The method seems interesting and potentially useful, but I'm skeptical of the evaluation for two reasons. First, R2 is not a fair way to compare simple (linear

The method seems interesting and potentially useful, but I'm skeptical of the evaluation for two reasons. First, R2 is not a fair way to compare simple (linear regression, kNN) and complex (deep neural net) models, as it will always prefer a more complex model. Second, there was no indication how the error was computed. Was there a hold out set or cross-validation for accuracy? Without any more details, I have to assume they measured error on the the training data, which will also prefer the more complex model. Also, as a public service announcement: "The authors are affiliated with Insilico Medicine, Inc, a commercial company developing differential pathway activation scoring-based and deep learned biomarkers of multiple diseases and aging and engaging in drug discovery and drug repurposing."