scikit-learn AgglomerativeClustering and connectivity -



scikit-learn AgglomerativeClustering and connectivity -

i trying utilize agglomerativeclustering scikit-learn cluster points on place. points defined coordinates (x,y) stored in _xy.

cluster limited few neighbours through connectivity matrix defined c = kneighbors_graph(_xy, n_neighbors = 20).

i want points not part of same cluster, if neighbours, modified connectivity matrix set 0 between these points.

the algorithm runs smoothly but, @ end, clusters contain points should not together, i.e. couple imposed _c = 0.

from children, can see problem arises when cluster of 2 points (i, j) formed , k joins (i,j) if _c[i,k]=0.

so wondering how connectivity constraint propagated when size of clusters larger 2, _c beingness not defined in case.

thanks !

so seems happening in case despite active disconnection of point not want have in 1 cluster, these points still part of same connected component , info associated them still imply should connected same cluster level up.

in general, agglomerativeclustering works follows: @ beginning, info points separate clusters. then, @ each iteration, 2 adjacent clusters merged, such overall increment in discrepancy original info minimal if compare original info cluster means in l2 distance.

hence, although sever direct link between 2 nodes, can clustered 1 level higher intermediate node.

scikit-learn connectivity hierarchical-clustering

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