Markus Bujotzek

Stefan Denner, Markus Bujotzek, Dimitrios Bounias et al.

Medical image classification plays a crucial role in clinical decision-making, yet most models are constrained to a fixed set of predefined classes, limiting their adaptability to new conditions. Contrastive Language-Image Pretraining (CLIP) offers a promising solution by enabling zero-shot classification through multimodal large-scale pretraining. However, while CLIP effectively captures global image content, radiology requires a more localized focus on specific pathology regions to enhance both interpretability and diagnostic accuracy. To address this, we explore the potential of incorporating visual cues into zero-shot classification, embedding visual markers, such as arrows, bounding boxes, and circles, directly into radiological images to guide model attention. Evaluating across four public chest X-ray datasets, we demonstrate that visual markers improve AUROC by up to 0.185, highlighting their effectiveness in enhancing classification performance. Furthermore, attention map analysis confirms that visual cues help models focus on clinically relevant areas, leading to more interpretable predictions.To support further research, we use public datasets and provide our codebase and preprocessing pipeline under https://github.com/MIC-DKFZ/VPE-in-Radiology, serving as a reference point for future work on localized classification in medical imaging.

Stefan Denner, Jonas Scherer, Klaus Kades et al.

In the rapidly evolving field of medical imaging, machine learning algorithms have become indispensable for enhancing diagnostic accuracy. However, the effectiveness of these algorithms is contingent upon the availability and organization of high-quality medical imaging datasets. Traditional Digital Imaging and Communications in Medicine (DICOM) data management systems are inadequate for handling the scale and complexity of data required to be facilitated in machine learning algorithms. This paper introduces an innovative data curation tool, developed as part of the Kaapana open-source toolkit, aimed at streamlining the organization, management, and processing of large-scale medical imaging datasets. The tool is specifically tailored to meet the needs of radiologists and machine learning researchers. It incorporates advanced search, auto-annotation and efficient tagging functionalities for improved data curation. Additionally, the tool facilitates quality control and review, enabling researchers to validate image and segmentation quality in large datasets. It also plays a critical role in uncovering potential biases in datasets by aggregating and visualizing metadata, which is essential for developing robust machine learning models. Furthermore, Kaapana is integrated within the Radiological Cooperative Network (RACOON), a pioneering initiative aimed at creating a comprehensive national infrastructure for the aggregation, transmission, and consolidation of radiological data across all university clinics throughout Germany. A supplementary video showcasing the tool's functionalities can be accessed at https://bit.ly/MICCAI-DEMI2023.

Ünal Akünal, Markus Bujotzek, Stefan Denner et al.

Developing generalizable AI for medical imaging requires both access to large, multi-center datasets and standardized, reproducible tooling within research environments. However, leveraging real-world imaging data in clinical research environments is still hampered by strict regulatory constraints, fragmented software infrastructure, and the challenges inherent in conducting large-cohort multicentre studies. This leads to projects that rely on ad-hoc toolchains that are hard to reproduce, difficult to scale beyond single institutions and poorly suited for collaboration between clinicians and data scientists. We present Kaapana, a comprehensive open-source platform for medical imaging research that is designed to bridge this gap. Rather than building single-use, site-specific tooling, Kaapana provides a modular, extensible framework that unifies data ingestion, cohort curation, processing workflows and result inspection under a common user interface. By bringing the algorithm to the data, it enables institutions to keep control over their sensitive data while still participating in distributed experimentation and model development. By integrating flexible workflow orchestration with user-facing applications for researchers, Kaapana reduces technical overhead, improves reproducibility and enables conducting large-scale, collaborative, multi-centre imaging studies. We describe the core concepts of the platform and illustrate how they can support diverse use cases, from local prototyping to nation-wide research networks. The open-source codebase is available at https://github.com/kaapana/kaapana

Stefan Denner, David Zimmerer, Dimitrios Bounias et al.

Content-based image retrieval (CBIR) has the potential to significantly improve diagnostic aid and medical research in radiology. However, current CBIR systems face limitations due to their specialization to certain pathologies, limiting their utility. On the other hand, several vision foundation models have been shown to produce general-purpose visual features. Therefore, in this work, we propose using vision foundation models as powerful and versatile off-the-shelf feature extractors for content-based image retrieval. Our contributions include: (1) benchmarking a diverse set of vision foundation models on an extensive dataset comprising 1.6 million 2D radiological images across four modalities and 161 pathologies; (2) identifying weakly-supervised models, particularly BiomedCLIP, as highly effective, achieving a achieving a P@1 of up to 0.594 (P@3: 0.590, P@5: 0.588, P@10: 0.583), comparable to specialized CBIR systems but without additional training; (3) conducting an in-depth analysis of the impact of index size on retrieval performance; (4) evaluating the quality of embedding spaces generated by different models; and (5) investigating specific challenges associated with retrieving anatomical versus pathological structures. Despite these challenges, our research underscores the vast potential of foundation models for CBIR in radiology, proposing a shift towards versatile, general-purpose medical image retrieval systems that do not require specific tuning. Our code, dataset splits and embeddings are publicly available under https://github.com/MIC-DKFZ/foundation-models-for-cbmir.

Markus Bujotzek, Evelyn Trautmann, Calum Hand et al.

AI methods are increasingly shaping pharmaceutical drug discovery. However, their translation to industrial applications remains limited due to their reliance on public datasets, lacking scale and diversity of proprietary pharmaceutical data. Federated learning (FL) offers a promising approach to integrate private data into privacy-preserving, collaborative model training across data silos. This federated data access complicates important data-centric tasks such as estimating dataset diversity, performing informed data splits, and understanding the structure of the combined chemical space. To address this gap, we investigate how well federated clustering methods can disentangle and represent distributed molecular data. We benchmark three approaches, Federated kMeans (Fed-kMeans), Federated Principal Component Analysis combined with Fed-kMeans (Fed-PCA+Fed-kMeans), and Federated Locality-Sensitive Hashing (Fed-LSH), against their centralized counterparts on eight diverse molecular datasets. Our evaluation utilizes both, standard mathematical and a chemistry-informed evaluation metrics, SF-ICF, that we introduce in this work. The large-scale benchmarking combined with an in-depth explainability analysis shows the importance of incorporating domain knowledge through chemistry-informed metrics, and on-client explainability analyses for federated diversity analysis on molecular data.

Kendall Schmidt, Benjamin Bearce, Ken Chang et al.

The correct interpretation of breast density is important in the assessment of breast cancer risk. AI has been shown capable of accurately predicting breast density, however, due to the differences in imaging characteristics across mammography systems, models built using data from one system do not generalize well to other systems. Though federated learning (FL) has emerged as a way to improve the generalizability of AI without the need to share data, the best way to preserve features from all training data during FL is an active area of research. To explore FL methodology, the breast density classification FL challenge was hosted in partnership with the American College of Radiology, Harvard Medical School's Mass General Brigham, University of Colorado, NVIDIA, and the National Institutes of Health National Cancer Institute. Challenge participants were able to submit docker containers capable of implementing FL on three simulated medical facilities, each containing a unique large mammography dataset. The breast density FL challenge ran from June 15 to September 5, 2022, attracting seven finalists from around the world. The winning FL submission reached a linear kappa score of 0.653 on the challenge test data and 0.413 on an external testing dataset, scoring comparably to a model trained on the same data in a central location.