Embodiments of the present disclosure provide methods, apparatus, systems, computing devices, computing entities, and/or the like for generating a protocol recommendation for an application data object. In accordance with one embodiment, a method is provided comprising: extracting application codes from the application data object representing application codes; generating a graph representation data object that includes code nodes representing the application codes, and edges connecting code nodes to indicate an association between the code nodes; identifying a replaceable code node; extracting substitute code nodes from the graph representation data object; identifying a replacement configuration of the graph representation data object with the replaceable code node with one of the substitute code nodes; and generating the protocol recommendation based at least in part on the replacement configuration.