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SLINK: Single-link agglomerative clusterer - #525
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andrewdalpino wants to merge 5 commits into
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andrewdalpino wants to merge 5 commits into
andrewdalpino wants to merge 5 commits into
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andrewdalpino
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a balanced review from Copilot
October 21, 2026 00:50
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🟡 Changes recommended
Recovered cluster memberships are lost, NaN distances bypass detection, and probability normalization adds avoidable quadratic work per sample.
3 open issues
What changed in this PR
Adds SLINK single-link agglomerative clustering to Rubix ML.
Changes:
- Implements distance-limited clustering, medoid-based prediction, probabilities, and progress reporting.
- Adds tests and a training/prediction benchmark.
- Documents SLINK and adds it to estimator listings and navigation.
| File | Description |
|---|---|
| tests/Clusterers/SLINKTest.php | Tests clustering, prediction, validation, and persistence. |
| src/Clusterers/SLINK.php | Implements the SLINK estimator. |
| mkdocs.yml | Adds SLINK navigation. |
| docs/clusterers/slink.md | Documents behavior and public methods. |
| docs/choosing-an-estimator.md | Lists SLINK among clusterers. |
| benchmarks/Clusterers/SLINKBench.php | Benchmarks training and prediction. |
Review effort: Balanced
| $lambda[$i] = INF; | ||
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| for ($j = 0; $j < $i; ++$j) { | ||
| $mu[$j] = $this->kernel->compute($samples[$j], $samples[$i]); |
| */ | ||
| public function predictSample(array $sample) : int | ||
| { | ||
| return argmin($this->medoidDistances($sample)); |
Comment on lines
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| foreach ($distances as $distanceA) { | ||
| $sigma = 0.0; | ||
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| foreach ($distances as $distanceB) { | ||
| $sigma += $distanceA / $distanceB; | ||
| } | ||
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| $proba[] = 1.0 / $sigma; | ||
| } |
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