arXiv subjects

André Homeyer

Publications and source records attributed to André Homeyer.

11 recordsLinked to original sources

arXiv2026

Sharing standardized image-derived data in computational pathology using DICOM

Development and evaluation of computational pathology methods require access to large and diverse datasets. Over the past decade, various initiatives invested significantly into collecting, centralizing, and sharing pathology imaging data. In contrast, sharing of image-derived data such as region-of-interest delineations or segmentation masks is less well developed. In this work, we describe our approach to encoding and sharing image-derived pathology data in a standardized manner within the National Cancer Institute (NCI) Imaging Data Commons (IDC), a platform that hosts and provides public access to de-identified radiology and pathology data. The IDC relies on the Digital Imaging and Communications in Medicine (DICOM) standard for data harmonization, yet the adoption of DICOM for pathology image-derived content has remained largely unexplored until now. Here, we present five representative datasets harmonized by conversion from their original representations into DICOM and shared publicly in the IDC. We demonstrate the benefits of this harmonization, describe contributions to critical open-source tooling, and discuss technical considerations relevant to broader adoption of DICOM for pathology image-derived data.

cs.CV↗

arXiv2026

Untargeted analysis of volatile markers of post-exercise fat oxidation in exhaled breath

Breath acetone represents a promising non-invasive biomarker for monitoring fat oxidation during exercise. However, its utility is limited by confounding factors, as well as by the fact that significant changes in concentration occur only hours post-exercise, which makes real-time assessment difficult. We performed an untargeted screening for volatile organic compounds (VOCs) that could serve as markers of fat oxidation beyond acetone, and investigated whether breath measurements taken during exercise could predict post-exercise changes in fat oxidation. Nineteen participants completed two 25-min cycling sessions separated by a brief 5-min rest period. VOC emissions were analysed using proton-transfer-reaction time-of-flight mass spectrometry (PTR-TOF-MS) during exercise and after a 90-min recovery period. Blood $β$-hydroxybutyrate (BOHB) concentrations served as the reference marker for fat oxidation. Among 773 relevant analytical features detected in the PTR-TOF-MS measurements, only four signals exhibited strong correlations with BOHB ($ρ$ $\geq$ 0.82, p = 0.0002)-all attributable to acetone or its isotopologues or fragments. End-of-exercise measurements of these signals enabled accurate prediction of participants with substantial post-exercise BOHB changes (F1 score $\geq$ 0.83, accuracy = 0.89). Our study did not reveal any novel breath-based biomarkers of fat oxidation, but it confirmed acetone as the key marker. Moreover, our findings suggest that breath acetone measurements during exercise may already enable basic predictions of post-exercise fat oxidation.

physics.med-ph↗

arXiv2026

Explainable histomorphology-based survival prediction of glioblastoma, IDH-wildtype

Glioblastoma, IDH-wildtype (GBM-IDHwt) is the most common malignant brain tumor. While histomorphology is a crucial component of GBM-IDHwt diagnosis, it is not further considered for prognosis. Here, we present an explainable artificial intelligence (AI) framework to identify and interpret histomorphological features associated with patient survival. The framework combines an explainable multiple instance learning (MIL) architecture that directly identifies prognostically relevant image tiles with a sparse autoencoder (SAE) that maps these tiles to interpretable visual patterns. The MIL model was trained and evaluated on a new real-world dataset of 720 GBM-IDHwt cases from three hospitals and four cancer registries across Germany. The SAE was trained on 1,878 whole-slide images from five independent public glioblastoma collections. Despite the many factors influencing survival time, our method showed some ability to discriminate between patients living less than 180 days or more than 360 days solely based on histomorphology (AUC: 0.67; 95% CI: 0.63-0.72). Cox proportional hazards regression confirmed a significant survival difference between predicted groups after adjustment for established prognostic factors (hazard ratio: 1.47; 95% CI: 1.26-1.72). Three neuropathologists categorized the identified visual patterns into seven distinct histomorphological groups, revealing both established prognostic features and unexpected associations, the latter being potentially attributable to surgery-related confounders. The presented explainable AI framework facilitates prognostic biomarker discovery in GBM-IDHwt and beyond, highlighting promising histomorphological features for further analysis and exposing potential confounders that would be hidden in black-box models.

eess.IV↗

arXiv2026

Whole Slide Concepts: A Supervised Foundation Model For Pathological Images

Foundation models (FMs) are transforming computational pathology by offering new ways to analyze histopathology images. However, FMs typically require weeks of training on large databases, making their creation a resource-intensive process. In this paper, we present a training for foundation models from whole slide images using supervised, end-to-end, multitask learning on slide-level labels. Notably, it is the first model to incorporate cancer subtyping, risk estimation, and genetic mutation prediction into one model. The presented model outperforms self-supervised models on seven benchmark tasks while the training only required 5% of the computational resources. The results not only show that supervised training can outperform self-supervision with less data, but also offer a solution to annotation problems, as patient-based labels are widely available through routine clinical processes. Furthermore, an attention module provides a layer of explainability across different tasks and serves as a tumor detector for unseen cancer types. To address the issue of closed-source datasets, the model was fully trained on openly available data. The code and model weights are made available under https://github.com/FraunhoferMEVIS/MedicalMultitaskModeling.

eess.IV↗

arXiv2025

Automatic Extraction of Rules for Generating Synthetic Patient Data From Real-World Population Data Using Glioblastoma as an Example

The generation of synthetic data is a promising technology to make medical data available for secondary use in a privacy-compliant manner. A popular method for creating realistic patient data is the rule-based Synthea data generator. Synthea generates data based on rules describing the lifetime of a synthetic patient. These rules typically express the probability of a condition occurring, such as a disease, depending on factors like age. Since they only contain statistical information, rules usually have no specific data protection requirements. However, creating meaningful rules can be a very complex process that requires expert knowledge and realistic sample data. In this paper, we introduce and evaluate an approach to automatically generate Synthea rules based on statistics from tabular data, which we extracted from cancer reports. As an example use case, we created a Synthea module for glioblastoma from a real-world dataset and used it to generate a synthetic dataset. Compared to the original dataset, the synthetic data reproduced known disease courses and mostly retained the statistical properties. Overall, synthetic patient data holds great potential for privacy-preserving research. The data can be used to formulate hypotheses and to develop prototypes, but medical interpretation should consider the specific limitations as with any currently available approach.

cs.LG↗

arXiv2024

Applications of artificial intelligence in the analysis of histopathology images of gliomas: a review

In recent years, the diagnosis of gliomas has become increasingly complex. Analysis of glioma histopathology images using artificial intelligence (AI) offers new opportunities to support diagnosis and outcome prediction. To give an overview of the current state of research, this review examines 83 publicly available research studies that have proposed AI-based methods for whole-slide histopathology images of human gliomas, covering the diagnostic tasks of subtyping (23/83), grading (27/83), molecular marker prediction (20/83), and survival prediction (29/83). All studies were reviewed with regard to methodological aspects as well as clinical applicability. It was found that the focus of current research is the assessment of hematoxylin and eosin-stained tissue sections of adult-type diffuse gliomas. The majority of studies (52/83) are based on the publicly available glioblastoma and low-grade glioma datasets from The Cancer Genome Atlas (TCGA) and only a few studies employed other datasets in isolation (16/83) or in addition to the TCGA datasets (15/83). Current approaches mostly rely on convolutional neural networks (63/83) for analyzing tissue at 20x magnification (35/83). A new field of research is the integration of clinical data, omics data, or magnetic resonance imaging (29/83). So far, AI-based methods have achieved promising results, but are not yet used in real clinical settings. Future work should focus on the independent validation of methods on larger, multi-site datasets with high-quality and up-to-date clinical and molecular pathology annotations to demonstrate routine applicability.

eess.IV↗

arXiv2024

Joining Forces for Pathology Diagnostics with AI Assistance: The EMPAIA Initiative

Over the past decade, artificial intelligence (AI) methods in pathology have advanced substantially. However, integration into routine clinical practice has been slow due to numerous challenges, including technical and regulatory hurdles in translating research results into clinical diagnostic products and the lack of standardized interfaces. The open and vendor-neutral EMPAIA initiative addresses these challenges. Here, we provide an overview of EMPAIA's achievements and lessons learned. EMPAIA integrates various stakeholders of the pathology AI ecosystem, i.e., pathologists, computer scientists, and industry. In close collaboration, we developed technical interoperability standards, recommendations for AI testing and product development, and explainability methods. We implemented the modular and open-source EMPAIA platform and successfully integrated 14 AI-based image analysis apps from 8 different vendors, demonstrating how different apps can use a single standardized interface. We prioritized requirements and evaluated the use of AI in real clinical settings with 14 different pathology laboratories in Europe and Asia. In addition to technical developments, we created a forum for all stakeholders to share information and experiences on digital pathology and AI. Commercial, clinical, and academic stakeholders can now adopt EMPAIA's common open-source interfaces, providing a unique opportunity for large-scale standardization and streamlining of processes. Further efforts are needed to effectively and broadly establish AI assistance in routine laboratory use. To this end, a sustainable infrastructure, the non-profit association EMPAIA International, has been established to continue standardization and support broad implementation and advocacy for an AI-assisted digital pathology future.

cs.CY↗

arXiv2023

The NCI Imaging Data Commons as a platform for reproducible research in computational pathology

Background and Objectives: Reproducibility is a major challenge in developing machine learning (ML)-based solutions in computational pathology (CompPath). The NCI Imaging Data Commons (IDC) provides >120 cancer image collections according to the FAIR principles and is designed to be used with cloud ML services. Here, we explore its potential to facilitate reproducibility in CompPath research. Methods: Using the IDC, we implemented two experiments in which a representative ML-based method for classifying lung tumor tissue was trained and/or evaluated on different datasets. To assess reproducibility, the experiments were run multiple times with separate but identically configured instances of common ML services. Results: The AUC values of different runs of the same experiment were generally consistent. However, we observed small variations in AUC values of up to 0.045, indicating a practical limit to reproducibility. Conclusions: We conclude that the IDC facilitates approaching the reproducibility limit of CompPath research (i) by enabling researchers to reuse exactly the same datasets and (ii) by integrating with cloud ML services so that experiments can be run in identically configured computing environments.

cs.CV↗

arXiv2023

Digitization of Pathology Labs: A Review of Lessons Learned

Pathology laboratories are increasingly using digital workflows. This has the potential of increasing lab efficiency, but the digitization process also involves major challenges. Several reports have been published describing the individual experiences of specific laboratories with the digitization process. However, a comprehensive overview of the lessons learned is still lacking. We provide an overview of the lessons learned for different aspects of the digitization process, including digital case management, digital slide reading, and computer-aided slide reading. We also cover metrics used for monitoring performance and pitfalls and corresponding values observed in practice. The overview is intended to help pathologists, IT decision-makers, and administrators to benefit from the experiences of others and to implement the digitization process in an optimal way to make their own laboratory future-proof.

cs.HC↗

arXiv2022

Recommendations on test datasets for evaluating AI solutions in pathology

Artificial intelligence (AI) solutions that automatically extract information from digital histology images have shown great promise for improving pathological diagnosis. Prior to routine use, it is important to evaluate their predictive performance and obtain regulatory approval. This assessment requires appropriate test datasets. However, compiling such datasets is challenging and specific recommendations are missing. A committee of various stakeholders, including commercial AI developers, pathologists, and researchers, discussed key aspects and conducted extensive literature reviews on test datasets in pathology. Here, we summarize the results and derive general recommendations for the collection of test datasets. We address several questions: Which and how many images are needed? How to deal with low-prevalence subsets? How can potential bias be detected? How should datasets be reported? What are the regulatory requirements in different countries? The recommendations are intended to help AI developers demonstrate the utility of their products and to help regulatory agencies and end users verify reported performance measures. Further research is needed to formulate criteria for sufficiently representative test datasets so that AI solutions can operate with less user intervention and better support diagnostic workflows in the future.

eess.IV↗

arXiv2021

Evaluating Generic Auto-ML Tools for Computational Pathology

Image analysis tasks in computational pathology are commonly solved using convolutional neural networks (CNNs). The selection of a suitable CNN architecture and hyperparameters is usually done through exploratory iterative optimization, which is computationally expensive and requires substantial manual work. The goal of this article is to evaluate how generic tools for neural network architecture search and hyperparameter optimization perform for common use cases in computational pathology. For this purpose, we evaluated one on-premises and one cloud-based tool for three different classification tasks for histological images: tissue classification, mutation prediction, and grading. We found that the default CNN architectures and parameterizations of the evaluated AutoML tools already yielded classification performance on par with the original publications. Hyperparameter optimization for these tasks did not substantially improve performance, despite the additional computational effort. However, performance varied substantially between classifiers obtained from individual AutoML runs due to non-deterministic effects. Generic CNN architectures and AutoML tools could thus be a viable alternative to manually optimizing CNN architectures and parametrizations. This would allow developers of software solutions for computational pathology to focus efforts on harder-to-automate tasks such as data curation.

eess.IV↗