Dataset Information

Detecting Spatial Patterns of Disease in Large Collections of Electronic Medical Records Using Neighbor-Based Bootstrapping.

ABSTRACT: We introduce a method called neighbor-based bootstrapping (NB2) that can be used to quantify the geospatial variation of a variable. We applied this method to an analysis of the incidence rates of disease from electronic medical record data (International Classification of Diseases, Ninth Revision codes) for ?100 million individuals in the United States over a period of 8 years. We considered the incidence rate of disease in each county and its geospatially contiguous neighbors and rank ordered diseases in terms of their degree of geospatial variation as quantified by the NB2 method. We show that this method yields results in good agreement with established methods for detecting spatial autocorrelation (Moran's I method and kriging). Moreover, the NB2 method can be tuned to identify both large area and small area geospatial variations. This method also applies more generally in any parameter space that can be partitioned to consist of regions and their neighbors.

SUBMITTER: Patterson MT

PROVIDER: S-EPMC5647508 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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Publications

Detecting Spatial Patterns of Disease in Large Collections of Electronic Medical Records Using Neighbor-Based Bootstrapping.

Patterson Maria T MT Grossman Robert L RL

Big data 20170901 3

We introduce a method called neighbor-based bootstrapping (NB2) that can be used to quantify the geospatial variation of a variable. We applied this method to an analysis of the incidence rates of disease from electronic medical record data (International Classification of Diseases, Ninth Revision codes) for ∼100 million individuals in the United States over a period of 8 years. We considered the incidence rate of disease in each county and its geospatially contiguous neighbors and rank ordered ...[more]

PMID: 28933946

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Project description:Post-market medical device surveillance is a challenge facing manufacturers, regulatory agencies, and health care providers. Electronic health records are valuable sources of real-world evidence for assessing device safety and tracking device-related patient outcomes over time. However, distilling this evidence remains challenging, as information is fractured across clinical notes and structured records. Modern machine learning methods for machine reading promise to unlock increasingly complex information from text, but face barriers due to their reliance on large and expensive hand-labeled training sets. To address these challenges, we developed and validated state-of-the-art deep learning methods that identify patient outcomes from clinical notes without requiring hand-labeled training data. Using hip replacements-one of the most common implantable devices-as a test case, our methods accurately extracted implant details and reports of complications and pain from electronic health records with up to 96.3% precision, 98.5% recall, and 97.4% F1, improved classification performance by 12.8-53.9% over rule-based methods, and detected over six times as many complication events compared to using structured data alone. Using these additional events to assess complication-free survivorship of different implant systems, we found significant variation between implants, including for risk of revision surgery, which could not be detected using coded data alone. Patients with revision surgeries had more hip pain mentions in the post-hip replacement, pre-revision period compared to patients with no evidence of revision surgery (mean hip pain mentions 4.97 vs. 3.23; t?=?5.14; p?<?0.001). Some implant models were associated with higher or lower rates of hip pain mentions. Our methods complement existing surveillance mechanisms by requiring orders of magnitude less hand-labeled training data, offering a scalable solution for national medical device surveillance using electronic health records.

Dataset Information

Detecting Spatial Patterns of Disease in Large Collections of Electronic Medical Records Using Neighbor-Based Bootstrapping.

Publications

Detecting Spatial Patterns of Disease in Large Collections of Electronic Medical Records Using Neighbor-Based Bootstrapping.

Similar Datasets

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