Machine 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. Generalized 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/ . The 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.

The encounter of large amounts of biological sequence data generated during the last decades and the algorithmic and hardware improvements have offered the possibility to apply machine learning techniques in bioinformatics. While the machine learning community is aware of the necessity to rigorously distinguish data transformation from data comparison and adopt reasonable combinations thereof, this awareness is often lacking in the field of comparative sequence analysis. With realization of the disadvantages of alignments for sequence comparison, some typical applications use more and more so-called alignment-free approaches. In light of this development, we present a conceptual framework for alignment-free sequence comparison, which highlights the delineation of: 1) the sequence data transformation comprising of adequate mathematical sequence coding and feature generation, from 2) the subsequent (dis-)similarity evaluation of the transformed data by means of problem-specific but mathematically consistent proximity measures. We consider coding to be an information-loss free data transformation in order to get an appropriate representation, whereas feature generation is inevitably information-lossy with the intention to extract just the task-relevant information. This distinction sheds light on the plethora of methods available and assists in identifying suitable methods in machine learning and data analysis to compare the sequences under these premises.

Prototype-based models like the Generalized Learning Vector Quantization (GLVQ) belong to the class of interpretable classifiers. Moreover, quantum-inspired methods get more and more into focus in machine learning due to its potential efficient computing. Further, its interesting mathematical perspectives offer new ideas for alternative learning scenarios. This paper proposes a quantum computing-inspired variant of the prototype-based GLVQ for classification learning. We start considering kernelized GLVQ with real- and complex-valued kernels and their respective feature mapping. Thereafter, we explain how quantum space ideas could be integrated into a GLVQ using quantum bit vector space in the quantum state space $${\mathcal {H}}^{n}$$Hn and show the relations to kernelized GLVQ. In particular, we explain the related feature mapping of data into the quantum state space $${\mathcal {H}}^{n}$$Hn . A key feature for this approach is that $${\mathcal {H}}^{n}$$Hn is an Hilbert space with particular inner product properties, which finally restrict the prototype adaptations to be unitary transformations. The resulting approach is denoted as Qu-GLVQ. We provide the mathematical framework and give exemplary numerical results.

Sensor fusion has gained a great deal of attention in recent years. It is used as an application tool in many different fields, especially the semiconductor, automotive, and medical industries. However, this field of research, regardless of the field of application, still presents different challenges concerning the choice of the sensors to be combined and the fusion architecture to be developed. To decrease application costs and engineering efforts, it is very important to analyze the sensors’ data beforehand once the application target is defined. This pre-analysis is a basic step to establish a working environment with fewer misclassification cases and high safety. One promising approach to do so is to analyze the system using deep neural networks. The disadvantages of this approach are mainly the required huge storage capacity, the big training effort, and that these networks are difficult to interpret. In this paper, we focus on developing a smart and interpretable bi-functional artificial intelligence (AI) system, which has to discriminate the combined data regarding predefined classes. Furthermore, the system can evaluate the single source signals used in the classification task. The evaluation here covers each sensor contribution and robustness. More precisely, we train a smart and interpretable prototype-based neural network, which learns automatically to weight the influence of the sensors for the classification decision. Moreover, the prototype-based classifier is equipped with a reject option to measure classification certainty. To validate our approach’s efficiency, we refer to different industrial sensor fusion applications.

In the present article we propose the application of variants of the mutual information function as characteristic fingerprints of biomolecular sequences for classification analysis. In particular, we consider the resolved mutual information functions based on Shannon-, Rényi-, and Tsallis-entropy. In combination with interpretable machine learning classifier models based on generalized learning vector quantization, a powerful methodology for sequence classification is achieved which allows substantial knowledge extraction in addition to the high classification ability due to the model-inherent robustness. Any potential (slightly) inferior performance of the used classifier is compensated by the additional knowledge provided by interpretable models. This knowledge may assist the user in the analysis and understanding of the used data and considered task. After theoretical justification of the concepts, we demonstrate the approach for various example data sets covering different areas in biomolecular sequence analysis.