Background: The development of algorithms to infer the structure of gene regulatory networks based on expression data is an important subject in bioinformatics research. Validation of these algorithms requires benchmark data sets for which the underlying network is known. Since experimental data sets of the appropriate size and design are usually not available, there is a clear need to generate well-characterized synthetic data sets that allow thorough testing of learning algorithms in a fast and reproducible manner.
Abstract.Comparative machine learning experiments have become an important methodology in empirical approaches to natural language processing (i) to investigate which machine learning algorithms have the 'right bias' to solve specific natural language processing tasks, and (ii) to investigate which sources of information add to accuracy in a learning approach. Using automatic word sense disambiguation as an example task, we show that with the methodology currently used in comparative machine learning experiments, the results may often not be reliable because of the role of and interaction between feature selection and algorithm parameter optimization. We propose genetic algorithms as a practical approach to achieve both higher accuracy within a single approach, and more reliable comparisons.
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