Explainable Artificial Intelligence (XAI) is an increasingly important field of research required to bring AI to the next level in real-world applications. Global sensitivity analysis (GSA) methods... Show moreExplainable Artificial Intelligence (XAI) is an increasingly important field of research required to bring AI to the next level in real-world applications. Global sensitivity analysis (GSA) methods play an important role in XAI, as they can provide an understanding of which (groups of) parameters have high influence in the predictions of machine learning models and the output of simulators and real-world processes. In this paper, we conduct a survey into global sensitivity methods in an XAI context and present both a qualitative and a quantitative analysis of these methods under different conditions. In addition to the overview and comparison, we propose an open source application, GSAreport, that allows you to easily generate extensive reports using a carefully selected set of global sensitivity analysis methods depending on the number of dimensions and samples, to gain a deep understanding of the role of each feature for a given model or data set. We finally present the methods discussed in a complex real-world application of genomic prediction and draw conclusions about when to use which GSA methods. Show less
Motivation: Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these... Show moreMotivation: Protein function prediction is a difficult bioinformatics problem. Many recent methods use deep neural networks to learn complex sequence representations and predict function from these. Deep supervised models require a lot of labeled training data which are not available for this task. However, a very large amount of protein sequences without functional labels is available.Results: We applied an existing deep sequence model that had been pretrained in an unsupervised setting on the supervised task of protein molecular function prediction. We found that this complex feature representation is effective for this task, outperforming hand-crafted features such as one-hot encoding of amino acids, k-mer counts, secondary structure and backbone angles. Also, it partly negates the need for complex prediction models, as a two-layer perceptron was enough to achieve competitive performance in the third Critical Assessment of Functional Annotation benchmark. We also show that combining this sequence representation with protein 3D structure information does not lead to performance improvement, hinting that 3D structure is also potentially learned during the unsupervised pretraining. Show less
