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Evaluating explanations of image classifiers regarding ground truth, e.g. segmentation masks defined by human perception, primarily evaluates the quality of the models under consideration rather than the explanation methods themselves. Driven by this observation, we propose a framework for $\textit{jointly}$ evaluating the robustness of safety-critical systems that $\textit{combine}$ a deep neural network with an explanation method. These are increasingly used in real-world applications like medical image analysis or robotics. We introduce a fine-tuning procedure to (mis)align model$\unicode{x2013}$explanation pipelines with ground truth and use it to quantify the potential discrepancy between worst and best-case scenarios of human alignment. Experiments across various model architectures and post-hoc local interpretation methods provide insights into the robustness of vision transformers and the overall vulnerability of such AI systems to potential adversarial attacks.

As systems based on opaque Artificial Intelligence (AI) continue to flourish in diverse real-world applications, understanding these black box models has become paramount. In response, Explainable AI (XAI) has emerged as a field of research with practical and ethical benefits across various domains. This paper not only highlights the advancements in XAI and its application in real-world scenarios but also addresses the ongoing challenges within XAI, emphasizing the need for broader perspectives and collaborative efforts. We bring together experts from diverse fields to identify open problems, striving to synchronize research agendas and accelerate XAI in practical applications. By fostering collaborative discussion and interdisciplinary cooperation, we aim to propel XAI forward, contributing to its continued success. Our goal is to put forward a comprehensive proposal for advancing XAI. To achieve this goal, we present a manifesto of 27 open problems categorized into nine categories. These challenges encapsulate the complexities and nuances of XAI and offer a road map for future research. For each problem, we provide promising research directions in the hope of harnessing the collective intelligence of interested stakeholders.

Explainable AI (XAI) is an increasingly important area of machine learning research, which aims to make black-box models transparent and interpretable. In this paper, we propose a novel approach to XAI that uses the so-called counterfactual paths generated by conditional permutations of features. The algorithm measures feature importance by identifying sequential permutations of features that most influence changes in model predictions. It is particularly suitable for generating explanations based on counterfactual paths in knowledge graphs incorporating domain knowledge. Counterfactual paths introduce an additional graph dimension to current XAI methods in both explaining and visualizing black-box models. Experiments with synthetic and medical data demonstrate the practical applicability of our approach.

Large language models, e.g. ChatGPT are currently contributing enormously to make artificial intelligence even more popular, especially among the general population. However, such chatbot models were developed as tools to support natural language communication between humans. Problematically, it is very much a ``statistical correlation machine" (correlation instead of causality) and there are indeed ethical concerns associated with the use of AI language models such as ChatGPT, such as Bias, Privacy, and Abuse. This paper highlights specific ethical concerns on ChatGPT and articulates key challenges when ChatGPT is used in various applications. Practical commandments for different stakeholders of ChatGPT are also proposed that can serve as checklist guidelines for those applying ChatGPT in their applications. These commandment examples are expected to motivate the ethical use of ChatGPT., Comment: 8 pages, 2 figures

There is a broad consensus on the importance of deep learning models in tasks involving complex data. Often, an adequate understanding of these models is required when focusing on the transparency of decisions in human-critical applications. Besides other explainability techniques, trustworthiness can be achieved by using counterfactuals, like the way a human becomes familiar with an unknown process: by understanding the hypothetical circumstances under which the output changes. In this work we argue that automated counterfactual generation should regard several aspects of the produced adversarial instances, not only their adversarial capability. To this end, we present a novel framework for the generation of counterfactual examples which formulates its goal as a multi-objective optimization problem balancing three different objectives: 1) plausibility, i.e., the likeliness of the counterfactual of being possible as per the distribution of the input data; 2) intensity of the changes to the original input; and 3) adversarial power, namely, the variability of the model's output induced by the counterfactual. The framework departs from a target model to be audited and uses a Generative Adversarial Network to model the distribution of input data, together with a multi-objective solver for the discovery of counterfactuals balancing among these objectives. The utility of the framework is showcased over six classification tasks comprising image and three-dimensional data. The experiments verify that the framework unveils counterfactuals that comply with intuition, increasing the trustworthiness of the user, and leading to further insights, such as the detection of bias and data misrepresentation., Comment: 52 pages, 14 figures, under review

Last years have been characterized by an upsurge of opaque automatic decision support systems, such as Deep Neural Networks (DNNs). Although they have great generalization and prediction skills, their functioning does not allow obtaining detailed explanations of their behaviour. As opaque machine learning models are increasingly being employed to make important predictions in critical environments, the danger is to create and use decisions that are not justifiable or legitimate. Therefore, there is a general agreement on the importance of endowing machine learning models with explainability. EXplainable Artificial Intelligence (XAI) techniques can serve to verify and certify model outputs and enhance them with desirable notions such as trustworthiness, accountability, transparency and fairness. This guide is meant to be the go-to handbook for any audience with a computer science background aiming at getting intuitive insights on machine learning models, accompanied with straight, fast, and intuitive explanations out of the box. This article aims to fill the lack of compelling XAI guide by applying XAI techniques in their particular day-to-day models, datasets and use-cases. Figure 1 acts as a flowchart/map for the reader and should help him to find the ideal method to use according to his type of data. In each chapter, the reader will find a description of the proposed method as well as an example of use on a Biomedical application and a Python notebook. It can be easily modified in order to be applied to specific applications.

Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in the form of graphs or networks, and its use can improve model performance. We need network-based algorithms that are versatile and applicable in many research areas. In this work, we demonstrate subnetwork detection based on multi-modal node features using a novel Greedy Decision Forest with inherent interpretability. The latter will be a crucial factor to retain experts and gain their trust in such algorithms. To demonstrate a concrete application example, we focus on bioinformatics, systems biology and particularly biomedicine, but the presented methodology is applicable in many other domains as well. Systems biology is a good example of a field in which statistical data-driven machine learning enables the analysis of large amounts of multi-modal biomedical data. This is important to reach the future goal of precision medicine, where the complexity of patients is modeled on a system level to best tailor medical decisions, health practices and therapies to the individual patient. Our proposed approach can help to uncover disease-causing network modules from multi-omics data to better understand complex diseases such as cancer.

Machine Learning (ML) and Artificial Intelligence (AI) have shown promising results in many areas and are driven by the increasing amount of available data. However, this data is often distributed across different institutions and cannot be shared due to privacy concerns. Privacy-preserving methods, such as Federated Learning (FL), allow for training ML models without sharing sensitive data, but their implementation is time-consuming and requires advanced programming skills. Here, we present the FeatureCloud AI Store for FL as an all-in-one platform for biomedical research and other applications. It removes large parts of this complexity for developers and end-users by providing an extensible AI Store with a collection of ready-to-use apps. We show that the federated apps produce similar results to centralized ML, scale well for a typical number of collaborators and can be combined with Secure Multiparty Computation (SMPC), thereby making FL algorithms safely and easily applicable in biomedical and clinical environments.

Optimal performance is critical for decision-making tasks from medicine to autonomous driving, however common performance measures may be too general or too specific. For binary classifiers, diagnostic tests or prognosis at a timepoint, measures such as the area under the receiver operating characteristic curve, or the area under the precision recall curve, are too general because they include unrealistic decision thresholds. On the other hand, measures such as accuracy, sensitivity or the F1 score are measures at a single threshold that reflect an individual single probability or predicted risk, rather than a range of individuals or risk. We propose a method in between, deep ROC analysis, that examines groups of probabilities or predicted risks for more insightful analysis. We translate esoteric measures into familiar terms: AUC and the normalized concordant partial AUC are balanced average accuracy (a new finding); the normalized partial AUC is average sensitivity; and the normalized horizontal partial AUC is average specificity. Along with post-test measures, we provide a method that can improve model selection in some cases and provide interpretation and assurance for patients in each risk group. We demonstrate deep ROC analysis in two case studies and provide a toolkit in Python., Comment: 14 pages, 6 Figures, submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), currently under review

Machine intelligence is very successful at standard recognition tasks when having high-quality training data. There is still a significant gap between machine-level pattern recognition and human-level concept learning. Humans can learn under uncertainty from only a few examples and generalize these concepts to solve new problems. The growing interest in explainable machine intelligence, requires experimental environments and diagnostic tests to analyze weaknesses in existing approaches to drive progress in the field. In this paper, we discuss existing diagnostic tests and test data sets such as CLEVR, CLEVERER, CLOSURE, CURI, Bongard-LOGO, V-PROM, and present our own experimental environment: The KANDINSKYPatterns, named after the Russian artist Wassily Kandinksy, who made theoretical contributions to compositivity, i.e. that all perceptions consist of geometrically elementary individual components. This was experimentally proven by Hubel &Wiesel in the 1960s and became the basis for machine learning approaches such as the Neocognitron and the even later Deep Learning. While KANDINSKYPatterns have computationally controllable properties on the one hand, bringing ground truth, they are also easily distinguishable by human observers, i.e., controlled patterns can be described by both humans and algorithms, making them another important contribution to international research in machine intelligence., Comment: 12 pages, submitted to IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI), currently under review

Gleason grading of prostate cancer is an important prognostic factor but suffers from poor reproducibility, particularly among non-subspecialist pathologists. Although artificial intelligence (A.I.) tools have demonstrated Gleason grading on-par with expert pathologists, it remains an open question whether A.I. grading translates to better prognostication. In this study, we developed a system to predict prostate-cancer specific mortality via A.I.-based Gleason grading and subsequently evaluated its ability to risk-stratify patients on an independent retrospective cohort of 2,807 prostatectomy cases from a single European center with 5-25 years of follow-up (median: 13, interquartile range 9-17). The A.I.'s risk scores produced a C-index of 0.84 (95%CI 0.80-0.87) for prostate cancer-specific mortality. Upon discretizing these risk scores into risk groups analogous to pathologist Grade Groups (GG), the A.I. had a C-index of 0.82 (95%CI 0.78-0.85). On the subset of cases with a GG in the original pathology report (n=1,517), the A.I.'s C-indices were 0.87 and 0.85 for continuous and discrete grading, respectively, compared to 0.79 (95%CI 0.71-0.86) for GG obtained from the reports. These represent improvements of 0.08 (95%CI 0.01-0.15) and 0.07 (95%CI 0.00-0.14) respectively. Our results suggest that A.I.-based Gleason grading can lead to effective risk-stratification and warrants further evaluation for improving disease management.

Artificial intelligence (AI) has been successfully applied in numerous scientific domains. In biomedicine, AI has already shown tremendous potential, e.g. in the interpretation of next-generation sequencing data and in the design of clinical decision support systems. However, training an AI model on sensitive data raises concerns about the privacy of individual participants. For example, summary statistics of a genome-wide association study can be used to determine the presence or absence of an individual in a given dataset. This considerable privacy risk has led to restrictions in accessing genomic and other biomedical data, which is detrimental for collaborative research and impedes scientific progress. Hence, there has been a substantial effort to develop AI methods that can learn from sensitive data while protecting individuals' privacy. This paper provides a structured overview of recent advances in privacy-preserving AI techniques in biomedicine. It places the most important state-of-the-art approaches within a unified taxonomy and discusses their strengths, limitations, and open problems. As the most promising direction, we suggest combining federated machine learning as a more scalable approach with other additional privacy preserving techniques. This would allow to merge the advantages to provide privacy guarantees in a distributed way for biomedical applications. Nonetheless, more research is necessary as hybrid approaches pose new challenges such as additional network or computation overhead., Comment: 17 pages, 3 figures, 3 tables. Methods of Information in Medicine (2022)

Recent success in Artificial Intelligence (AI) and Machine Learning (ML) allow problem solving automatically without any human intervention. Autonomous approaches can be very convenient. However, in certain domains, e.g., in the medical domain, it is necessary to enable a domain expert to understand, why an algorithm came up with a certain result. Consequently, the field of Explainable AI (xAI) rapidly gained interest worldwide in various domains, particularly in medicine. Explainable AI studies transparency and traceability of opaque AI/ML and there are already a huge variety of methods. For example with layer-wise relevance propagation relevant parts of inputs to, and representations in, a neural network which caused a result, can be highlighted. This is a first important step to ensure that end users, e.g., medical professionals, assume responsibility for decision making with AI/ML and of interest to professionals and regulators. Interactive ML adds the component of human expertise to AI/ML processes by enabling them to re-enact and retrace AI/ML results, e.g. let them check it for plausibility. This requires new human-AI interfaces for explainable AI. In order to build effective and efficient interactive human-AI interfaces we have to deal with the question of how to evaluate the quality of explanations given by an explainable AI system. In this paper we introduce our System Causability Scale (SCS) to measure the quality of explanations. It is based on our notion of Causability (Holzinger et al., 2019) combined with concepts adapted from a widely accepted usability scale., Comment: 6 pages, 1 figure, 1 table, will appear in Springer/Nature KI - K\"unstliche Intelligenz (2020), Volume 34, Issue 2

In this paper a neural network is trained to perform simple arithmetic using images of concatenated handwritten digit pairs. A convolutional neural network was trained with images consisting of two side-by-side handwritten digits, where the image's label is the summation of the two digits contained in the combined image. Crucially, the network was tested on permutation pairs that were not present during training in an effort to see if the network could learn the task of addition, as opposed to simply mapping images to labels. A dataset was generated for all possible permutation pairs of length 2 for the digits 0-9 using MNIST as a basis for the images, with one thousand samples generated for each permutation pair. For testing the network, samples generated from previously unseen permutation pairs were fed into the trained network, and its predictions measured. Results were encouraging, with the network achieving an accuracy of over 90% on some permutation train/test splits. This suggests that the network learned at first digit recognition, and subsequently the further task of addition based on the two recognised digits. As far as the authors are aware, no previous work has concentrated on learning a mathematical operation in this way.

In this paper we propose a new augmentation technique, called patch augmentation, that, in our experiments, improves model accuracy and makes networks more robust to adversarial attacks. In brief, this data-independent approach creates new image data based on image/label pairs, where a patch from one of the two images in the pair is superimposed on to the other image, creating a new augmented sample. The new image's label is a linear combination of the image pair's corresponding labels. Initial experiments show a several percentage point increase in accuracy on CIFAR-10, from a baseline of approximately 81% to 89%. CIFAR-100 sees larger improvements still, from a baseline of 52% to 68% accuracy. Networks trained using patch augmentation are also more robust to adversarial attacks, which we demonstrate using the Fast Gradient Sign Method., Comment: Version 2: updated author list, reduced abstract length, plots consolidated as sub-plots

Kandinsky Figures and Kandinsky Patterns are mathematically describable, simple self-contained hence controllable test data sets for the development, validation and training of explainability in artificial intelligence. Whilst Kandinsky Patterns have these computationally manageable properties, they are at the same time easily distinguishable from human observers. Consequently, controlled patterns can be described by both humans and computers. We define a Kandinsky Pattern as a set of Kandinsky Figures, where for each figure an "infallible authority" defines that the figure belongs to the Kandinsky Pattern. With this simple principle we build training and validation data sets for automatic interpretability and context learning. In this paper we describe the basic idea and some underlying principles of Kandinsky Patterns and provide a Github repository to invite the international machine learning research community to a challenge to experiment with our Kandinsky Patterns to expand and thus make progress in the field of explainable AI and to contribute to the upcoming field of explainability and causability., Comment: 13 pages, 13 Figures