A method may include receiving a graph-based model in a first format, including a static topology of the graph-based model. The method may also include encoding the graph-based model from the first format into a neural network topology optimizer (NNTO) readable format such that the topology of the encoded graph-based model is configured to be altered; creating a first group of entities based on at least a same portion of the encoded graph-based model; and performing a learning operation by tuning parameters of the first group of entities to produce an optimization score for each entity. Additionally, the method may include performing a validation operation; determining that an improvement in validation performance for at least one entity is within a threshold amount of improvement; selecting a solution entity; and adding the selected solution entity into the graph-based model in place of the same portion.