Issues in Process Variants Mining

In today's dynamic business world economic success of an enterprise increasingly depends on its ability to react to internal and external changes in a quick and flexible way. In response to this need, process-aware information systems (PAIS) emerged, which support the modeling, orchestration and monitoring of business processes and services respectively. Recently, a new generation of flexible PAIS was introduced, which additionally allows for dynamic process and service changes. This, in turn, will lead to a large number of process variants, which are created from the same original process model, but might slightly differ from each other. This paper deals with issues related to the mining of such process variant collections. Our overall goal is to learn from process changes and to merge the resulting model variants into a generic process model in the best possible way. By adopting this generic process model in the PAIS, future cost of process change and need for process adaptations will decrease. Finally, we compare our approach with existing process mining techniques, and show that process variants mining is additionally needed to learn from process changes

ALOJA: A framework for benchmarking and predictive analytics in Hadoop deployments

This article presents the ALOJA project and its analytics tools, which leverages machine learning to interpret Big Data benchmark performance data and tuning. ALOJA is part of a long-term collaboration between BSC and Microsoft to automate the characterization of cost-effectiveness on Big Data deployments, currently focusing on Hadoop. Hadoop presents a complex run-time environment, where costs and performance depend on a large number of configuration choices. The ALOJA project has created an open, vendor-neutral repository, featuring over 40,000 Hadoop job executions and their performance details. The repository is accompanied by a test-bed and tools to deploy and evaluate the cost-effectiveness of different hardware configurations, parameters and Cloud services. Despite early success within ALOJA, a comprehensive study requires automation of modeling procedures to allow an analysis of large and resource-constrained search spaces. The predictive analytics extension, ALOJA-ML, provides an automated system allowing knowledge discovery by modeling environments from observed executions. The resulting models can forecast execution behaviors, predicting execution times for new configurations and hardware choices. That also enables model-based anomaly detection or efficient benchmark guidance by prioritizing executions. In addition, the community can benefit from ALOJA data-sets and framework to improve the design and deployment of Big Data applications.This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 639595). This work is partially supported by the Ministry of Economy of Spain under contracts TIN2012-34557 and 2014SGR1051.Peer ReviewedPostprint (published version

Pairwise gene GO-based measures for biclustering of high-dimensional expression data

Background: Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be used to drive these algorithms to find biclusters composed of groups of genes functionally coherent. On the other hand, a distance among genes can be defined according to their information stored in Gene Ontology (GO). Gene pairwise GO semantic similarity measures report a value for each pair of genes which establishes their functional similarity. A scatter search-based algorithm that optimizes a merit function that integrates GO information is studied in this paper. This merit function uses a term that addresses the information through a GO measure. Results: The effect of two possible different gene pairwise GO measures on the performance of the algorithm is analyzed. Firstly, three well known yeast datasets with approximately one thousand of genes are studied. Secondly, a group of human datasets related to clinical data of cancer is also explored by the algorithm. Most of these data are high-dimensional datasets composed of a huge number of genes. The resultant biclusters reveal groups of genes linked by a same functionality when the search procedure is driven by one of the proposed GO measures. Furthermore, a qualitative biological study of a group of biclusters show their relevance from a cancer disease perspective. Conclusions: It can be concluded that the integration of biological information improves the performance of the biclustering process. The two different GO measures studied show an improvement in the results obtained for the yeast dataset. However, if datasets are composed of a huge number of genes, only one of them really improves the algorithm performance. This second case constitutes a clear option to explore interesting datasets from a clinical point of view.Ministerio de Economía y Competitividad TIN2014-55894-C2-

Extending fragment-based free energy calculations with library Monte Carlo simulation: Annealing in interaction space

Pre-calculated libraries of molecular fragment configurations have previously been used as a basis for both equilibrium sampling (via "library-based Monte Carlo") and for obtaining absolute free energies using a polymer-growth formalism. Here, we combine the two approaches to extend the size of systems for which free energies can be calculated. We study a series of all-atom poly-alanine systems in a simple dielectric "solvent" and find that precise free energies can be obtained rapidly. For instance, for 12 residues, less than an hour of single-processor is required. The combined approach is formally equivalent to the "annealed importance sampling" algorithm; instead of annealing by decreasing temperature, however, interactions among fragments are gradually added as the molecule is "grown." We discuss implications for future binding affinity calculations in which a ligand is grown into a binding site

Is One Hyperparameter Optimizer Enough?

Hyperparameter tuning is the black art of automatically finding a good combination of control parameters for a data miner. While widely applied in empirical Software Engineering, there has not been much discussion on which hyperparameter tuner is best for software analytics. To address this gap in the literature, this paper applied a range of hyperparameter optimizers (grid search, random search, differential evolution, and Bayesian optimization) to defect prediction problem. Surprisingly, no hyperparameter optimizer was observed to be `best' and, for one of the two evaluation measures studied here (F-measure), hyperparameter optimization, in 50\% cases, was no better than using default configurations. We conclude that hyperparameter optimization is more nuanced than previously believed. While such optimization can certainly lead to large improvements in the performance of classifiers used in software analytics, it remains to be seen which specific optimizers should be applied to a new dataset.Comment: 7 pages, 2 columns, accepted for SWAN1