One way is the authentication method (authentication at connection time or message level).
Another is a "keep alive".
But I am wondering why a non-dialog application has SAPGui timeouts. You should use a SYSTEM user.
A hint might be in transaction ST22. How many dumps do you have per day and what are the mesage types. Anything related to this in the Sm21 system log. Those are the first 2 places you should look into.
ps: I also allow myself to ask you what you have tried so far? You question does not provide enough information other than making some guesses.
Cheers,
Julius