Search results for "data structure"
showing 10 items of 441 documents
"Acceptance by Final State in SR4$\ell$" of "Search for trilepton resonances from chargino and neutralino pair production in $\sqrt{s}$ = 13 TeV $pp$…
2021
The truth-level acceptances for each decay mode of the generated $\tilde\chi^{\pm}_{1}\tilde\chi^{\mp}_{1} + \tilde\chi^{\pm}_{1}\tilde\chi^{0}_{1}$ signals in the SR4$\ell$ region. Results are given as a function of $\tilde\chi^{0}_{1}/\tilde\chi^{0}_{1}$ mass and the final state boson and lepton combination.
A Model for Capturing Product Assembly Information
2005
The important issue of mechanical assemblies has been a subject of intense research over the past several years. Most electromechanical products are assemblies of several components, for various technical as well as economic reasons. This paper provides an object-oriented definition of an assembly model called the Open Assembly Model (OAM) and defines an extension to the NIST Core Product Model (NIST-CPM). The assembly model represents the function, form, and behavior of the assembly and defines both a system level conceptual model and associated hierarchical relationships. The model provides a way for tolerance representation and propagation, kinematics representation, and engineering anal…
Epigenomic k-mer dictionaries: shedding light on how sequence composition influences in vivo nucleosome positioning
2014
Abstract Motivation: Information-theoretic and compositional analysis of biological sequences, in terms of k-mer dictionaries, has a well established role in genomic and proteomic studies. Much less so in epigenomics, although the role of k-mers in chromatin organization and nucleosome positioning is particularly relevant. Fundamental questions concerning the informational content and compositional structure of nucleosome favouring and disfavoring sequences with respect to their basic building blocks still remain open. Results: We present the first analysis on the role of k-mers in the composition of nucleosome enriched and depleted genomic regions (NER and NDR for short) that is: (i) exhau…
A New Time Dependent Model Based on Level Set Motion for Nonlinear Deblurring and Noise Removal
1999
In this paper we summarize the main features of a new time dependent model to approximate the solution to the nonlinear total variation optimization problem for deblurring and noise removal introduced by Rudin, Osher and Fatemi. Our model is based on level set motion whose steady state is quickly reached by means of an explicit procedure based on an ENO Hamilton-Jacobi version of Roe's scheme. We show numerical evidence of the speed, resolution and stability of this simple explicit procedure in two representative 1D and 2D numerical examples.
On the Greedy Algorithm for the Shortest Common Superstring Problem with Reversals
2015
We study a variation of the classical Shortest Common Superstring (SCS) problem in which a shortest superstring of a finite set of strings $S$ is sought containing as a factor every string of $S$ or its reversal. We call this problem Shortest Common Superstring with Reversals (SCS-R). This problem has been introduced by Jiang et al., who designed a greedy-like algorithm with length approximation ratio $4$. In this paper, we show that a natural adaptation of the classical greedy algorithm for SCS has (optimal) compression ratio $\frac12$, i.e., the sum of the overlaps in the output string is at least half the sum of the overlaps in an optimal solution. We also provide a linear-time implement…
Inducing the Lyndon Array
2019
In this paper we propose a variant of the induced suffix sorting algorithm by Nong (TOIS, 2013) that computes simultaneously the Lyndon array and the suffix array of a text in $O(n)$ time using $\sigma + O(1)$ words of working space, where $n$ is the length of the text and $\sigma$ is the alphabet size. Our result improves the previous best space requirement for linear time computation of the Lyndon array. In fact, all the known linear algorithms for Lyndon array computation use suffix sorting as a preprocessing step and use $O(n)$ words of working space in addition to the Lyndon array and suffix array. Experimental results with real and synthetic datasets show that our algorithm is not onl…
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.
Sorting suffixes of a text via its Lyndon Factorization
2013
The process of sorting the suffixes of a text plays a fundamental role in Text Algorithms. They are used for instance in the constructions of the Burrows-Wheeler transform and the suffix array, widely used in several fields of Computer Science. For this reason, several recent researches have been devoted to finding new strategies to obtain effective methods for such a sorting. In this paper we introduce a new methodology in which an important role is played by the Lyndon factorization, so that the local suffixes inside factors detected by this factorization keep their mutual order when extended to the suffixes of the whole word. This property suggests a versatile technique that easily can b…
Novel Results on the Number of Runs of the Burrows-Wheeler-Transform
2021
The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms for sequence data, such as webpages, genomic and other biological sequences, or indeed any textual data. The BWT lends itself well to compression because its number of equal-letter-runs (usually referred to as $r$) is often considerably lower than that of the original string; in particular, it is well suited for strings with many repeated factors. In fact, much attention has been paid to the $r$ parameter as measure of repetitiveness, especially to evalua…
Adaptive learning of compressible strings
2020
Suppose an oracle knows a string $S$ that is unknown to us and that we want to determine. The oracle can answer queries of the form "Is $s$ a substring of $S$?". In 1995, Skiena and Sundaram showed that, in the worst case, any algorithm needs to ask the oracle $\sigma n/4 -O(n)$ queries in order to be able to reconstruct the hidden string, where $\sigma$ is the size of the alphabet of $S$ and $n$ its length, and gave an algorithm that spends $(\sigma-1)n+O(\sigma \sqrt{n})$ queries to reconstruct $S$. The main contribution of our paper is to improve the above upper-bound in the context where the string is compressible. We first present a universal algorithm that, given a (computable) compre…