A user interface (UI), data structures and algorithms facilitate programming, analyzing, debugging, embedding, and/or modifying problems that are embedded or to be embedded on an analog processor (e.g., quantum processor), increasing computational efficiency and/or accuracy of problem solutions. The UI provides graph representations (e.g., source graph, target graph and correspondence therebetween) with nodes and edges which may map to hardware components (e.g., qubits, couplers) of the analog processor. Characteristics of solutions are advantageously represented spatially associated (e.g., overlaid or nested) with characteristics of a problem. Characteristics (e.g., bias state) may be represented by color, pattern, values, icons. Issues (e.g., broken chains) may be detected and alerts provided. Problem representations may be modified via the UI, and a computer system may autonomously generate new instances of the problem representation, update data structures, embed the new instance and cause the new instance to be executed by the analog processor.