Reading through the paper it seems obvious to me (please correct me if I am wrong) that that the structure of the Input Layer of a column is equivalent to the (mini)Column, Cells, Connections, etc. objects of the NUPIC library and are acted on by the standard SP and TM algorithms:
In the first set of simulations the input layer of each column consists of 150 mini-columns, with 16 cells per mini-column, for a total of 2,400 cells.
I do not see, though, a corresponding data structure/algorithm for the Output layer of the column as described in the paper in the NUPIC code:
The output layer of each column consists of 4,096 cells, which are not arranged in mini-columns.
Is there code for this paper that illustrates the Output Layer? If not, is there any guidance/psuedo code for connecting the Output Layer to the Input Layer and for growing/removing connections to other Output cells in the column or other columns?