24,689 research outputs found
Tree Compression with Top Trees Revisited
We revisit tree compression with top trees (Bille et al, ICALP'13) and
present several improvements to the compressor and its analysis. By
significantly reducing the amount of information stored and guiding the
compression step using a RePair-inspired heuristic, we obtain a fast compressor
achieving good compression ratios, addressing an open problem posed by Bille et
al. We show how, with relatively small overhead, the compressed file can be
converted into an in-memory representation that supports basic navigation
operations in worst-case logarithmic time without decompression. We also show a
much improved worst-case bound on the size of the output of top-tree
compression (answering an open question posed in a talk on this algorithm by
Weimann in 2012).Comment: SEA 201
Universal Indexes for Highly Repetitive Document Collections
Indexing highly repetitive collections has become a relevant problem with the
emergence of large repositories of versioned documents, among other
applications. These collections may reach huge sizes, but are formed mostly of
documents that are near-copies of others. Traditional techniques for indexing
these collections fail to properly exploit their regularities in order to
reduce space.
We introduce new techniques for compressing inverted indexes that exploit
this near-copy regularity. They are based on run-length, Lempel-Ziv, or grammar
compression of the differential inverted lists, instead of the usual practice
of gap-encoding them. We show that, in this highly repetitive setting, our
compression methods significantly reduce the space obtained with classical
techniques, at the price of moderate slowdowns. Moreover, our best methods are
universal, that is, they do not need to know the versioning structure of the
collection, nor that a clear versioning structure even exists.
We also introduce compressed self-indexes in the comparison. These are
designed for general strings (not only natural language texts) and represent
the text collection plus the index structure (not an inverted index) in
integrated form. We show that these techniques can compress much further, using
a small fraction of the space required by our new inverted indexes. Yet, they
are orders of magnitude slower.Comment: This research has received funding from the European Union's Horizon
2020 research and innovation programme under the Marie Sk{\l}odowska-Curie
Actions H2020-MSCA-RISE-2015 BIRDS GA No. 69094
XML Compression via DAGs
Unranked trees can be represented using their minimal dag (directed acyclic
graph). For XML this achieves high compression ratios due to their repetitive
mark up. Unranked trees are often represented through first child/next sibling
(fcns) encoded binary trees. We study the difference in size (= number of
edges) of minimal dag versus minimal dag of the fcns encoded binary tree. One
main finding is that the size of the dag of the binary tree can never be
smaller than the square root of the size of the minimal dag, and that there are
examples that match this bound. We introduce a new combined structure, the
hybrid dag, which is guaranteed to be smaller than (or equal in size to) both
dags. Interestingly, we find through experiments that last child/previous
sibling encodings are much better for XML compression via dags, than fcns
encodings. We determine the average sizes of unranked and binary dags over a
given set of labels (under uniform distribution) in terms of their exact
generating functions, and in terms of their asymptotical behavior.Comment: A short version of this paper appeared in the Proceedings of ICDT
201
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
. (...continues...
Fast and Tiny Structural Self-Indexes for XML
XML document markup is highly repetitive and therefore well compressible
using dictionary-based methods such as DAGs or grammars. In the context of
selectivity estimation, grammar-compressed trees were used before as synopsis
for structural XPath queries. Here a fully-fledged index over such grammars is
presented. The index allows to execute arbitrary tree algorithms with a
slow-down that is comparable to the space improvement. More interestingly,
certain algorithms execute much faster over the index (because no decompression
occurs). E.g., for structural XPath count queries, evaluating over the index is
faster than previous XPath implementations, often by two orders of magnitude.
The index also allows to serialize XML results (including texts) faster than
previous systems, by a factor of ca. 2-3. This is due to efficient copy
handling of grammar repetitions, and because materialization is totally
avoided. In order to compare with twig join implementations, we implemented a
materializer which writes out pre-order numbers of result nodes, and show its
competitiveness.Comment: 13 page
Abnormal wave reflections and left ventricular hypertrophy late after coarctation of the aorta repair
Patients with repaired coarctation of the aorta are thought to have increased afterload due to abnormalities in vessel structure and function. We have developed a novel cardiovascular magnetic resonance protocol that allows assessment of central hemodynamics, including central aortic systolic blood pressure, resistance, total arterial compliance, pulse wave velocity, and wave reflections. The main study aims were to (1) characterize group differences in central aortic systolic blood pressure and peripheral systolic blood pressure, (2) comprehensively evaluate afterload (including wave reflections) in the 2 groups, and (3) identify possible biomarkers among covariates associated with elevated left ventricular mass (LVM). Fifty adult patients with repaired coarctation and 25 age- and sex-matched controls were recruited. Ascending aorta area and flow waveforms were obtained using a high temporal-resolution spiral phase-contrast cardiovascular magnetic resonance flow sequence. These data were used to derive central hemodynamics and to perform wave intensity analysis noninvasively. Covariates associated with LVM were assessed using multivariable linear regression analysis. There were no significant group differences (P≥0.1) in brachial systolic, mean, or diastolic BP. However central aortic systolic blood pressure was significantly higher in patients compared with controls (113 versus 107 mm Hg, P=0.002). Patients had reduced total arterial compliance, increased pulse wave velocity, and larger backward compression waves compared with controls. LVM index was significantly higher in patients than controls (72 versus 59 g/m(2), P<0.0005). The magnitude of the backward compression waves was independently associated with variation in LVM (P=0.01). Using a novel, noninvasive hemodynamic assessment, we have shown abnormal conduit vessel function after coarctation of the aorta repair, including abnormal wave reflections that are associated with elevated LVM
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