Evaluating the quality of process models discovered from event logs is a fundamental challenge in process mining. Traditional evaluation relies on conformance metrics such as fitness and precision, which are highly sensitive to noise and deviations in event logs and therefore often fail to give a consistent assessment of discovery algorithms. We introduce a model-centric evaluation framework that combines node embeddings with Procrustes alignment to enable cross-graph comparability, since embeddings derived from different graphs reside in distinct vector spaces. The proposed PetriNetGraph method transforms Petri net process models into graph representations compatible with embedding algorithms. Comparing the node embeddings of ground-truth and discovered models through a parameterized cosine distance yields a unified and bounded metric for evaluating process discovery across datasets and methods. We evaluate the framework under static and context-aware scenarios to examine how prior knowledge of activity existence influences the assessment of structural similarity. The framework also integrates a compliance checking mechanism that localizes deviations at the activity level and an entropy-regularized node distance aggregation function that quantifies global deviations across the model. Experiments on nine publicly available event logs show that the approach provides a reliable embedding-based conformance indicator that reflects the behavior of fitness and precision. Experiments on synthetic logs with controlled noise levels confirm that it is substantially more robust to log deviations than traditional conformance metrics, PetriNet2Vec, and its dynamic-window and Procrustes-aligned variants, while remaining sensitive to process model degradation. All implementation details and datasets are publicly available.

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