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Deep Unsupervised Anomaly Detection in Brain Imaging: Large-Scale Benchmarking and Bias Analysis

Frotscher, Alexander, Baumgartner, Christian F., Wolfers, Thomas

arXiv.org Artificial Intelligence

Deep unsupervised anomaly detection in brain magnetic resonance imaging offers a promising route to identify pathological deviations without requiring lesion-specific annotations. Yet, fragmented evaluations, heterogeneous datasets, and inconsistent metrics have hindered progress toward clinical translation. Here, we present a large-scale, multi-center benchmark of deep unsupervised anomaly detection for brain imaging. The training cohort comprised 2,976 T1 and 2,972 T2-weighted scans from healthy individuals across six scanners, with ages ranging from 6 to 89 years. Validation used 92 scans to tune hyperparameters and estimate unbiased thresholds. Testing encompassed 2,221 T1w and 1,262 T2w scans spanning healthy datasets and diverse clinical cohorts. Across all algorithms, the Dice-based segmentation performance varied between 0.03 and 0.65, indicating substantial variability. To assess robustness, we systematically evaluated the impact of different scanners, lesion types and sizes, as well as demographics (age, sex). Reconstruction-based methods, particularly diffusion-inspired approaches, achieved the strongest lesion segmentation performance, while feature-based methods showed greater robustness under distributional shifts. However, systematic biases, such as scanner-related effects, were observed for the majority of algorithms, including that small and low-contrast lesions were missed more often, and that false positives varied with age and sex. Increasing healthy training data yields only modest gains, underscoring that current unsupervised anomaly detection frameworks are limited algorithmically rather than by data availability. Our benchmark establishes a transparent foundation for future research and highlights priorities for clinical translation, including image native pretraining, principled deviation measures, fairness-aware modeling, and robust domain adaptation.


Data-Driven Discovery of Feature Groups in Clinical Time Series

Sergeev, Fedor, Burger, Manuel, Leshetkina, Polina, Fortuin, Vincent, Rätsch, Gunnar, Kuznetsova, Rita

arXiv.org Artificial Intelligence

Clinical time series data are critical for patient monitoring and predictive modeling. These time series are typically multivariate and often comprise hundreds of heterogeneous features from different data sources. The grouping of features based on similarity and relevance to the prediction task has been shown to enhance the performance of deep learning architectures. However, defining these groups a priori using only semantic knowledge is challenging, even for domain experts. To address this, we propose a novel method that learns feature groups by clustering weights of feature-wise embedding layers. This approach seamlessly integrates into standard supervised training and discovers the groups that directly improve downstream performance on clinically relevant tasks. We demonstrate that our method outperforms static clustering approaches on synthetic data and achieves performance comparable to expert-defined groups on real-world medical data. Moreover, the learned feature groups are clinically interpretable, enabling data-driven discovery of task-relevant relationships between variables.


Systematic Evaluation of Multi-modal Approaches to Complex Player Profile Classification

Starace, Jason, Soule, Terence

arXiv.org Artificial Intelligence

Modern adaptive games require nuanced player understanding, yet most models use simplified 5-10 category taxonomies that fail to capture diversity. Behavioral clustering cannot distinguish players with different motivations who act similarly. We present a systematic evaluation of multi-modal classification at scale, combining behavioral telemetry with semantic context to support 36 player profiles. Using 19,413 gameplay sessions from an AI-controlled text-based RPG, we compared behavioral-only baselines with multi-modal approaches that integrate action sequences and semantic descriptions. Traditional clustering achieved only 10% accuracy for 36-category classification, limited by semantic conflation where opposite actions produced identical features. Our multi-modal LSTM processing action-text pairs improved accuracy to 21%, showing both potential and limits of non-conversational data. Analysis by behavioral complexity revealed that non-neutral profiles reached 42% accuracy (15x above random), while neutral profiles dropped to 25% (9x above random). Identical actions such as "help the merchant" cannot reveal whether a player is neutral or strategically waiting. Without access to reasoning, even multi-modal models struggle, though above-baseline results confirm a meaningful signal. Since prediction beyond 20 categories remains unexplored, our findings establish benchmarks for complex player modeling. Behavioral data alone plateaus near 10% for 36 categories, while multi-modal integration enables 25%. For designers, this shows that personality-based adaptation requires conversational interaction, as predefined choices cannot capture intent. Our evaluation at 36-category scale offers guidance for building adaptive games that better understand their players.


Barlow-Swin: Toward a novel siamese-based segmentation architecture using Swin-Transformers

Haftlang, Morteza Kiani, Malmir, Mohammadhossein, Parand, Foroutan, Michelucci, Umberto, Ghazouali, Safouane El

arXiv.org Artificial Intelligence

Medical image segmentation is a critical task in clinical workflows, particularly for the detection and delineation of pathological regions. While convolutional architectures like U-Net have become standard for such tasks, their limited receptive field restricts global context modeling. Recent efforts integrating transformers have addressed this, but often result in deep, computationally expensive models unsuitable for real-time use. In this work, we present a novel end-to-end lightweight architecture designed specifically for real-time binary medical image segmentation. Our model combines a Swin Transformer-like encoder with a U-Net-like decoder, connected via skip pathways to preserve spatial detail while capturing contextual information. Unlike existing designs such as Swin Transformer or U-Net, our architecture is significantly shallower and competitively efficient. To improve the encoder's ability to learn meaningful features without relying on large amounts of labeled data, we first train it using Barlow Twins, a self-supervised learning method that helps the model focus on important patterns by reducing unnecessary repetition in the learned features. After this pretraining, we fine-tune the entire model for our specific task. Experiments on benchmark binary segmentation tasks demonstrate that our model achieves competitive accuracy with substantially reduced parameter count and faster inference, positioning it as a practical alternative for deployment in real-time and resource-limited clinical environments. The code for our method is available at Github repository: https://github.com/mkianih/Barlow-Swin.


Benchmarking the State of Networks with a Low-Cost Method Based on Reservoir Computing

Reimers, Felix Simon, Peters, Carl-Hendrik, Nichele, Stefano

arXiv.org Artificial Intelligence

Using data from mobile network utilization in Norway, we showcase the possibility of monitoring the state of communication and mobility networks with a non-invasive, low-cost method. This method transforms the network data into a model within the framework of reservoir computing and then measures the model's performance on proxy tasks. Experimentally, we show how the performance on these proxies relates to the state of the network. A key advantage of this approach is that it uses readily available data sets and leverages the reservoir computing framework for an inexpensive and largely agnostic method. Data from mobile network utilization is available in an anonymous, aggregated form with multiple snapshots per day. This data can be treated like a weighted network. Reservoir computing allows the use of weighted, but untrained networks as a machine learning tool. The network, initialized as a so-called echo state network (ESN), projects incoming signals into a higher dimensional space, on which a single trained layer operates. This consumes less energy than deep neural networks in which every weight of the network is trained. We use neuroscience inspired tasks and trained our ESN model to solve them. We then show how the performance depends on certain network configurations and also how it visibly decreases when perturbing the network. While this work serves as proof of concept, we believe it can be elevated to be used for near-real-time monitoring as well as the identification of possible weak spots of both mobile communication networks as well as transportation networks.


MRExtrap: Longitudinal Aging of Brain MRIs using Linear Modeling in Latent Space

Kapoor, Jaivardhan, Macke, Jakob H., Baumgartner, Christian F.

arXiv.org Artificial Intelligence

Simulating aging in 3D brain MRI scans can reveal disease progression patterns in neurological disorders such as Alzheimer's disease. Current deep learning-based generative models typically approach this problem by predicting future scans from a single observed scan. We investigate modeling brain aging via linear models in the latent space of convolutional autoencoders (MRExtrap). Our approach, MRExtrap, is based on our observation that autoencoders trained on brain MRIs create latent spaces where aging trajectories appear approximately linear. We train autoencoders on brain MRIs to create latent spaces, and investigate how these latent spaces allow predicting future MRIs through linear extrapolation based on age, using an estimated latent progression rate $\boldsymbolβ$. For single-scan prediction, we propose using population-averaged and subject-specific priors on linear progression rates. We also demonstrate that predictions in the presence of additional scans can be flexibly updated using Bayesian posterior sampling, providing a mechanism for subject-specific refinement. On the ADNI dataset, MRExtrap predicts aging patterns accurately and beats a GAN-based baseline for single-volume prediction of brain aging. We also demonstrate and analyze multi-scan conditioning to incorporate subject-specific progression rates. Finally, we show that the latent progression rates in MRExtrap's linear framework correlate with disease and age-based aging patterns from previously studied structural atrophy rates. MRExtrap offers a simple and robust method for the age-based generation of 3D brain MRIs, particularly valuable in scenarios with multiple longitudinal observations.


CUTE-MRI: Conformalized Uncertainty-based framework for Time-adaptivE MRI

Fischer, Paul, Morshuis, Jan Nikolas, Küstner, Thomas, Baumgartner, Christian

arXiv.org Artificial Intelligence

Magnetic Resonance Imaging (MRI) offers unparalleled soft-tissue contrast but is fundamentally limited by long acquisition times. While deep learning-based accelerated MRI can dramatically shorten scan times, the reconstruction from undersampled data introduces ambiguity resulting from an ill-posed problem with infinitely many possible solutions that propagates to downstream clinical tasks. This uncertainty is usually ignored during the acquisition process as acceleration factors are often fixed a priori, resulting in scans that are either unnecessarily long or of insufficient quality for a given clinical endpoint. This work introduces a dynamic, uncertainty-aware acquisition framework that adjusts scan time on a per-subject basis. Our method leverages a probabilistic reconstruction model to estimate image uncertainty, which is then propagated through a full analysis pipeline to a quantitative metric of interest (e.g., patellar cartilage volume or cardiac ejection fraction). We use conformal prediction to transform this uncertainty into a rigorous, calibrated confidence interval for the metric. During acquisition, the system iteratively samples k-space, updates the reconstruction, and evaluates the confidence interval. The scan terminates automatically once the uncertainty meets a user-predefined precision target. We validate our framework on both knee and cardiac MRI datasets. Our results demonstrate that this adaptive approach reduces scan times compared to fixed protocols while providing formal statistical guarantees on the precision of the final image. This framework moves beyond fixed acceleration factors, enabling patient-specific acquisitions that balance scan efficiency with diagnostic confidence, a critical step towards personalized and resource-efficient MRI.


Reinforcement Twinning for Hybrid Control of Flapping-Wing Drones

Poletti, Romain, Schena, Lorenzo, Koloszar, Lilla, Degroote, Joris, Mendez, Miguel Alfonso

arXiv.org Artificial Intelligence

Controlling the flight of flapping-wing drones requires versatile controllers that handle their time-varying, nonlinear, and underactuated dynamics from incomplete and noisy sensor data. Model-based methods struggle with accurate modeling, while model-free approaches falter in efficiently navigating very high-dimensional and nonlinear control objective landscapes. This article presents a novel hybrid model-free/model-based approach to flight control based on the recently proposed reinforcement twinning algorithm. The model-based (MB) approach relies on an adjoint formulation using an adaptive digital twin, continuously identified from live trajectories, while the model-free (MF) approach relies on reinforcement learning. The two agents collaborate through transfer learning, imitation learning, and experience sharing using the real environment, the digital twin and a referee. The latter selects the best agent to interact with the real environment based on performance within the digital twin and a real-to-virtual environment consistency ratio. The algorithm is evaluated for controlling the longitudinal dynamics of a flapping-wing drone, with the environment simulated as a nonlinear, time-varying dynamical system under the influence of quasi-steady aerodynamic forces. The hybrid control learning approach is tested with three types of initialization of the adaptive model: (1) offline identification using previously available data, (2) random initialization with full online identification, and (3) offline pre-training with an estimation bias, followed by online adaptation. In all three scenarios, the proposed hybrid learning approach demonstrates superior performance compared to purely model-free and model-based methods.


Label-free Concept Based Multiple Instance Learning for Gigapixel Histopathology

Sun, Susu, Tessier, Leslie, Meeuwsen, Frédérique, Grisi, Clément, van Midden, Dominique, Litjens, Geert, Baumgartner, Christian F.

arXiv.org Artificial Intelligence

Multiple Instance Learning (MIL) methods allow for gigapixel Whole-Slide Image (WSI) analysis with only slide-level annotations. Interpretability is crucial for safely deploying such algorithms in high-stakes medical domains. Traditional MIL methods offer explanations by highlighting salient regions. However, such spatial heatmaps provide limited insights for end users. To address this, we propose a novel inherently interpretable WSI-classification approach that uses human-understandable pathology concepts to generate explanations. Our proposed Concept MIL model leverages recent advances in vision-language models to directly predict pathology concepts based on image features. The model's predictions are obtained through a linear combination of the concepts identified on the top-K patches of a WSI, enabling inherent explanations by tracing each concept's influence on the prediction. In contrast to traditional concept-based interpretable models, our approach eliminates the need for costly human annotations by leveraging the vision-language model. We validate our method on two widely used pathology datasets: Camelyon16 and PANDA. On both datasets, Concept MIL achieves AUC and accuracy scores over 0.9, putting it on par with state-of-the-art models. We further find that 87.1\% (Camelyon16) and 85.3\% (PANDA) of the top 20 patches fall within the tumor region. A user study shows that the concepts identified by our model align with the concepts used by pathologists, making it a promising strategy for human-interpretable WSI classification.


Knowledge-Augmented Explainable and Interpretable Learning for Anomaly Detection and Diagnosis

Atzmueller, Martin, Bohne, Tim, Windler, Patricia

arXiv.org Artificial Intelligence

Knowledge-augmented learning enables the combination of knowledge-based and data-driven approaches. For anomaly detection and diagnosis, understandability is typically an important factor, especially in high-risk areas. Therefore, explainability and interpretability are also major criteria in such contexts. This chapter focuses on knowledge-augmented explainable and interpretable learning to enhance understandability, transparency and ultimately computational sensemaking. We exemplify different approaches and methods in the domains of anomaly detection and diagnosis - from comparatively simple interpretable methods towards more advanced neuro-symbolic approaches.