The problem I am trying to solve is as follows: Given two lists of equal length containing points, find a mapping that minimizes the sum of distances between pairs. The reason I'm trying to do this is to find the closest points in two polygons for a genetic algorithm I'm building, that would ideally line up two genes based on the output of this computation to maximize the spatial similarity.
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that's a little vague, more info please? – Chris Ballance Feb 20 '09 at 05:40
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This is known as the linear assignment problem. The Hungarian algorithm is one way to solve it.

Zach Scrivena
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I actually asked basically the same question a few days ago here. There are a bunch of good links to explanations of possible solutions including simulated annealing.

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MahlerFive
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