Similarity search for scientific workflows

Abstract

With the increasing popularity of scientific workflows, public repositories are gaining importance as a means to share, find, and reuse such workflows. As the sizes of these repositories grow, methods to compare the scientific workflows stored in them become a necessity, for instance, to allow duplicate detection or similarity search. Scientific workflows are complex objects, and their comparison entails a number of distinct steps from comparing atomic elements to comparison of the workflows as a whole. Various studies have implemented methods for scientific workflow comparison and came up with often contradicting conclusions upon which algorithms work best. Comparing these results is cumbersome, as the original studies mixed different approaches for different steps and used different evaluation data and metrics. We contribute to the field (i) by disecting each previous approach into an explicitly defined and comparable set of subtasks, (ii) by comparing in isolation different approaches taken at each step of scientific workflow comparison, reporting on an number of unexpected findings, (iii) by investigating how these can best be combined into aggregated measures, and (iv) by making available a gold standard of over 2000 similarity ratings contributed by 15 workflow experts on a corpus of almost 1500 workflows and re-implementations of all methods we evaluated.

Layer Decomposition: An Effective Structure-Based Approach for Scientific Workflow Similarity

“…However, these comparisons were performed on very small and welldocumented workflow sets, and thus the results should not be extrapolated to the large, but shallowly annotated repositories that exist today. To verify this hypothesis, in prior work we performed a large-scale comparative evaluation of workflow similarity search algorithms [14]. Our results indicated that a) structure-based methods are indispensable for some current repositories which lack rich annotations, b) structure-based methods, once properly configured, outperform annotationbased methods even when such rich annotations are available, and c) any such standalone approach is further beaten by ensembles of annotation-based and structure-based methods.…”

Cross-domain graph based similarity measurement of workflows

“…Some workflow similarity measurements are text based [19], and some others consider different aspects of workflows (such as workflow motifs [17], or workflow structures [1,20]). For example a workflow similarity measurement method is the work at [19] that used feature selection techniques based on text.…”

“…The tool used was Protégé 4.x 1 . Protégé is mainly used for ontology demonstration but it also provides some features to workflow demonstration.…”

“…Both authors read and approved the final manuscript. 1 International Campus of Kharazmi, Shahrood University of Technology, Shahrood, Iran.…”

Scientific Workflow Clustering Based on Motif Discovery

“…Note that the clustering is done on the entire workflows without considering the sub-clustering of individual workflow tasks. In spite of some other works similar the work of [22]. In the work of [22] normalization with regard to sizes of compared workflows is done as a post processing step.…”