1,812 research outputs found
On Longest Repeat Queries Using GPU
Repeat finding in strings has important applications in subfields such as
computational biology. The challenge of finding the longest repeats covering
particular string positions was recently proposed and solved by \.{I}leri et
al., using a total of the optimal time and space, where is the
string size. However, their solution can only find the \emph{leftmost} longest
repeat for each of the string position. It is also not known how to
parallelize their solution. In this paper, we propose a new solution for
longest repeat finding, which although is theoretically suboptimal in time but
is conceptually simpler and works faster and uses less memory space in practice
than the optimal solution. Further, our solution can find \emph{all} longest
repeats of every string position, while still maintaining a faster processing
speed and less memory space usage. Moreover, our solution is
\emph{parallelizable} in the shared memory architecture (SMA), enabling it to
take advantage of the modern multi-processor computing platforms such as the
general-purpose graphics processing units (GPU). We have implemented both the
sequential and parallel versions of our solution. Experiments with both
biological and non-biological data show that our sequential and parallel
solutions are faster than the optimal solution by a factor of 2--3.5 and 6--14,
respectively, and use less memory space.Comment: 14 page
A framework for space-efficient string kernels
String kernels are typically used to compare genome-scale sequences whose
length makes alignment impractical, yet their computation is based on data
structures that are either space-inefficient, or incur large slowdowns. We show
that a number of exact string kernels, like the -mer kernel, the substrings
kernels, a number of length-weighted kernels, the minimal absent words kernel,
and kernels with Markovian corrections, can all be computed in time and
in bits of space in addition to the input, using just a
data structure on the Burrows-Wheeler transform of the
input strings, which takes time per element in its output. The same
bounds hold for a number of measures of compositional complexity based on
multiple value of , like the -mer profile and the -th order empirical
entropy, and for calibrating the value of using the data
Space-efficient detection of unusual words
Detecting all the strings that occur in a text more frequently or less
frequently than expected according to an IID or a Markov model is a basic
problem in string mining, yet current algorithms are based on data structures
that are either space-inefficient or incur large slowdowns, and current
implementations cannot scale to genomes or metagenomes in practice. In this
paper we engineer an algorithm based on the suffix tree of a string to use just
a small data structure built on the Burrows-Wheeler transform, and a stack of
bits, where is the length of the string and
is the size of the alphabet. The size of the stack is except for very
large values of . We further improve the algorithm by removing its time
dependency on , by reporting only a subset of the maximal repeats and
of the minimal rare words of the string, and by detecting and scoring candidate
under-represented strings that in the string. Our
algorithms are practical and work directly on the BWT, thus they can be
immediately applied to a number of existing datasets that are available in this
form, returning this string mining problem to a manageable scale.Comment: arXiv admin note: text overlap with arXiv:1502.0637
Composite repetition-aware data structures
In highly repetitive strings, like collections of genomes from the same
species, distinct measures of repetition all grow sublinearly in the length of
the text, and indexes targeted to such strings typically depend only on one of
these measures. We describe two data structures whose size depends on multiple
measures of repetition at once, and that provide competitive tradeoffs between
the time for counting and reporting all the exact occurrences of a pattern, and
the space taken by the structure. The key component of our constructions is the
run-length encoded BWT (RLBWT), which takes space proportional to the number of
BWT runs: rather than augmenting RLBWT with suffix array samples, we combine it
with data structures from LZ77 indexes, which take space proportional to the
number of LZ77 factors, and with the compact directed acyclic word graph
(CDAWG), which takes space proportional to the number of extensions of maximal
repeats. The combination of CDAWG and RLBWT enables also a new representation
of the suffix tree, whose size depends again on the number of extensions of
maximal repeats, and that is powerful enough to support matching statistics and
constant-space traversal.Comment: (the name of the third co-author was inadvertently omitted from
previous version
Lempel-Ziv Parsing in External Memory
For decades, computing the LZ factorization (or LZ77 parsing) of a string has
been a requisite and computationally intensive step in many diverse
applications, including text indexing and data compression. Many algorithms for
LZ77 parsing have been discovered over the years; however, despite the
increasing need to apply LZ77 to massive data sets, no algorithm to date scales
to inputs that exceed the size of internal memory. In this paper we describe
the first algorithm for computing the LZ77 parsing in external memory. Our
algorithm is fast in practice and will allow the next generation of text
indexes to be realised for massive strings and string collections.Comment: 10 page
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