SCALPEL3: a scalable open-source library for healthcare claims databases

TL;DR

SCALPEL3 is a scalable, open-source framework built on Apache Spark that streamlines the analysis of large healthcare claims databases, enabling efficient data extraction, manipulation, and machine learning integration.

Contribution

It introduces a modular, scalable library suite for healthcare claims data analysis, improving efficiency and reproducibility over previous methods.

Findings

Successfully processed 14.5 million patients' data in under 49 minutes

Enabled complex concept extraction for large observational studies

Provided interactive tools for cohort analysis and data flow monitoring

Abstract

This article introduces SCALPEL3, a scalable open-source framework for studies involving Large Observational Databases (LODs). Its design eases medical observational studies thanks to abstractions allowing concept extraction, high-level cohort manipulation, and production of data formats compatible with machine learning libraries. SCALPEL3 has successfully been used on the SNDS database (see Tuppin et al. (2017)), a huge healthcare claims database that handles the reimbursement of almost all French citizens. SCALPEL3 focuses on scalability, easy interactive analysis and helpers for data flow analysis to accelerate studies performed on LODs. It consists of three open-source libraries based on Apache Spark. SCALPEL-Flattening allows denormalization of the LOD (only SNDS for now) by joining tables sequentially in a big table. SCALPEL-Extraction provides fast concept extraction from a big table such as the one produced by SCALPEL-Flattening. Finally, SCALPEL-Analysis allows interactive cohort manipulations, monitoring statistics of cohort flows and building datasets to be used with machine learning libraries. The first two provide a Scala API while the last one provides a Python API that can be used in an interactive environment. Our code is available on GitHub. SCALPEL3 allowed to extract successfully complex concepts for studies such as Morel et al (2017) or studies with 14.5 million patients observed over three years (corresponding to more than 15 billion healthcare events and roughly 15 TeraBytes of data) in less than 49 minutes on a small 15 nodes HDFS cluster. SCALPEL3 provides a sharp interactive control of data processing through legible code, which helps to build studies with full reproducibility, leading to improved maintainability and audit of studies performed on LODs.