7,297 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
Fully-Functional Suffix Trees and Optimal Text Searching in BWT-runs Bounded Space
Indexing highly repetitive texts - such as genomic databases, software
repositories and versioned text collections - has become an important problem
since the turn of the millennium. A relevant compressibility measure for
repetitive texts is r, the number of runs in their Burrows-Wheeler Transforms
(BWTs). One of the earliest indexes for repetitive collections, the Run-Length
FM-index, used O(r) space and was able to efficiently count the number of
occurrences of a pattern of length m in the text (in loglogarithmic time per
pattern symbol, with current techniques). However, it was unable to locate the
positions of those occurrences efficiently within a space bounded in terms of
r. In this paper we close this long-standing problem, showing how to extend the
Run-Length FM-index so that it can locate the occ occurrences efficiently
within O(r) space (in loglogarithmic time each), and reaching optimal time, O(m
+ occ), within O(r log log w ({\sigma} + n/r)) space, for a text of length n
over an alphabet of size {\sigma} on a RAM machine with words of w =
{\Omega}(log n) bits. Within that space, our index can also count in optimal
time, O(m). Multiplying the space by O(w/ log {\sigma}), we support count and
locate in O(dm log({\sigma})/we) and O(dm log({\sigma})/we + occ) time, which
is optimal in the packed setting and had not been obtained before in compressed
space. We also describe a structure using O(r log(n/r)) space that replaces the
text and extracts any text substring of length ` in almost-optimal time
O(log(n/r) + ` log({\sigma})/w). Within that space, we similarly provide direct
access to suffix array, inverse suffix array, and longest common prefix array
cells, and extend these capabilities to full suffix tree functionality,
typically in O(log(n/r)) time per operation.Comment: submitted version; optimal count and locate in smaller space: O(r log
log_w(n/r + sigma)
Linear pattern matching on sparse suffix trees
Packing several characters into one computer word is a simple and natural way
to compress the representation of a string and to speed up its processing.
Exploiting this idea, we propose an index for a packed string, based on a {\em
sparse suffix tree} \cite{KU-96} with appropriately defined suffix links.
Assuming, under the standard unit-cost RAM model, that a word can store up to
characters ( the alphabet size), our index takes
space, i.e. the same space as the packed string itself.
The resulting pattern matching algorithm runs in time ,
where is the length of the pattern, is the actual number of characters
stored in a word and is the number of pattern occurrences
Full-fledged Real-Time Indexing for Constant Size Alphabets
In this paper we describe a data structure that supports pattern matching
queries on a dynamically arriving text over an alphabet ofconstant size. Each
new symbol can be prepended to in O(1) worst-case time. At any moment, we
can report all occurrences of a pattern in the current text in
time, where is the length of and is the number of occurrences.
This resolves, under assumption of constant-size alphabet, a long-standing open
problem of existence of a real-time indexing method for string matching (see
\cite{AmirN08})
Sublinear Space Algorithms for the Longest Common Substring Problem
Given documents of total length , we consider the problem of finding a
longest string common to at least of the documents. This problem is
known as the \emph{longest common substring (LCS) problem} and has a classic
space and time solution (Weiner [FOCS'73], Hui [CPM'92]).
However, the use of linear space is impractical in many applications. In this
paper we show that for any trade-off parameter , the LCS
problem can be solved in space and time, thus providing
the first smooth deterministic time-space trade-off from constant to linear
space. The result uses a new and very simple algorithm, which computes a
-additive approximation to the LCS in time and
space. We also show a time-space trade-off lower bound for deterministic
branching programs, which implies that any deterministic RAM algorithm solving
the LCS problem on documents from a sufficiently large alphabet in
space must use
time.Comment: Accepted to 22nd European Symposium on Algorithm
A representation of a compressed de Bruijn graph for pan-genome analysis that enables search
Recently, Marcus et al. (Bioinformatics 2014) proposed to use a compressed de
Bruijn graph to describe the relationship between the genomes of many
individuals/strains of the same or closely related species. They devised an
time algorithm called splitMEM that constructs this graph
directly (i.e., without using the uncompressed de Bruijn graph) based on a
suffix tree, where is the total length of the genomes and is the length
of the longest genome. In this paper, we present a construction algorithm that
outperforms their algorithm in theory and in practice. Moreover, we propose a
new space-efficient representation of the compressed de Bruijn graph that adds
the possibility to search for a pattern (e.g. an allele - a variant form of a
gene) within the pan-genome.Comment: Submitted to Algorithmica special issue of CPM201
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