Making head and neck cancer clinical data Findable-Accessible-Interoperable-Reusable to support multi-institutional collaboration and federated learning
Varsha Gouthamchand, Ananya Choudhury, Frank J P Hoebers, Frederik W. R. Wesseling, Mattea L. Welch, Sejin Kim, Joanna Kaźmierska, Andre L.A.J. Dekker, Benjamin Haibe‐Kains, Johan van Soest, Leonard Wee · BJR|Artificial Intelligence · 2024
Objectives: Federated learning (FL) is a group of methodologies where statistical modelling can be performed without exchanging identifiable patient data between cooperating institutions. To realize its potential for AI development on clinical data, a number of bottlenecks need to be addressed. One of these is making data Findable-Accessible-Interoperable-Reusable (FAIR). The primary aim of this work is to show that tools making data FAIR allow consortia to collaborate on privacy-aware data exploration, data visualization, and training of models on each other's original data. Methods: We propose a "Schema-on-Read" FAIR-ification method that adapts for different (re)analyses without needing to change the underlying original data. The procedure involves (1) decoupling the contents of the data from its schema and database structure, (2) annotation with semantic ontologies as a metadata layer, and (3) readout using semantic queries. Open-source tools are given as Docker containers to help local investigators prepare their data on-premises. Results: We created a federated privacy-preserving visualization dashboard for case mix exploration of 5 distributed datasets with no common schema at the point of origin. We demonstrated robust and flexible prognostication model development and validation, linking together different data sources-clinical risk factors and radiomics. Conclusions: Our procedure leads to successful (re)use of data in FL-based consortia without the need to impose a common schema at every point of origin of data. Advances in knowledge: This work supports the adoption of FL within the healthcare AI community by sharing means to make data more FAIR.