33,685 research outputs found
Improved Approximate String Matching and Regular Expression Matching on Ziv-Lempel Compressed Texts
We study the approximate string matching and regular expression matching
problem for the case when the text to be searched is compressed with the
Ziv-Lempel adaptive dictionary compression schemes. We present a time-space
trade-off that leads to algorithms improving the previously known complexities
for both problems. In particular, we significantly improve the space bounds,
which in practical applications are likely to be a bottleneck
Prospects and limitations of full-text index structures in genome analysis
The combination of incessant advances in sequencing technology producing large amounts of data and innovative bioinformatics approaches, designed to cope with this data flood, has led to new interesting results in the life sciences. Given the magnitude of sequence data to be processed, many bioinformatics tools rely on efficient solutions to a variety of complex string problems. These solutions include fast heuristic algorithms and advanced data structures, generally referred to as index structures. Although the importance of index structures is generally known to the bioinformatics community, the design and potency of these data structures, as well as their properties and limitations, are less understood. Moreover, the last decade has seen a boom in the number of variant index structures featuring complex and diverse memory-time trade-offs. This article brings a comprehensive state-of-the-art overview of the most popular index structures and their recently developed variants. Their features, interrelationships, the trade-offs they impose, but also their practical limitations, are explained and compared
Pattern matching in Lempel-Ziv compressed strings: fast, simple, and deterministic
Countless variants of the Lempel-Ziv compression are widely used in many
real-life applications. This paper is concerned with a natural modification of
the classical pattern matching problem inspired by the popularity of such
compression methods: given an uncompressed pattern s[1..m] and a Lempel-Ziv
representation of a string t[1..N], does s occur in t? Farach and Thorup gave a
randomized O(nlog^2(N/n)+m) time solution for this problem, where n is the size
of the compressed representation of t. We improve their result by developing a
faster and fully deterministic O(nlog(N/n)+m) time algorithm with the same
space complexity. Note that for highly compressible texts, log(N/n) might be of
order n, so for such inputs the improvement is very significant. A (tiny)
fragment of our method can be used to give an asymptotically optimal solution
for the substring hashing problem considered by Farach and Muthukrishnan.Comment: submitte
TAPER: query-aware, partition-enhancement for large, heterogenous, graphs
Graph partitioning has long been seen as a viable approach to address Graph
DBMS scalability. A partitioning, however, may introduce extra query processing
latency unless it is sensitive to a specific query workload, and optimised to
minimise inter-partition traversals for that workload. Additionally, it should
also be possible to incrementally adjust the partitioning in reaction to
changes in the graph topology, the query workload, or both. Because of their
complexity, current partitioning algorithms fall short of one or both of these
requirements, as they are designed for offline use and as one-off operations.
The TAPER system aims to address both requirements, whilst leveraging existing
partitioning algorithms. TAPER takes any given initial partitioning as a
starting point, and iteratively adjusts it by swapping chosen vertices across
partitions, heuristically reducing the probability of inter-partition
traversals for a given pattern matching queries workload. Iterations are
inexpensive thanks to time and space optimisations in the underlying support
data structures. We evaluate TAPER on two different large test graphs and over
realistic query workloads. Our results indicate that, given a hash-based
partitioning, TAPER reduces the number of inter-partition traversals by around
80%; given an unweighted METIS partitioning, by around 30%. These reductions
are achieved within 8 iterations and with the additional advantage of being
workload-aware and usable online.Comment: 12 pages, 11 figures, unpublishe
Universal Compressed Text Indexing
The rise of repetitive datasets has lately generated a lot of interest in
compressed self-indexes based on dictionary compression, a rich and
heterogeneous family that exploits text repetitions in different ways. For each
such compression scheme, several different indexing solutions have been
proposed in the last two decades. To date, the fastest indexes for repetitive
texts are based on the run-length compressed Burrows-Wheeler transform and on
the Compact Directed Acyclic Word Graph. The most space-efficient indexes, on
the other hand, are based on the Lempel-Ziv parsing and on grammar compression.
Indexes for more universal schemes such as collage systems and macro schemes
have not yet been proposed. Very recently, Kempa and Prezza [STOC 2018] showed
that all dictionary compressors can be interpreted as approximation algorithms
for the smallest string attractor, that is, a set of text positions capturing
all distinct substrings. Starting from this observation, in this paper we
develop the first universal compressed self-index, that is, the first indexing
data structure based on string attractors, which can therefore be built on top
of any dictionary-compressed text representation. Let be the size of a
string attractor for a text of length . Our index takes
words of space and supports locating the
occurrences of any pattern of length in
time, for any constant . This is, in particular, the first index
for general macro schemes and collage systems. Our result shows that the
relation between indexing and compression is much deeper than what was
previously thought: the simple property standing at the core of all dictionary
compressors is sufficient to support fast indexed queries.Comment: Fixed with reviewer's comment
Fast, Small and Exact: Infinite-order Language Modelling with Compressed Suffix Trees
Efficient methods for storing and querying are critical for scaling
high-order n-gram language models to large corpora. We propose a language model
based on compressed suffix trees, a representation that is highly compact and
can be easily held in memory, while supporting queries needed in computing
language model probabilities on-the-fly. We present several optimisations which
improve query runtimes up to 2500x, despite only incurring a modest increase in
construction time and memory usage. For large corpora and high Markov orders,
our method is highly competitive with the state-of-the-art KenLM package. It
imposes much lower memory requirements, often by orders of magnitude, and has
runtimes that are either similar (for training) or comparable (for querying).Comment: 14 pages in Transactions of the Association for Computational
Linguistics (TACL) 201
A Compression Technique Exploiting References for Data Synchronization Services
Department of Computer Science and EngineeringIn a variety of network applications, there exists significant amount of shared data between two end hosts. Examples include data synchronization services that replicate data from one node to another. Given that shared data may have high correlation with new data to transmit, we question how such shared data can be best utilized to improve the efficiency of data transmission. To answer this, we develop an encoding technique, SyncCoding, that effectively replaces bit sequences of the data to be transmitted with the pointers to their matching bit sequences in the shared data so called references. By doing so, SyncCoding can reduce data traffic, speed up data transmission, and save energy consumption for transmission. Our evaluations of SyncCoding implemented in Linux show that it outperforms existing popular encoding techniques, Brotli, LZMA, Deflate, and Deduplication. The gains of SyncCoding over those techniques in the perspective of data size after compression in a cloud storage scenario are about 12.4%, 20.1%, 29.9%, and 61.2%, and are about 78.3%, 79.6%, 86.1%, and 92.9% in a web browsing scenario, respectively.ope
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