Abstract. Classification is one of the most frequent tasks in machine learning. However, the variety of classification tasks as well as classifier methods is huge. Thus the question is coming up: which classifier is suitable for a given problem or how can we utilize a certain classifier model for different tasks in classification learning. This paper focuses on learning vector quantization classifiers as one of the most intuitive prototype based classification models. Recent extensions and modifications of the basic learning vector quantization algorithm, which are proposed in the last years, are highlighted and also discussed in relation to particular classification task scenarios like imbalanced and/or incomplete data, prior data knowledge, classification guarantees or adaptive data metrics for optimal classification.

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BackgroundMachine learning strategies are prominent tools for data analysis. Especially in life sciences, they have become increasingly important to handle the growing datasets collected by the scientific community. Meanwhile, algorithms improve in performance, but also gain complexity, and tend to neglect interpretability and comprehensiveness of the resulting models.ResultsGeneralized Matrix Learning Vector Quantization (GMLVQ) is a supervised, prototype-based machine learning method and provides comprehensive visualization capabilities not present in other classifiers which allow for a fine-grained interpretation of the data. In contrast to commonly used machine learning strategies, GMLVQ is well-suited for imbalanced classification problems which are frequent in life sciences. We present a Weka plug-in implementing GMLVQ. The feasibility of GMLVQ is demonstrated on a dataset of Early Folding Residues (EFR) that have been shown to initiate and guide the protein folding process. Using 27 features, an area under the receiver operating characteristic of 76.6% was achieved which is comparable to other state-of-the-art classifiers. The obtained model is accessible at https://biosciences.hs-mittweida.de/efpred/.ConclusionsThe application on EFR prediction demonstrates how an easy interpretation of classification models can promote the comprehension of biological mechanisms. The results shed light on the special features of EFR which were reported as most influential for the classification: EFR are embedded in ordered secondary structure elements and they participate in networks of hydrophobic residues. Visualization capabilities of GMLVQ are presented as we demonstrate how to interpret the results.Electronic supplementary materialThe online version of this article (10.1186/s13040-018-0188-2) contains supplementary material, which is available to authorized users.

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