One simple improvement would be to precompute the k nearest neighbors for each region based on region centers and then do comparisons only over those neighbors, under the (correct) assumption that valid merges will be local.
cc @jwittenbach @j-friedrich might be interested in working on it
freeman-lab
commented
8 years ago
A generic greedy merging method was added in https://github.com/thunder-project/thunder-extraction/commit/aecd49348540e3b92def4e443f7d2551aa1dbb2a but the performance is quite poor in practice, sometimes taking longer than the initial fitting itself! We should find an implementation that doesn't require
n^2region comparisons.One simple improvement would be to precompute the
knearest neighbors for each region based on region centers and then do comparisons only over those neighbors, under the (correct) assumption that valid merges will be local.cc @jwittenbach @j-friedrich might be interested in working on it