Speeding up algorithm selection using average ranking and active testing by introducing runtime

Algorithm selection methods can be speeded-up substantially by incorporating multi-objective measures that give preference to algorithms that are both promising and fast to evaluate. In this paper, we introduce such a measure, A3R, and incorporate it into two algorithm selection techniques: average ranking and active testing. Average ranking combines algorithm rankings observed on prior datasets to identify the best algorithms for a new dataset. The aim of the second method is to iteratively select algorithms to be tested on the new dataset, learning from each new evaluation to intelligently select the next best candidate. We show how both methods can be upgraded to incorporate a multi-objective measure A3R that combines accuracy and runtime. It is necessary to establish the correct balance between accuracy and runtime, as otherwise time will be wasted by conducting less informative tests. The correct balance can be set by an appropriate parameter setting within function A3R that trades off accuracy and runtime. Our results demonstrate that the upgraded versions of Average Ranking and Active Testing lead to much better mean interval loss values than their accuracy-based counterparts.     

Experiment databases

Thousands of machine learning research papers contain extensive experimental comparisons. However, the details of those experiments are often lost after publication, making it impossible to reuse these experiments in further research, or reproduce them to verify the claims made. In this paper, we present a collaboration framework designed to easily share machine learning experiments with the community, and automatically organize them in public databases. This enables immediate reuse of experiments for subsequent, possibly much broader investigation and offers faster and more thorough analysis based on a large set of varied results. We describe how we designed such an experiment database, currently holding over 650,000 classification experiments, and demonstrate its use by answering a wide range of interesting research questions and by verifying a number of recent studies.     

Meta-QSAR: a large-scale application of meta-learning to drug design and discovery

We investigate the learning of quantitative structure activity relationships (QSARs) as a case-study of meta-learning. This application area is of the highest societal importance, as it is a key step in the development of new medicines. The standard QSAR learning problem is: given a target (usually a protein) and a set of chemical compounds (small molecules) with associated bioactivities (e.g. inhibition of the target), learn a predictive mapping from molecular representation to activity. Although almost every type of machine learning method has been applied to QSAR learning there is no agreed single best way of learning QSARs, and therefore the problem area is well-suited to meta-learning. We first carried out the most comprehensive ever comparison of machine learning methods for QSAR learning: 18 regression methods, 3 molecular representations, applied to more than 2700 QSAR problems. (These results have been made publicly available on OpenML and represent a valuable resource for testing novel meta-learning methods.) We then investigated the utility of algorithm selection for QSAR problems. We found that this meta-learning approach outperformed the best individual QSAR learning method (random forests using a molecular fingerprint representation) by up to 13%, on average. We conclude that meta-learning outperforms base-learning methods for QSAR learning, and as this investigation is one of the most extensive ever comparisons of base and meta-learning methods ever made, it provides evidence for the general effectiveness of meta-learning over base-learning.     

The online performance estimation framework: heterogeneous ensemble learning for data streams

Ensembles of classifiers are among the best performing classifiers available in many data mining applications, including the mining of data streams. Rather than training one classifier, multiple classifiers are trained, and their predictions are combined according to a given voting schedule. An important prerequisite for ensembles to be successful is that the individual models are diverse. One way to vastly increase the diversity among the models is to build an heterogeneous ensemble, comprised of fundamentally different model types. However, most ensembles developed specifically for the dynamic data stream setting rely on only one type of base-level classifier, most often Hoeffding Trees. We study the use of heterogeneous ensembles for data streams. We introduce the Online Performance Estimation framework, which dynamically weights the votes of individual classifiers in an ensemble. Using an internal evaluation on recent training data, it measures how well ensemble members performed on this and dynamically updates their weights. Experiments over a wide range of data streams show performance that is competitive with state of the art ensemble techniques, including Online Bagging and Leveraging Bagging, while being significantly faster. All experimental results from this work are easily reproducible and publicly available online.