6,780 research outputs found
Weighted ancestors in suffix trees
The classical, ubiquitous, predecessor problem is to construct a data
structure for a set of integers that supports fast predecessor queries. Its
generalization to weighted trees, a.k.a. the weighted ancestor problem, has
been extensively explored and successfully reduced to the predecessor problem.
It is known that any solution for both problems with an input set from a
polynomially bounded universe that preprocesses a weighted tree in O(n
polylog(n)) space requires \Omega(loglogn) query time. Perhaps the most
important and frequent application of the weighted ancestors problem is for
suffix trees. It has been a long-standing open question whether the weighted
ancestors problem has better bounds for suffix trees. We answer this question
positively: we show that a suffix tree built for a text w[1..n] can be
preprocessed using O(n) extra space, so that queries can be answered in O(1)
time. Thus we improve the running times of several applications. Our
improvement is based on a number of data structure tools and a
periodicity-based insight into the combinatorial structure of a suffix tree.Comment: 27 pages, LNCS format. A condensed version will appear in ESA 201
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
Managing Unbounded-Length Keys in Comparison-Driven Data Structures with Applications to On-Line Indexing
This paper presents a general technique for optimally transforming any
dynamic data structure that operates on atomic and indivisible keys by
constant-time comparisons, into a data structure that handles unbounded-length
keys whose comparison cost is not a constant. Examples of these keys are
strings, multi-dimensional points, multiple-precision numbers, multi-key data
(e.g.~records), XML paths, URL addresses, etc. The technique is more general
than what has been done in previous work as no particular exploitation of the
underlying structure of is required. The only requirement is that the insertion
of a key must identify its predecessor or its successor.
Using the proposed technique, online suffix tree can be constructed in worst
case time per input symbol (as opposed to amortized
time per symbol, achieved by previously known algorithms). To our knowledge,
our algorithm is the first that achieves worst case time per input
symbol. Searching for a pattern of length in the resulting suffix tree
takes time, where is the
number of occurrences of the pattern. The paper also describes more
applications and show how to obtain alternative methods for dealing with suffix
sorting, dynamic lowest common ancestors and order maintenance
Computing Lempel-Ziv Factorization Online
We present an algorithm which computes the Lempel-Ziv factorization of a word
of length on an alphabet of size online in the
following sense: it reads starting from the left, and, after reading each
characters of , updates the Lempel-Ziv
factorization. The algorithm requires bits of space and O(n
\log^2 n) time. The basis of the algorithm is a sparse suffix tree combined
with wavelet trees
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
CiNCT: Compression and retrieval for massive vehicular trajectories via relative movement labeling
In this paper, we present a compressed data structure for moving object
trajectories in a road network, which are represented as sequences of road
edges. Unlike existing compression methods for trajectories in a network, our
method supports pattern matching and decompression from an arbitrary position
while retaining a high compressibility with theoretical guarantees.
Specifically, our method is based on FM-index, a fast and compact data
structure for pattern matching. To enhance the compression, we incorporate the
sparsity of road networks into the data structure. In particular, we present
the novel concepts of relative movement labeling and PseudoRank, each
contributing to significant reductions in data size and query processing time.
Our theoretical analysis and experimental studies reveal the advantages of our
proposed method as compared to existing trajectory compression methods and
FM-index variants
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