arXiv subjects

Benjamin Risse

Publications and source records attributed to Benjamin Risse.

At least 19 recordsLinked to original sources

arXiv2026

Seeing Beyond the Lesion: Disease Recognition from Reactive CNS Tissue

Sampling error yields exclusively reactive, non-lesional brain parenchyma in a significant proportion of intracranial biopsies, leaving the underlying disease undiagnosed. We benchmark four pathology foundation models (UNI2-h, Virchow2, Prov-GigaPath, H-optimus-0) as frozen patch encoders within a shared attention-based multiple-instance learning framework using 245 whole-slide images from 186 patients with confirmed downstream diagnoses. We first show that coarse disease-category prediction can be reproduced largely from slide size alone. After restricting classification to three finer diagnostic distinctions within common tissue categories, this confound no longer explains performance, yet disease labels remain predictable above chance under permutation testing (p $\le 10^{-4}$ throughout). Surprisingly, performance is statistically indistinguishable across all foundation-model encoders, suggesting that recovering these weak morphological signatures is not limited by current patch representations. Signed instance-contribution maps and expert review further test whether predictive evidence localizes to reactive parenchyma rather than sampling-induced bias like blood introduced during tissue sampling. These results position acquisition-shortcut auditing via a provenance-only baseline as a necessary control in computational-pathology benchmarks, and show, once that confound is removed, that weakly supervised models still recover disease signal from tissue conventionally regarded as non-diagnostic.

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arXiv2026

Random Label Prediction Heads for Studying Memorization in Deep Neural Networks

We introduce a straightforward yet effective method to empirically study memorization in deep neural networks for classification tasks. Our approach augments each training sample with auxiliary random labels, which are then predicted by a random label prediction head (RLP-head). RLP-heads can be attached at arbitrary depths of a network, predicting random labels from the corresponding intermediate representation and thereby enabling analysis of how memorization capacity evolves across layers. By interpreting the RLP-head performance as an empirical estimate of Rademacher complexity, we obtain a direct measure of both sample-level memorization and model capacity. We leverage this random label accuracy metric to analyze generalization and overfitting in different models and datasets. Building on this approach, we further propose a novel regularization technique based on the output of the RLP-head, which demonstrably reduces memorization. Interestingly, our experiments reveal that reducing memorization can either improve or impair generalization, depending on the dataset and training setup. These findings challenge the traditional assumption that overfitting is equivalent to memorization and suggest new hypotheses to reconcile these seemingly contradictory results. The source code is available at https://github.com/MarlonBecker/RandomLabelHeads

cs.LG↗

arXiv2026

Population-Scale Segmentation of Penile Tissue in DIXON MRI using Deep Learning for Quantitative Phenotyping in Male Reproductive Health

Penile measurement is clinically relevant across male reproductive and urogenital health, including conditions such as micropenis, congenital and endocrine disorders, and sexual or urinary dysfunction. However, quantitative assessment of penile size has relied mainly on external length or circumference measurements, which are difficult to standardize, sensitive to measurement conditions, and unable to capture the internal portion of the penis. MRI enables volumetric assessment of the whole penis in vivo, but automated segmentation has not previously been established at population scale. Automated whole-organ volumetry would enable high-throughput phenotyping for multi-omics and clinical studies of male reproductive disease. Here, we present a deep learning framework for whole-penis segmentation in multi-channel DIXON MRI. Using a newly curated expert-annotated training dataset ($n = 145$ subjects; $13,050$ annotated slices) and a double-annotated independent test benchmark ($n = 24$ subjects; $2,160$ double-annotated slices), we optimized a 3D nnU-Net architecture. The model achieved a 5-fold cross-validation Dice score of $0.90$ and performed at observer-level accuracy on the independent test set (Dice: $0.92$; Hausdorff distance: $3.58$). We deployed the model in $34,412$ UK Biobank participants, enabling automated quantification of total penile tissue, including both external and internal components. Longitudinal evaluation in 2,282 men demonstrated high inter-session reproducibility ($r = 0.87$). This framework establishes a reproducible and population-scalable method for MRI-based assessment of penile anatomy and provides an open technical resource for future studies in urological imaging and male reproductive health. The trained model weights will be publicly released.

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arXiv2026

WildBox: A Dataset and Benchmark for Aerial Monocular 3D Detection of African Savanna Wildlife

We introduce WildBox, a dataset and benchmark for monocular 3D detection of wildlife from drone video, comprising 237,505 3D bounding box annotations across seven African savanna species grouped into six benchmark classes. Annotations follow a KITTI/Omni3D-compatible format in a per-segment scale-normalised camera frame, with instance identities maintained across each segment. We evaluate two open-vocabulary monocular 3D architectures, OVMono3D-LIFT and DetAny3D, under zero-shot, ground-truth 2D box prompt, and supervised fine-tuning protocols. Open-vocabulary 2D foundation models provide usable zero-shot wildlife localisation (50.55 AP@50), but zero-shot 3D detection collapses to 0.00 AP across both architectures and every 2D-input condition tested, including ground-truth 2D box prompts, thus isolating the failure to the 3D stage. Fine-tuning on WildBox recovers performance to 8.68 +/- 0.47 AP-BEV@0.50 and 13.17 +/- 0.69 AP3D macro. Depth contributes 84% of normalised Hausdorff distance after fine-tuning and over 99% in zero-shot, identifying monocular aerial depth as the dominant open problem in this regime. A coarse-to-fine curriculum, i.e. pretraining on a merged zebra class before fine-tuning on the Grevy's/plains split, improves macro 3D performance with less total compute, with the largest gains on the two zebra subclasses. WildBox is released with video-level splits, evaluation code, and baseline checkpoints to enable progress in 3D wildlife perception from drone video.

cs.CV↗

arXiv2026

NEST3D: A High-Resolution Multimodal Dataset of Sociable Weaver Tree Nests

Sociable weaver nests function as complex ecological structures offering thermoregulatory microhabitats and sustaining diverse species; however, datasets used in prior studies lack fine-grained 3D structural detail. Producing usable and accurate 3D weaver nest data is challenging due to their irregular geometry and integration with complex host vegetation. We bridge this gap with an open-access, 1.4 TB multimodal drone dataset of 104 nest-bearing trees, comprising 27,945 RGB images, 111,780 multispectral images, approximately 781 million 3D points, and expert-annotated semantic segmentation labels. We benchmark semantic segmentation using KPConv, RandLA-Net, and Point Transformer V3, with PT-v3 achieving an mIoU of 86.35% on the test set. While the results demonstrate strong performance for transformer-based and point-wise methods, they also highlight architecture-dependent challenges, particularly for convolution-based approaches such as KPConv. By uniquely combining spectral, spatial, and structural information, the presented dataset advances 3D reconstruction, segmentation, and classification algorithms, enabling ecological applications from nest volume estimation to species conservation, and serves as a demanding benchmark that exposes architecture-dependent performance under extreme class imbalance.

cs.CV↗

arXiv2026

FAIR^2 Drones: An AI-Ready Standard for Cross-Domain Wildlife Drone Datasets

Animal ecology data collection using drones represents a substantial investment of time, expertise, and financial resources. Yet most existing datasets serve only a single research community, limiting interdisciplinary reuse. We propose a unified drone dataset standard, FAIR^2 Drones, that bridges ecology, robotics, and computer vision by building on existing FAIR and AI-ready data frameworks while adding essential platform metadata and annotation specifications. Our standard enables datasets to simultaneously support ecological analysis, robotics algorithm development, and computer vision benchmarking. We provide open-source validation tools, reference implementations, and multimodal extensions linking drone imagery with complementary sensors such as camera traps, GPS, and acoustics. By standardizing metadata across disciplines, this framework maximizes the scientific return on investment for costly field deployments and accelerates cross-domain collaboration in environmental monitoring.

cs.RO↗

arXiv2026

WildLIFT: Lifting monocular drone video to 3D for species-agnostic wildlife monitoring

Monocular RGB cameras mounted on drones are widely used for wildlife monitoring, yet most analytical pipelines remain confined to two-dimensional image space, leaving geometric information in video underexploited. We present WildLIFT, a computational framework that integrates three-dimensional scene geometry from monocular drone video with open-vocabulary 2D instance segmentation to enable species-agnostic 3D detection and tracking. Oriented 3D bounding box labels with semantic face information enable quantitative assessment of viewpoint coverage and inter-animal occlusion, producing structured metadata for downstream ecological analyses. We validate the framework on 2,581 manually curated frames comprising over 6,700 3D detections across four large mammal species. WildLIFT maintains high identity consistency in multi-animal scenes and substantially reduces manual 3D annotation effort through keyframe-based refinement. By transforming standard drone footage into structured 3D and viewpoint-aware representations, WildLIFT extends the analytical utility of aerial wildlife datasets for behavioural research and population monitoring.

cs.CV↗

arXiv2026

Adding Another Dimension to Image-based Animal Detection

Monocular imaging of animals inherently reduces 3D structures to 2D projections. Detection algorithms lead to 2D bounding boxes that lack information about animal's orientation relative to the camera. To build 3D detection methods for RGB animal images, there is a lack of labeled datasets; such labeling processes require 3D input streams along with RGB data. We present a pipeline that utilises Skinned Multi Animal Linear models to estimate 3D bounding boxes and to project them as robust labels into 2D image space using a dedicated camera pose refinement algorithm. To assess which sides of the animal are captured, cuboid face visibility metrics are computed. These 3D bounding boxes and metrics form a crucial step toward developing and benchmarking future monocular 3D animal detection algorithms. We evaluate our method on the Animal3D dataset, demonstrating accurate performance across species and settings.

cs.CV↗

arXiv2026

FixationFormer: Direct Utilization of Expert Gaze Trajectories for Chest X-Ray Classification

Expert eye movements provide a rich, passive source of domain knowledge in radiology, offering a powerful cue for integrating diagnostic reasoning into computer-aided analysis. However, direct integration into CNN-based systems, which historically have dominated the medical image analysis domain, is challenging: gaze recordings are sequential, temporally dense yet spatially sparse, noisy, and variable across experts. As a consequence, most existing image-based models utilize reduced representations such as heatmaps. In contrast, gaze naturally aligns with transformer architectures, as both are sequential in nature and rely on attention to highlight relevant input regions. In this work, we introduce FixationFormer, a transformer-based architecture that represents expert gaze trajectories as sequences of tokens, thereby preserving their temporal and spatial structure. By modeling gaze sequences jointly with image features, our approach addresses sparsity and variability in gaze data while enabling a more direct and fine-grained integration of expert diagnostic cues through explicit cross-attention between the image and gaze token sequences. We evaluate our method on three publicly available benchmark chest X-ray datasets and demonstrate that it achieves state-of-the-art classification performance, highlighting the value of representing gaze as a sequence in transformer-based medical image analysis.

cs.CV↗

arXiv2026

GazeXPErT: An Expert Eye-tracking Dataset for Interpretable and Explainable AI in Oncologic FDG-PET/CT Scans

[18F]FDG-PET/CT is a cornerstone imaging modality for guiding oncology therapies, yet human expert shortages necessitate more efficient diagnostic aids. While standalone AI models for automatic lesion detection exist, clinical translation remains hindered by AI explainability, reliability, and workflow integration. Meanwhile, human-computer-interaction in radiology remain limited to keyboard, mouse and voice, ignoring experts' faster, natural gaze signal. We present GazeXPErT, a 4D eye-tracking dataset with annotated expert decision windows for tumor detection and measurement on 346 dual-read FDG-PET/CTs. The dataset contributes 9,030 gaze-to-lesion trajectories derived from 3,948 minutes of 60 Hz eye-tracking data, rendered in COCO-style format. GazeXPErT captures experts' visual reasoning patterns when adjudicating suspicious lesions. It aims to facilitate development of trusted, explainable and interactive AI models through understanding expert gaze patterns. Baseline feasibility experiments suggest salient signal is extractable from routinely collected expert gaze (3D nnU-Net Dice: 0.6819 versus 0.6008 without), that gaze-trained vision transformers may aid dynamic lesion localization (74.95% predicted gaze closer to tumor), and that experts' intent may be predictable from raw gaze (Accuracy 67.53%, AUROC 0.747).

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arXiv2026

Dynamic Personality Adaptation in Large Language Models via State Machines

The inability of Large Language Models (LLMs) to modulate their personality expression in response to evolving dialogue dynamics hinders their performance in complex, interactive contexts. We propose a model-agnostic framework for dynamic personality simulation that employs state machines to represent latent personality states, where transition probabilities are dynamically adapted to the conversational context. Part of our architecture is a modular pipeline for continuous personality scoring that evaluates dialogues along latent axes while remaining agnostic to the specific personality models, their dimensions, transition mechanisms, or LLMs used. These scores function as dynamic state variables that systematically reconfigure the system prompt, steering behavioral alignment throughout the interaction.We evaluate this framework by operationalizing the Interpersonal Circumplex (IPC) in a medical education setting. Results demonstrate that the system successfully adapts its personality state to user inputs, but also influences user behavior, thereby facilitating de-escalation training. Notably, the scoring pipeline maintains comparable precision even when utilizing lightweight, fine-tuned classifiers instead of large-scale LLMs. This work demonstrates the feasibility of modular, personality-adaptive architectures for education, customer support, and broader human-computer interaction.

cs.CL↗

arXiv2025

ShelfOcc: Native 3D Supervision beyond LiDAR for Vision-Based Occupancy Estimation

Recent progress in self- and weakly supervised occupancy estimation has largely relied on 2D projection or rendering-based supervision, which suffers from geometric inconsistencies and severe depth bleeding. We thus introduce ShelfOcc, a vision-only method that overcomes these limitations without relying on LiDAR. ShelfOcc brings supervision into native 3D space by generating metrically consistent semantic voxel labels from video, enabling true 3D supervision without any additional sensors or manual 3D annotations. While recent vision-based 3D geometry foundation models provide a promising source of prior knowledge, they do not work out of the box as a prediction due to sparse or noisy and inconsistent geometry, especially in dynamic driving scenes. Our method introduces a dedicated framework that mitigates these issues by filtering and accumulating static geometry consistently across frames, handling dynamic content and propagating semantic information into a stable voxel representation. This data-centric shift in supervision for weakly/shelf-supervised occupancy estimation allows the use of essentially any SOTA occupancy model architecture without relying on LiDAR data. We argue that such high-quality supervision is essential for robust occupancy learning and constitutes an important complementary avenue to architectural innovation. On the Occ3D-nuScenes benchmark, ShelfOcc substantially outperforms all previous weakly/shelf-supervised methods (up to a 34% relative improvement), establishing a new data-driven direction for LiDAR-free 3D scene understanding.

cs.CV↗

arXiv2025

Palace: A Library for Interactive GPU-Accelerated Large Tensor Processing and Visualization

Tensor datasets (two-, three-, or higher-dimensional) are fundamental to many scientific fields utilizing imaging or simulation technologies. Advances in these methods have led to ever-increasing data sizes and, consequently, interest and development of out-of-core processing and visualization techniques, although mostly as specialized solutions. Here we present Palace, an open-source, cross-platform, general-purpose library for interactive and accelerated out-of-core tensor processing and visualization. Through a high-performance asynchronous concurrent architecture and a simple compute-graph interface, Palace enables the interactive development of out-of-core pipelines on workstation hardware. We demonstrate on benchmarks that Palace outperforms or matches state-of-the-art systems for volume rendering and hierarchical random-walker segmentation and demonstrate applicability in use cases involving tensors from 2D images up to 4D time series datasets.

cs.GR↗

arXiv2025

GaussianFlowOcc: Sparse and Weakly Supervised Occupancy Estimation using Gaussian Splatting and Temporal Flow

Occupancy estimation has become a prominent task in 3D computer vision, particularly within the autonomous driving community. In this paper, we present a novel approach to occupancy estimation, termed GaussianFlowOcc, which is inspired by Gaussian Splatting and replaces traditional dense voxel grids with a sparse 3D Gaussian representation. Our efficient model architecture based on a Gaussian Transformer significantly reduces computational and memory requirements by eliminating the need for expensive 3D convolutions used with inefficient voxel-based representations that predominantly represent empty 3D spaces. GaussianFlowOcc effectively captures scene dynamics by estimating temporal flow for each Gaussian during the overall network training process, offering a straightforward solution to a complex problem that is often neglected by existing methods. Moreover, GaussianFlowOcc is designed for scalability, as it employs weak supervision and does not require costly dense 3D voxel annotations based on additional data (e.g., LiDAR). Through extensive experimentation, we demonstrate that GaussianFlowOcc significantly outperforms all previous methods for weakly supervised occupancy estimation on the nuScenes dataset while featuring an inference speed that is 50 times faster than current SOTA.

cs.CV↗

arXiv2024

Learned Random Label Predictions as a Neural Network Complexity Metric

We empirically investigate the impact of learning randomly generated labels in parallel to class labels in supervised learning on memorization, model complexity, and generalization in deep neural networks. To this end, we introduce a multi-head network architecture as an extension of standard CNN architectures. Inspired by methods used in fair AI, our approach allows for the unlearning of random labels, preventing the network from memorizing individual samples. Based on the concept of Rademacher complexity, we first use our proposed method as a complexity metric to analyze the effects of common regularization techniques and challenge the traditional understanding of feature extraction and classification in CNNs. Second, we propose a novel regularizer that effectively reduces sample memorization. However, contrary to the predictions of classical statistical learning theory, we do not observe improvements in generalization.

cs.LG↗

arXiv2024

The Hatching-Box: A Novel System for Automated Monitoring and Quantification of Drosophila melanogaster Developmental Behavior

In this paper we propose the Hatching-Box, a novel imaging and analysis system to automatically monitor and quantify the developmental behavior of Drosophila in standard rearing vials and during regular rearing routines, rendering explicit experiments obsolete. This is achieved by combining custom tailored imaging hardware with dedicated detection and tracking algorithms, enabling the quantification of larvae, filled/empty pupae and flies over multiple days. Given the affordable and reproducible design of the Hatching-Box in combination with our generic client/server-based software, the system can easily be scaled to monitor an arbitrary amount of rearing vials simultaneously. We evaluated our system on a curated image dataset comprising nearly 470,000 annotated objects and performed several studies on real world experiments. We successfully reproduced results from well-established circadian experiments by comparing the eclosion periods of wild type flies to the clock mutants $\textit{per}^{short}$, $\textit{per}^{long}$ and $\textit{per}^0$ without involvement of any manual labor. Furthermore we show, that the Hatching-Box is able to extract additional information about group behavior as well as to reconstruct the whole life-cycle of the individual specimens. These results not only demonstrate the applicability of our system for long-term experiments but also indicate its benefits for automated monitoring in the general cultivation process.

cs.CV↗

arXiv2024

Towards Population Scale Testis Volume Segmentation in DIXON MRI

Testis size is known to be one of the main predictors of male fertility, usually assessed in clinical workup via palpation or imaging. Despite its potential, population-level evaluation of testicular volume using imaging remains underexplored. Previous studies, limited by small and biased datasets, have demonstrated the feasibility of machine learning for testis volume segmentation. This paper presents an evaluation of segmentation methods for testicular volume using Magnet Resonance Imaging data from the UKBiobank. The best model achieves a median dice score of $0.87$, compared to median dice score of $0.83$ for human interrater reliability on the same dataset, enabling large-scale annotation on a population scale for the first time. Our overall aim is to provide a trained model, comparative baseline methods, and annotated training data to enhance accessibility and reproducibility in testis MRI segmentation research.

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arXiv2024

deepmriprep: Voxel-based Morphometry (VBM) Preprocessing via Deep Neural Networks

Voxel-based Morphometry (VBM) has emerged as a powerful approach in neuroimaging research, utilized in over 7,000 studies since the year 2000. Using Magnetic Resonance Imaging (MRI) data, VBM assesses variations in the local density of brain tissue and examines its associations with biological and psychometric variables. Here, we present deepmriprep, a neural network-based pipeline that performs all necessary preprocessing steps for VBM analysis of T1-weighted MR images using deep neural networks. Utilizing the Graphics Processing Unit (GPU), deepmriprep is 37 times faster than CAT12, the leading VBM preprocessing toolbox. The proposed method matches CAT12 in accuracy for tissue segmentation and image registration across more than 100 datasets and shows strong correlations in VBM results. Tissue segmentation maps from deepmriprep have over 95% agreement with ground truth maps, and its non-linear registration, using supervised SYMNet, predicts smooth deformation fields comparable to CAT12. The high processing speed of deepmriprep enables rapid preprocessing of extensive datasets and thereby fosters the application of VBM analysis to large-scale neuroimaging studies and opens the door to real-time applications. Finally, deepmripreps straightforward, modular design enables researchers to easily understand, reuse, and advance the underlying methods, fostering further advancements in neuroimaging research. deepmriprep can be conveniently installed as a Python package and is publicly accessible at https://github.com/wwu-mmll/deepmriprep.

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