SCARF: A Biomedical Association Rule Finding Webserver

TL;DR

SCARF is a webserver tool for generalized association rule mining in biomedical datasets, enabling discovery of complex multi-parametric relations including disjunctions, which helps identify combinatorial biomarkers in large, incomplete datasets.

Contribution

The paper introduces a webserver implementation of a novel generalized association rule mining algorithm that incorporates logical disjunctions to find complex rules in biomedical data.

Findings

Demonstrated in Alzheimer's disease dataset analysis

Reduces large result tables with OR-based rules

Enables discovery of complex multi-parametric relations

Abstract

The analysis of enormous datasets with missing data entries is a standard task in biological and medical data processing. Large-scale, multi-institution clinical studies are the typical examples of such datasets. These sets make possible the search for multi-parametric relations since from the plenty of the data one is likely to find a satisfying number of subjects with the required parameter ensembles. Specifically, finding combinatorial biomarkers for some given condition also needs a very large dataset to analyze. For this goal, statistical regression analysis is not the preferred tool of choice, since (i) the {\em a priori} knowledge of the parameter-sets to analyze is missing, and (ii) typically relatively few subjects have the interesting parameter-value ensembles for the analysis. For fast and automatic multi-parametric relation discovery association-rule finding tools are used for more than two decades in the data-mining community. Here we present the SCARF webserver for {\em generalized} association rule mining. Association rules are of the form: $a$ AND $b$ AND ... AND $x \rightarrow y$, meaning that the presence of properties $a$ AND $b$ AND ... AND $x$ implies property $y$; our algorithm finds generalized association rules, since it also finds logical disjunctions (i.e., ORs) at the left-hand side, allowing the discovery of more complex rules in a more compressed form in the database. This feature also helps reducing the typically very large result-tables of such studies, since allowing ORs in the left-hand side of a single rule could include dozens of classical rules. The capabilities of the SCARF algorithm were demonstrated in mining the Alzheimer's database of the Coalition Against Major Diseases (CAMD) in our recent publication (Archives of Gerontology and Geriatrics Vol. 73, pp. 300-307, 2017). Here we describe the webserver implementation of the algorithm.