[maltekuehl]

Mutual k-nearest neighbor graphs

so.neighbor.mnn_graph.create(data, neighbor_count=20, connect_isolated_nodes=True, distance_metric=..., accuracy=..., job_count=..., use_gpu=...) connects two data points only if each is among the neighbor_count nearest neighbors of the other. The result is an undirected, unweighted nx.Graph with one node per data point, built with the same neighbor finder as knn_graph and snn_graph. It accepts an array or a fitted SOM.

• In a k-nearest neighbor graph, a small group of data points far from the rest is still connected to it whenever the group has fewer members than neighbor_count. In the mutual graph it is not, because the rest of the data does not list the group's points among its own nearest neighbors.
• With connect_isolated_nodes=True (the default), a data point without any mutual neighbor keeps the edge to its nearest neighbor, as in snn_graph.
• The removal of each data point from its own neighbor list moves from KnnGraph.get_edges into a private helper, _exclude_self, which both graphs use. knn_graph is unchanged.

Tests (test/neighbor/test_mnn_graph.py, 15):

• The edges equal a brute-force mutual k-nearest neighbor set for neighbor_count 1, 5 and 15 under all four distance metrics.
• A distant group of 4 points among 500 is connected to the rest in the kNN graph but not in the mutual graph.
• connect_isolated_nodes on and off.
• A fitted SOM as input.

fastersom 0.5.0

• pyproject.toml and uv.lock require fastersom 0.5.0, which finds the best-matching units of so.dimension.som on Apple GPUs (MPS) with fused Metal kernels.
• The full example tutorial is re-run with it.

Release notes in docs/source/release-notes/0.12.0.md; please rename the file if the next release gets another number.

Checks

• test/neighbor, test/cluster, test/dimension and test/test_public_api.py with fastersom 0.5.0 on the CPU: 130 passed (-m "not gpu and not no_github_ci").
• ruff, ruff format, mypy (-p spatiomic) and bandit clean.
• The full CPU suite (make unittest) was not run locally.

🤖 Generated with Claude Code

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 82.51%. Comparing base (3d167c9) to head (57e04d4).

Additional details and impacted files

@@            Coverage Diff             @@
##             main      #33      +/-   ##
==========================================
+ Coverage   82.22%   82.51%   +0.28%     
==========================================
  Files          55       56       +1     
  Lines        1975     2007      +32     
==========================================
+ Hits         1624     1656      +32     
  Misses        351      351              

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