Transfer learning improves resting-state functional connectivity pattern analysis using convolutional neural networks

Abstract Background Deep learning is gaining importance in the prediction of cognitive states and brain pathology based on neuroimaging data. Including multiple hidden layers in artificial neural networks enables unprecedented predictive power; however, the proper training of deep neural networks requires thousands of exemplars. Collecting this amount of data is not feasible in typical neuroimaging experiments. A handy solution to this problem, which has largely fallen outside the scope of deep learning applications in neuroimaging, is to repurpose deep networks that have already been trained on large datasets by fine-tuning them to target datasets/tasks with fewer exemplars. Here, we investigated how this method, called transfer learning, can aid age category classification and regression based on brain functional connectivity patterns derived from resting-state functional magnetic resonance imaging. We trained a connectome-convolutional neural network on a larger public dataset and then examined how the knowledge learned can be used effectively to perform these tasks on smaller target datasets collected with a different type of scanner and/or imaging protocol and pre-processing pipeline. Results Age classification on the target datasets benefitted from transfer learning. Significant improvement (∼9%–13% increase in accuracy) was observed when the convolutional layers’ weights were initialized based on the values learned on the public dataset and then fine-tuned to the target datasets. Transfer learning also appeared promising in improving the otherwise poor prediction of chronological age. Conclusions Transfer learning is a plausible solution to adapt convolutional neural networks to neuroimaging data with few exemplars and different data acquisition and pre-processing protocols.