Search results for "CODE"
showing 10 items of 1180 documents
A loop-free two-close Gray-code algorithm for listing k-ary Dyck words
2006
AbstractP. Chase and F. Ruskey each published a Gray code for length n binary strings with m occurrences of 1, coding m-combinations of n objects, which is two-close—that is, in passing from one binary string to its successor a single 1 exchanges positions with a 0 which is either adjacent to the 1 or separated from it by a single 0. If we impose the restriction that any suffix of a string contains at least k−1 times as many 0's as 1's, we obtain k-suffixes: suffixes of k-ary Dyck words. Combinations are retrieved as special case by setting k=1 and k-ary Dyck words are retrieved as a special case by imposing the additional condition that the entire string has exactly k−1 times as many 0's a…
Parallel Calculation of CCSDT and Mk-MRCCSDT Energies.
2010
A scheme for the parallel calculation of energies at the coupled-cluster singles, doubles, and triples (CCSDT) level of theory, several approximate iterative CCSDT schemes (CCSDT-1a, CCSDT-1b, CCSDT-2, CCSDT-3, and CC3), and for the state-specific multireference coupled-cluster ansatz suggested by Mukherjee with a full treatment of triple excitations (Mk-MRCCSDT) is presented. The proposed scheme is based on the adaptation of a highly efficient serial coupled-cluster code leading to a communication-minimized implementation by parallelizing the time-determining steps. The parallel algorithm is tailored for affordable cluster architectures connected by standard communication networks such as …
"Master-Slave" Biological Network Alignment
2010
Performing global alignment between protein-protein interaction (PPI) networks of different organisms is important to infer knowledge about conservation across species. Known methods that perform this task operate symmetrically, that is to say, 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 well the corresponding organism is biologically well-characterized. For well-characterized organisms the associated PPI network supposedly encode in a sound manner all the information about their proteins and associated interactions, which is far from being the case for not well characterized ones. He…
A study on graph representations for genetic programming
2020
Graph representations promise several desirable properties for Genetic Programming (GP); multiple-output programs, natural representations of code reuse and, in many cases, an innate mechanism for neutral drift. Each graph GP technique provides a program representation, genetic operators and overarching evolutionary algorithm. This makes it difficult to identify the individual causes of empirical differences, both between these methods and in comparison to traditional GP. In this work, we empirically study the behavior of Cartesian Genetic Programming (CGP), Linear Genetic Programming (LGP), Evolving Graphs by Graph Programming (EGGP) and traditional GP. By fixing some aspects of the config…
On the role of non-effective code in linear genetic programming
2019
In linear variants of Genetic Programming (GP) like linear genetic programming (LGP), structural introns can emerge, which are nodes that are not connected to the final output and do not contribute to the output of a program. There are claims that such non-effective code is beneficial for search, as it can store relevant and important evolved information that can be reactivated in later search phases. Furthermore, introns can increase diversity, which leads to higher GP performance. This paper studies the role of non-effective code by comparing the performance of LGP variants that deal differently with non-effective code for standard symbolic regression problems. As we find no decrease in p…
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) …
Statistical analysis of RaptorQ failure probability applied to a data recovery software
2014
In this work, we have implemented a data recovery software integrating the most recent rateless codes, i.e., RaptorQ codes. Thanks to the above-mentioned software, it is possible to recover data loss occurring on several kinds of network conditions. We have performed a statistical analysis of failure probabilities at several configurations of RaptorQ parameters. We have found a good agreement with the theoretical values of a random linear fountain code over Galois Field GF(256). Moreover, we have shown that the probability of having a certain number of failed decoded source blocks - when sending a fixed size file - follows a Poisson distribution.
Recursive modeling for completed code generation
2009
Model-Driven Development is promising to software development because it can reduce the complexity and cost of developing large software systems. The basic idea is the use of different kinds of models during the software development process, transformations between them, and automatic code generation at the end of the development. But unlike the structural parts, fully-automated code generation from the behavior parts is still hard, if it works at all, restricted to specific application areas using a domain specific language, DSL.This paper proposes an approach to model the behavior parts of a system and to embed them into the structural models. The underlying idea is recursive refinements …
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
2015
This is a post-peer-review, pre-copyedit version of an article published in Journal of Computational Science. The final authenticated version is available online at: https://doi.org/10.1016/j.jocs.2015.04.001 [Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting epistasis, i.e. interactions among k markers (k ≥ 2), is an important but time consuming operation since statistical computations have to be performed for each k-tuple of measured markers. Efficient exhaustive methods have been proposed for k = 2, but exhaustive thi…
Challenges of Program Synthesis with Grammatical Evolution
2020
Program synthesis is an emerging research topic in the field of EC with the potential to improve real-world software development. Grammar-guided approaches like GE are suitable for program synthesis as they can express common programming languages with their required properties. This work uses common software metrics (lines of code, McCabe metric, size and depth of the abstract syntax tree) for an analysis of GE’s search behavior and the resulting problem structure. We find that GE is not able to solve program synthesis problems, where correct solutions have higher values of the McCabe metric (which means they require conditions or loops). Since small mutations of high-quality solutions str…