Understanding the relationship between antibody sequence, structure and function is essential for the design of antibody-based therapeutics and research tools. Recently, machine learning (ML) models mostly based on the application of large language models to sequence information have been developed to predict antibody properties. Yet there are open directions to incorporate structural information, not only to enhance prediction but also to offer insights into the underlying molecular mechanisms. This chapter provides an overview of these approaches and describes two ML frameworks that integrate structural data (via graph representations) with neural networks to predict properties of antibodies: ANTIPASTI predicts binding affinity (a global property) whereas INFUSSE predicts residue flexibility (a local property). We survey the principles underpinning these models; the ways in which they encode structural knowledge; and the strategies that can be used to extract biologically relevant statistical signals that can help discover and disentangle molecular determinants of the properties of interest.

There has been a large number of studies in interpretable and explainable ML for cybersecurity, in particular, for intrusion detection. Many of these studies have significant amount of overlapping and repeated evaluations and analysis. At the same time, these studies overlook crucial model, data, learning process, and utility related issues and many times completely disregard them. These issues include the use of overly complex and opaque ML models, unaccounted data imbalances and correlated features, inconsistent influential features across different explanation methods, the inconsistencies stemming from the constituents of a learning process, and the implausible utility of explanations. In this work, we empirically demonstrate these issues, analyze them and propose practical solutions in the context of feature-based model explanations. Specifically, we advise avoiding complex opaque models such as Deep Neural Networks and instead using interpretable ML models such as Decision Trees as the available intrusion datasets are not difficult for such interpretable models to classify successfully. Then, we bring attention to the binary classification metrics such as Matthews Correlation Coefficient (which are well-suited for imbalanced datasets. Moreover, we find that feature-based model explanations are most often inconsistent across different settings. In this respect, to further gauge the extent of inconsistencies, we introduce the notion of cross explanations which corroborates that the features that are determined to be impactful by one explanation method most often differ from those by another method. Furthermore, we show that strongly correlated data features and the constituents of a learning process, such as hyper-parameters and the optimization routine, become yet another source of inconsistent explanations. Finally, we discuss the utility of feature-based explanations.