9,036 research outputs found
Optimal Substring-Equality Queries with Applications to Sparse Text Indexing
We consider the problem of encoding a string of length from an integer
alphabet of size 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
bits. We describe a new data
structure matching this lower bound when while supporting
both queries in optimal time. Furthermore, we show that the string can
be overwritten in-place with this structure. The redundancy of
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 time and to the first Las Vegas in-place algorithms
solving the sparse suffix sorting and sparse LCP array construction problems in
time. Running times of these Las Vegas
algorithms hold in the worst case with high probability.Comment: Refactored according to TALG's reviews. New w.h.p. bounds and Las
Vegas algorithm
Sorting suffixes of a text via its Lyndon Factorization
The process of sorting the suffixes of a text plays a fundamental role in
Text Algorithms. They are used for instance in the constructions of the
Burrows-Wheeler transform and the suffix array, widely used in several fields
of Computer Science. For this reason, several recent researches have been
devoted to finding new strategies to obtain effective methods for such a
sorting. In this paper we introduce a new methodology in which an important
role is played by the Lyndon factorization, so that the local suffixes inside
factors detected by this factorization keep their mutual order when extended to
the suffixes of the whole word. This property suggests a versatile technique
that easily can be adapted to different implementative scenarios.Comment: Submitted to the Prague Stringology Conference 2013 (PSC 2013
On the combinatorics of suffix arrays
We prove several combinatorial properties of suffix arrays, including a
characterization of suffix arrays through a bijection with a certain
well-defined class of permutations. Our approach is based on the
characterization of Burrows-Wheeler arrays given in [1], that we apply by
reducing suffix sorting to cyclic shift sorting through the use of an
additional sentinel symbol. We show that the characterization of suffix arrays
for a special case of binary alphabet given in [2] easily follows from our
characterization. Based on our results, we also provide simple proofs for the
enumeration results for suffix arrays, obtained in [3]. Our approach to
characterizing suffix arrays is the first that exploits their relationship with
Burrows-Wheeler permutations
Regular Languages meet Prefix Sorting
Indexing strings via prefix (or suffix) sorting is, arguably, one of the most
successful algorithmic techniques developed in the last decades. Can indexing
be extended to languages? The main contribution of this paper is to initiate
the study of the sub-class of regular languages accepted by an automaton whose
states can be prefix-sorted. Starting from the recent notion of Wheeler graph
[Gagie et al., TCS 2017]-which extends naturally the concept of prefix sorting
to labeled graphs-we investigate the properties of Wheeler languages, that is,
regular languages admitting an accepting Wheeler finite automaton.
Interestingly, we characterize this family as the natural extension of regular
languages endowed with the co-lexicographic ordering: when sorted, the strings
belonging to a Wheeler language are partitioned into a finite number of
co-lexicographic intervals, each formed by elements from a single Myhill-Nerode
equivalence class. Moreover: (i) We show that every Wheeler NFA (WNFA) with
states admits an equivalent Wheeler DFA (WDFA) with at most
states that can be computed in time. This is in sharp contrast with
general NFAs. (ii) We describe a quadratic algorithm to prefix-sort a proper
superset of the WDFAs, a -time online algorithm to sort acyclic
WDFAs, and an optimal linear-time offline algorithm to sort general WDFAs. By
contribution (i), our algorithms can also be used to index any WNFA at the
moderate price of doubling the automaton's size. (iii) We provide a
minimization theorem that characterizes the smallest WDFA recognizing the same
language of any input WDFA. The corresponding constructive algorithm runs in
optimal linear time in the acyclic case, and in time in the
general case. (iv) We show how to compute the smallest WDFA equivalent to any
acyclic DFA in nearly-optimal time.Comment: added minimization theorems; uploaded submitted version; New version
with new results (W-MH theorem, linear determinization), added author:
Giovanna D'Agostin
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