Well, trying to understand Mother Nature is like 'crypto-analysis' in some metaphorical sense, but the methods of real crypto-analysis do not carry over well to, say, physics, or? Except for 'rubber hose crypto-analysis' which is better known as 'experimentation' :)

What can be done is the kind advanced statistical analysis, where you take all you measurements, tabulate them and calculate the correlations between them. Current statistical tools may not be too good at the kind of relations there exists, that may be an area for research...You take your AI capable of doing that, feed it the LHC-data, and a new quantum theory rolls out...