Machine Learning Predictive Models Can Improve Efficacy of Clinical Trials for Alzheimer's Disease

Abstract

Background: The ideal participants for Alzheimer's disease (AD) clinical trials would show cognitive decline in the absence of treatment (i.e., placebo arm) and also would be responsive to the therapeutic intervention being studied (i.e., drug arm). One strategy to boost the power of trials is to enroll individuals who are more likely to progress targeted using data-driven predictive models.

Objective: To investigate if machine learning (ML) models can effectively predict clinical disease progression (cognitive decline) in mild-to-moderate AD patients during the timeframe of a phase III clinical trial.

Methods: Data from 202 participants with a diagnosis of AD at baseline from the Alzheimer's Disease Neuroimaging Initiative (ADNI) was used to train ML classifiers that can differentiate between individuals who had declining cognitive function (DC) and individuals with stable cognitive function (SC). DC was defined as any downward change in the Alzheimer's Disease Assessment Scale cognitive subscale (ADAS-cog) score over 12 months of follow-up. SC was defined by the absence of decline in ADAS-cog. Trained models were applied to data from 77 participants from the placebo arm of the phase III trial of Semagacestat (LFAN study) to identify subgroups of SC versus DC.

Results: Only 74.8% of ADNI participants and 63.6% of LFAN participants had cognitive decline after one year of follow up. K-nearest neighbors (kNN) classifier had an accuracy of 68.3%, sensitivity of 80.1%, and specificity of 33.3% for identifying decliners in ADNI (training sample). In LFAN (validation sample), the model showed an overall accuracy of 61.3%, sensitivity of 65.5%, and specificity of 47.0% in identifying decliners at the 12 months of follow-up. The model had a positive predictive value of 80.8%, which was 17.2% more than the base prevalence of decliners.

Conclusions: Machine learning predictive models can be effectively used to boost the power of clinical trials by reducing the sample size.

Keywords: Alzheimer’s disease; clinical trial; cognitive decline; machine learning; predictive analytics.

Fig. 1.

Study design diagram and schematic illustration of training models and prediction of cognitive decline. Data from ADNI were used for training the models. Participants were dichotomized to two groups based on the longitudinal change in ADAS-cog score at 12 months: stable cognition (SC) and declining cognition (DC). Models were trained to classify participants of training data-set (Yellow block). Subsequently, participants from LFAN study were introduced to the newly developed model to predict if they will have decline in cognition or will remain cognitively stable in longitudinal follow-up (Orange block).