Some months ago I filed an application for a national patent (in an EU country). The examiner pointed out several amendments to be made, which I did after I discussed with him twice.
Eventually the application was rejected at the examination stage (i.e. before reaching the prior art search) on the grounds of exclusions from patentability. Afaik there is no way to appeal.
How would it be best for me to proceed?
The rejection invoked the exclusion area of scientific theories and software. The material is actually neither, although it could be mistaken for them by someone not familiar with the field.
One of the pillars in the (attempted) patent is the application of machine learning methods, which the examiner sounded like he isn't quite familiar with. At one point during our discussions he exclaimed "do you mean to tell me that you'll input data and you'll just get an answer?", which is exactly what machine learning is supposed to be about when handled properly.
As an aside, this is not about improving a machine learning algorithm or about a trivial application; unfortunately you'll have to take my word for it for the time being, given the situation :)
An acquaintance, an engineer who collaborates with patent attorneys, read the application and agreed that there is no ground for rejection. He added that it's the first time he hears about an application being rejected before the prior art search.
All in all, I believe that the rejection is due to a combination of novelty, unfamiliarity of the examiner with the field, and rather abstract nature of the material (although its practical applications in industry were described in detail).
Lastly, during the examination period I contributed a poster to a conference, which included a description of the main concept used in the patent.
At the moment I'm speaking with patent attorneys in order to find the best way forward, but I'd like to hear the opinion of people with similar experience or expertise...