H2: A Dual Hybrid Semantic Data Lake Architecture for Medical Data Harmonization with Human-In-the-Loop verified, LLM Driven Metadata Annotation System

Abstract

Medical data, by its nature, exhibit a high degree of heterogeneity on multiple levels ranging from (a) different modalities like images, text and time series, (b) diverse tabular schemata introduced by institutions and (c) completely unstructured textual information data provided by healthcare professionals. Data lakes are often used in medical data storage to consolidate all heterogeneous diverse data in a single, central location, where it can be saved "as is", without the need to impose a schema like a data warehouse does. Despite their flexibility, though, data lakes are notorious for the "data swamp" failure. Thus, providing a reliable data harmonization mechanism through metadata, without compromising integrity or flexibility, is a real challenge. To this end, knowledge graphs have attracted attention since they provide a dynamic way to depict relationships without a rigid schema-on-write approach. Additionally, another rigorous task relies on the interoperability of data: application of appropriate ML techniques on such a diverse nature of data is not an easy task, as a domain expert must decide the efficacy of a method to a specific data type or dataset. Metadata annotation can aid by tagging applicable operations, however this requires manual intervention, not to mention the plethora of existing datasets which lack such information. To tackle both challenges, in this paper, we propose a semantic data lake architecture that promotes data harmonization and incorporates a generative annotation process (i.e. LLMs) of non-labeled metadata collections to support the application of meaningful ML techniques. Building on top of this approach, we create a higher level of knowledge, identifying suitability of data with respect to applicable ML operations based on their data nature...