Does filing a patent application require disclosure in the paper publication process?
The answer to this depends on the state of the filing and the particulars of the publication venue.  


If you haven't filed anything yet, you definitely aren't required to disclose, and more than you are required to cite a paper that hasn't been submitted yet.  After all, any number of things might prevent the filing from happening.  Also, if you disclose before filing, it could screw up your patent.
If you have filed, then it depends on whether the venue requires you to disclose a conflict of interest.  For example, PLoS ONE is very picky about conflict disclosure, but most IEEE venues do not care.  A patent filing (preliminary or full), is reasonable to treat as a conflict of interest.


If you're not sure, though, then the people handling your patent will almost certainly be willing to help you figure out the right way to handle it.  In my experience, the IP offices of many institutions are very happy when researchers are actually willing to engage with them and will be very helpful to you.