arXiv subjects

Gregor Köhler

Publications and source records attributed to Gregor Köhler.

8 recordsLinked to original sources

arXiv2026

Primus: Enforcing Attention Usage for 3D Medical Image Segmentation

Transformers have achieved remarkable success across multiple fields, yet their impact on 3D medical image segmentation remains limited with convolutional networks still dominating major benchmarks. In this work, (A) we analyze current Transformer-based segmentation models and identify critical shortcomings, particularly their over-reliance on convolutional blocks. Further, we demonstrate that in some architectures, performance is unaffected by the absence of the Transformer, thereby demonstrating their limited effectiveness. To address these challenges, we move away from hybrid architectures and (B) introduce Transformer-centric segmentation architectures, termed Primus and PrimusV2. Primus leverages high-resolution tokens, combined with advances in positional embeddings and block design, to maximally leverage its Transformer blocks, while PrimusV2 expands on this through an iterative patch embedding. Through these adaptations, Primus surpasses current Transformer-based methods and competes with a default nnU-Net while PrimusV2 exceeds it and is on par with the state-of-the-art CNNs such as ResEnc-L and MedNeXt architectures across nine public datasets. In doing so, we introduce the first competitive Transformer-centric model, making Transformers state-of-the-art in 3D medical image segmentation. The code is available here: https://github.com/MIC-DKFZ/nnUNet/blob/master/documentation/primus.md.

cs.CV↗

arXiv2025

An OpenMind for 3D medical vision self-supervised learning

The field of self-supervised learning (SSL) for 3D medical images lacks consistency and standardization. While many methods have been developed, it is impossible to identify the current state-of-the-art, due to i) varying and small pretraining datasets, ii) varying architectures, and iii) being evaluated on differing downstream datasets. In this paper, we bring clarity to this field and lay the foundation for further method advancements through three key contributions: We a) publish the largest publicly available pre-training dataset comprising 114k 3D brain MRI volumes, enabling all practitioners to pre-train on a large-scale dataset. We b) benchmark existing 3D self-supervised learning methods on this dataset for a state-of-the-art CNN and Transformer architecture, clarifying the state of 3D SSL pre-training. Among many findings, we show that pre-trained methods can exceed a strong from-scratch nnU-Net ResEnc-L baseline. Lastly, we c) publish the code of our pre-training and fine-tuning frameworks and provide the pre-trained models created during the benchmarking process to facilitate rapid adoption and reproduction.

cs.CV↗

arXiv2024

Decoupling Semantic Similarity from Spatial Alignment for Neural Networks

What representation do deep neural networks learn? How similar are images to each other for neural networks? Despite the overwhelming success of deep learning methods key questions about their internal workings still remain largely unanswered, due to their internal high dimensionality and complexity. To address this, one approach is to measure the similarity of activation responses to various inputs. Representational Similarity Matrices (RSMs) distill this similarity into scalar values for each input pair. These matrices encapsulate the entire similarity structure of a system, indicating which input leads to similar responses. While the similarity between images is ambiguous, we argue that the spatial location of semantic objects does neither influence human perception nor deep learning classifiers. Thus this should be reflected in the definition of similarity between image responses for computer vision systems. Revisiting the established similarity calculations for RSMs we expose their sensitivity to spatial alignment. In this paper, we propose to solve this through semantic RSMs, which are invariant to spatial permutation. We measure semantic similarity between input responses by formulating it as a set-matching problem. Further, we quantify the superiority of semantic RSMs over spatio-semantic RSMs through image retrieval and by comparing the similarity between representations to the similarity between predicted class probabilities.

cs.CV↗

arXiv2024

Physics-based vs. data-driven 24-hour probabilistic forecasts of precipitation for northern tropical Africa

Numerical weather prediction (NWP) models struggle to skillfully predict tropical precipitation occurrence and amount, calling for alternative approaches. For instance, it has been shown that fairly simple, purely data-driven logistic regression models for 24-hour precipitation occurrence outperform both climatological and NWP forecasts for the West African summer monsoon. More complex neural network based approaches, however, remain underdeveloped due to the non-Gaussian character of precipitation. In this study, we develop, apply and evaluate a novel two-stage approach, where we train a U-Net convolutional neural network (CNN) model on gridded rainfall data to obtain a deterministic forecast and then apply the recently developed, nonparametric Easy Uncertainty Quantification (EasyUQ) approach to convert it into a probabilistic forecast. We evaluate CNN+EasyUQ for one-day ahead 24-hour accumulated precipitation forecasts over northern tropical Africa for 2011--2019, with the Integrated Multi-satellitE Retrievals for GPM (IMERG) data serving as ground truth. In the most comprehensive assessment to date we compare CNN+EasyUQ to state-of-the-art physics-based and data-driven approaches such as a monthly probabilistic climatology, raw and postprocessed ensemble forecasts from the European Centre for Medium-Range Weather Forecasts (ECMWF), and traditional statistical approaches that use up to 25 predictor variables from IMERG and the ERA5 reanalysis.Generally, statistical approaches perform about en par with post-processed ECMWF ensemble forecasts. The CNN+EasyUQ approach, however, clearly outperforms all competitors for both occurrence and amount. Hybrid methods that merge CNN+EasyUQ and physics-based forecasts show slight further improvement. Thus, the CNN+EasyUQ approach can likely improve operational probabilistic forecasts of rainfall in the tropics, and potentially even beyond.

physics.ao-ph↗

arXiv2021

Continuous-Time Deep Glioma Growth Models

The ability to estimate how a tumor might evolve in the future could have tremendous clinical benefits, from improved treatment decisions to better dose distribution in radiation therapy. Recent work has approached the glioma growth modeling problem via deep learning and variational inference, thus learning growth dynamics entirely from a real patient data distribution. So far, this approach was constrained to predefined image acquisition intervals and sequences of fixed length, which limits its applicability in more realistic scenarios. We overcome these limitations by extending Neural Processes, a class of conditional generative models for stochastic time series, with a hierarchical multi-scale representation encoding including a spatio-temporal attention mechanism. The result is a learned growth model that can be conditioned on an arbitrary number of observations, and that can produce a distribution of temporally consistent growth trajectories on a continuous time axis. On a dataset of 379 patients, the approach successfully captures both global and finer-grained variations in the images, exhibiting superior performance compared to other learned growth models.

eess.IV↗

arXiv2021

GP-ConvCNP: Better Generalization for Convolutional Conditional Neural Processes on Time Series Data

Neural Processes (NPs) are a family of conditional generative models that are able to model a distribution over functions, in a way that allows them to perform predictions at test time conditioned on a number of context points. A recent addition to this family, Convolutional Conditional Neural Processes (ConvCNP), have shown remarkable improvement in performance over prior art, but we find that they sometimes struggle to generalize when applied to time series data. In particular, they are not robust to distribution shifts and fail to extrapolate observed patterns into the future. By incorporating a Gaussian Process into the model, we are able to remedy this and at the same time improve performance within distribution. As an added benefit, the Gaussian Process reintroduces the possibility to sample from the model, a key feature of other members in the NP family.

cs.LG↗

arXiv2021

Sample-Efficient Automated Deep Reinforcement Learning

Despite significant progress in challenging problems across various domains, applying state-of-the-art deep reinforcement learning (RL) algorithms remains challenging due to their sensitivity to the choice of hyperparameters. This sensitivity can partly be attributed to the non-stationarity of the RL problem, potentially requiring different hyperparameter settings at various stages of the learning process. Additionally, in the RL setting, hyperparameter optimization (HPO) requires a large number of environment interactions, hindering the transfer of the successes in RL to real-world applications. In this work, we tackle the issues of sample-efficient and dynamic HPO in RL. We propose a population-based automated RL (AutoRL) framework to meta-optimize arbitrary off-policy RL algorithms. In this framework, we optimize the hyperparameters and also the neural architecture while simultaneously training the agent. By sharing the collected experience across the population, we substantially increase the sample efficiency of the meta-optimization. We demonstrate the capabilities of our sample-efficient AutoRL approach in a case study with the popular TD3 algorithm in the MuJoCo benchmark suite, where we reduce the number of environment interactions needed for meta-optimization by up to an order of magnitude compared to population-based training.

cs.LG↗

arXiv2020

Neural Architecture Evolution in Deep Reinforcement Learning for Continuous Control

Current Deep Reinforcement Learning algorithms still heavily rely on handcrafted neural network architectures. We propose a novel approach to automatically find strong topologies for continuous control tasks while only adding a minor overhead in terms of interactions in the environment. To achieve this, we combine Neuroevolution techniques with off-policy training and propose a novel architecture mutation operator. Experiments on five continuous control benchmarks show that the proposed Actor-Critic Neuroevolution algorithm often outperforms the strong Actor-Critic baseline and is capable of automatically finding topologies in a sample-efficient manner which would otherwise have to be found by expensive architecture search.

cs.LG↗