Structure-Aware Message Passing on Petri Nets through Directed Walks and Incidence Diffusion

Process discovery is one of the central challenges in process mining. Petri nets are particularly attractive because simple local constructs can express complex behavior, including concurrency. While their global behavior may be difficult to analyze, individual places can be efficiently characterized using monotonic properties, enabling bottom-up discovery. Unlike top-down approaches such as the Inductive Miner, which rely on predefined constructs for sequences, choices, loops, and concurrency, our approach allows such structures to emerge organically and can exploit the full expressive power of Petri nets, including free-choice constructs and long-term dependencies. The main challenge is the exponential number of candidate places and their combinations. We present the SPECpp framework which implements strategies to obtain high-quality models under time and resource constraints. SPECpp supports rapid experimentation and is used to evaluate these strategies using both synthetic and real-life event data.

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.

Petri nets have been used to describe chemical processes such as reactions.They map well to chemistry: Places are the bonds between atoms and the free valence of each atom, a token is a unit of bond order, a transition forms or breaks a bond, the conserved quantities are the valence budgets of the atoms, and the enabling rule is the valence rule. These semantics are not guaranteed by learned models of reactions or neural networks that are built on Petri nets that use the net as a scaffold for message passing. Here, we ask what architecture remains a Petri net for every value of its weights. We find the answer in the theory, where all semantics of a net share the firing form $m^\prime=m+Cσ$, locality, as enabling reads only the inputs of a transition, and the enabling rule, and we prove that conservation forces the firing form and that non-negativity forces the enabling rule on local rate laws. This leaves free the rate law, which is the propensity of each transition to fire. We introduce Neural Petri Flow, which learns this rate law, or a readout for classification, and hard-wires the rest as parameter-free layers. On what we denote a valence net, atom mapping, reaction classification, and forward prediction become three tasks on one firing vector. Without training, the minimum firing vector maps 88.8% of the curated Golden set against 85.6% for RXNMapper, and 88.7 against 77.9% of the enzymatic reactions of EnzymeMap. On USPTO-480K, NPF trained on these firing vectors predicts 87.7% of the products and 67.4% when trained on a 1% subset of the training reactions. EC numbers of ECREACT are predicted at the third level for 90.2% of reactions, 5.6 points ahead of the best published method. With electrons as tokens, the same token game predicts 90.5% of the elementary steps of FlowER first, ahead of the published baseline, and every top-1 prediction is a valid molecule without a filter.