Fast and Memory-Efficient Significant Pattern Mining via Permutation Testing

We present a novel algorithm for significant pattern mining, Westfall-Young light. The target patterns are statistically significantly enriched in one of two classes of objects. Our method corrects for multiple hypothesis testing and correlations between patterns via the Westfall-Young permutation procedure, which empirically estimates the null distribution of pattern frequencies in each class via permutations. In our experiments, Westfall-Young light dramatically outperforms the current state-of-the-art approach, both in terms of runtime and memory efficiency on popular real-world benchmark datasets for pattern mining. The key to this efficiency is that, unlike all existing methods, our algorithm does not need to solve the underlying frequent pattern mining problem anew for each permutation and does not need to store the occurrence list of all frequent patterns. Westfall-Young light opens the door to significant pattern mining on large datasets that previously involved prohibitive runtime or memory costs. Our code is available from http://www.bsse.ethz.ch/mlcb/research/machine-learning/wylight.html