Decided to try and implement one of the Korbell algorithms. After much angst managed to get their IncFctr algorithm working (although not producing quite such good results). It doesn't seem to lead to much better results than the Funkian gradient approach but it sure is a lot faster. It must be at least 10* faster than the gradient approach. The Korbell team are to be congratulated.
I wish I'd tried implementing it earlier - it would haved saved considerable time.
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As far as I can determine, I have something very similar to the IncFctr. My best probe RMSE on it is 0.93.
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