Ensembles of Randomized Time Series Shapelets Provide Improved Accuracy while Reducing Computational Costs

Shapelets are discriminative time series subsequences that allow generation of interpretable classification models, which provide faster and generally better classification than the nearest neighbor approach. However, the shapelet discovery process requires the evaluation of all possible subsequences of all time series in the training set, making it extremely computation intensive. Consequently, shapelet discovery for large time series datasets quickly becomes intractable. A number of improvements have been proposed to reduce the training time. These techniques use approximation or discretization and often lead to reduced classification accuracy compared to the exact method. We are proposing the use of ensembles of shapelet-based classifiers obtained using random sampling of the shapelet candidates. Using random sampling reduces the number of evaluated candidates and consequently the required computational cost, while the classification accuracy of the resulting models is also not significantly different than that of the exact algorithm. The combination of randomized classifiers rectifies the inaccuracies of individual models because of the diversity of the solutions. Based on the experiments performed, it is shown that the proposed approach of using an ensemble of inexpensive classifiers provides better classification accuracy compared to the exact method at a significantly lesser computational cost

Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources