UWB-Biocomputing / Graphitti

A project to facilitate construction of high-performance simulations of graph-structured systems.
https://uwb-biocomputing.github.io/Graphitti/
Apache License 2.0
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Remove sumation_map references from the 911 model implementation #485

Open jardiamj opened 1 year ago

jardiamj commented 1 year ago

The summation_map data structure is not used in the 911 models. right now, the references are present and initialized to avoid breaking the code in other parts but is should be removed to decouple the neural network model from the base classes.

jardiamj commented 1 year ago

@KamathScience, as per our conversation this evening I looked into removing the summation_map from the NG911 model. The following is what I found:

The addEdge method in AllEdges.cpp assumes that all models would have a summation_point by requiring it in the method's signature. This is the reason it is there even though is it not used nor needed.

My suggestion is to make addEdge and createEdge take only the edgeType, srcVertex, and destVertex to add the new edge. The method then would return the new edge index (iEdg) so that other parameters needed by specific models could be added after the edge has been created.

deltaT is not needed in the method's signature either because it is a Simulator's class member, making it in essence a global variable because of the singleton nature of the Simulator class.

Finally, the iEdg (edge index) is required by addEdge but in reality, we search for the first unused edge available for the destination vertex within it. We should return that index instead so it can be used to assign model-specific parameters to a given edge post-creation.