all automata can always be co-lexicographically partially ordered, and an intrinsic measure of their complexity can be defined and effectively determined, namely, the minimum width $p$ of one of their admissible co-lex partial orders - dubbed here the automaton's co-lex width. We first show that this new measure captures at once the complexity of several seemingly-unrelated hard problems on automata. Any NFA of co-lex width $p$: (i) has an equivalent powerset DFA whose size is exponential in $p$ rather than (as a classic analysis shows) in the NFA's size; (ii) can be encoded using just $Θ(\log p)$ bits per transition; (iii) admits a linear-space data structure solving regular expression matching queries in time proportional to $p^2$ per matched character. Some consequences of this new parametrization of automata are that PSPACE-hard problems such as NFA equivalence are FPT in $p$, and quadratic lower bounds for the regular expression matching problem do not hold for sufficiently small $p$. We prove that a canonical minimum-width DFA accepting a language $\mathcal L$ - dubbed the Hasse automaton $\mathcal H$ of $\mathcal L$ - can be exhibited. Finally, we explore the relationship between two conflicting objectives: minimizing the width and minimizing the number of states of a DFA. In this context, we provide an analogous of the Myhill-Nerode Theorem for co-lexicographically ordered regular languages.

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arXiv2023

Faster Prefix-Sorting Algorithms for Deterministic Finite Automata

Sorting is a fundamental algorithmic pre-processing technique which often allows to represent data more compactly and, at the same time, speeds up search queries on it. In this paper, we focus on the well-studied problem of sorting and indexing string sets. Since the introduction of suffix trees in 1973, dozens of suffix sorting algorithms have been described in the literature. In 2017, these techniques were extended to sets of strings described by means of finite automata: the theory of Wheeler graphs [Gagie et al., TCS'17] introduced automata whose states can be totally-sorted according to the co-lexicographic (co-lex in the following) order of the prefixes of words accepted by the automaton. More recently, in [Cotumaccio, Prezza, SODA'21] it was shown how to extend these ideas to arbitrary automata by means of partial co-lex orders. This work showed that a co-lex order of minimum width (thus optimizing search query times) on deterministic finite automata (DFAs) can be computed in $O(m^2 + n^{5/2})$ time, $m$ being the number of transitions and $n$ the number of states of the input DFA. In this paper, we exhibit new combinatorial properties of the minimum-width co-lex order of DFAs and exploit them to design faster prefix sorting algorithms. In particular, we describe two algorithms sorting arbitrary DFAs in $O(mn)$ and $O(n^2\log n)$ time, respectively, and an algorithm sorting acyclic DFAs in $O(m\log n)$ time. Within these running times, all algorithms compute also a smallest chain partition of the partial order (required to index the DFA). We present an experiment result to show that an optimized implementation of the $O(n^2\log n)$-time algorithm exhibits a nearly-linear behaviour on large deterministic pan-genomic graphs and is thus also of practical interest.

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arXiv2023

Co-lexicographically Ordering Automata and Regular Languages -- Part II

In the present work, we tackle the regular language indexing problem by first studying the hierarchy of $p$-sortable languages: regular languages accepted by automata of width $p$. We show that the hierarchy is strict and does not collapse, and provide (exponential in $p$) upper and lower bounds relating the minimum widths of equivalent NFAs and DFAs. Our bounds indicate the importance of being able to index NFAs, as they enable indexing regular languages with much faster and smaller indexes. Our second contribution solves precisely this problem, optimally: we devise a polynomial-time algorithm that indexes any NFA with the optimal value $p$ for its width, without explicitly computing $p$ (NP-hard to find). In particular, this implies that we can index in polynomial time the well-studied case $p=1$ (Wheeler NFAs). More in general, in polynomial time we can build an index breaking the worst-case conditional lower bound of $Ω(|P| m)$, whenever the input NFA's width is $p \in o(\sqrt{m})$.

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arXiv2023

Computing matching statistics on Wheeler DFAs

Matching statistics were introduced to solve the approximate string matching problem, which is a recurrent subroutine in bioinformatics applications. In 2010, Ohlebusch et al. [SPIRE 2010] proposed a time and space efficient algorithm for computing matching statistics which relies on some components of a compressed suffix tree - notably, the longest common prefix (LCP) array. In this paper, we show how their algorithm can be generalized from strings to Wheeler deterministic finite automata. Most importantly, we introduce a notion of LCP array for Wheeler automata, thus establishing a first clear step towards extending (compressed) suffix tree functionalities to labeled graphs.

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arXiv2021

HOLZ: High-Order Entropy Encoding of Lempel-Ziv Factor Distances

We propose a new representation of the offsets of the Lempel-Ziv (LZ) factorization based on the co-lexicographic order of the processed prefixes. The selected offsets tend to approach the k-th order empirical entropy. Our evaluations show that this choice of offsets is superior to the rightmost LZ parsing and the bit-optimal LZ parsing on datasets with small high-order entropy.

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arXiv2021

Linear-time Minimization of Wheeler DFAs

Wheeler DFAs (WDFAs) are a sub-class of finite-state automata which is playing an important role in the emerging field of compressed data structures: as opposed to general automata, WDFAs can be stored in just $\logσ+ O(1)$ bits per edge, $σ$ being the alphabet's size, and support optimal-time pattern matching queries on the substring closure of the language they recognize. An important step to achieve further compression is minimization. When the input $\mathcal A$ is a general deterministic finite-state automaton (DFA), the state-of-the-art is represented by the classic Hopcroft's algorithm, which runs in $O(|\mathcal A|\log |\mathcal A|)$ time. This algorithm stands at the core of the only existing minimization algorithm for Wheeler DFAs, which inherits its complexity. In this work, we show that the minimum WDFA equivalent to a given input WDFA can be computed in linear $O(|\mathcal A|)$ time. When run on de Bruijn WDFAs built from real DNA datasets, an implementation of our algorithm reduces the number of nodes from 14% to 51% at a speed of more than 1 million nodes per second.

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arXiv2021

Adaptive Learning of Compressible Strings

Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm needs to ask the oracle $σn/4 -O(n)$ queries in order to be able to reconstruct the hidden string, where $σ$ is the size of the alphabet of $S$ and $n$ its length, and gave an algorithm that spends $(σ-1)n+O(σ\sqrt{n})$ queries to reconstruct $S$. The main contribution of our paper is to improve the above upper-bound in the context where the string is compressible. We first present a universal algorithm that, given a (computable) compressor that compresses the string to $τ$ bits, performs $q=O(τ)$ substring queries; this algorithm, however, runs in exponential time. For this reason, the second part of the paper focuses on more time-efficient algorithms whose number of queries is bounded by specific compressibility measures. We first show that any string of length $n$ over an integer alphabet of size $σ$ with $rle$ runs can be reconstructed with $q=O(rle (σ+ \log \frac{n}{rle}))$ substring queries in linear time and space. We then present an algorithm that spends $q \in O(σg\log n)$ substring queries and runs in $O(n(\log n + \log σ)+ q)$ time using linear space, where $g$ is the size of a smallest straight-line program generating the string.

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arXiv2021

On (co-lex) Ordering Automata

The states of a deterministic finite automaton A can be identified with collections of words in Pf(L(A)) -- the set of prefixes of words belonging to the regular language accepted by A. But words can be ordered and among the many possible orders a very natural one is the co-lexicographic one. Such naturalness stems from the fact that it suggests a transfer of the order from words to the automaton's states. In a number of papers automata admitting a total ordering of states coherent with the ordering of the set of words reaching them have been proposed. Such class of ordered automata -- the Wheeler automata -- turned out to be efficiently stored/searched using an index. Unfortunately not all automata can be totally ordered as previously outlined. However, automata can always be partially ordered and an intrinsic measure of their complexity can be defined and effectively determined, as the minimum width of one of their admissible partial orders. As shown in previous works, this new concept of width of an automaton has useful consequences in the fields of graph compression, indexing data structures, and automata theory. In this paper we prove that a canonical, minimum-width, partially-ordered automaton accepting a language L -- dubbed the Hasse automaton H of L -- can be exhibited. H provides, in a precise sense, the best possible way to (partially) order the states of any automaton accepting L, as long as we want to maintain an operational link with the (co-lexicographic) order of Pf(L(A)). Using H we prove that the width of the language can be effectively computed from the minimum automaton recognizing the language. Finally, we explore the relationship between two (often conflicting) objectives: minimizing the width and minimizing the number of states of an automaton.

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arXiv2021

Towards a Definitive Compressibility Measure for Repetitive Sequences

Unlike in statistical compression, where Shannon's entropy is a definitive lower bound, no such clear measure exists for the compressibility of repetitive sequences. Since statistical entropy does not capture repetitiveness, ad-hoc measures like the size $z$ of the Lempel--Ziv parse are frequently used to estimate it. The size $b \le z$ of the smallest bidirectional macro scheme captures better what can be achieved via copy-paste processes, though it is NP-complete to compute and it is not monotonic upon symbol appends. Recently, a more principled measure, the size $γ$ of the smallest string \emph{attractor}, was introduced. The measure $γ\le b$ lower bounds all the previous relevant ones, yet length-$n$ strings can be represented and efficiently indexed within space $O(γ\log\frac{n}γ)$, which also upper bounds most measures. While $γ$ is certainly a better measure of repetitiveness than $b$, it is also NP-complete to compute and not monotonic, and it is unknown if one can always represent a string in $o(γ\log n)$ space. In this paper, we study an even smaller measure, $δ\le γ$, which can be computed in linear time, is monotonic, and allows encoding every string in $O(δ\log\frac{n}δ)$ space because $z = O(δ\log\frac{n}δ)$. We show that $δ$ better captures the compressibility of repetitive strings. Concretely, we show that (1) $δ$ can be strictly smaller than $γ$, by up to a logarithmic factor; (2) there are string families needing $Ω(δ\log\frac{n}δ)$ space to be encoded, so this space is optimal for every $n$ and $δ$; (3) one can build run-length context-free grammars of size $O(δ\log\frac{n}δ)$, whereas the smallest (non-run-length) grammar can be up to $Θ(\log n/\log\log n)$ times larger; and (4) within $O(δ\log\frac{n}δ)$ space we can not only...

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arXiv2020

On Locating Paths in Compressed Tries

In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on top of the XBWT tree transform of Ferragina et al. [FOCS 2005] and generalizes the \emph{r-index} locate machinery of Gagie et al. [SODA 2018, JACM 2020] based on the run-length encoded Burrows-Wheeler transform (BWT). Our first contribution is to propose a suitable generalization of the run-length BWT to tries. We show that this natural generalization enjoys several of the useful properties of its counterpart on strings: in particular, the transform natively supports counting occurrences of a query pattern on the trie's paths and its size $r$ captures the trie's repetitiveness and lower-bounds a natural notion of trie entropy. Our main contribution is a much deeper insight into the combinatorial structure of this object. In detail, we show that a data structure of $O(r\log n) + 2n + o(n)$ bits, where $n$ is the number of nodes, allows locating the $occ$ occurrences of a pattern of length $m$ in nearly-optimal $O(m\logσ+ occ)$ time, where $σ$ is the alphabet's size. Our solution consists in sampling $O(r)$ nodes that can be used as "anchor points" during the locate process. Once obtained the pre-order identifier of the first pattern occurrence (in co-lexicographic order), we show that a constant number of constant-time jumps between those anchor points lead to the identifier of the next pattern occurrence, thus enabling locating in optimal $O(1)$ time per occurrence.

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arXiv2020

Subpath Queries on Compressed Graphs: a Survey

Text indexing is a classical algorithmic problem that has been studied for over four decades: given a text $T$, pre-process it off-line so that, later, we can quickly count and locate the occurrences of any string (the query pattern) in $T$ in time proportional to the query's length. The earliest optimal-time solution to the problem, the suffix tree, dates back to 1973 and requires up to two orders of magnitude more space than the plain text just to be stored. In the year 2000, two breakthrough works showed that efficient queries can be achieved without this space overhead: a fast index be stored in a space proportional to the text's entropy. These contributions had an enormous impact in bioinformatics: nowadays, virtually any DNA aligner employs compressed indexes. Recent trends considered more powerful compression schemes (dictionary compressors) and generalizations of the problem to labeled graphs: after all, texts can be viewed as labeled directed paths. In turn, since finite state automata can be considered as a particular case of labeled graphs, these findings created a bridge between the fields of compressed indexing and regular language theory, ultimately allowing to index regular languages and promising to shed new light on problems such as regular expression matching. This survey is a gentle introduction to the main landmarks of the fascinating journey that took us from suffix trees to today's compressed indexes for labeled graphs and regular languages.

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arXiv2020

Novel Results on the Number of Runs of the Burrows-Wheeler-Transform

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms for sequence data, such as webpages, genomic and other biological sequences, or indeed any textual data. The BWT lends itself well to compression because its number of equal-letter-runs (usually referred to as $r$) is often considerably lower than that of the original string; in particular, it is well suited for strings with many repeated factors. In fact, much attention has been paid to the $r$ parameter as measure of repetitiveness, especially to evaluate the performance in terms of both space and time of compressed indexing data structures. In this paper, we investigate $ρ(v)$, the ratio of $r$ and of the number of runs of the BWT of the reverse of $v$. Kempa and Kociumaka [FOCS 2020] gave the first non-trivial upper bound as $ρ(v) = O(\log^2(n))$, for any string $v$ of length $n$. However, nothing is known about the tightness of this upper bound. We present infinite families of binary strings for which $ρ(v) = Θ(\log n)$ holds, thus giving the first non-trivial lower bound on $ρ(n)$, the maximum over all strings of length $n$. Our results suggest that $r$ is not an ideal measure of the repetitiveness of the string, since the number of repeated factors is invariant between the string and its reverse. We believe that there is a more intricate relationship between the number of runs of the BWT and the string's combinatorial properties.

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arXiv2020

On Indexing and Compressing Finite Automata

An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of indexing arbitrary finite automata. Our solution consists in finding a partial co-lexicographic order of the states and proving, as in the total order case, that states reached by a given string form one interval on the partial order, thus enabling indexing. We provide a lower bound stating that such an interval requires $O(p)$ words to be represented, $p$ being the order's width (i.e. the size of its largest antichain). Indeed, we show that $p$ determines the complexity of several fundamental problems on finite automata: (i) Letting $σ$ be the alphabet size, we provide an encoding for NFAs using $\lceil\log σ\rceil + 2\lceil\log p\rceil + 2$ bits per transition and a smaller encoding for DFAs using $\lceil\log σ\rceil + \lceil\log p\rceil + 2$ bits per transition. This is achieved by generalizing the Burrows-Wheeler transform to arbitrary automata. (ii) We show that indexed pattern matching can be solved in $\tilde O(m\cdot p^2)$ query time on NFAs. (iii) We provide a polynomial-time algorithm to index DFAs, while matching the optimal value for $ p $. On the other hand, we prove that the problem is NP-hard on NFAs. (iv) We show that, in the worst case, the classic powerset construction algorithm for NFA determinization generates an equivalent DFA of size $2^p(n-p+1)-1$, where $n$ is the number of NFA's states.

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arXiv2020

Optimal Substring-Equality Queries with Applications to Sparse Text Indexing

We consider the problem of encoding a string of length $n$ from an integer alphabet of size $σ$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any uniquely-decodable encoding supporting access must take $n\logσ+ Θ(\log (n\logσ))$ bits. We describe a new data structure matching this lower bound when $σ\leq n^{O(1)}$ while supporting both queries in optimal $O(1)$ time. Furthermore, we show that the string can be overwritten in-place with this structure. The redundancy of $Θ(\log n)$ bits and the constant query time break exponentially a lower bound that is known to hold in the read-only model. Using our new string representation, we obtain the first in-place subquadratic (indeed, even sublinear in some cases) algorithms for several string-processing problems in the restore model: the input string is rewritable and must be restored before the computation terminates. In particular, we describe the first in-place subquadratic Monte Carlo solutions to the sparse suffix sorting, sparse LCP array construction, and suffix selection problems. With the sole exception of suffix selection, our algorithms are also the first running in sublinear time for small enough sets of input suffixes. Combining these solutions, we obtain the first sublinear-time Monte Carlo algorithm for building the sparse suffix tree in compact space. We also show how to derandomize our algorithms using small space. This leads to the first Las Vegas in-place algorithm computing the full LCP array in $O(n\log n)$ time and to the first Las Vegas in-place algorithms solving the sparse suffix sorting and sparse LCP array construction problems in $O(n^{1.5}\sqrt{\log σ})$ time. Running times of these Las Vegas algorithms hold in the worst case with high probability.

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arXiv2020

Wheeler Languages

The recently introduced class of Wheeler graphs, inspired by the Burrows-Wheeler Transform (BWT) of a given string, admits an efficient index data structure for searching for subpaths with a given path label, and lifts the applicability of the Burrows-Wheeler transform from strings to languages. In this paper we study the regular languages accepted by automata having a Wheeler graph as transition function, and prove results on determination, Myhill_Nerode characterization, decidability, and closure properties for this class of languages.

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arXiv2019

On the Reproducibility of Experiments of Indexing Repetitive Document Collections

This work introduces a companion reproducible paper with the aim of allowing the exact replication of the methods, experiments, and results discussed in a previous work [5]. In that parent paper, we proposed many and varied techniques for compressing indexes which exploit that highly repetitive collections are formed mostly of documents that are near-copies of others. More concretely, we describe a replication framework, called uiHRDC (universal indexes for Highly Repetitive Document Collections), that allows our original experimental setup to be easily replicated using various document collections. The corresponding experimentation is carefully explained, providing precise details about the parameters that can be tuned for each indexing solution. Finally, note that we also provide uiHRDC as reproducibility package.

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