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In the present paper we present the potential of Explainable Artificial Intelligence methods for decision-support in medical image analysis scenarios. With three types of explainable methods applied to the same medical image data set our…

Explainable Artificial Intelligence (XAI) addresses the growing need for transparency and interpretability in AI systems, enabling trust and accountability in decision-making processes. This book offers a comprehensive guide to XAI,…

Artificial Intelligence has emerged as a useful aid in numerous clinical applications for diagnosis and treatment decisions. Deep neural networks have shown same or better performance than clinicians in many tasks owing to the rapid…

As machine learning algorithms are increasingly applied to high impact yet high risk tasks, such as medical diagnosis or autonomous driving, it is critical that researchers can explain how such algorithms arrived at their predictions. In…

Black box neural networks are an indispensable part of modern robots. Nevertheless, deploying such high-stakes systems in real-world scenarios poses significant challenges when the stakeholders, such as engineers and legislative bodies,…

Post-hoc explainability methods aim to clarify predictions of black-box machine learning models. However, it is still largely unclear how well users comprehend the provided explanations and whether these increase the users ability to…

AI systems' ability to explain their reasoning is critical to their utility and trustworthiness. Deep neural networks have enabled significant progress on many challenging problems such as visual question answering (VQA). However, most of…

Providing high quality explanations for AI predictions based on machine learning is a challenging and complex task. To work well it requires, among other factors: selecting a proper level of generality/specificity of the explanation;…

Predicting the structure of multi-protein complexes is a grand challenge in biochemistry, with major implications for basic science and drug discovery. Computational structure prediction methods generally leverage pre-defined structural…

In medical imaging, particularly in early disease detection and prognosis tasks, discerning the rationale behind an AI model's predictions is crucial for evaluating the reliability of its decisions. Conventional explanation methods face…

The application of deep learning in medical imaging has significantly advanced diagnostic capabilities, enhancing both accuracy and efficiency. Despite these benefits, the lack of transparency in these AI models, often termed "black boxes,"…

In recent years, machine learning (ML) has become a key enabling technology for the sciences and industry. Especially through improvements in methodology, the availability of large databases and increased computational power, today's ML…

Artificial Intelligence/Machine Learning techniques have been widely used in software engineering to improve developer productivity, the quality of software systems, and decision-making. However, such AI/ML models for software engineering…

Protein structure prediction is a critical and longstanding challenge in biology, garnering widespread interest due to its significance in understanding biological processes. A particular area of focus is the prediction of missing loops in…

There is a growing concern that the recent progress made in AI, especially regarding the predictive competence of deep learning models, will be undermined by a failure to properly explain their operation and outputs. In response to this…

Deep learning models achieve remarkable predictive performance, yet their black-box nature limits transparency and trustworthiness. Although numerous explainable artificial intelligence (XAI) methods have been proposed, they primarily…

How do protein structure prediction models fold proteins? We investigate this question by tracing how ESMFold folds a beta hairpin, a prevalent structural motif. Through counterfactual interventions on model latents, we identify two…

Protein function prediction is currently achieved by encoding its sequence or structure, where the sequence-to-function transcendence and high-quality structural data scarcity lead to obvious performance bottlenecks. Protein domains are…

The large and still increasing popularity of deep learning clashes with a major limit of neural network architectures, that consists in their lack of capability in providing human-understandable motivations of their decisions. In situations…

We introduce IntFold, a controllable foundation model for general and specialized biomolecular structure prediction. Utilizing a high-performance custom attention kernel, IntFold achieves accuracy comparable to the state-of-the-art…