Search results for " computing"
showing 10 items of 2075 documents
Scavenger – A Framework for Efficient Evaluation of Dynamic and Modular Algorithms
2015
Machine Learning methods and algorithms are often highly modular in the sense that they rely on a large number of subalgorithms that are in principle interchangeable. For example, it is often possible to use various kinds of pre- and post-processing and various base classifiers or regressors as components of the same modular approach. We propose a framework, called Scavenger, that allows evaluating whole families of conceptually similar algorithms efficiently. The algorithms are represented as compositions, couplings and products of atomic subalgorithms. This allows partial results to be cached and shared between different instances of a modular algorithm, so that potentially expensive part…
Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform
2012
Unprecedented production of short reads from the new high-throughput sequencers has posed challenges to align short reads to reference genomes with high sensitivity and high speed. Many CPU-based short read aligners have been developed to address this challenge. Among them, one popular approach is the seed-and-extend heuristic. For this heuristic, the first and foremost step is to generate seeds between the input reads and the reference genome, where hash tables are the most frequently used data structure. However, hash tables are memory-consuming, making it not well-suited to memory-stringent many-core architectures, like GPUs, even though they usually have a nearly constant query time com…
Work Partitioning on Parallel and Distributed Agent-Based Simulation
2017
Work partitioning is a key challenge with ap- plications in many scientific and technological fields. The problem is very well studied with a rich literature on both distributed and parallel computing architectures. In this paper we deal with the work partitioning problem for parallel and distributed agent-based simulations which aims at (i) balancing the overall load distribution, (ii) minimizing, at the same time, the communication overhead due to agents' inter-dependencies. We introduce a classification taxonomy of work partitioning strategies and present a space-based work partitioning ap- proach, based on a Quad-tree data structure, which enables to: identify a good space partitioning …
Movie Script Similarity Using Multilayer Network Portrait Divergence
2020
International audience; This paper addresses the question of movie similarity through multilayer graph similarity measures. Recent work has shown how to construct multilayer networks using movie scripts, and how they capture different aspects of the stories. Based on this modeling, we propose to rely on the multilayer structure and compute different similarities, so we may compare movies, not from their visual content, summary, or actors, but actually from their own storyboard. We propose to do so using “portrait divergence”, which has been recently introduced to compute graph distances from summarizing graph characteristics. We illustrate our approach on the series of six Star Wars movies.
On implicit data structures for priority queues
1985
Comparaison avec une structure liee simple et implementation de certaines structures de donnees implicites pour les files d'attente de priorite. Le minutage des experiences montre que les structures implicites sont plutot lentes
HOW SMART DOES AN AGENT NEED TO BE?
2005
The classic distributed computation is done by atoms, molecules or spins in vast numbers, each equipped with nothing more than the knowledge of their immediate neighborhood and the rules of statistical mechanics. These agents, 1023 or more, are able to form liquids and solids from gases, realize extremely complex ordered states, such as liquid crystals, and even decode encrypted messages. We will describe a study done for a sensor-array "challenge problem" in which we have based our approach on old-fashioned simulated annealing to accomplish target acquisition and tracking under the rules of statistical mechanics. We believe the many additional constraints that occur in the real problem ca…
Supervised learning of time-independent Hamiltonians for gate design
2018
We present a general framework to tackle the problem of finding time-independent dynamics generating target unitary evolutions. We show that this problem is equivalently stated as a set of conditions over the spectrum of the time-independent gate generator, thus transforming the task to an inverse eigenvalue problem. We illustrate our methodology by identifying suitable time-independent generators implementing Toffoli and Fredkin gates without the need for ancillae or effective evolutions. We show how the same conditions can be used to solve the problem numerically, via supervised learning techniques. In turn, this allows us to solve problems that are not amenable, in general, to direct ana…
A Logical Key Hierarchy Based approach to preserve content privacy in Decentralized Online Social Networks
2020
Distributed Online Social Networks (DOSNs) have been proposed to shift the control over user data from a unique entity, the online social network provider, to the users of the DOSN themselves. In this paper we focus on the problem of preserving the privacy of the contents shared to large groups of users. In general, content privacy is enforced by encrypting the content, having only authorized parties being able to decrypt it. When efficiency has to be taken into account, new solutions have to be devised that: i) minimize the re-encryption of the contents published in a group when the composition of the group changes; and, ii) enable a fast distribution of the cryptographic keys to all the m…
Code Interoperability and Standard Data Formats in Quantum Chemistry and Quantum Dynamics: The Q5/Q5cost Data Model
2014
Code interoperability and the search for domain-specific standard data formats represent critical issues in many areas of computational science. The advent of novel computing infrastructures such as computational grids and clouds make these issues even more urgent. The design and implementation of a common data format for quantum chemistry (QC) and quantum dynamics (QD) computer programs is discussed with reference to the research performed in the course of two Collaboration in Science and Technology Actions. The specific data models adopted, Q5Cost and D5Cost, are shown to work for a number of interoperating codes, regardless of the type and amount of information (small or large datasets) …
Parallel Collision Queries on the GPU
2013
We present parallel algorithms to accelerate collision tests of rigid body objects for a high number of independent transformations as they occur in sampling-based motion planning and path validation problems. We compare various GPU approaches with a different level of parallelism against each other and against a parallel CPU implementation. Our algorithms require no sophisticated load balancing schemes. They make no assumption on the distribution of the input transformations and require no pre-processing. Yet, we can perform up to 1 million collision tests per second with our best GPU implementation in our benchmarks. This is about 2.5X faster than our reference multi-core CPU implementati…