Search results for " data structure."
showing 8 items of 88 documents
A Big Data Approach for Sequences Indexing on the Cloud via Burrows Wheeler Transform
2020
Indexing sequence data is important in the context of Precision Medicine, where large amounts of ``omics'' data have to be daily collected and analyzed in order to categorize patients and identify the most effective therapies. Here we propose an algorithm for the computation of Burrows Wheeler transform relying on Big Data technologies, i.e., Apache Spark and Hadoop. Our approach is the first that distributes the index computation and not only the input dataset, allowing to fully benefit of the available cloud resources.
Normal, Abby Normal, Prefix Normal
2014
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present results about the number $pnw(n)$ of prefix normal words of length $n$, showing that $pnw(n) =\Omega\left(2^{n - c\sqrt{n\ln n}}\right)$ for some $c$ and $pnw(n) = O \left(\frac{2^n (\ln n)^2}{n}\right)$. We introduce efficient algorithms for testing the prefix normal property and a "mechanical algorithm" for computing prefix normal forms. We also include games which can be played with prefix normal words. In these games Alice wishes to stay normal but Bob wants t…
2D-Pattern Indexing
2008
Data Structures for two-dimensional pattern matching are presented and discussed.
The Alternating BWT: an algorithmic perspective
2020
Abstract The Burrows-Wheeler Transform (BWT) is a word transformation introduced in 1994 for Data Compression. It has become a fundamental tool for designing self-indexing data structures, with important applications in several areas in science and engineering. The Alternating Burrows-Wheeler Transform (ABWT) is another transformation recently introduced in Gessel et al. (2012) [21] and studied in the field of Combinatorics on Words. It is analogous to the BWT, except that it uses an alternating lexicographical order instead of the usual one. Building on results in Giancarlo et al. (2018) [23] , where we have shown that BWT and ABWT are part of a larger class of reversible transformations, …
Enhanced query processing for NoSQL crowdsourcing systems
2014
In this paper, we provide a novel approach for effectively and efficiently support query processing tasks in novel NoSQL crowdsourcing systems. The idea of our method is to exploit the social knowledge available from reviews about products of any kind, freely provided by customers through specialized web sites. We thus define a NoSQL database system for large collections of product reviews, where queries can be expressed in terms of natural language sentences whose answers are modeled as lists of products ranked based on the relevance of reviews w.r.t. the natural language sentences. The best ranked products in the result list can be seen as the best hints for the user based on crowd opinio…
Uncommon Suffix Tries
2011
Common assumptions on the source producing the words inserted in a suffix trie with $n$ leaves lead to a $\log n$ height and saturation level. We provide an example of a suffix trie whose height increases faster than a power of $n$ and another one whose saturation level is negligible with respect to $\log n$. Both are built from VLMC (Variable Length Markov Chain) probabilistic sources; they are easily extended to families of sources having the same properties. The first example corresponds to a ''logarithmic infinite comb'' and enjoys a non uniform polynomial mixing. The second one corresponds to a ''factorial infinite comb'' for which mixing is uniform and exponential.
Adaptive reference-free compression of sequence quality scores
2014
Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…
Algorithms for Computing Abelian Periods of Words
2012
Constantinescu and Ilie (Bulletin EATCS 89, 167--170, 2006) introduced the notion of an \emph{Abelian period} of a word. A word of length $n$ over an alphabet of size $\sigma$ can have $\Theta(n^{2})$ distinct Abelian periods. The Brute-Force algorithm computes all the Abelian periods of a word in time $O(n^2 \times \sigma)$ using $O(n \times \sigma)$ space. We present an off-line algorithm based on a $\sel$ function having the same worst-case theoretical complexity as the Brute-Force one, but outperforming it in practice. We then present on-line algorithms that also enable to compute all the Abelian periods of all the prefixes of $w$.