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* '''Implicit places:''' Alpha miner cannot distinguish between implicit and required places and thus might result in additional non required places in the discovered petri net.<ref>{{Cite web|title=(PDF) Discovering Petri Nets from Event Logs|url=https://www.researchgate.net/publication/265764352_Discovering_Petri_Nets_from_Event_Logs|access-date=2021-08-31|website=ResearchGate|language=en}}</ref>
* '''Loops:''' Alpha miner cannot discover loops in the process model.<ref name=":1">{{Cite web|title=Limitations of Alpha miner|url=https://courses.edsa-project.eu/pluginfile.php/281/mod_resource/content/0/17%20Alpha%20Algorithm%20-%20Limitations.pdf|url-status=live|archive-url=https://web.archive.org/web/20210831175934/https://courses.edsa-project.eu/pluginfile.php/281/mod_resource/content/0/17%20Alpha%20Algorithm%20-%20Limitations.pdf |archive-date=2021-08-31 }}</ref>
* Local dependencies are often missed in alpha miner.<ref name=":1" />
* '''Representational bias:''' Alpha miner can only discover petri net thus adding representational bias such as requirement on unique visible labels for every transition.<ref name=":1" />
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