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.

Hatching-Box: Monitoring the Rearing Process of Drosophila Using an Embedded Imaging and in-vial Detection System

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.

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.

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.

LangOcc: Self-Supervised Open Vocabulary Occupancy Estimation via Volume Rendering

The 3D occupancy estimation task has become an important challenge in the area of vision-based autonomous driving recently. However, most existing camera-based methods rely on costly 3D voxel labels or LiDAR scans for training, limiting their practicality and scalability. Moreover, most methods are tied to a predefined set of classes which they can detect. In this work we present a novel approach for open vocabulary occupancy estimation called LangOcc, that is trained only via camera images, and can detect arbitrary semantics via vision-language alignment. In particular, we distill the knowledge of the strong vision-language aligned encoder CLIP into a 3D occupancy model via differentiable volume rendering. Our model estimates vision-language aligned features in a 3D voxel grid using only images. It is trained in a self-supervised manner by rendering our estimations back to 2D space, where ground-truth features can be computed. This training mechanism automatically supervises the scene geometry, allowing for a straight-forward and powerful training method without any explicit geometry supervision. LangOcc outperforms LiDAR-supervised competitors in open vocabulary occupancy by a large margin, solely relying on vision-based training. We also achieve state-of-the-art results in self-supervised semantic occupancy estimation on the Occ3D-nuScenes dataset, despite not being limited to a specific set of categories, thus demonstrating the effectiveness of our proposed vision-language training.

OccFlowNet: Towards Self-supervised Occupancy Estimation via Differentiable Rendering and Occupancy Flow

Semantic occupancy has recently gained significant traction as a prominent 3D scene representation. However, most existing methods rely on large and costly datasets with fine-grained 3D voxel labels for training, which limits their practicality and scalability, increasing the need for self-monitored learning in this domain. In this work, we present a novel approach to occupancy estimation inspired by neural radiance field (NeRF) using only 2D labels, which are considerably easier to acquire. In particular, we employ differentiable volumetric rendering to predict depth and semantic maps and train a 3D network based on 2D supervision only. To enhance geometric accuracy and increase the supervisory signal, we introduce temporal rendering of adjacent time steps. Additionally, we introduce occupancy flow as a mechanism to handle dynamic objects in the scene and ensure their temporal consistency. Through extensive experimentation we demonstrate that 2D supervision only is sufficient to achieve state-of-the-art performance compared to methods using 3D labels, while outperforming concurrent 2D approaches. When combining 2D supervision with 3D labels, temporal rendering and occupancy flow we outperform all previous occupancy estimation models significantly. We conclude that the proposed rendering supervision and occupancy flow advances occupancy estimation and further bridges the gap towards self-supervised learning in this domain.

pyAKI -- An Open Source Solution to Automated KDIGO classification

Acute Kidney Injury (AKI) is a frequent complication in critically ill patients, affecting up to 50% of patients in the intensive care units. The lack of standardized and open-source tools for applying the Kidney Disease Improving Global Outcomes (KDIGO) criteria to time series data has a negative impact on workload and study quality. This project introduces pyAKI, an open-source pipeline addressing this gap by providing a comprehensive solution for consistent KDIGO criteria implementation. The pyAKI pipeline was developed and validated using a subset of the Medical Information Mart for Intensive Care (MIMIC)-IV database, a commonly used database in critical care research. We defined a standardized data model in order to ensure reproducibility. Validation against expert annotations demonstrated pyAKI's robust performance in implementing KDIGO criteria. Comparative analysis revealed its ability to surpass the quality of human labels. This work introduces pyAKI as an open-source solution for implementing the KDIGO criteria for AKI diagnosis using time series data with high accuracy and performance.

Momentum-SAM: Sharpness Aware Minimization without Computational Overhead

The recently proposed optimization algorithm for deep neural networks Sharpness Aware Minimization (SAM) suggests perturbing parameters before gradient calculation by a gradient ascent step to guide the optimization into parameter space regions of flat loss. While significant generalization improvements and thus reduction of overfitting could be demonstrated, the computational costs are doubled due to the additionally needed gradient calculation, making SAM unfeasible in case of limited computationally capacities. Motivated by Nesterov Accelerated Gradient (NAG) we propose Momentum-SAM (MSAM), which perturbs parameters in the direction of the accumulated momentum vector to achieve low sharpness without significant computational overhead or memory demands over SGD or Adam. We evaluate MSAM in detail and reveal insights on separable mechanisms of NAG, SAM and MSAM regarding training optimization and generalization. Code is available at https://github.com/MarlonBecker/MSAM.

Deepbet: Fast brain extraction of T1-weighted MRI using Convolutional Neural Networks

Brain extraction in magnetic resonance imaging (MRI) data is an important segmentation step in many neuroimaging preprocessing pipelines. Image segmentation is one of the research fields in which deep learning had the biggest impact in recent years enabling high precision segmentation with minimal compute. Consequently, traditional brain extraction methods are now being replaced by deep learning-based methods. Here, we used a unique dataset comprising 568 T1-weighted (T1w) MR images from 191 different studies in combination with cutting edge deep learning methods to build a fast, high-precision brain extraction tool called deepbet. deepbet uses LinkNet, a modern UNet architecture, in a two stage prediction process. This increases its segmentation performance, setting a novel state-of-the-art performance during cross-validation with a median Dice score (DSC) of 99.0% on unseen datasets, outperforming current state of the art models (DSC = 97.8% and DSC = 97.9%). While current methods are more sensitive to outliers, resulting in Dice scores as low as 76.5%, deepbet manages to achieve a Dice score of > 96.9% for all samples. Finally, our model accelerates brain extraction by a factor of ~10 compared to current methods, enabling the processing of one image in ~2 seconds on low level hardware.

From Group-Differences to Single-Subject Probability: Conformal Prediction-based Uncertainty Estimation for Brain-Age Modeling

The brain-age gap is one of the most investigated risk markers for brain changes across disorders. While the field is progressing towards large-scale models, recently incorporating uncertainty estimates, no model to date provides the single-subject risk assessment capability essential for clinical application. In order to enable the clinical use of brain-age as a biomarker, we here combine uncertainty-aware deep Neural Networks with conformal prediction theory. This approach provides statistical guarantees with respect to single-subject uncertainty estimates and allows for the calculation of an individual's probability for accelerated brain-aging. Building on this, we show empirically in a sample of N=16,794 participants that 1. a lower or comparable error as state-of-the-art, large-scale brain-age models, 2. the statistical guarantees regarding single-subject uncertainty estimation indeed hold for every participant, and 3. that the higher individual probabilities of accelerated brain-aging derived from our model are associated with Alzheimer's Disease, Bipolar Disorder and Major Depressive Disorder.