11,160 research outputs found
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology
Essential guidelines for computational method benchmarking
In computational biology and other sciences, researchers are frequently faced
with a choice between several computational methods for performing data
analyses. Benchmarking studies aim to rigorously compare the performance of
different methods using well-characterized benchmark datasets, to determine the
strengths of each method or to provide recommendations regarding suitable
choices of methods for an analysis. However, benchmarking studies must be
carefully designed and implemented to provide accurate, unbiased, and
informative results. Here, we summarize key practical guidelines and
recommendations for performing high-quality benchmarking analyses, based on our
experiences in computational biology.Comment: Minor update
The SOS Platform: Designing, Tuning and Statistically Benchmarking Optimisation Algorithms
open access articleWe present Stochastic Optimisation Software (SOS), a Java platform facilitating the algorithmic design process and the evaluation of metaheuristic optimisation algorithms. SOS reduces the burden of coding miscellaneous methods for dealing with several bothersome and time-demanding tasks such as parameter tuning, implementation of comparison algorithms and testbed problems, collecting and processing data to display results, measuring algorithmic overhead, etc. SOS provides numerous off-the-shelf methods including: (1) customised implementations of statistical tests, such as the Wilcoxon rank-sum test and the Holm–Bonferroni procedure, for comparing the performances of optimisation algorithms and automatically generating result tables in PDF and formats; (2) the implementation of an original advanced statistical routine for accurately comparing couples of stochastic optimisation algorithms; (3) the implementation of a novel testbed suite for continuous optimisation, derived from the IEEE CEC 2014 benchmark, allowing for controlled activation of the rotation on each testbed function. Moreover, we briefly comment on the current state of the literature in stochastic optimisation and highlight similarities shared by modern metaheuristics inspired by nature. We argue that the vast majority of these algorithms are simply a reformulation of the same methods and that metaheuristics for optimisation should be simply treated as stochastic processes with less emphasis on the inspiring metaphor behind them
A Benchmark for Image Retrieval using Distributed Systems over the Internet: BIRDS-I
The performance of CBIR algorithms is usually measured on an isolated
workstation. In a real-world environment the algorithms would only constitute a
minor component among the many interacting components. The Internet
dramati-cally changes many of the usual assumptions about measuring CBIR
performance. Any CBIR benchmark should be designed from a networked systems
standpoint. These benchmarks typically introduce communication overhead because
the real systems they model are distributed applications. We present our
implementation of a client/server benchmark called BIRDS-I to measure image
retrieval performance over the Internet. It has been designed with the trend
toward the use of small personalized wireless systems in mind. Web-based CBIR
implies the use of heteroge-neous image sets, imposing certain constraints on
how the images are organized and the type of performance metrics applicable.
BIRDS-I only requires controlled human intervention for the compilation of the
image collection and none for the generation of ground truth in the measurement
of retrieval accuracy. Benchmark image collections need to be evolved
incrementally toward the storage of millions of images and that scaleup can
only be achieved through the use of computer-aided compilation. Finally, our
scoring metric introduces a tightly optimized image-ranking window.Comment: 24 pages, To appear in the Proc. SPIE Internet Imaging Conference
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