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I use some math notation in my software/method patent application to make the description precise. I am not claiming any mathematical operations. Could it be that just the usage of math notations causes application rejection?

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IMHO the answer is No*. The way a method is described should not effect whether it is simply a digitization of an "abstract idea" or not.

*But it is possible that the use of math notation will make it seem more like and abstract idea, and that could draw attention to it if it were a borderline case.

I agree that consulting a patent lawyer about this may be a good idea, but I would personally focus primarily on adding language that highlights reasons why your patent is more than just a digitization of an abstract concept.

The main advantage gained by avoiding math notation would be a potentially increased probability of a weak patent flying under the radar, and the value of this stealth would depend on the costs and risks of utilizing the weak patent. If the patented software or method is easy to implement this could actually add significant value, especially if it would be produced/used even without the patent. But adding stealth to a weak patent would add little to no value if implementing the requires a major financial investment that could not be recouped if the patent were invalidated.

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  • I don't want a weak patent. I want potential investors be assured that the business is protected. Also I hope to use a patent as a marketing tool, so people familiar with the field can appreciate its value.
    – Pol99
    Commented Mar 21, 2015 at 22:34
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You need to hire a patent lawyer to answer this question. Making that all the more annoying, even the best patent lawyers are just guessing at how Alice will be implemented going forward. For my own inventions, if I have code, formulas, etc., that are helpful to others understanding the invention, I include them. Even before Alice, you couldn't claim laws of nature, so I don't know that Alice really changes things in this aspect. But until the implications of Alice shake out -- and until the Supreme Court lets patent law kind of settle down before taking new cases -- well, talk to a patent lawyer.

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