I would love to have such a model tell me how to prune my fruit trees as they grow up. Should be a fairly straightforward supervised problem with the right front end for the graph generation.
You can start right now with an algorithm I learned from an expert when I was working in a landscaping business.
It is a very simple three-pass plan: "Deadwood, Crossovers, Aesthetics".
So, first pass, go through the tree cutting out only and all the dead branches. Cut back to live stock, and as always make good clean angle cuts at a proper angle (many horticulture books will provide far better instructions on this).
Second pass, look only for branches that cross-over other branches and especially those that show rubbing or friction marks against other branches. Cut the ones that are either least healthy or grow in the craziest direction (i.e., crazy away from the normal more-or-less not radially away from the trunk).
Then, and only after the other two passes are complete, start pruning for the desired look and/or size & shape for planned growth or bearing fruit.
This method is simple and saves a LOT of ruined trees from trying to first cut to size and appearance, then by the time the deadwood and crossovers are taken later, it is a scraggly mess that takes years to grow back. And it even works well for novices, as long as they pay attention.
I'd suspect entering the state and direction of every branch to an app would take longer than just pruning with the above method, although for trees that haven't fully leafed out, perhaps a 360° angle set of drone pics could make an adequate 3D model to use for planning?
In any case, good luck with your fruit trees — may they grow healthy and provide you with great bounty for many years!
When i read OP this is what I thought it was going to be - these branches are going to be apex competitors, these are crossing or going to cross, this one shows signs of disease, this one interrupts air flow through the centre, etc.
