Predicting Phase 3 Clinical Trial Results by Modeling Phase 2 Clinical Trial Subject Level Data Using Deep Learning

Youran Qi, Qi Tang

Abstract:

Predicting Phase 3 clinical trial results is a critical step of Go/No-Go decision making
and Phase 3 trial design optimization. To predict the overall treatment effect for patients
enrolled into a Phase 3 trial, we propose a framework consisting of two models. First, an
individual trough pharmacokinetic concentration (Ctrough) model is developed to predict
the trough pharmacokinetic concentration for a potentially new treatment regime planned
for Phase 3. Second, an individual treatment effect model is built to model the relationship
between patient baseline characteristics, Ctrough and clinical outcomes. These two models
are combined together to predict Phase 3 clinical trial results. Since the clinical outcomes
to be predicted are longitudinal and the predictors are a mix of time-invariant and time-variant
variables, a novel neural network, Residual Semi-Recurrent Neural Network, is
developed for both models. The proposed framework is applied in a post-hoc prediction of
Phase 3 clinical trial results, and it outperforms the traditional method.