I believe they refer to the ideas involving what comprehends your solution to a problem (idea). It's obvious that the problem(idea) you are solving it self cannot be patented, although I think you could just refer to just the problem(idea) you are solving...
A patent (software patent) should never be presented as algorithm in the patent application, but rather as a mechansism that automates a process and has results that solve the problem. This is essential difference between papers. And if you study software patents, you will see a ton of claims reffering to the previous claims, in order to describe your mechanism, in order someone could re-create your solution, thats why some companies decide to go the trade-secret way...
A patent (software patent) should never be presented as algorithm in the patent application, but rather as a mechansism that automates a process and has results that solve the problem. This is essential difference between papers. And if you study software patents, you will see a ton of claims reffering to the previous claims, in order to describe your mechanism, in order someone could re-create your solution, thats why some companies decide to go the trade-secret way...