Search results for "benchmark"
showing 10 items of 310 documents
Implementation of the full explicitly correlated coupled-cluster singles and doubles model CCSD-F12 with optimally reduced auxiliary basis dependence.
2008
An implementation of the full explicitly correlated coupled-cluster singles and doubles model CCSD-F12 using a single Slater-type geminal has been obtained with the aid of automated term generation and evaluation techniques. In contrast to a previously reported computer code [T. Shiozaki et al., J. Chem. Phys. 129, 071101 (2008)], our implementation features a reduced dependence on the auxiliary basis set due to the use of a reformulated evaluation of the so-called Z-intermediate rather than straight forward insertion of an auxiliary basis expansion, which allows an unambiguous comparison to more approximate CCSD-F12 models. First benchmark results for total correlation energies and reactio…
CUDA-enabled Sparse Matrix–Vector Multiplication on GPUs using atomic operations
2013
We propose the Sliced Coordinate Format (SCOO) for Sparse Matrix-Vector Multiplication on GPUs.An associated CUDA implementation which takes advantage of atomic operations is presented.We propose partitioning methods to transform a given sparse matrix into SCOO format.An efficient Dual-GPU implementation which overlaps computation and communication is described.Extensive performance comparisons of SCOO compared to other formats on GPUs and CPUs are provided. Existing formats for Sparse Matrix-Vector Multiplication (SpMV) on the GPU are outperforming their corresponding implementations on multi-core CPUs. In this paper, we present a new format called Sliced COO (SCOO) and an efficient CUDA i…
A branch-and-cut algorithm for the soft-clustered vehicle-routing problem
2021
Abstract The soft-clustered vehicle-routing problem is a variant of the classical capacitated vehicle-routing problem (CVRP) in which customers are partitioned into clusters and all customers of the same cluster must be served by the same vehicle. We introduce a novel symmetric formulation of the problem in which the clustering part is modeled with an asymmetric sub-model. We solve the new model with a branch-and-cut algorithm exploiting some known valid inequalities for the CVRP that can be adapted. In addition, we derive problem-specific cutting planes and new heuristic and exact separation procedures. For square grid instances in the Euclidean plane, we provide lower-bounding techniques …
Textual data compression in computational biology: a synopsis.
2009
Abstract Motivation: Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. Results: The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been use…
Iterative Cluster Analysis of Protein Interaction Data
2004
Abstract Motivation: Generation of fast tools of hierarchical clustering to be applied when distances among elements of a set are constrained, causing frequent distance ties, as happens in protein interaction data. Results: We present in this work the program UVCLUSTER, that iteratively explores distance datasets using hierarchical clustering. Once the user selects a group of proteins, UVCLUSTER converts the set of primary distances among them (i.e. the minimum number of steps, or interactions, required to connect two proteins) into secondary distances that measure the strength of the connection between each pair of proteins when the interactions for all the proteins in the group are consid…
ArtiFuse—computational validation of fusion gene detection tools without relying on simulated reads
2019
Abstract Motivation Gene fusions are an important class of transcriptional variants that can influence cancer development and can be predicted from RNA sequencing (RNA-seq) data by multiple existing tools. However, the real-world performance of these tools is unclear due to the lack of known positive and negative events, especially with regard to fusion genes in individual samples. Often simulated reads are used, but these cannot account for all technical biases in RNA-seq data generated from real samples. Results Here, we present ArtiFuse, a novel approach that simulates fusion genes by sequence modification to the genomic reference, and therefore, can be applied to any RNA-seq dataset wit…
Bond-based 3D-chiral linear indices: Theory and QSAR applications to central chirality codification
2008
The recently introduced non-stochastic and stochastic bond-based linear indices are been generalized to codify chemical structure information for chiral drugs, making use of a trigonometric 3D-chirality correction factor. These improved modified descriptors are applied to several well-known data sets to validate each one of them. Particularly, Cramer's steroid data set has become a benchmark for the assessment of novel quantitative structure activity relationship methods. This data set has been used by several researchers using 3D-QSAR approaches such as Comparative Molecular Field Analysis, Molecular Quantum Similarity Measures, Comparative Molecular Moment Analysis, E-state, Mapping Prope…
STRATEGIC PLANNING AND MANAGEMENT IN GOVERNMENTAL AND PRIVATE SECTOR IN LATVIA: COMPARATIVE ANALYSIS AND OPPORTUNITIES FOR IMPROVEMENT
2012
Management issues can be divided in two large groups: governmental, with its specific aims, methods and challenges, and private sector responsible for economical results, competitiveness and state revenues. Although these sectors have so much in common in sustaining the state, striving for excellence, fulfilment of European Union 2020 strategy and for the best results, they are at the same time very different. By theory and practice, one of the greatest methods how to improve performance, is benchmarking- both looking for the best in the concrete field and in different area. In the article authors compare strategic planning and management issues in governmental and private sector, thus iden…
Large‐scale set partitioning problems: Some real‐world instances hide a beneficial structure
2006
In this paper we consider large‐scale set partitioning problems. Our main purpose is to show that real‐world set partitioning problems originating from the container‐trucking industry are easier to tackle in respect to general ones. We show such different behavior through computational experiments: in particular, we have applied both a heuristic algorithm and some exact solution approaches to real‐world instances as well as to benchmark instances from Beasley OR‐library. Moreover, in order to gain an insight into the structure of the real‐world instances, we have performed and evaluated various instance perturbations. Didelės matematinės aibės dalijimo problemų sprendimas, nagrinėjant reali…
VoxelMages: a general-purpose graphical interface for designing geometries and processing DICOM images for PENELOPE
2016
The design and construction of geometries for Monte Carlo calculations is an error-prone, time-consuming, and complex step in simulations describing particle interactions and transport in the field of medical physics. The software VoxelMages has been developed to help the user in this task. It allows to design complex geometries and to process DICOM image files for simulations with the general-purpose Monte Carlo code PENELOPE in an easy and straightforward way. VoxelMages also allows to import DICOM-RT structure contour information as delivered by a treatment planning system. Its main characteristics, usage and performance benchmarking are described in detail.