Search results for "computational"
showing 10 items of 5884 documents
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 …
An improved quantum query algorithm for computing AND Boolean function
2010
We consider the quantum query model for computing Boolean functions. The definition of the function is known, but a black box contains the input X = (x 1 , x 2 , …, x n ). Black box can be accessed by querying x i values. The goal is to develop an algorithm, which would compute the function value for arbitrary input using as few queries to the black box as possible. We present two different quantum query algorithms for computing the basic Boolean function — logical AND of two bits. Both algorithms use only one query to determine the function value. Correct answer probability for the first algorithm is 80%, but for the second algorithm it is 90%. To compute this function with the same probab…
OpenCMISS: A multi-physics & multi-scale computational infrastructure for the VPH/Physiome project
2011
The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level b…
On parsing optimality for dictionary-based text compression—the Zip case
2013
Dictionary-based compression schemes are the most commonly used data compression schemes since they appeared in the foundational paper of Ziv and Lempel in 1977, and generally referred to as LZ77. Their work is the base of Zip, gZip, 7-Zip and many other compression software utilities. Some of these compression schemes use variants of the greedy approach to parse the text into dictionary phrases; others have left the greedy approach to improve the compression ratio. Recently, two bit-optimal parsing algorithms have been presented filling the gap between theory and best practice. We present a survey on the parsing problem for dictionary-based text compression, identifying noticeable results …
Psi4: an open-source ab initio electronic structure program
2011
The Psi4 program is a new approach to modern quantum chemistry, encompassing Hartree–Fock and density-functional theory to configuration interaction and coupled cluster. The program is written entirely in C++ and relies on a new infrastructure that has been designed to permit high-efficiency computations of both standard and emerging electronic structure methods on conventional and high-performance parallel computer architectures. Psi4 offers flexible user input built on the Python scripting language that enables both new and experienced users to make full use of the program's capabilities, and even to implement new functionality with moderate effort. To maximize its impact and usefulness, …
Dictionary-symbolwise flexible parsing
2012
AbstractLinear-time optimal parsing algorithms are rare in the dictionary-based branch of the data compression theory. A recent result is the Flexible Parsing algorithm of Matias and Sahinalp (1999) that works when the dictionary is prefix closed and the encoding of dictionary pointers has a constant cost. We present the Dictionary-Symbolwise Flexible Parsing algorithm that is optimal for prefix-closed dictionaries and any symbolwise compressor under some natural hypothesis. In the case of LZ78-like algorithms with variable costs and any, linear as usual, symbolwise compressor we show how to implement our parsing algorithm in linear time. In the case of LZ77-like dictionaries and any symbol…
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…
Statistically validated networks in bipartite complex systems.
2011
Many complex systems present an intrinsic bipartite nature and are often described and modeled in terms of networks [1-5]. Examples include movies and actors [1, 2, 4], authors and scientific papers [6-9], email accounts and emails [10], plants and animals that pollinate them [11, 12]. Bipartite networks are often very heterogeneous in the number of relationships that the elements of one set establish with the elements of the other set. When one constructs a projected network with nodes from only one set, the system heterogeneity makes it very difficult to identify preferential links between the elements. Here we introduce an unsupervised method to statistically validate each link of the pr…
Asymmetric Comparison and Querying of Biological Networks
2011
Comparing and querying the protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform these tasks operate symmetrically, i.e., they do not assign a distinct role to the input PPI networks. However, in most cases, the input networks are indeed distinguishable on the basis of how the corresponding organism is biologically well characterized. In this paper a new idea is developed, that is, to exploit differences in the characterization of organisms at hand in order to devise methods for comparing their PPI networks. We use the PPI network (called Master) of the best characterized organism as a …
Algorithmic Analysis of Programs with Well Quasi-ordered Domains
2000
AbstractOver the past few years increasing research effort has been directed towards the automatic verification of infinite-state systems. This paper is concerned with identifying general mathematical structures which can serve as sufficient conditions for achieving decidability. We present decidability results for a class of systems (called well-structured systems) which consist of a finite control part operating on an infinite data domain. The results assume that the data domain is equipped with a preorder which is a well quasi-ordering, such that the transition relation is “monotonic” (a simulation) with respect to the preorder. We show that the following properties are decidable for wel…