Explainable Artificial Intelligence for Drug Discovery and Development -- A Comprehensive Survey

The field of drug discovery has experienced a remarkable transformation with the advent of artificial intelligence (AI) and machine learning (ML) technologies. However, as these AI and ML models are becoming more complex, there is a growing need for transparency and interpretability of the models. Explainable Artificial Intelligence (XAI) is a novel approach that addresses this issue and provides a more interpretable understanding of the predictions made by machine learning models. In recent years, there has been an increasing interest in the application of XAI techniques to drug discovery. This review article provides a comprehensive overview of the current state-of-the-art in XAI for drug discovery, including various XAI methods, their application in drug discovery, and the challenges and limitations of XAI techniques in drug discovery. The article also covers the application of XAI in drug discovery, including target identification, compound design, and toxicity prediction. Furthermore, the article suggests potential future research directions for the application of XAI in drug discovery. The aim of this review article is to provide a comprehensive understanding of the current state of XAI in drug discovery and its potential to transform the field.Comment: 13 pages, 3 figure

The Role of Human Knowledge in Explainable AI

As the performance and complexity of machine learning models have grown significantly over the last years, there has been an increasing need to develop methodologies to describe their behaviour. Such a need has mainly arisen due to the widespread use of black-box models, i.e., high-performing models whose internal logic is challenging to describe and understand. Therefore, the machine learning and AI field is facing a new challenge: making models more explainable through appropriate techniques. The final goal of an explainability method is to faithfully describe the behaviour of a (black-box) model to users who can get a better understanding of its logic, thus increasing the trust and acceptance of the system. Unfortunately, state-of-the-art explainability approaches may not be enough to guarantee the full understandability of explanations from a human perspective. For this reason, human-in-the-loop methods have been widely employed to enhance and/or evaluate explanations of machine learning models. These approaches focus on collecting human knowledge that AI systems can then employ or involving humans to achieve their objectives (e.g., evaluating or improving the system). This article aims to present a literature overview on collecting and employing human knowledge to improve and evaluate the understandability of machine learning models through human-in-the-loop approaches. Furthermore, a discussion on the challenges, state-of-the-art, and future trends in explainability is also provided

ConceptExplainer: Understanding the Mental Model of Deep Learning Algorithms via Interactive Concept-based Explanations

Traditional deep learning interpretability methods which are suitable for non-expert users cannot explain network behaviors at the global level and are inflexible at providing fine-grained explanations. As a solution, concept-based explanations are gaining attention due to their human intuitiveness and their flexibility to describe both global and local model behaviors. Concepts are groups of similarly meaningful pixels that express a notion, embedded within the network's latent space and have primarily been hand-generated, but have recently been discovered by automated approaches. Unfortunately, the magnitude and diversity of discovered concepts makes it difficult for non-experts to navigate and make sense of the concept space, and lack of easy-to-use software also makes concept explanations inaccessible to many non-expert users. Visual analytics can serve a valuable role in bridging these gaps by enabling structured navigation and exploration of the concept space to provide concept-based insights of model behavior to users. To this end, we design, develop, and validate ConceptExplainer, a visual analytics system that enables non-expert users to interactively probe and explore the concept space to explain model behavior at the instance/class/global level. The system was developed via iterative prototyping to address a number of design challenges that non-experts face in interpreting the behavior of deep learning models. Via a rigorous user study, we validate how ConceptExplainer supports these challenges. Likewise, we conduct a series of usage scenarios to demonstrate how the system supports the interactive analysis of model behavior across a variety of tasks and explanation granularities, such as identifying concepts that are important to classification, identifying bias in training data, and understanding how concepts can be shared across diverse and seemingly dissimilar classes.Comment: 9 pages, 6 figure

Quantifying and Explaining Machine Learning Uncertainty in Predictive Process Monitoring: An Operations Research Perspective

This paper introduces a comprehensive, multi-stage machine learning methodology that effectively integrates information systems and artificial intelligence to enhance decision-making processes within the domain of operations research. The proposed framework adeptly addresses common limitations of existing solutions, such as the neglect of data-driven estimation for vital production parameters, exclusive generation of point forecasts without considering model uncertainty, and lacking explanations regarding the sources of such uncertainty. Our approach employs Quantile Regression Forests for generating interval predictions, alongside both local and global variants of SHapley Additive Explanations for the examined predictive process monitoring problem. The practical applicability of the proposed methodology is substantiated through a real-world production planning case study, emphasizing the potential of prescriptive analytics in refining decision-making procedures. This paper accentuates the imperative of addressing these challenges to fully harness the extensive and rich data resources accessible for well-informed decision-making

Tools of Trade of the Next Blue-Collar Job? Antecedents, Design Features, and Outcomes of Interactive Labeling Systems

Supervised machine learning is becoming increasingly popular - and so is the need for annotated training data. Such data often needs to be manually labeled by human workers, not unlikely to negatively impact the involved workforce. To alleviate this issue, a new information systems class has emerged - interactive labeling systems. However, this young, but rapidly growing field lacks guidance and structure regarding the design of such systems. Against this backdrop, this paper describes antecedents, design features, and outcomes of interactive labeling systems. We perform a systematic literature review, identifying 188 relevant articles. Our results are presented as a morphological box with 14 dimensions, which we evaluate using card sorting. By additionally offering this box as a web-based artifact, we provide actionable guidance for interactive labeling system development for scholars and practitioners. Lastly, we discuss imbalances in the article distribution of our morphological box and suggest future work directions

Explainable methods for knowledge graph refinement and exploration via symbolic reasoning

Knowledge Graphs (KGs) have applications in many domains such as Finance, Manufacturing, and Healthcare. While recent efforts have created large KGs, their content is far from complete and sometimes includes invalid statements. Therefore, it is crucial to refine the constructed KGs to enhance their coverage and accuracy via KG completion and KG validation. It is also vital to provide human-comprehensible explanations for such refinements, so that humans have trust in the KG quality. Enabling KG exploration, by search and browsing, is also essential for users to understand the KG value and limitations towards down-stream applications. However, the large size of KGs makes KG exploration very challenging. While the type taxonomy of KGs is a useful asset along these lines, it remains insufficient for deep exploration. In this dissertation we tackle the aforementioned challenges of KG refinement and KG exploration by combining logical reasoning over the KG with other techniques such as KG embedding models and text mining. Through such combination, we introduce methods that provide human-understandable output. Concretely, we introduce methods to tackle KG incompleteness by learning exception-aware rules over the existing KG. Learned rules are then used in inferring missing links in the KG accurately. Furthermore, we propose a framework for constructing human-comprehensible explanations for candidate facts from both KG and text. Extracted explanations are used to insure the validity of KG facts. Finally, to facilitate KG exploration, we introduce a method that combines KG embeddings with rule mining to compute informative entity clusters with explanations.Wissensgraphen haben viele Anwendungen in verschiedenen Bereichen, beispielsweise im Finanz- und Gesundheitswesen. Wissensgraphen sind jedoch unvollständig und enthalten auch ungültige Daten. Hohe Abdeckung und Korrektheit erfordern neue Methoden zur Wissensgraph-Erweiterung und Wissensgraph-Validierung. Beide Aufgaben zusammen werden als Wissensgraph-Verfeinerung bezeichnet. Ein wichtiger Aspekt dabei ist die Erklärbarkeit und Verständlichkeit von Wissensgraphinhalten für Nutzer. In Anwendungen ist darüber hinaus die nutzerseitige Exploration von Wissensgraphen von besonderer Bedeutung. Suchen und Navigieren im Graph hilft dem Anwender, die Wissensinhalte und ihre Limitationen besser zu verstehen. Aufgrund der riesigen Menge an vorhandenen Entitäten und Fakten ist die Wissensgraphen-Exploration eine Herausforderung. Taxonomische Typsystem helfen dabei, sind jedoch für tiefergehende Exploration nicht ausreichend. Diese Dissertation adressiert die Herausforderungen der Wissensgraph-Verfeinerung und der Wissensgraph-Exploration durch algorithmische Inferenz über dem Wissensgraph. Sie erweitert logisches Schlussfolgern und kombiniert es mit anderen Methoden, insbesondere mit neuronalen Wissensgraph-Einbettungen und mit Text-Mining. Diese neuen Methoden liefern Ausgaben mit Erklärungen für Nutzer. Die Dissertation umfasst folgende Beiträge: Insbesondere leistet die Dissertation folgende Beiträge: • Zur Wissensgraph-Erweiterung präsentieren wir ExRuL, eine Methode zur Revision von Horn-Regeln durch Hinzufügen von Ausnahmebedingungen zum Rumpf der Regeln. Die erweiterten Regeln können neue Fakten inferieren und somit Lücken im Wissensgraphen schließen. Experimente mit großen Wissensgraphen zeigen, dass diese Methode Fehler in abgeleiteten Fakten erheblich reduziert und nutzerfreundliche Erklärungen liefert. • Mit RuLES stellen wir eine Methode zum Lernen von Regeln vor, die auf probabilistischen Repräsentationen für fehlende Fakten basiert. Das Verfahren erweitert iterativ die aus einem Wissensgraphen induzierten Regeln, indem es neuronale Wissensgraph-Einbettungen mit Informationen aus Textkorpora kombiniert. Bei der Regelgenerierung werden neue Metriken für die Regelqualität verwendet. Experimente zeigen, dass RuLES die Qualität der gelernten Regeln und ihrer Vorhersagen erheblich verbessert. • Zur Unterstützung der Wissensgraph-Validierung wird ExFaKT vorgestellt, ein Framework zur Konstruktion von Erklärungen für Faktkandidaten. Die Methode transformiert Kandidaten mit Hilfe von Regeln in eine Menge von Aussagen, die leichter zu finden und zu validieren oder widerlegen sind. Die Ausgabe von ExFaKT ist eine Menge semantischer Evidenzen für Faktkandidaten, die aus Textkorpora und dem Wissensgraph extrahiert werden. Experimente zeigen, dass die Transformationen die Ausbeute und Qualität der entdeckten Erklärungen deutlich verbessert. Die generierten unterstützen Erklärungen unterstütze sowohl die manuelle Wissensgraph- Validierung durch Kuratoren als auch die automatische Validierung. • Zur Unterstützung der Wissensgraph-Exploration wird ExCut vorgestellt, eine Methode zur Erzeugung von informativen Entitäts-Clustern mit Erklärungen unter Verwendung von Wissensgraph-Einbettungen und automatisch induzierten Regeln. Eine Cluster-Erklärung besteht aus einer Kombination von Relationen zwischen den Entitäten, die den Cluster identifizieren. ExCut verbessert gleichzeitig die Cluster- Qualität und die Cluster-Erklärbarkeit durch iteratives Verschränken des Lernens von Einbettungen und Regeln. Experimente zeigen, dass ExCut Cluster von hoher Qualität berechnet und dass die Cluster-Erklärungen für Nutzer informativ sind

Data-Driven Design-by-Analogy: State of the Art and Future Directions

Design-by-Analogy (DbA) is a design methodology wherein new solutions, opportunities or designs are generated in a target domain based on inspiration drawn from a source domain; it can benefit designers in mitigating design fixation and improving design ideation outcomes. Recently, the increasingly available design databases and rapidly advancing data science and artificial intelligence technologies have presented new opportunities for developing data-driven methods and tools for DbA support. In this study, we survey existing data-driven DbA studies and categorize individual studies according to the data, methods, and applications in four categories, namely, analogy encoding, retrieval, mapping, and evaluation. Based on both nuanced organic review and structured analysis, this paper elucidates the state of the art of data-driven DbA research to date and benchmarks it with the frontier of data science and AI research to identify promising research opportunities and directions for the field. Finally, we propose a future conceptual data-driven DbA system that integrates all propositions.Comment: A Preprint Versio