A Privacy-Preserving Ecosystem for Developing Machine Learning Algorithms Using Patient Data: Insights from the TUM.ai Makeathon

TL;DR

This paper presents a multi-stage, privacy-preserving approach for developing machine learning models on sensitive patient data using federated learning and simulated knowledge graphs, validated during a healthcare AI challenge.

Contribution

It introduces a novel multi-stage method combining simulated knowledge graphs and federated learning to enable privacy-preserving AI development in healthcare.

Findings

Successful validation during TUM.ai Makeathon 2024 challenge

Models developed without access to real patient data

Demonstrated feasibility of privacy-preserving AI in clinical settings

Abstract

The integration of clinical data offers significant potential for the development of personalized medicine. However, its use is severely restricted by the General Data Protection Regulation (GDPR), especially for small cohorts with rare diseases. High-quality, structured data is essential for the development of predictive medical AI. In this case study, we propose a novel, multi-stage approach to secure AI training: (1) The model is designed on a simulated clinical knowledge graph (cKG). This graph is used exclusively to represent the structural characteristics of the real cKG without revealing any sensitive content. (2) The model is then integrated into the FeatureCloud (FC) federated learning framework, where it is prepared in a single-client configuration within a protected execution environment. (3) Training then takes place within the hospital environment on the real cKG, either under the direct supervision of hospital staff or via a fully automated pipeline controlled by the hospital. (4) Finally, verified evaluation scripts are executed, which only return aggregated performance metrics. This enables immediate performance feedback without sensitive patient data or individual predictions, leaving the clinic. A fundamental element of this approach involves the incorporation of a cKG, which serves to organize multi-omics and patient data within the context of real-world hospital environments. This approach was successfully validated during the TUM.ai Makeathon 2024 (TUMaiM24) challenge set by the Dr. von Hauner Children's Hospital (HCH-LMU): 50 students developed models for patient classification and diagnosis without access to real data. Deploying secure algorithms via federated frameworks, such as the FC framework, could be a practical way of achieving privacy-preserving AI in healthcare.