To which JC replied:

Dear Pieter,

The most recent work that enables the mining of hierarchical process models (process maps) is the one of http://www.win.tue.nl/~jcbose/Li_JCBose_Aalst_BPI2010_ExtendedAbstract.pdf.
This is a follow up to the abstractions paper that you referred to. You can find one case study in this paper. The discovery of process maps has been enabled/realized in ProM 6.0. In order to discover process maps, you need to use two packages in ProM 6.0 in the following order:

(i) Pattern Abstractions (This is implemented as a Visualizer). This plugin implements the functionality of (Abstractions in Process Mining: A Taxonomy of Patterns) and also provides rich functionality to prune/select patterns, define abstractions (sub-processes) based on the common execution patterns, and transform the log (as defined in the latest paper mentioned above). An analyst need to explore the patterns, select/define meaningful abstractions and use the transformation functionality. The transformation creates sub-logs for each of the sub-processed defined.
(ii) Fuzzy Miner. The original fuzzy miner has been enhanced to utilize the availabilty of sub-logs and mine sub-processes from these sub-logs. Just like cluster nodes, we now have abstract nodes in the fuzzy model which upon zooming-in can provide the sub-process captured underneath it.

Note that Fuzzy Miner is just one realization of step 1 above. You can customize any other process discovery algorithm to make use of the sub-logs and mine process maps.

We have recently applied this two-phase approach to process map discovery in the context of discovering the workflow of field service engineer at Philips the results of which is not yet publicly available. However, I would like to mention that this approach showed good promise in discovering comprehensible process maps.

Hope this helps. Should you have any queries, please feel free to contact me.

Thanks and Kind Regards,
JC