Papers by Jano van Hemert
IEEE Transactions on Evolutionary Computation, 2003
Constraint handling is not straightforward in evolutionary algorithms (ea) since the usual search... more Constraint handling is not straightforward in evolutionary algorithms (ea) since the usual search operators, mutation and recombination, are 'blind' to constraints. Nevertheless, the issue is highly relevant, for many challenging problems involve constraints. Over the last decade numerous eas for solving constraint satisfaction problems (csp) have been introduced and studied on various problems. The diversity of approaches and the variety of problems used to study the resulting algorithms prevents a fair and accurate comparison of these algorithms. This paper aligns related work by presenting a concise overview and an extensive performance comparison of all these eas on a systematically generated test suite of random binary csps. The random problem instance generator is based on a theoretical model that fixes deficiencies of models and respective generators that have been formerly used in the Evolutionary Computing (ec) field.
Bmc …, Jan 1, 2010
Background: Microarray technology is a popular means of producing whole genome transcriptional pr... more Background: Microarray technology is a popular means of producing whole genome transcriptional profiles, however high cost and scarcity of mRNA has led many studies to be conducted based on the analysis of single samples. We exploit the design of the Illumina platform, specifically multiple arrays on each chip, to evaluate intraexperiment technical variation using repeated hybridisations of universal human reference RNA (UHRR) and duplicate hybridisations of primary breast tumour samples from a clinical study. Results: A clear batch-specific bias was detected in the measured expressions of both the UHRR and clinical samples. This bias was found to persist following standard microarray normalisation techniques. However, when mean-centering or empirical Bayes batch-correction methods (ComBat) were applied to the data, inter-batch variation in the UHRR and clinical samples were greatly reduced. Correlation between replicate UHRR samples improved by two orders of magnitude following batch-correction using ComBat (ranging from 0.9833-0.9991 to 0.9997-0.9999) and increased the consistency of the gene-lists from the duplicate clinical samples, from 11.6% in quantile normalised data to 66.4% in batch-corrected data. The use of UHRR as an inter-batch calibrator provided a small additional benefit when used in conjunction with ComBat, further increasing the agreement between the two gene-lists, up to 74.1%. Conclusion: In the interests of practicalities and cost, these results suggest that single samples can generate reliable data, but only after careful compensation for technical bias in the experiment. We recommend that investigators appreciate the propensity for such variation in the design stages of a microarray experiment and that the use of suitable correction methods become routine during the statistical analysis of the data.
BMC Bioinformatics, 2011
Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multipl... more Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments.
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Papers by Jano van Hemert