Modern IT infrastructures, especially IoT and cyber-physical systems, require systematic and repeatable security assessment methods. A persistent challenge concerns the correctness and completeness of the system model underlying such analyses, which directly affect the quality of threat modeling and penetration test planning. Existing model-based approaches support these activities, but rarely ensure that the adopted model is both structurally valid and representative of the real system. This paper addresses this gap by introducing a formal modeling framework and extending a security assessment methodology (ESSecA) with a cyclical refinement process. At its core lies the Multi-purpose Application Composition Model (MACM), a property-graph formalism equipped with a schema and a set of syntactic and semantic constraints that define the space of admissible models. These constraints are automatically verified through formal checks (e.g., Cypher queries and Neo4j triggers), enabling automated verification of model correctness throughout the assessment lifecycle. As a result, any model accepted by the framework is guaranteed to comply with the rules of the modeling system. The cyclical refinement process complements this by addressing model completeness. Penetration testing results are iteratively reintegrated into the model, enriching it with newly discovered elements and interactions. This produces progressively more accurate system representations, which in turn yield more comprehensive threat models and increasingly precise penetration test plans, effectively mitigating grey-box limitations. The contribution is demonstrated through two case studies: the eWeLink IoT ecosystem, illustrating MACM’s modeling and validation capabilities, and the JetRacer autonomous vehicle platform, showcasing the full iterative methodology. Overall, the proposed approach combines a formal modeling system with a cyclic refinement process that exploits such formal guarantees to progressively enhance model completeness, ultimately strengthening threat modeling and penetration test planning.
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