  Precision medicine for chronic diseases such as multiple sclerosis (MS)
involves choosing a treatment which best balances efficacy and side
effects/preferences for individual patients. Making this choice as early as
possible is important, as delays in finding an effective therapy can lead to
irreversible disability accrual. To this end, we present the first deep neural
network model for individualized treatment decisions from baseline magnetic
resonance imaging (MRI) (with clinical information if available) for MS
patients. Our model (a) predicts future new and enlarging T2 weighted (NE-T2)
lesion counts on follow-up MRI on multiple treatments and (b) estimates the
conditional average treatment effect (CATE), as defined by the predicted future
suppression of NE-T2 lesions, between different treatment options relative to
placebo. Our model is validated on a proprietary federated dataset of 1817
multi-sequence MRIs acquired from MS patients during four multi-centre
randomized clinical trials. Our framework achieves high average precision in
the binarized regression of future NE-T2 lesions on five different treatments,
identifies heterogeneous treatment effects, and provides a personalized
treatment recommendation that accounts for treatment-associated risk (e.g. side
effects, patient preference, administration difficulties).
