974 research outputs found
Practical Evaluation of Lempel-Ziv-78 and Lempel-Ziv-Welch Tries
We present the first thorough practical study of the Lempel-Ziv-78 and the
Lempel-Ziv-Welch computation based on trie data structures. With a careful
selection of trie representations we can beat well-tuned popular trie data
structures like Judy, m-Bonsai or Cedar
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
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
Handling Massive N-Gram Datasets Efficiently
This paper deals with the two fundamental problems concerning the handling of
large n-gram language models: indexing, that is compressing the n-gram strings
and associated satellite data without compromising their retrieval speed; and
estimation, that is computing the probability distribution of the strings from
a large textual source. Regarding the problem of indexing, we describe
compressed, exact and lossless data structures that achieve, at the same time,
high space reductions and no time degradation with respect to state-of-the-art
solutions and related software packages. In particular, we present a compressed
trie data structure in which each word following a context of fixed length k,
i.e., its preceding k words, is encoded as an integer whose value is
proportional to the number of words that follow such context. Since the number
of words following a given context is typically very small in natural
languages, we lower the space of representation to compression levels that were
never achieved before. Despite the significant savings in space, our technique
introduces a negligible penalty at query time. Regarding the problem of
estimation, we present a novel algorithm for estimating modified Kneser-Ney
language models, that have emerged as the de-facto choice for language modeling
in both academia and industry, thanks to their relatively low perplexity
performance. Estimating such models from large textual sources poses the
challenge of devising algorithms that make a parsimonious use of the disk. The
state-of-the-art algorithm uses three sorting steps in external memory: we show
an improved construction that requires only one sorting step thanks to
exploiting the properties of the extracted n-gram strings. With an extensive
experimental analysis performed on billions of n-grams, we show an average
improvement of 4.5X on the total running time of the state-of-the-art approach.Comment: Published in ACM Transactions on Information Systems (TOIS), February
2019, Article No: 2
Fast and Lean Immutable Multi-Maps on the JVM based on Heterogeneous Hash-Array Mapped Tries
An immutable multi-map is a many-to-many thread-friendly map data structure
with expected fast insert and lookup operations. This data structure is used
for applications processing graphs or many-to-many relations as applied in
static analysis of object-oriented systems. When processing such big data sets
the memory overhead of the data structure encoding itself is a memory usage
bottleneck. Motivated by reuse and type-safety, libraries for Java, Scala and
Clojure typically implement immutable multi-maps by nesting sets as the values
with the keys of a trie map. Like this, based on our measurements the expected
byte overhead for a sparse multi-map per stored entry adds up to around 65B,
which renders it unfeasible to compute with effectively on the JVM.
In this paper we propose a general framework for Hash-Array Mapped Tries on
the JVM which can store type-heterogeneous keys and values: a Heterogeneous
Hash-Array Mapped Trie (HHAMT). Among other applications, this allows for a
highly efficient multi-map encoding by (a) not reserving space for empty value
sets and (b) inlining the values of singleton sets while maintaining a (c)
type-safe API.
We detail the necessary encoding and optimizations to mitigate the overhead
of storing and retrieving heterogeneous data in a hash-trie. Furthermore, we
evaluate HHAMT specifically for the application to multi-maps, comparing them
to state-of-the-art encodings of multi-maps in Java, Scala and Clojure. We
isolate key differences using microbenchmarks and validate the resulting
conclusions on a real world case in static analysis. The new encoding brings
the per key-value storage overhead down to 30B: a 2x improvement. With
additional inlining of primitive values it reaches a 4x improvement
Loom: Query-aware Partitioning of Online Graphs
As with general graph processing systems, partitioning data over a cluster of
machines improves the scalability of graph database management systems.
However, these systems will incur additional network cost during the execution
of a query workload, due to inter-partition traversals. Workload-agnostic
partitioning algorithms typically minimise the likelihood of any edge crossing
partition boundaries. However, these partitioners are sub-optimal with respect
to many workloads, especially queries, which may require more frequent
traversal of specific subsets of inter-partition edges. Furthermore, they
largely unsuited to operating incrementally on dynamic, growing graphs.
We present a new graph partitioning algorithm, Loom, that operates on a
stream of graph updates and continuously allocates the new vertices and edges
to partitions, taking into account a query workload of graph pattern
expressions along with their relative frequencies.
First we capture the most common patterns of edge traversals which occur when
executing queries. We then compare sub-graphs, which present themselves
incrementally in the graph update stream, against these common patterns.
Finally we attempt to allocate each match to single partitions, reducing the
number of inter-partition edges within frequently traversed sub-graphs and
improving average query performance.
Loom is extensively evaluated over several large test graphs with realistic
query workloads and various orderings of the graph updates. We demonstrate
that, given a workload, our prototype produces partitionings of significantly
better quality than existing streaming graph partitioning algorithms Fennel and
LDG
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