A Spark-based workflow for probabilistic record linkage of healthcare data *

ABSTRACT Several areas, such as science, economics, finance, business intelligence, health, and others are exploring big data as a way to produce new information, make better decisions, and move forward their related technologies and systems. Specifically in health, big data represents a challenging problem due to the poor quality of data in some circumstances and the need to retrieve, aggregate, and process a huge amount of data from disparate databases. In this work, we focused on Brazilian Public Health System and on large databases from Ministry of Health and Ministry of Social Development and Hunger Alleviation. We present our Spark-based approach to data processing and probabilistic record linkage of such databases in order to produce very accurate data marts. These data marts are used by statisticians and epidemiologists to assess the effectiveness of conditional cash transfer programs to poor families in respect with the occurrence of some diseases (tuberculosis, leprosy, and AIDS). The case study we made as a proof-of-concept presents a good performance with accurate results. For comparison, we also discuss an OpenMP-based implementation

Cloud-Scale Entity Resolution: Current State and Open Challenges

Entity resolution (ER) is a process to identify records in information systems, which refer to the same real-world entity. Because in the two recent decades the data volume has grown so large, parallel techniques are called upon to satisfy the ER requirements of high performance and scalability. The development of parallel ER has reached a relatively prosperous stage, and has found its way into several applications. In this work, we first comprehensively survey the state of the art of parallel ER approaches. From the comprehensive overview, we then extract the classification criteria of parallel ER, classify and compare these approaches based on these criteria. Finally, we identify open research questions and challenges and discuss potential solutions and further research potentials in this field

Accuracy of probabilistic record linkage applied to the Brazilian 100 million cohort project

This paper presents some current results obtained from our probabilistic record linkage methods applied to the integration of a 100 million cohort composed by socioeconomic data with health databases

A Machine Learning Trainable Model to Assess the Accuracy of Probabilistic Record Linkage

Record linkage (RL) is the process of identifying and linking data that relates to the same physical entity across multiple heterogeneous data sources. Deterministic linkage methods rely on the presence of common uniquely identifying attributes across all sources while probabilistic approaches use non-unique attributes and calculates similarity indexes for pair wise comparisons. A key component of record linkage is accuracy assessment — the process of manually verifying and validating matched pairs to further refine linkage parameters and increase its overall effectiveness. This process however is time-consuming and impractical when applied to large administrative data sources where millions of records must be linked. Additionally, it is potentially biased as the gold standard used is often the reviewer’s intuition. In this paper, we present an approach for assessing and refining the accuracy of probabilistic linkage based on different supervised machine learning methods (decision trees, naïve Bayes, logistic regression, random forest, linear support vector machines and gradient boosted trees). We used data sets extracted from huge Brazilian socioeconomic and public health care data sources. These models were evaluated using receiver operating characteristic plots, sensitivity, specificity and positive predictive values collected from a 10-fold cross-validation method. Results show that logistic regression outperforms other classifiers and enables the creation of a generalized, very accurate model to validate linkage results

Probabilistic integration of large Brazilian socioeconomic and clinical databases

The integration of disparate large and heterogeneous socioeconomic and clinical databases is considered essential to capture and model longitudinal and social aspects of diseases. However, such integration is challenging: databases are stored in disparate locations, make use of different identifiers, have variable data quality, record information in bespoke purpose-specific formats and have different levels of metadata. Novel computational methods are required to integrate them and enable their statistical analyses for epidemiological research purposes. In this paper, we describe a probabilistic approach for constructing a very large population-based cohort comprised of 114 million individuals using linkages between clinical databases from the National Health System and administrative databases from governmental social programmes. We present our data integration model for creating data marts (epidemiological data) and discuss our evaluation results in controlled and uncontrolled scenarios, which demonstrate that our model and tools achieve high accuracy (minimum of 91%) in different probabilistic data integration scenarios

Data Infrastructure for Medical Research

While we are witnessing rapid growth in data across the sciences and in many applications, this growth is particularly remarkable in the medical domain, be it because of higher resolution instruments and diagnostic tools (e.g. MRI), new sources of structured data like activity trackers, the wide-spread use of electronic health records and many others. The sheer volume of the data is not, however, the only challenge to be faced when using medical data for research. Other crucial challenges include data heterogeneity, data quality, data privacy and so on. In this article, we review solutions addressing these challenges by discussing the current state of the art in the areas of data integration, data cleaning, data privacy, scalable data access and processing in the context of medical data. The techniques and tools we present will give practitioners — computer scientists and medical researchers alike — a starting point to understand the challenges and solutions and ultimately to analyse medical data and gain better and quicker insights

Scalable Data Integration for Linked Data

Linked Data describes an extensive set of structured but heterogeneous datasources where entities are connected by formal semantic descriptions. In thevision of the Semantic Web, these semantic links are extended towards theWorld Wide Web to provide as much machine-readable data as possible forsearch queries. The resulting connections allow an automatic evaluation to findnew insights into the data. Identifying these semantic connections betweentwo data sources with automatic approaches is called link discovery. We derivecommon requirements and a generic link discovery workflow based on similaritiesbetween entity properties and associated properties of ontology concepts. Mostof the existing link discovery approaches disregard the fact that in times ofBig Data, an increasing volume of data sources poses new demands on linkdiscovery. In particular, the problem of complex and time-consuming linkdetermination escalates with an increasing number of intersecting data sources.To overcome the restriction of pairwise linking of entities, holistic clusteringapproaches are needed to link equivalent entities of multiple data sources toconstruct integrated knowledge bases. In this context, the focus on efficiencyand scalability is essential. For example, reusing existing links or backgroundinformation can help to avoid redundant calculations. However, when dealingwith multiple data sources, additional data quality problems must also be dealtwith. This dissertation addresses these comprehensive challenges by designingholistic linking and clustering approaches that enable reuse of existing links.Unlike previous systems, we execute the complete data integration workflowvia a distributed processing system. At first, the LinkLion portal will beintroduced to provide existing links for new applications. These links act asa basis for a physical data integration process to create a unified representationfor equivalent entities from many data sources. We then propose a holisticclustering approach to form consolidated clusters for same real-world entitiesfrom many different sources. At the same time, we exploit the semantic typeof entities to improve the quality of the result. The process identifies errorsin existing links and can find numerous additional links. Additionally, theentity clustering has to react to the high dynamics of the data. In particular,this requires scalable approaches for continuously growing data sources withmany entities as well as additional new sources. Previous entity clusteringapproaches are mostly static, focusing on the one-time linking and clustering ofentities from few sources. Therefore, we propose and evaluate new approaches for incremental entity clustering that supports the continuous addition of newentities and data sources. To cope with the ever-increasing number of LinkedData sources, efficient and scalable methods based on distributed processingsystems are required. Thus we propose distributed holistic approaches to linkmany data sources based on a clustering of entities that represent the samereal-world object. The implementation is realized on Apache Flink. In contrastto previous approaches, we utilize efficiency-enhancing optimizations for bothdistributed static and dynamic clustering. An extensive comparative evaluationof the proposed approaches with various distributed clustering strategies showshigh effectiveness for datasets from multiple domains as well as scalability on amulti-machine Apache Flink cluster