Journal Article

Development of a machine learning model to predict mild cognitive impairment using natural language processing in the absence of screening

Penfold, Robert B., Thompson, Ella, Pabiniak, Chester, Johnson, Eric, Glass, Ashley MH, Arrighi, H. Michael, Cronkite, David J., Dodd, Tammy, Carrell, David S., Stang, Paul E.

2022

Overview

Background Patients and their loved ones often report symptoms or complaints of cognitive decline that clinicians note in free clinical text, but no structured screening or diagnostic data are recorded. These symptoms/complaints may be signals that predict who will go on to be diagnosed with mild cognitive impairment (MCI) and ultimately develop Alzheimer’s Disease or related dementias. Our objective was to develop a natural language processing system and prediction model for identification of MCI from clinical text in the absence of screening or other structured diagnostic information. Methods There were two populations of patients: 1794 participants in the Adult Changes in Thought (ACT) study and 2391 patients in the general population of Kaiser Permanente Washington. All individuals had standardized cognitive assessment scores. We excluded patients with a diagnosis of Alzheimer’s Disease, Dementia or use of donepezil. We manually annotated 10,391 clinic notes to train the NLP model. Standard Python code was used to extract phrases from notes and map each phrase to a cognitive functioning concept. Concepts derived from the NLP system were used to predict future MCI. The prediction model was trained on the ACT cohort and 60% of the general population cohort with 40% withheld for validation. We used a least absolute shrinkage and selection operator logistic regression approach (LASSO) to fit a prediction model with MCI as the prediction target. Using the predicted case status from the LASSO model and known MCI from standardized scores, we constructed receiver operating curves to measure model performance. Results Chart abstraction identified 42 MCI concepts. Prediction model performance in the validation data set was modest with an area under the curve of 0.67. Setting the cutoff for correct classification at 0.60, the classifier yielded sensitivity of 1.7%, specificity of 99.7%, PPV of 70% and NPV of 70.5% in the validation cohort. Discussion and conclusion Although the sensitivity of the machine learning model was poor, negative predictive value was high, an important characteristic of models used for population-based screening. While an AUC of 0.67 is generally considered moderate performance, it is also comparable to several tests that are widely used in clinical practice.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Alzheimer Disease - diagnosis / Alzheimer's disease / Cognition & reasoning / Cognition disorders / Cognitive ability / Cognitive Dysfunction - diagnosis / Computational linguistics / Data warehouses / Dementia / Dementia disorders / Diagnostic systems / Donepezil / Early identification / Electronic health records / Enrollments / Geriatrics / Health Informatics / Health services utilization / Humans / Impairment / Information Systems and Communication Service / Language / Language processing / Learning algorithms / Machine Learning / Management of Computing and Information Systems / Mass Screening / MCI / Medicine / Medicine & Public Health / Memory / Mild cognitive impairment / Natural language interfaces / Natural Language Processing / Neurodegenerative diseases / NLP / Patients / Population / Prediction models / Predictions / Primary care / Research Article / Risk factors / Sensitivity / Signs and symptoms / Statistical models