Dataset Information

Feature engineering with clinical expert knowledge: A case study assessment of machine learning model complexity and performance.

ABSTRACT: Incorporating expert knowledge at the time machine learning models are trained holds promise for producing models that are easier to interpret. The main objectives of this study were to use a feature engineering approach to incorporate clinical expert knowledge prior to applying machine learning techniques, and to assess the impact of the approach on model complexity and performance. Four machine learning models were trained to predict mortality with a severe asthma case study. Experiments to select fewer input features based on a discriminative score showed low to moderate precision for discovering clinically meaningful triplets, indicating that discriminative score alone cannot replace clinical input. When compared to baseline machine learning models, we found a decrease in model complexity with use of fewer features informed by discriminative score and filtering of laboratory features with clinical input. We also found a small difference in performance for the mortality prediction task when comparing baseline ML models to models that used filtered features. Encoding demographic and triplet information in ML models with filtered features appeared to show performance improvements from the baseline. These findings indicated that the use of filtered features may reduce model complexity, and with little impact on performance.

SUBMITTER: Roe KD

PROVIDER: S-EPMC7179831 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Feature engineering with clinical expert knowledge: A case study assessment of machine learning model complexity and performance.

Roe Kenneth D KD Jawa Vibhu V Zhang Xiaohan X Chute Christopher G CG Epstein Jeremy A JA Matelsky Jordan J Shpitser Ilya I Taylor Casey Overby CO

PloS one 20200423 4

Incorporating expert knowledge at the time machine learning models are trained holds promise for producing models that are easier to interpret. The main objectives of this study were to use a feature engineering approach to incorporate clinical expert knowledge prior to applying machine learning techniques, and to assess the impact of the approach on model complexity and performance. Four machine learning models were trained to predict mortality with a severe asthma case study. Experiments to se ...[more]

PMID: 32324754

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Project description:BACKGROUND:With the growing adoption of the electronic health record (EHR) worldwide over the last decade, new opportunities exist for leveraging EHR data for detection of rare diseases. Rare diseases are often not diagnosed or delayed in diagnosis by clinicians who encounter them infrequently. One such rare disease that may be amenable to EHR-based detection is acute hepatic porphyria (AHP). AHP consists of a family of rare, metabolic diseases characterized by potentially life-threatening acute attacks and chronic debilitating symptoms. The goal of this study was to apply machine learning and knowledge engineering to a large extract of EHR data to determine whether they could be effective in identifying patients not previously tested for AHP who should receive a proper diagnostic workup for AHP. METHODS AND FINDINGS:We used an extract of the complete EHR data of 200,000 patients from an academic medical center and enriched it with records from an additional 5,571 patients containing any mention of porphyria in the record. After manually reviewing the records of all 47 unique patients with the ICD-10-CM code E80.21 (Acute intermittent [hepatic] porphyria), we identified 30 patients who were positive cases for our machine learning models, with the rest of the patients used as negative cases. We parsed the record into features, which were scored by frequency of appearance and filtered using univariate feature analysis. We manually choose features not directly tied to provider attributes or suspicion of the patient having AHP. We trained on the full dataset, with the best cross-validation performance coming from support vector machine (SVM) algorithm using a radial basis function (RBF) kernel. The trained model was applied back to the full data set and patients were ranked by margin distance. The top 100 ranked negative cases were manually reviewed for symptom complexes similar to AHP, finding four patients where AHP diagnostic testing was likely indicated and 18 patients where AHP diagnostic testing was possibly indicated. From the top 100 ranked cases of patients with mention of porphyria in their record, we identified four patients for whom AHP diagnostic testing was possibly indicated and had not been previously performed. Based solely on the reported prevalence of AHP, we would have expected only 0.002 cases out of the 200 patients manually reviewed. CONCLUSIONS:The application of machine learning and knowledge engineering to EHR data may facilitate the diagnosis of rare diseases such as AHP. Further work will recommend clinical investigation to identified patients' clinicians, evaluate more patients, assess additional feature selection and machine learning algorithms, and apply this methodology to other rare diseases. This work provides strong evidence that population-level informatics can be applied to rare diseases, greatly improving our ability to identify undiagnosed patients, and in the future improve the care of these patients and our ability study these diseases. The next step is to learn how best to apply these EHR-based machine learning approaches to benefit individual patients with a clinical study that provides diagnostic testing and clinical follow up for those identified as possibly having undiagnosed AHP.

Dataset Information

Feature engineering with clinical expert knowledge: A case study assessment of machine learning model complexity and performance.

Publications

Feature engineering with clinical expert knowledge: A case study assessment of machine learning model complexity and performance.

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