A unifying view for performance measures in multi-class prediction

In the last few years, many different performance measures have been introduced to overcome the weakness of the most natural metric, the Accuracy. Among them, Matthews Correlation Coefficient has recently gained popularity among researchers not only in machine learning but also in several application fields such as bioinformatics. Nonetheless, further novel functions are being proposed in literature. We show that Confusion Entropy, a recently introduced classifier performance measure for multi-class problems, has a strong (monotone) relation with the multi-class generalization of a classical metric, the Matthews Correlation Coefficient. Computational evidence in support of the claim is provided, together with an outline of the theoretical explanation

Using machine learning methods to determine a typology of patients with HIV-HCV infection to be treated with antivirals

Several European countries have established criteria for prioritising initiation of treatment in patients infected with the hepatitis C virus (HCV) by grouping patients according to clinical characteristics. Based on neural network techniques, our objective was to identify those factors for HIV/HCV co-infected patients (to which clinicians have given careful consideration before treatment uptake) that have not being included among the prioritisation criteria. This study was based on the Spanish HERACLES cohort (NCT02511496) (April-September 2015, 2940 patients) and involved application of different neural network models with different basis functions (product-unit, sigmoid unit and radial basis function neural networks) for automatic classification of patients for treatment. An evolutionary algorithm was used to determine the architecture and estimate the coefficients of the model. This machine learning methodology found that radial basis neural networks provided a very simple model in terms of the number of patient characteristics to be considered by the classifier (in this case, six), returning a good overall classification accuracy of 0.767 and a minimum sensitivity (for the classification of the minority class, untreated patients) of 0.550. Finally, the area under the ROC curve was 0.802, which proved to be exceptional. The parsimony of the model makes it especially attractive, using just eight connections. The independent variable "recent PWID" is compulsory due to its importance. The simplicity of the model means that it is possible to analyse the relationship between patient characteristics and the probability of belonging to the treated group

Stratification bias in low signal microarray studies

BACKGROUND: When analysing microarray and other small sample size biological datasets, care is needed to avoid various biases. We analyse a form of bias, stratification bias, that can substantially affect analyses using sample-reuse validation techniques and lead to inaccurate results. This bias is due to imperfect stratification of samples in the training and test sets and the dependency between these stratification errors, i.e. the variations in class proportions in the training and test sets are negatively correlated. RESULTS: We show that when estimating the performance of classifiers on low signal datasets (i.e. those which are difficult to classify), which are typical of many prognostic microarray studies, commonly used performance measures can suffer from a substantial negative bias. For error rate this bias is only severe in quite restricted situations, but can be much larger and more frequent when using ranking measures such as the receiver operating characteristic (ROC) curve and area under the ROC (AUC). Substantial biases are shown in simulations and on the van 't Veer breast cancer dataset. The classification error rate can have large negative biases for balanced datasets, whereas the AUC shows substantial pessimistic biases even for imbalanced datasets. In simulation studies using 10-fold cross-validation, AUC values of less than 0.3 can be observed on random datasets rather than the expected 0.5. Further experiments on the van 't Veer breast cancer dataset show these biases exist in practice. CONCLUSION: Stratification bias can substantially affect several performance measures. In computing the AUC, the strategy of pooling the test samples from the various folds of cross-validation can lead to large biases; computing it as the average of per-fold estimates avoids this bias and is thus the recommended approach. As a more general solution applicable to other performance measures, we show that stratified repeated holdout and a modified version of k-fold cross-validation, balanced, stratified cross-validation and balanced leave-one-out cross-validation, avoids the bias. Therefore for model selection and evaluation of microarray and other small biological datasets, these methods should be used and unstratified versions avoided. In particular, the commonly used (unbalanced) leave-one-out cross-validation should not be used to estimate AUC for small datasets

Multi-objective optimisation for receiver operating characteristic analysis

Copyright © 2006 Springer-Verlag Berlin Heidelberg. The final publication is available at link.springer.comBook title: Multi-Objective Machine LearningSummary Receiver operating characteristic (ROC) analysis is now a standard tool for the comparison of binary classifiers and the selection operating parameters when the costs of misclassification are unknown. This chapter outlines the use of evolutionary multi-objective optimisation techniques for ROC analysis, in both its traditional binary classification setting, and in the novel multi-class ROC situation. Methods for comparing classifier performance in the multi-class case, based on an analogue of the Gini coefficient, are described, which leads to a natural method of selecting the classifier operating point. Illustrations are given concerning synthetic data and an application to Short Term Conflict Alert

Formulation and comparison of multi-class ROC surfaces

2nd ROCML workshop, held within the 22nd International Conference on Machine Learning (ICML 2005), Bonn, Germany, 7-11 August 2005The Receiver Operating Characteristic (ROC) has become a standard tool for the analysis and comparison of classifiers when the costs of misclassification are unknown. There has been relatively little work, however, examining ROC for more than two classes. Here we define the ROC surface for the Q-class problem in terms of a multi-objective optimisation problem in which the goal is to simultaneously minimise the Q(Q − 1) mis-classification rates, when the misclassification costs and parameters governing the classifier’s behaviour are unknown. We present an evolutionary algorithm to locate the optimal trade-off surface between misclassifications of different types. The performance of the evolutionary algorithm is illustrated on a synthetic three class problem. In addition the use of the Pareto optimal surface to compare classifiers is discussed, and we present a straightforward multi-class analogue of the Gini coefficient. This is illustrated on synthetic and standard machine learning dat

Support Vector Machine classification of strong gravitational lenses

The imminent advent of very large-scale optical sky surveys, such as Euclid and LSST, makes it important to find efficient ways of discovering rare objects such as strong gravitational lens systems, where a background object is multiply gravitationally imaged by a foreground mass. As well as finding the lens systems, it is important to reject false positives due to intrinsic structure in galaxies, and much work is in progress with machine learning algorithms such as neural networks in order to achieve both these aims. We present and discuss a Support Vector Machine (SVM) algorithm which makes use of a Gabor filterbank in order to provide learning criteria for separation of lenses and non-lenses, and demonstrate using blind challenges that under certain circumstances it is a particularly efficient algorithm for rejecting false positives. We compare the SVM engine with a large-scale human examination of 100000 simulated lenses in a challenge dataset, and also apply the SVM method to survey images from the Kilo-Degree Survey.Comment: Accepted by MNRA

Multi-Objective Supervised Learning

Copyright © 2008 Springer-Verlag Berlin Heidelberg. The final publication is available at link.springer.comBook title: Multiobjective Problem Solving from NatureExtended version of the 2006 workshop paper presented at the Workshop on Multiobjective Problem-Solving from Nature, 9th International Conference on Parallel Problem Solving from Nature (PPSN IX), Reykjavik, Iceland, 9-13 September 2006; see: http://hdl.handle.net/10871/11785This chapter sets out a number of the popular areas in multiobjective supervised learning. It gives empirical examples of model complexity optimization and competing error terms, and presents the recent advances in multi-class receiver operating characteristic analysis enabled by multiobjective optimization. It concludes by highlighting some specific areas of interest/concern when dealing with multiobjective supervised learning problems, and sets out future areas of potential research

Multi-class ROC analysis from a multi-objective optimisation perspective

Copyright © 2006 Elsevier. NOTICE: this is the author’s version of a work that was accepted for publication in Pattern Recognition Letters . Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Pattern Recognition Letters, Vol. 27 Issue 8 (2006), DOI: 10.1016/j.patrec.2005.10.016Notes: Receiver operating characteristics (ROC) are traditionally used for assessing and tuning classifiers discriminating between two classes. This paper is the first to set ROC analysis in a multi-objective optimisation framework and thus generalise ROC curves to any number of classes, showing how multi-objective optimisation may be used to optimise classifier performance. An important new result is that the appropriate measure for assessing overall classifier quality is the Gini coefficient, rather than the volume under the ROC surface as previously thought. The method is currently being exploited in a KTP project with AI Corporation on detecting credit card fraud.The receiver operating characteristic (ROC) has become a standard tool for the analysis and comparison of classifiers when the costs of misclassification are unknown. There has been relatively little work, however, examining ROC for more than two classes. Here we discuss and present an extension to the standard two-class ROC for multi-class problems. We define the ROC surface for the Q-class problem in terms of a multi-objective optimisation problem in which the goal is to simultaneously minimise the Q(Q − 1) misclassification rates, when the misclassification costs and parameters governing the classifier’s behaviour are unknown. We present an evolutionary algorithm to locate the Pareto front—the optimal trade-off surface between misclassifications of different types. The use of the Pareto optimal surface to compare classifiers is discussed and we present a straightforward multi-class analogue of the Gini coefficient. The performance of the evolutionary algorithm is illustrated on a synthetic three class problem, for both k-nearest neighbour and multi-layer perceptron classifiers