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Here, I assume you are using a bag-of-words like approach. Therefore, you have histograms of your descriptors, which seems more efficient in your case. The idea is to build a tree of histograms. You can use different solutions:
I think there is many others solutions, but I'm not familiar with image retrieving optimization, try Google it and read some papers... This is only the "first" solutions I will use if I have to do something similar. Let us know the methods you've try!
Enjoy.