FIX Fixes AgglomerativeClustering with precomputed affinity #20597
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| if affinity == "precomputed": | ||
| D = X[np.ix_(idx_i, idx_j)] |
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Completing the connectivity based on the affinity is a hack, because the connectivity can be arbitrary and unrelated to X and its affinity matrix. For example in this example, the connectivity is based on the pixel grid and has nothing to do with the pixel value. But if we do not question this hack, your fix makes it work with precomputed affinity, which does fix the linked issue.
In #20531, the situation is a bit different because the connectivity is not separate from the distance matrix. So if the distance matrix is precomputed as a sparse graph, the connectivity is directly given by the sparse graph connectivity, and there is no way to reconnect disconnected components based on the precomputed sparse graph. So I raise en error instead.
| if affinity == "precomputed": | ||
| D = X[np.ix_(idx_i, idx_j)] |
There was a problem hiding this comment.
Completing the connectivity based on the affinity is a hack, because the connectivity can be arbitrary and unrelated to X and its affinity matrix. For example in this example, the connectivity is based on the pixel grid and has nothing to do with the pixel value. But if we do not question this hack, your fix makes it work with precomputed affinity, which does fix the linked issue.
In #20531, the situation is a bit different because the connectivity is not separate from the distance matrix. So if the distance matrix is precomputed as a sparse graph, the connectivity is directly given by the sparse graph connectivity, and there is no way to reconnect disconnected components based on the precomputed sparse graph. So I raise en error instead.
Co-authored-by: Tom Dupré la Tour <[email protected]>
ogrisel
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LGTM as well. I am convinced that the enforced consistency makes sense. The non-regression test makes sense.
…earn#20597) Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Tom Dupré la Tour <[email protected]>
…earn#20597) Co-authored-by: Olivier Grisel <[email protected]> Co-authored-by: Tom Dupré la Tour <[email protected]>
Reference Issues/PRs
Fixes #16151
What does this implement/fix? Explain your changes.
Queries
Xwhen it is precomputed.