6,071 research outputs found
Compressed Text Indexes:From Theory to Practice!
A compressed full-text self-index represents a text in a compressed form and
still answers queries efficiently. This technology represents a breakthrough
over the text indexing techniques of the previous decade, whose indexes
required several times the size of the text. Although it is relatively new,
this technology has matured up to a point where theoretical research is giving
way to practical developments. Nonetheless this requires significant
programming skills, a deep engineering effort, and a strong algorithmic
background to dig into the research results. To date only isolated
implementations and focused comparisons of compressed indexes have been
reported, and they missed a common API, which prevented their re-use or
deployment within other applications.
The goal of this paper is to fill this gap. First, we present the existing
implementations of compressed indexes from a practitioner's point of view.
Second, we introduce the Pizza&Chili site, which offers tuned implementations
and a standardized API for the most successful compressed full-text
self-indexes, together with effective testbeds and scripts for their automatic
validation and test. Third, we show the results of our extensive experiments on
these codes with the aim of demonstrating the practical relevance of this novel
and exciting technology
Optimal-Time Text Indexing 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 , the number of runs in their Burrows-Wheeler Transform
(BWT). One of the earliest indexes for repetitive collections, the Run-Length
FM-index, used space and was able to efficiently count the number of
occurrences of a pattern of length 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
. Since then, a number of other indexes with space bounded by other measures
of repetitiveness --- the number of phrases in the Lempel-Ziv parse, the size
of the smallest grammar generating the text, the size of the smallest automaton
recognizing the text factors --- have been proposed for efficiently locating,
but not directly counting, the occurrences of a pattern. In this paper we close
this long-standing problem, showing how to extend the Run-Length FM-index so
that it can locate the occurrences efficiently within space (in
loglogarithmic time each), and reaching optimal time within
space, on a RAM machine of bits. Within
space, our index can also count in optimal time .
Raising the space to , we support count and locate in
and time, which is optimal in the
packed setting and had not been obtained before in compressed space. We also
describe a structure using space that replaces the text and
extracts any text substring of length in almost-optimal time
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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)
Document Retrieval on Repetitive Collections
Document retrieval aims at finding the most important documents where a
pattern appears in a collection of strings. Traditional pattern-matching
techniques yield brute-force document retrieval solutions, which has motivated
the research on tailored indexes that offer near-optimal performance. However,
an experimental study establishing which alternatives are actually better than
brute force, and which perform best depending on the collection
characteristics, has not been carried out. In this paper we address this
shortcoming by exploring the relationship between the nature of the underlying
collection and the performance of current methods. Via extensive experiments we
show that established solutions are often beaten in practice by brute-force
alternatives. We also design new methods that offer superior time/space
trade-offs, particularly on repetitive collections.Comment: Accepted to ESA 2014. Implementation and experiments at
http://www.cs.helsinki.fi/group/suds/rlcsa
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