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Leveraging profiling to bridge healthcare silos for federated analyses

Barret, Nelly

Publisher
Zenodo
DOI
10.5281/zenodo.17642200
Repository
zenodo.org
Language
en

Abstract

The unprecedented creation, use and share of data around the world has led to new applications and economic opportunities. This data is often large, heterogeneous at a schema and model level, and more or less structured. To bring more order, the World Wide Web consortium recommends sharing data as RDF graphs, which has been mostly adopted in the Open Data initiative, but many other formats are used in practice. Moreover, data is now scattered across places and owners (enterprise silos, open data, Big Tech clouds, etc.) and this adds to the complexity of managing, joining, processing and using various data together. Finally, end users, such as domain experts or decision makers, need tools to generate tangible results they can rely on and share. In this presentation, I will present post-doctoral work on this domain. I will show how to homogenize healthcare silos in order to run various federated learning tasks on the underlying data.

Full text

Leveraging profiling to bridge healthcare silos for federated analyses Nelly Barret, Anna Bernasconi, Cinzia Cappiello, Giacomo Palu, and Pietro Pinoli Politecnico di Milano June 27th, 2025 Context: Federated Learning for healthcare 27/06/2025 Profiling healthcare silos - Nelly Barret et al. Which genes favor intelligence disability in children? How do genetic and clinical data correlate in eye dystrophies? 2/18 Context: Federated Learning for healthcare 27/06/2025 Profiling healthcare silos - Nelly Barret et al. Which genes favor intelligence disability in children? How do genetic and clinical data correlate in eye dystrophies? I-ETL [1] [1] N. Barret et al. I-ETL: an interoperability-aware health (meta)data pipeline to enable federated analyses. Under review. 3/18 Context: Federated Learning for healthcare 27/06/2025 Profiling healthcare silos - Nelly Barret et al. Which genes favor intelligence disability in children? How do genetic and clinical data correlate in eye dystrophies? I-ETL [1] [1] N. Barret et al. I-ETL: an interoperability-aware health (meta)data pipeline to enable federated analyses. Under review. [2] O. Beyan, et al. Distributed analytics on sensitive medical data: the personal health train. Data Intelligence. 2020 Jan 1;2(1-2):96-107. PHT [2] 4/18 Modeling and profiling healthcare silos 27/06/2025 Profiling healthcare silos - Nelly Barret et al. 5/18 Modeling and profiling healthcare silos 27/06/2025 Profiling healthcare silos - Nelly Barret et al. FAIRification 6/18 FAIRification in a nutshell For a given hospital: 27/06/2025 Profiling healthcare silos - Nelly Barret et al. Data Any patient data (real or synthetic) Metadata Any information providing context/semantic on the data I-ETL Extract Transform Load FAIR database 7/18 Our FAIR data model Modeling and profiling healthcare silos 27/06/2025 Profiling healthcare silos - Nelly Barret et al. 8/18 Problem statement How to help users discover homogenized silos to design FL algorithms? We aim at a catalogue which: •General and adaptive •Discover data and metadata 27/06/2025 Profiling healthcare silos - Nelly Barret et al. 9/18 Building the global catalogue Combine individual catalogues of each silo: •Union of all the individual catalogues (one per hospital) •Easy thanks to our general catalogue model •Allows to implement visualisations for all centers at a time When hospitals update their data: •Recompute the underlying catalogue •Replace the old with the new individual catalogue 27/06/2025 Profiling healthcare silos - Nelly Barret et al. 16/18 Lessons learnt and our vision •Existing works: lack of generality, approach per use-case •FL requires highly homogenized infrastructures •Balance generalization vs. domain knowledge •Data and metadata are both necessary Abstracting current conceptual models is promising: → Reuse, use case-agnostic pipelines, various settings → Easy exploration of large and complex silos 27/06/2025 Profiling healthcare silos - Nelly Barret et al. 17/18 Thank you! 27/06/2025 Profiling healthcare silos - Nelly Barret et al. https://www.better-health-project.eu/ Next steps: silo template queries, LLM-assisted queries, … 18/18