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Explainable Artificial Intelligence (xAI) is an established field with a vibrant community that has developed a variety of very successful approaches to explain and interpret predictions of complex machine learning models such as deep neural networks. In this article, we briefly introduce a few selected methods and discuss them in a short, clear and concise way. The goal of this article is to give beginners, especially application engineers and data scientists, a quick overview of the state of the art in this current topic. The following 17 methods are covered in this chapter: LIME, Anchors, GraphLIME, LRP, DTD, PDA, TCAV, XGNN, SHAP, ASV, Break-Down, Shapley Flow, Textual Explanations of Visual Models, Integrated Gradients, Causal Models, Meaningful Perturbations, and X-NeSyL.

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Motivation The tremendous success of graphical neural networks (GNNs) already had a major impact on systems biology research. For example, GNNs are currently being used for drug target recognition in protein–drug interaction networks, as well as for cancer gene discovery and more. Important aspects whose practical relevance is often underestimated are comprehensibility, interpretability and explainability. Results In this work, we present a novel graph-based deep learning framework for disease subnetwork detection via explainable GNNs. Each patient is represented by the topology of a protein–protein interaction (PPI) network, and the nodes are enriched with multi-omics features from gene expression and DNA methylation. In addition, we propose a modification of the GNNexplainer that provides model-wide explanations for improved disease subnetwork detection. Availability and implementation The proposed methods and tools are implemented in the GNN-SubNet Python package, which we have made available on our GitHub for the international research community (https://github.com/pievos101/GNN-SubNet). Supplementary information Supplementary data are available at Bioinformatics online.