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Clinical pathways, structured plans for managing specific conditions, are critical but challenging to design and update. This paper introduces a methodology combining pattern mining and Probabilistic Timed Petri Nets (PTPN) to model, simulate, and evaluate clinical pathways, incorporating probabilistic transitions and continuous-time distributions for activity durations. In collaboration with medical professionals, the proposed methodology has been successfully applied to develop a clinical pathway for anterior cruciate ligament (ACL) ruptures using real data. Iterative refinement addressed data inconsistencies, producing a robust PTPN model that optimizes patient care and resource allocation. Validation using the CASAS database demonstrate the adaptability of the method to different healthcare contexts.<\/jats:p>","DOI":"10.1007\/s10626-025-00419-4","type":"journal-article","created":{"date-parts":[[2025,7,23]],"date-time":"2025-07-23T12:54:32Z","timestamp":1753275272000},"page":"205-231","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Probabilistic timed Petri nets for clinical pathway design and analysis: a case study"],"prefix":"10.1007","volume":"35","author":[{"given":"Manon","family":"Le Moigne","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cristian","family":"Mahulea","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gregory","family":"Faraut","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Simona","family":"Bernardi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorge","family":"Albareda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lidia","family":"Cast\u00e1n","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2025,7,23]]},"reference":[{"key":"419_CR1","unstructured":"Aalst WMP, Carmona J (eds) (2022) Process mining handbook 448. 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