Thanks for your interest in HTM and asking on the forum.
I’m not very familiar with the reasons API. But I do think that is the way to go. Maybe another forum member can help.
You predict all of them. A standard HTM network is composed with 2 layers. A SP, which reduces noise and unneeded information. And a TM, which predicts the next time step. Given a predicted SDR, you can ask SP to walk back it’s synapses to reconstruct the input field.
Unfortunately staking layers in NuPIC although is doable, it will not give you any extra performance in standard HTM. I (and other community members) am working on an implementation of the thousand brains theory which will allow multiple cortical columns to work together. But unlike staking CNN layers and extracting higher and higher level features, it utilizes multiple cortical columns to predicting simultaneously.