Jackie Ma

Maximilian Springenberg, Annika Frommholz, Markus Wenzel et al.

While machine learning is currently transforming the field of histopathology, the domain lacks a comprehensive evaluation of state-of-the-art models based on essential but complementary quality requirements beyond a mere classification accuracy. In order to fill this gap, we developed a new methodology to extensively evaluate a wide range of classification models, including recent vision transformers, and convolutional neural networks such as: ConvNeXt, ResNet (BiT), Inception, ViT and Swin transformer, with and without supervised or self-supervised pretraining. We thoroughly tested the models on five widely used histopathology datasets containing whole slide images of breast, gastric, and colorectal cancer and developed a novel approach using an image-to-image translation model to assess the robustness of a cancer classification model against stain variations. Further, we extended existing interpretability methods to previously unstudied models and systematically reveal insights of the models' classifications strategies that can be transferred to future model architectures.

Mohammad Mahdi Mesgari, Jackie Ma, Wojciech Samek et al.

In the evaluation of attribution quality, the quantitative assessment of explanation legibility is particularly difficult, as it is influenced by varying shapes and internal organization of attributions not captured by simple statistics. To address this issue, we introduce Minimum Spanning Tree Compactness (MST-C), a graph-based structural metric that captures higher-order geometric properties of attributions, such as spread and cohesion. These components are combined into a single score that evaluates compactness, favoring attributions with salient points spread across a small area and spatially organized into few but cohesive clusters. We show that MST-C reliably distinguishes between explanation methods, exposes fundamental structural differences between models, and provides a robust, self-contained diagnostic for explanation compactness that complements existing notions of attribution complexity.

Tobias Labarta, Nhi Hoang, Maximilian Dreyer et al.

The explainable AI (XAI) research community has proposed numerous technical methods, yet deploying explainability as systems remains challenging: Interactive explanation systems require both suitable algorithms and system capabilities that maintain explanation usability across repeated queries, evolving models and data, and governance constraints. We argue that operationalizing XAI requires treating explainability as an information systems problem where user interaction demands induce specific system requirements. We introduce X-SYS, a reference architecture for interactive explanation systems, that guides (X)AI researchers, developers and practitioners in connecting interactive explanation user interfaces (XUI) with system capabilities. X-SYS organizes around four quality attributes named STAR (scalability, traceability, responsiveness, and adaptability), and specifies a five-component decomposition (XUI Services, Explanation Services, Model Services, Data Services, Orchestration and Governance). It maps interaction patterns to system capabilities to decouple user interface evolution from backend computation. We implement X-SYS through SemanticLens, a system for semantic search and activation steering in vision-language models. SemanticLens demonstrates how contract-based service boundaries enable independent evolution, offline/online separation ensures responsiveness, and persistent state management supports traceability. Together, this work provides a reusable blueprint and concrete instantiation for interactive explanation systems supporting end-to-end design under operational constraints.

Raunak Agarwal, Markus Wenzel, Simon Baur et al.

Machine learning in high-stakes domains such as healthcare requires not only strong predictive performance but also reliable uncertainty quantification (UQ) to support human oversight. Multi-label text classification (MLTC) is a central task in this domain, yet remains challenging due to label imbalances, dependencies, and combinatorial complexity. Existing MLTC benchmarks are increasingly saturated and may be affected by training data contamination, making it difficult to distinguish genuine reasoning capabilities from memorization. We introduce MADE, a living MLTC benchmark derived from {m}edical device {ad}verse {e}vent reports and continuously updated with newly published reports to prevent contamination. MADE features a long-tailed distribution of hierarchical labels and enables reproducible evaluation with strict temporal splits. We establish baselines across more than 20 encoder- and decoder-only models under fine-tuning and few-shot settings (instruction-tuned/reasoning variants, local/API-accessible). We systematically assess entropy-/consistency-based and self-verbalized UQ methods. Results show clear trade-offs: smaller discriminatively fine-tuned decoders achieve the strongest head-to-tail accuracy while maintaining competitive UQ; generative fine-tuning delivers the most reliable UQ; large reasoning models improve performance on rare labels yet exhibit surprisingly weak UQ; and self-verbalized confidence is not a reliable proxy for uncertainty. Our work is publicly available at https://hhi.fraunhofer.de/aml-demonstrator/made-benchmark.

Simon Baur, Tristan Ruhwedel, Ekin Böke et al.

Peptide receptor radionuclide therapy (PRRT) is an established treatment for metastatic neuroendocrine tumors (NETs), yet long-term disease control occurs only in a subset of patients. Predicting progression-free survival (PFS) could support individualized treatment planning. This study evaluates laboratory, imaging, and multimodal deep learning models for PFS prediction in PRRT-treated patients. In this retrospective, single-center study 116 patients with metastatic NETs undergoing 177Lu-DOTATOC were included. Clinical characteristics, laboratory values, and pretherapeutic somatostatin receptor positron emission tomography/computed tomographies (SR-PET/CT) were collected. Seven models were trained to classify low- vs. high-PFS groups, including unimodal (laboratory, SR-PET, or CT) and multimodal fusion approaches. Explainability was evaluated by feature importance analysis and gradient maps. Forty-two patients (36%) had short PFS (< 1 year), 74 patients long PFS (>1 year). Groups were similar in most characteristics, except for higher baseline chromogranin A (p = 0.003), elevated gamma-GT (p = 0.002), and fewer PRRT cycles (p < 0.001) in short-PFS patients. The Random Forest model trained only on laboratory biomarkers reached an AUROC of 0.59 +- 0.02. Unimodal three-dimensional convolutional neural networks using SR-PET or CT performed worse (AUROC 0.42 +- 0.03 and 0.54 +- 0.01, respectively). A multimodal fusion model laboratory values, SR-PET, and CT -augmented with a pretrained CT branch - achieved the best results (AUROC 0.72 +- 0.01, AUPRC 0.80 +- 0.01). Multimodal deep learning combining SR-PET, CT, and laboratory biomarkers outperformed unimodal approaches for PFS prediction after PRRT. Upon external validation, such models may support risk-adapted follow-up strategies.

Katinka Becker, Maximilian P. Oppelt, Tobias S. Zech et al.

Machine learning (ML) in medicine has transitioned from research to concrete applications aimed at supporting several medical purposes like therapy selection, monitoring and treatment. Acceptance and effective adoption by clinicians and patients, as well as regulatory approval, require evidence of trustworthiness. A major factor for the development of trustworthy AI is the quantification of data quality for AI model training and testing. We have recently proposed the METRIC-framework for systematically evaluating the suitability (fit-for-purpose) of data for medical ML for a given task. Here, we operationalize this theoretical framework by introducing a collection of data quality metrics - the metric library - for practically measuring data quality dimensions. For each metric, we provide a metric card with the most important information, including definition, applicability, examples, pitfalls and recommendations, to support the understanding and implementation of these metrics. Furthermore, we discuss strategies and provide decision trees for choosing an appropriate set of data quality metrics from the metric library given specific use cases. We demonstrate the impact of our approach exemplarily on the PTB-XL ECG-dataset. This is a first step to enable fit-for-purpose evaluation of training and test data in practice as the base for establishing trustworthy AI in medicine.

Jost Arndt, Utku Isil, Michael Detzel et al.

Many physical processes can be expressed through partial differential equations (PDEs). Real-world measurements of such processes are often collected at irregularly distributed points in space, which can be effectively represented as graphs; however, there are currently only a few existing datasets. Our work aims to make advancements in the field of PDE-modeling accessible to the temporal graph machine learning community, while addressing the data scarcity problem, by creating and utilizing datasets based on PDEs. In this work, we create and use synthetic datasets based on PDEs to support spatio-temporal graph modeling in machine learning for different applications. More precisely, we showcase three equations to model different types of disasters and hazards in the fields of epidemiology, atmospheric particles, and tsunami waves. Further, we show how such created datasets can be used by benchmarking several machine learning models on the epidemiological dataset. Additionally, we show how pre-training on this dataset can improve model performance on real-world epidemiological data. The presented methods enable others to create datasets and benchmarks customized to individual requirements. The source code for our methodology and the three created datasets can be found on https://github.com/github-usr-ano/Temporal_Graph_Data_PDEs.

Marc Aurel Vischer, Noelia Otero, Jackie Ma

We present a dataset for rainfall streamflow modeling that is fully spatially resolved with the aim of taking neural network-driven hydrological modeling beyond lumped catchments. To this end, we compiled data covering five river basins in central Europe: upper Danube, Elbe, Oder, Rhine, and Weser. The dataset contains meteorological forcings, as well as ancillary information on soil, rock, land cover, and orography. The data is harmonized to a regular 9km times 9km grid and contains daily values that span from October 1981 to September 2011. We also provide code to further combine our dataset with publicly available river discharge data for end-to-end rainfall streamflow modeling.

Simon Baur, Alexandra Benova, Emilio Dolgener Cantú et al.

Deploying deep learning models in clinical practice often requires leveraging multiple data modalities, such as images, text, and structured data, to achieve robust and trustworthy decisions. However, not all modalities are always available at inference time. In this work, we propose multimodal privileged knowledge distillation (MMPKD), a training strategy that utilizes additional modalities available solely during training to guide a unimodal vision model. Specifically, we used a text-based teacher model for chest radiographs (MIMIC-CXR) and a tabular metadata-based teacher model for mammography (CBIS-DDSM) to distill knowledge into a vision transformer student model. We show that MMPKD can improve the resulting attention maps' zero-shot capabilities of localizing ROI in input images, while this effect does not generalize across domains, as contrarily suggested by prior research.

Maximilian Springenberg, Noelia Otero, Yuxin Xue et al.

Renewable resources are strongly dependent on local and large-scale weather situations. Skillful subseasonal to seasonal (S2S) forecasts -- beyond two weeks and up to two months -- can offer significant socioeconomic advantages to the energy sector. This study aims to enhance wind speed predictions using a diffusion model with classifier-free guidance to downscale S2S forecasts of surface wind speed. We propose DiffScale, a diffusion model that super-resolves spatial information for continuous downscaling factors and lead times. Leveraging weather priors as guidance for the generative process of diffusion models, we adopt the perspective of conditional probabilities on sampling super-resolved S2S forecasts. We aim to directly estimate the density associated with the target S2S forecasts at different spatial resolutions and lead times without auto-regression or sequence prediction, resulting in an efficient and flexible model. Synthetic experiments were designed to super-resolve wind speed S2S forecasts from the European Center for Medium-Range Weather Forecast (ECMWF) from a coarse resolution to a finer resolution of ERA5 reanalysis data, which serves as a high-resolution target. The innovative aspect of DiffScale lies in its flexibility to downscale arbitrary scaling factors, enabling it to generalize across various grid resolutions and lead times -without retraining the model- while correcting model errors, making it a versatile tool for improving S2S wind speed forecasts. We achieve a significant improvement in prediction quality, outperforming baselines up to week 3.

Rodrigo Almeida, Noelia Otero, Miguel-Ángel Fernández-Torres et al.

Accurate prediction of extreme weather events remains a major challenge for artificial intelligence based weather prediction systems. While deterministic models such as FuXi, GraphCast, and SFNO have achieved competitive forecast skill relative to numerical weather prediction, their ability to represent uncertainty and capture extremes is still limited. This study investigates how state of the art deterministic artificial intelligence based models respond to initial-condition perturbations and evaluates the resulting ensembles in forecasting extremes. Using three perturbation strategies (Gaussian noise, Hemispheric Centered Bred Vectors, and Huge Ensembles), we generate 50 member ensembles for two major events in August 2022: the Pakistan floods and the China heatwave. Ensemble skill is assessed against ERA5 and compared with IFS ENS and the probabilistic AIFSENS model using deterministic and probabilistic metrics. Results show that flow dependent perturbations produce the most realistic ensemble spread and highest probabilistic skill, narrowing but not closing the performance gap with numerical weather prediction ensembles. Across variables, artificial intelligence based weather models capture temperature extremes more effectively than precipitation. These findings demonstrate that input perturbations can extend deterministic models toward probabilistic forecasting, paving the way for approaches that combine flow dependent perturbations with generative or latent-space uncertainty modeling for reliable artificial intelligence-driven early warning systems.

Simon Baur, Wojciech Samek, Jackie Ma

Reliable uncertainty quantification is crucial for trustworthy decision-making and the deployment of AI models in medical imaging. While prior work has explored the ability of neural networks to quantify predictive, epistemic, and aleatoric uncertainties using an information-theoretical approach in synthetic or well defined data settings like natural image classification, its applicability to real life medical diagnosis tasks remains underexplored. In this study, we provide an extensive uncertainty quantification benchmark for multi-label chest X-ray classification using the MIMIC-CXR-JPG dataset. We evaluate 13 uncertainty quantification methods for convolutional (ResNet) and transformer-based (Vision Transformer) architectures across a wide range of tasks. Additionally, we extend Evidential Deep Learning, HetClass NNs, and Deep Deterministic Uncertainty to the multi-label setting. Our analysis provides insights into uncertainty estimation effectiveness and the ability to disentangle epistemic and aleatoric uncertainties, revealing method- and architecture-specific strengths and limitations.

Michael Detzel, Gabriel Nobis, Jackie Ma et al.

We incorporate prior graph topology information into a Neural Controlled Differential Equation (NCDE) to predict the future states of a dynamical system defined on a graph. The informed NCDE infers the future dynamics at the vertices of simulated advection data on graph edges with a known causal graph, observed only at vertices during training. We investigate different positions in the model architecture to inform the NCDE with graph information and identify an outer position between hidden state and control as theoretically and empirically favorable. Our such informed NCDE requires fewer parameters to reach a lower Mean Absolute Error (MAE) compared to previous methods that do not incorporate additional graph topology information.

Vignesh Srinivasan, Nils Strodthoff, Jackie Ma et al.

There is an increasing number of medical use-cases where classification algorithms based on deep neural networks reach performance levels that are competitive with human medical experts. To alleviate the challenges of small dataset sizes, these systems often rely on pretraining. In this work, we aim to assess the broader implications of these approaches. For diabetic retinopathy grading as exemplary use case, we compare the impact of different training procedures including recently established self-supervised pretraining methods based on contrastive learning. To this end, we investigate different aspects such as quantitative performance, statistics of the learned feature representations, interpretability and robustness to image distortions. Our results indicate that models initialized from ImageNet pretraining report a significant increase in performance, generalization and robustness to image distortions. In particular, self-supervised models show further benefits to supervised models. Self-supervised models with initialization from ImageNet pretraining not only report higher performance, they also reduce overfitting to large lesions along with improvements in taking into account minute lesions indicative of the progression of the disease. Understanding the effects of pretraining in a broader sense that goes beyond simple performance comparisons is of crucial importance for the broader medical imaging community beyond the use-case considered in this work.

Felix Sattler, Jackie Ma, Patrick Wagner et al.

Digital contact tracing approaches based on Bluetooth low energy (BLE) have the potential to efficiently contain and delay outbreaks of infectious diseases such as the ongoing SARS-CoV-2 pandemic. In this work we propose a novel machine learning based approach to reliably detect subjects that have spent enough time in close proximity to be at risk of being infected. Our study is an important proof of concept that will aid the battery of epidemiological policies aiming to slow down the rapid spread of COVID-19.

Jackie Ma, Maximilian März, Stephanie Funk et al.

High-resolution three-dimensional (3D) cardiovascular magnetic resonance (CMR) is a valuable medical imaging technique, but its widespread application in clinical practice is hampered by long acquisition times. Here we present a novel compressed sensing (CS) reconstruction approach using shearlets as a sparsifying transform allowing for fast 3D CMR (3DShearCS). Shearlets are mathematically optimal for a simplified model of natural images and have been proven to be more efficient than classical systems such as wavelets. Data is acquired with a 3D Radial Phase Encoding (RPE) trajectory and an iterative reweighting scheme is used during image reconstruction to ensure fast convergence and high image quality. In our in-vivo cardiac MRI experiments we show that the proposed method 3DShearCS has lower relative errors and higher structural similarity compared to the other reconstruction techniques especially for high undersampling factors, i.e. short scan times. In this paper, we further show that 3DShearCS provides improved depiction of cardiac anatomy (measured by assessing the sharpness of coronary arteries) and two clinical experts qualitatively analyzed the image quality.