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Life sciences · Preprint
arXiv · October 21, 2026
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A common application of the process mining discipline is to connect observed event data with Petri nets, which are bipartite, directed graphical process models with rich formal underpinnings. Recent work learns vector representations of Petri nets to retrieve process models and relate them to event logs, but leaves implicit two key aspects hidden within the net's structure: directed cycles (process loops) and invariants recorded by the net's incidence matrix. We expose both of these to message-passing graph neural networks, through a positional encoding built from return probabilities of directed place-transition walks (PNRWPE), and through same-type messages gated by diffusion kernels of the incidence matrix (DA-PNGNN). Our constructions raise macro balanced accuracy in predicting the generation factors of the 96 Process Discovery Contest 2023 models from 0.751 to 0.796 with PNRWPE, which nearly doubles accuracy on process loops, and to 0.830 with DA-PNGNN, which, without retuning, also improves net-to-tree retrieval top-1 accuracy on the self-supervised ProcRosetta benchmark by 4.1 to 5.9 points.