yEd is still responsive, I can close it and it asks me if I want to save the changes, but the layout never finishes. The problem disappears if I uncheck BEAUTIFIED_ENABLED. Version 3.11.
Sample Graph
Settings
Please upload the GraphML file of your diagram and mention your exact settings (or post screen shots) so we are able to reproduce the problem.
(See How to upload files to yEd Q&A? for details on uploading files.)