Advancements in high-throughput technologies have led to a shift from traditional hypothesis-driven methodologies to data-driven approaches. Multi-omics refers to the integrative analysis of data derived from multiple 'omes', such as genomics, proteomics, transcriptomics, metabolomics, and microbiomics. This approach enables a comprehensive understanding of biological systems by capturing different layers of biological information. Deep learning methods are increasingly utilized to integrate multi-omics data, offering insights into molecular interactions and enhancing research into complex diseases. However, these models, with their numerous interconnected layers and nonlinear relationships, often function as black boxes, lacking transparency in decision-making processes. To overcome this challenge, explainable artificial intelligence (xAI) methods are crucial for creating transparent models that allow clinicians to interpret and work with complex data more effectively. This review explores how xAI can improve the interpretability of deep learning models in multi-omics research, highlighting its potential to provide clinicians with clear insights, thereby facilitating the effective application of such models in clinical settings.

Explainable artificial intelligence (XAI) methods shed light on the predictions of deep neural networks (DNNs). Several different approaches exist and have partly already been successfully applied in climate science. However, the often missing ground truth explanations complicate their evaluation and validation, subsequently compounding the choice of the XAI method. Therefore, in this work, we introduce XAI evaluation in the context of climate research and assess different desired explanation properties, namely, robustness, faithfulness, randomization, complexity, and localization. To this end we build upon previous work and train a multi-layer perceptron (MLP) and a convolutional neural network (CNN) to predict the decade based on annual-mean temperature maps. Next, multiple local XAI methods are applied and their performance is quantified for each evaluation property and compared against a baseline test. Independent of the network type, we find that the XAI methods Integrated Gradients, Layer-wise relevance propagation, and InputGradients exhibit considerable robustness, faithfulness, and complexity while sacrificing randomization. The opposite is true for Gradient, SmoothGrad, NoiseGrad, and FusionGrad. Notably, explanations using input perturbations, such as SmoothGrad and Integrated Gradients, do not improve robustness and faithfulness, contrary to previous claims. Overall, our experiments offer a comprehensive overview of different properties of explanation methods in the climate science context and supports users in the selection of a suitable XAI method.

The explanation to an AI model's prediction used to support decision making in cyber security, is of critical importance. It is especially so when the model's incorrect prediction can lead to severe damages or even losses to lives and critical assets. However, most existing AI models lack the ability to provide explanations on their prediction results, despite their strong performance in most scenarios. In this work, we propose a novel explainable AI method, called PhilaeX, that provides the heuristic means to identify the optimized subset of features to form the complete explanations of AI models' predictions. It identifies the features that lead to the model's borderline prediction, and those with positive individual contributions are extracted. The feature attributions are then quantified through the optimization of a Ridge regression model. We verify the explanation fidelity through two experiments. First, we assess our method's capability in correctly identifying the activated features in the adversarial samples of Android malwares, through the features attribution values from PhilaeX. Second, the deduction and augmentation tests, are used to assess the fidelity of the explanations. The results show that PhilaeX is able to explain different types of classifiers correctly, with higher fidelity explanations, compared to the state-of-the-arts methods such as LIME and SHAP.

Established approaches to assuring safety-critical systems and software are difficult to apply to systems employing machine learning (ML). In many cases, ML is used on ill-defined problems, e.g. optimising sepsis treatment, where there is no clear, pre-defined specification against which to assess validity. This problem is exacerbated by the "opaque" nature of ML where the learnt model is not amenable to human scrutiny. Explainable AI methods have been proposed to tackle this issue by producing human-interpretable representations of ML models which can help users to gain confidence and build trust in the ML system. However, there is not much work explicitly investigating the role of explainability for safety assurance in the context of ML development. This paper identifies ways in which explainable AI methods can contribute to safety assurance of ML-based systems. It then uses a concrete ML-based clinical decision support system, concerning weaning of patients from mechanical ventilation, to demonstrate how explainable AI methods can be employed to produce evidence to support safety assurance. The results are also represented in a safety argument to show where, and in what way, explainable AI methods can contribute to a safety case. Overall, we conclude that explainable AI methods have a valuable role in safety assurance of ML-based systems in healthcare but that they are not sufficient in themselves to assure safety.

Artificial intelligence (AI) has huge potential to improve the health and well-being of people, but adoption in clinical practice is still limited. Lack of transparency is identified as one of the main barriers to implementation, as clinicians should be confident the AI system can be trusted. Explainable AI has the potential to overcome this issue and can be a step towards trustworthy AI. In this paper we review the recent literature to provide guidance to researchers and practitioners on the design of explainable AI systems for the health-care domain and contribute to formalization of the field of explainable AI. We argue the reason to demand explainability determines what should be explained as this determines the relative importance of the properties of explainability (i.e. interpretability and fidelity). Based on this, we give concrete recommendations to choose between classes of explainable AI methods (explainable modelling versus post-hoc explanation; model-based, attribution-based, or example-based explanations; global and local explanations). Furthermore, we find that quantitative evaluation metrics, which are important for objective standardized evaluation, are still lacking for some properties (e.g. clarity) and types of explanators (e.g. example-based methods). We conclude that explainable modelling can contribute to trustworthy AI, but recognize that complementary measures might be needed to create trustworthy AI (e.g. reporting data quality, performing extensive (external) validation, and regulation).