Search results for " distributed"
showing 10 items of 235 documents
Stealthy Attacks in Cloud-Connected Linear Impulsive Systems
2018
This paper studies a security problem for a class cloud-connected multi-agent systems, where autonomous agents coordinate via a combination of short-range ad-hoc commu- nication links and long-range cloud services. We consider a simplified model for the dynamics of a cloud-connected multi- agent system and attacks, where the states evolve according to linear time-invariant impulsive dynamics, and attacks are modeled as exogenous inputs designed by an omniscent attacker that alters the continuous and impulsive updates. We propose a definition of attack detectability, characterize the existence of stealthy attacks as a function of the system parameters and attack properties, and design a fami…
Parallel distributed compensation for voltage controlled active magnetic bearing system using integral fuzzy model
2018
Parallel Distributed Compensation (PDC) for current-controlled Active Magnetic Bearing System (AMBS) has been quite effective in recent years. However, this method does not take into account the dynamics associated with the electromagnet. This limits the method to smaller scale applications where the electromagnet dynamics can be neglected. Voltage-controlled AMBS is used to overcome this limitation but this comes with serious challenges such as complex mathematical modelling and higher order system control. In this work, a PDC with integral part is proposed for position and input tracking control of voltage-controlled AMBS. PDC method is based on nonlinear Takagi-Sugeno (T-S) fuzzy model. …
A new parallel pipeline for DNA methylation analysis of long reads datasets
2017
Background DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. Results In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while…
On the Use of Binary Trees for DNA Hydroxymethylation Analysis
2017
DNA methylation (mC) and hydroxymethylation (hmC) can have a significant effect on normal human development, health and disease status. Hydroxymethylation studies require specific treatment of DNA, as well as software tools for their analysis. In this paper, we propose a parallel software tool for analyzing the DNA hydroxymethylation data obtained by TAB-seq. The software is based on the use of binary trees for searching the different occurrences of methylation and hydroxymethylation in DNA samples. The binary trees allow to efficiently store and access the information about the methylation of each methylated/hydroxymethylated cytosines in the samples. Evaluation results shows that the perf…
Informational and linguistic analysis of large genomic sequence collections via efficient Hadoop cluster algorithms
2018
Abstract Motivation Information theoretic and compositional/linguistic analysis of genomes have a central role in bioinformatics, even more so since the associated methodologies are becoming very valuable also for epigenomic and meta-genomic studies. The kernel of those methods is based on the collection of k-mer statistics, i.e. how many times each k-mer in {A,C,G,T}k occurs in a DNA sequence. Although this problem is computationally very simple and efficiently solvable on a conventional computer, the sheer amount of data available now in applications demands to resort to parallel and distributed computing. Indeed, those type of algorithms have been developed to collect k-mer statistics in…
2016
The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown to obtain high quality mappings at the expense of long execution times. Finding fast yet accurate software solutions is of high importance to research, since availability and size of NGS datasets continue to increase. In this work we present an efficient parallelization approach for NGS short-read alignment on multi-core clusters. Our approach takes advantage of a distributed shared memory programming model based on the new UPC++ language. Experimental results using the CUSHAW3 alig…
An effective extension of the applicability of alignment-free biological sequence comparison algorithms with Hadoop
2016
Alignment-free methods are one of the mainstays of biological sequence comparison, i.e., the assessment of how similar two biological sequences are to each other, a fundamental and routine task in computational biology and bioinformatics. They have gained popularity since, even on standard desktop machines, they are faster than methods based on alignments. However, with the advent of Next-Generation Sequencing Technologies, datasets whose size, i.e., number of sequences and their total length, is a challenge to the execution of alignment-free methods on those standard machines are quite common. Here, we propose the first paradigm for the computation of k-mer-based alignment-free methods for…
Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters
2016
Computing alignments between two or more sequences are common operations frequently performed in computational molecular biology. The continuing growth of biological sequence databases establishes the need for their efficient parallel implementation on modern accelerators. This paper presents new approaches to high performance biological sequence database scanning with the Smith-Waterman algorithm and the first stage of progressive multiple sequence alignment based on the ClustalW heuristic on a Xeon Phi-based compute cluster. Our approach uses a three-level parallelization scheme to take full advantage of the compute power available on this type of architecture; i.e. cluster-level data par…
A Smart Contract Based Recommender System
2019
Nowadays information available on the World Wide Web has reached unprecedented growth and it makes difficult for users to find the most relevant for them. In order to alleviate such issue, Recommender Systems (RSs) have been proposed to collect opinions and preferences about a set of items, process such preferences and build a personalized information access. While the most part of current RSs exploit centralized architecture to provide the service, in this manuscript we propose an alternative approach for building a general purpose RSs that provides to users with more transparent and decentralized rating strategy. Indeed, the proposed framework is built on top of a Distributed Ledger techn…