> I can't seem to find a USPTO link for their patent but their J Comp
> Chem paper came out online on March 6th, 2007. If they filed after
> that, is such an application valid?

 From what I remember, you have X number of days to ensure the patent  
is filed after public notice. So frequently US academics will "race"  
like this to make simultaneous disclosure. That way they get the  
patent AND the paper. (If the patent is filed several months before  
the paper is submitted, the ACS can sometimes consider this "prior  
publication" and reject the manuscript.)

I don't remember what X is, but it's probably something like 60 or 90  
days.

> It's easy to change the code to consider higher order moments, at the
> expense of time efficiency. But would that make it sufficiently
> different?

That depends on the "extension" of their patent. You make a claim  
based on what you've done that the work can be extended to other  
ideas/molecules/whatever based on obvious work to anyone "skilled in  
the art." (In normal words, the patent will claim that certain things  
are covered because any expert in the area (i.e., cheminformatics)  
could take the patent and extend it to higher orders.

I can't find this particular application (probably not published  
yet?) so I can't help much.

Cheers,
-Geoff

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