> Plus, the author gives some good examples like pulse ox%, doctors and nurses are not at all concerned with or trained to record data in a way that makes sense to use programmatically. They're typically thinking only as if they're recording it for another human to read.

The unstructured doctor's notes may be where the best signal lies. Thet should be mostly uncorrupted by the billing/process related trash. Deep learning does not need data to be formatted to be read "programmatically", in fact it shines most on data that isn't.