More than twelve years have elapsed since the first public release of WEKA. In that time, the software has been rewritten entirely from scratch, evolved substantially and now accompanies a text on data mining [35]. These days, WEKA enjoys widespread acceptance in both academia and business, has an active community, and has been downloaded more than 1.4 million times since being placed on Source-Forge in April 2000. This paper provides an introduction to the WEKA workbench, reviews the history of the project, and, in light of the recent 3.6 stable release, briefly discusses what has been added since the last stable version (Weka 3.4) released in 2003.

/pdf/the-weka-data-mining-software-an-update-3zs9onav7o.pdf

The WEKA data mining software: an update

As computational work becomes more and more integral to many aspects of scientific research, computational reproducibility has become an issue of increasing importance to computer systems researchers and domain scientists alike Though computational reproducibility seems more straight forward than replicating physical experiments, the complex and rapidly changing nature of computer environments makes being able to reproduce and extend such work a serious challenge In this paper, I explore common reasons that code developed for one research project cannot be successfully executed or extended by subsequent researchers I review current approaches to these issues, including virtual machines and workflow systems, and their limitations I then examine how the popular emerging technology Docker combines several areas from systems research - such as operating system virtualization, cross-platform portability, modular re-usable elements, versioning, and a 'DevOps' philosophy, to address these challenges I illustrate this with several examples of Docker use with a focus on the R statistical environment

An introduction to Docker for reproducible research

Workflows and e-Science: An overview of workflow system features and capabilities

Pegasus, a workflow management system for science automation

Motivation: Classification and feature selection of genomics or transcriptomics data is often hampered by the large number of features as compared with the small number of samples available. Moreover, features represented by probes that either have similar molecular functions (gene expression analysis) or genomic locations (DNA copy number analysis) are highly correlated. Classical model selection methods such as penalized logistic regression or random forest become unstable in the presence of high feature correlations. Sophisticated penalties such as group Lasso or fused Lasso can force the models to assign similar weights to correlated features and thus improve model stability and interpretability. In this article, we show that the measures of feature relevance corresponding to the above-mentioned methods are biased such that the weights of the features belonging to groups of correlated features decrease as the sizes of the groups increase, which leads to incorrect model interpretation and misleading feature ranking.

Results: With simulation experiments, we demonstrate that Lasso logistic regression, fused support vector machine, group Lasso and random forest models suffer from correlation bias. Using simulations, we show that two related methods for group selection based on feature clustering can be used for correcting the correlation bias. These techniques also improve the stability and the accuracy of the baseline models. We apply all methods investigated to a breast cancer and a bladder cancer arrayCGH dataset and in order to identify copy number aberrations predictive of tumor phenotype.

Availability: R code can be found at: http://www.mpi-inf.mpg.de/~laura/Clustering.r.

Contact: laura.tolosi@mpi-inf.mpg.de

Supplementary information:Supplementary data are available at Bioinformatics online.

/pdf/classification-with-correlated-features-100k5lt2i0.pdf

Classification with correlated features

Most scientists conduct analyses and run models in several different software and hardware environments, mentally coordinating the export and import of data from one environment to another. The Kepler scientific workflow system provides domain scientists with an easy-to-use yet powerful system for capturing scientific workflows (SWFs). SWFs are a formalization of the ad-hoc process that a scientist may go through to get from raw data to publishable results. Kepler attempts to streamline the workflow creation and execution process so that scientists can design, execute, monitor, re-run, and communicate analytical procedures repeatedly with minimal effort. Kepler is unique in that it seamlessly combines high-level workflow design with execution and runtime interaction, access to local and remote data, and local and remote service invocation. SWFs are superficially similar to business process workflows but have several challenges not present in the business workflow scenario. For example, they often operate on large, complex and heterogeneous data, can be computationally intensive and produce complex derived data products that may be archived for use in reparameterized runs or other workflows. Moreover, unlike business workflows, SWFs are often dataflow-oriented as witnessed by a number of recent academic systems (e.g., DiscoveryNet, Taverna and Triana) and commercial systems (Scitegic/Pipeline-Pilot, Inforsense). In a sense, SWFs are often closer to signal-processing and data streaming applications than they are to control-oriented business workflow applications.

/pdf/kepler-an-extensible-system-for-design-and-execution-of-4nt3chsgqp.pdf

Kepler: an extensible system for design and execution of scientific workflows

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Kepler: an extensible system for design and execution of scientific workflows