arXiv subjects

Lucas Zimmer

Publications and source records attributed to Lucas Zimmer.

10 recordsLinked to original sources

arXiv2026

TumorFlow: Physics-Guided Longitudinal MRI Synthesis of Glioblastoma Growth

Glioblastoma exhibits diverse, infiltrative, and patient-specific growth patterns that are only partially visible on routine MRI, making it difficult to reliably assess true tumor extent and personalize treatment planning and follow-up. We present a biophysically-conditioned generative framework that synthesizes biologically realistic 3D brain MRI volumes from estimated, spatially continuous tumor-concentration fields. Our approach combines a generative model with tumor-infiltration maps that can be propagated through time using a biophysical growth model, enabling fine-grained control over tumor shape and growth while preserving patient anatomy. This enables us to synthesize consistent tumor growth trajectories directly in the space of real patients, providing interpretable, controllable estimation of tumor infiltration and progression beyond what is explicitly observed in imaging. We evaluate the framework on longitudinal glioblastoma cases and demonstrate that it can generate temporally coherent sequences with realistic changes in tumor appearance and surrounding tissue response. These results suggest that integrating mechanistic tumor growth priors with modern generative modeling can provide a practical tool for patient-specific progression visualization and for generating controlled synthetic data to support downstream neuro-oncology workflows. In longitudinal extrapolation, we achieve a consistent 75% Dice overlap with the biophysical model while maintaining a constant PSNR of 25 in the surrounding tissue. Our code is available at: https://github.com/valentin-biller/lgm.git

cs.CV↗

arXiv2025

A Biophysically-Conditioned Generative Framework for 3D Brain Tumor MRI Synthesis

Magnetic resonance imaging (MRI) inpainting supports numerous clinical and research applications. We introduce the first generative model that conditions on voxel-level, continuous tumor concentrations to synthesize high-fidelity brain tumor MRIs. For the BraTS 2025 Inpainting Challenge, we adapt this architecture to the complementary task of healthy tissue restoration by setting the tumor concentrations to zero. Our latent diffusion model conditioned on both tissue segmentations and the tumor concentrations generates 3D spatially coherent and anatomically consistent images for both tumor synthesis and healthy tissue inpainting. For healthy inpainting, we achieve a PSNR of 18.5, and for tumor inpainting, we achieve 17.4. Our code is available at: https://github.com/valentin-biller/ldm.git

eess.IV↗

arXiv2025

From Fiber Tracts to Tumor Spread: Biophysical Modeling of Butterfly Glioma Growth Using Diffusion Tensor Imaging

Butterfly tumors are a distinct class of gliomas that span the corpus callosum, producing a characteristic butterfly-shaped appearance on MRI. The distinctive growth pattern of these tumors highlights how white matter fibers and structural connectivity influence brain tumor cell migration. To investigate this relation, we applied biophysical tumor growth models to a large patient cohort, systematically comparing models that incorporate fiber tract information with those that do not. Our results demonstrate that including fiber orientation data significantly improves model accuracy, particularly for a subset of butterfly tumors. These findings highlight the critical role of white matter architecture in tumor spread and suggest that integrating fiber tract information can enhance the precision of radiotherapy target volume delineation.

physics.med-ph↗

arXiv2025

BrainLesion Suite: A Flexible and User-Friendly Framework for Modular Brain Lesion Image Analysis

BrainLesion Suite is a versatile toolkit for building modular brain lesion image analysis pipelines in Python. Following Pythonic principles, BrainLesion Suite is designed to provide a 'brainless' development experience, minimizing cognitive effort and streamlining the creation of complex workflows for clinical and scientific practice. At its core is an adaptable preprocessing module that performs co-registration, atlas registration, and optional skull-stripping and defacing on arbitrary multi-modal input images. BrainLesion Suite leverages algorithms from the BraTS challenge to synthesize missing modalities, inpaint lesions, and generate pathology-specific tumor segmentations. BrainLesion Suite also enables quantifying segmentation model performance, with tools such as panoptica to compute lesion-wise metrics. Although BrainLesion Suite was originally developed for image analysis pipelines of brain lesions such as glioma, metastasis, and multiple sclerosis, it can be adapted for other biomedical image analysis applications. The individual BrainLesion Suite packages and tutorials are accessible on GitHub.

cs.CV↗

arXiv2024

A Lightweight Optimization Framework for Estimating 3D Brain Tumor Infiltration

Glioblastoma, the most aggressive primary brain tumor, poses a severe clinical challenge due to its diffuse microscopic infiltration, which remains largely undetected on standard MRI. As a result, current radiotherapy planning employs a uniform 15 mm margin around the resection cavity, failing to capture patient-specific tumor spread. Tumor growth modeling offers a promising approach to reveal this hidden infiltration. However, methods based on partial differential equations or physics-informed neural networks tend to be computationally intensive or overly constrained, limiting their clinical adaptability to individual patients. In this work, we propose a lightweight, rapid, and robust optimization framework that estimates the 3D tumor concentration by fitting it to MRI tumor segmentations while enforcing a smooth concentration landscape. This approach achieves superior tumor recurrence prediction on 192 brain tumor patients across two public datasets, outperforming state-of-the-art baselines while reducing runtime from 30 minutes to less than one minute. Furthermore, we demonstrate the framework's versatility and adaptability by showing its ability to seamlessly integrate additional imaging modalities or physical constraints.

physics.med-ph↗

arXiv2024

QUBIQ: Uncertainty Quantification for Biomedical Image Segmentation Challenge

Uncertainty in medical image segmentation tasks, especially inter-rater variability, arising from differences in interpretations and annotations by various experts, presents a significant challenge in achieving consistent and reliable image segmentation. This variability not only reflects the inherent complexity and subjective nature of medical image interpretation but also directly impacts the development and evaluation of automated segmentation algorithms. Accurately modeling and quantifying this variability is essential for enhancing the robustness and clinical applicability of these algorithms. We report the set-up and summarize the benchmark results of the Quantification of Uncertainties in Biomedical Image Quantification Challenge (QUBIQ), which was organized in conjunction with International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2020 and 2021. The challenge focuses on the uncertainty quantification of medical image segmentation which considers the omnipresence of inter-rater variability in imaging datasets. The large collection of images with multi-rater annotations features various modalities such as MRI and CT; various organs such as the brain, prostate, kidney, and pancreas; and different image dimensions 2D-vs-3D. A total of 24 teams submitted different solutions to the problem, combining various baseline models, Bayesian neural networks, and ensemble model techniques. The obtained results indicate the importance of the ensemble models, as well as the need for further research to develop efficient 3D methods for uncertainty quantification methods in 3D segmentation tasks.

eess.IV↗

arXiv2022

Learn-Morph-Infer: a new way of solving the inverse problem for brain tumor modeling

Current treatment planning of patients diagnosed with a brain tumor, such as glioma, could significantly benefit by accessing the spatial distribution of tumor cell concentration. Existing diagnostic modalities, e.g. magnetic resonance imaging (MRI), contrast sufficiently well areas of high cell density. In gliomas, however, they do not portray areas of low cell concentration, which can often serve as a source for the secondary appearance of the tumor after treatment. To estimate tumor cell densities beyond the visible boundaries of the lesion, numerical simulations of tumor growth could complement imaging information by providing estimates of full spatial distributions of tumor cells. Over recent years a corpus of literature on medical image-based tumor modeling was published. It includes different mathematical formalisms describing the forward tumor growth model. Alongside, various parametric inference schemes were developed to perform an efficient tumor model personalization, i.e. solving the inverse problem. However, the unifying drawback of all existing approaches is the time complexity of the model personalization which prohibits a potential integration of the modeling into clinical settings. In this work, we introduce a deep learning based methodology for inferring the patient-specific spatial distribution of brain tumors from T1Gd and FLAIR MRI medical scans. Coined as Learn-Morph-Infer the method achieves real-time performance in the order of minutes on widely available hardware and the compute time is stable across tumor models of different complexity, such as reaction-diffusion and reaction-advection-diffusion models. We believe the proposed inverse solution approach not only bridges the way for clinical translation of brain tumor personalization but can also be adopted to other scientific and engineering domains.

physics.med-ph↗

arXiv2022

A for-loop is all you need. For solving the inverse problem in the case of personalized tumor growth modeling

Solving the inverse problem is the key step in evaluating the capacity of a physical model to describe real phenomena. In medical image computing, it aligns with the classical theme of image-based model personalization. Traditionally, a solution to the problem is obtained by performing either sampling or variational inference based methods. Both approaches aim to identify a set of free physical model parameters that results in a simulation best matching an empirical observation. When applied to brain tumor modeling, one of the instances of image-based model personalization in medical image computing, the overarching drawback of the methods is the time complexity for finding such a set. In a clinical setting with limited time between imaging and diagnosis or even intervention, this time complexity may prove critical. As the history of quantitative science is the history of compression, we align in this paper with the historical tendency and propose a method compressing complex traditional strategies for solving an inverse problem into a simple database query task. We evaluated different ways of performing the database query task assessing the trade-off between accuracy and execution time. On the exemplary task of brain tumor growth modeling, we prove that the proposed method achieves one order speed-up compared to existing approaches for solving the inverse problem. The resulting compute time offers critical means for relying on more complex and, hence, realistic models, for integrating image preprocessing and inverse modeling even deeper, or for implementing the current model into a clinical workflow.

cs.CE↗

arXiv2022

Surrogate NAS Benchmarks: Going Beyond the Limited Search Spaces of Tabular NAS Benchmarks

The most significant barrier to the advancement of Neural Architecture Search (NAS) is its demand for large computational resources, which hinders scientifically sound empirical evaluations of NAS methods. Tabular NAS benchmarks have alleviated this problem substantially, making it possible to properly evaluate NAS methods in seconds on commodity machines. However, an unintended consequence of tabular NAS benchmarks has been a focus on extremely small architectural search spaces since their construction relies on exhaustive evaluations of the space. This leads to unrealistic results that do not transfer to larger spaces. To overcome this fundamental limitation, we propose a methodology to create cheap NAS surrogate benchmarks for arbitrary search spaces. We exemplify this approach by creating surrogate NAS benchmarks on the existing tabular NAS-Bench-101 and on two widely used NAS search spaces with up to $10^{21}$ architectures ($10^{13}$ times larger than any previous tabular NAS benchmark). We show that surrogate NAS benchmarks can model the true performance of architectures better than tabular benchmarks (at a small fraction of the cost), that they lead to faithful estimates of how well different NAS methods work on the original non-surrogate benchmark, and that they can generate new scientific insight. We open-source all our code and believe that surrogate NAS benchmarks are an indispensable tool to extend scientifically sound work on NAS to large and exciting search spaces.

cs.LG↗

arXiv2021

Auto-PyTorch Tabular: Multi-Fidelity MetaLearning for Efficient and Robust AutoDL

While early AutoML frameworks focused on optimizing traditional ML pipelines and their hyperparameters, a recent trend in AutoML is to focus on neural architecture search. In this paper, we introduce Auto-PyTorch, which brings the best of these two worlds together by jointly and robustly optimizing the architecture of networks and the training hyperparameters to enable fully automated deep learning (AutoDL). Auto-PyTorch achieves state-of-the-art performance on several tabular benchmarks by combining multi-fidelity optimization with portfolio construction for warmstarting and ensembling of deep neural networks (DNNs) and common baselines for tabular data. To thoroughly study our assumptions on how to design such an AutoDL system, we additionally introduce a new benchmark on learning curves for DNNs, dubbed LCBench, and run extensive ablation studies of the full Auto-PyTorch on typical AutoML benchmarks, eventually showing that Auto-PyTorch performs better than several state-of-the-art competitors on average.

cs.LG↗