Dataset Information

Temporal condition pattern mining in large, sparse electronic health record data: A case study in characterizing pediatric asthma.

ABSTRACT: OBJECTIVE:This study introduces a temporal condition pattern mining methodology to address the sparse nature of coded condition concept utilization in electronic health record data. As a validation study, we applied this method to reveal condition patterns surrounding an initial diagnosis of pediatric asthma. MATERIALS AND METHODS:The SPADE (Sequential PAttern Discovery using Equivalence classes) algorithm was used to identify common temporal condition patterns surrounding the initial diagnosis of pediatric asthma in a study population of 71 824 patients from the Children's Hospital of Philadelphia. SPADE was applied to a dataset with diagnoses coded using International Classification of Diseases (ICD) concepts and separately to a dataset with the ICD codes mapped to their corresponding expanded diagnostic clusters (EDCs). Common temporal condition patterns surrounding the initial diagnosis of pediatric asthma ascertained by SPADE from both the ICD and EDC datasets were compared. RESULTS:SPADE identified 36 unique diagnoses in the mapped EDC dataset, whereas only 19 were recognized in the ICD dataset. Temporal trends in condition diagnoses ascertained from the EDC data were not discoverable in the ICD dataset. DISCUSSION:Mining frequent temporal condition patterns from large electronic health record datasets may reveal previously unknown associations between diagnoses that could inform future research into causation or other relationships. Mapping sparsely coded medical concepts into homogenous groups was essential to discovering potentially useful information from our dataset. CONCLUSIONS:We expect that the presented methodology is applicable to the study of diagnostic trajectories for other clinical conditions and can be extended to study temporal patterns of other coded medical concepts such as medications and procedures.

SUBMITTER: Campbell EA

PROVIDER: S-EPMC7075539 | biostudies-literature | 2020 Apr

REPOSITORIES: biostudies-literature

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Temporal condition pattern mining in large, sparse electronic health record data: A case study in characterizing pediatric asthma.

Campbell Elizabeth A EA Bass Ellen J EJ Masino Aaron J AJ

Journal of the American Medical Informatics Association : JAMIA 20200401 4

<h4>Objective</h4>This study introduces a temporal condition pattern mining methodology to address the sparse nature of coded condition concept utilization in electronic health record data. As a validation study, we applied this method to reveal condition patterns surrounding an initial diagnosis of pediatric asthma.<h4>Materials and methods</h4>The SPADE (Sequential PAttern Discovery using Equivalence classes) algorithm was used to identify common temporal condition patterns surrounding the ini ...[more]

PMID: 32049282

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Project description:Background:Polycystic ovary syndrome (PCOS) is characterized by hyperandrogenemia, oligo-anovulation, and numerous ovarian cysts. Hospital electronic medical records provide an avenue for investigating polycystic ovary morphology commonly seen in PCOS at a large scale. The purpose of this study was to develop and evaluate the performance of two machine learning text algorithms, for classification of polycystic ovary morphology (PCOM) in pelvic ultrasounds. Methods:Pelvic ultrasound reports from patients at Boston Medical Center between October 1, 2003 and December 12, 2016 were included for analysis, which resulted in 39,093 ultrasound reports from 25,535 unique women. Following the 2003 Rotterdam Consensus Criteria for polycystic ovary syndrome, 2000 randomly selected ultrasounds were expert labeled for PCOM status as present, absent, or unidentifiable (not able to be determined from text alone). An ovary was marked as having PCOM if there was mention of numerous peripheral follicles or if the volume was greater than 10?ml in the absence of a dominant follicle or other confounding pathology. Half of the labeled data was used to develop and refine the algorithms, and the other half was used as a test set for evaluating its accuracy. Results:On the evaluation set of 1000 random US reports, the accuracy of the classifiers were 97.6% (95% CI: 96.5, 98.5%) and 96.1% (94.7, 97.2%). Both models were more adept at identifying PCOM-absent ultrasounds than either PCOM-unidentifiable or PCOM-present ultrasounds. The two classifiers estimated prevalence of PCOM within the whole set of 39,093 ultrasounds to be 44% PCOM-absent, 32% PCOM-unidentifiable, and 24% PCOM-present. Conclusions:Although accuracy measured on the test set and inter-rater agreement between the two classifiers (Cohen's Kappa?=?0.988) was high, a major limitation of our approach is that it uses the ultrasound report text as a proxy and does not directly count follicles from the ultrasound images themselves.

Project description:BackgroundAsthma exacerbation leading to emergency department (ED) visit is prevalent, an indicator of poor control of asthma, and is a potentially preventable clinical outcome.ObjectiveWe propose to utilize multiple data elements available in electronic medical records (EMRs) and claims database to create separate algorithms with high validity for clinical and research purposes to identify asthma exacerbation-related ED visit among the general population.MethodsWe performed a retrospective study with inclusion criteria of patients aged 4 to 40 years, a visit to Geisinger ED from January 1, 2006, to October 28, 2013, with asthma on their problem list. Different electronic data elements including chief complaints, vitals, season, smoking, medication use, and discharge diagnoses were obtained to create the algorithm. A stratified random sample was generated to select the charts for review. Chart review was performed to classify patients with asthma-related ED visit, that is, the gold standard. Two reviewers performed the chart review and validation was done on a small subset.ResultsThere were 966 eligible ED visits in the EMR sample and 731 in the claims sample. Agreement between reviewers was 95.45% and kappa statistic was 0.91. Mean age of the EMR sample was 22 years, and mostly white (93%). Multiple models conventionally used in studies were evaluated and the final model chosen included principal diagnosis, bronchodilator, and steroid use for both algorithms, chief complaints for EMR, and secondary diagnosis for claims. Area under the curve was 0.93 (95% confidence interval: 0.91-0.94) and 0.94 (0.93-0.96), respectively, for EMR and claims data, with positive predictive value of > 94%. The algorithms are visually presented using nomograms.ConclusionWe were able to develop two separate algorithms for EMR and claims to identify asthma exacerbation-related ED visit with excellent diagnostic ability and varying discrimination threshold for clinical and research purposes.

Dataset Information

Temporal condition pattern mining in large, sparse electronic health record data: A case study in characterizing pediatric asthma.

Publications

Temporal condition pattern mining in large, sparse electronic health record data: A case study in characterizing pediatric asthma.

Similar Datasets

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