mixdist 0.1.0

Distances, nearest-neighbour search and clustering for mixed numeric/categorical tabular data.

mixdist

Distances, nearest-neighbour search and clustering for mixed numeric/categorical tables.

日本語 README

Real customer tables mix age and spend with gender and plan_tier. The standard answers — Gower's distance and k-prototypes — handle that, but with two well-known problems: you have to hand-pick the numeric/categorical balance, and high-cardinality categorical columns quietly dominate the distance regardless of whether they carry signal.

mixdist makes the weighting explicit and inspectable, scales past the n × n wall, and hands the resulting geometry to ordinary Euclidean tooling.

pip install mixdist

Requires Python ≥ 3.9, NumPy and pandas. Nothing else.

---

The problem, in one table

from mixdist import MixedMetric, make_mixed_blobs

# 3 informative numeric + 2 informative categorical + 2 pure-noise categorical
X, y_true = make_mixed_blobs(n_samples=800, random_state=0)

MixedMetric(weights="equal").fit(X).column_report()

            kind  n_levels  expected_dissimilarity  weight  share
column
noise_0  nominal      30.0                   0.965     1.0  0.246
noise_1  nominal      30.0                   0.965     1.0  0.246
cat_1    nominal       3.0                   0.666     1.0  0.170
cat_0    nominal       3.0                   0.665     1.0  0.170
num_1    numeric       NaN                   0.246     1.0  0.063
num_2    numeric       NaN                   0.210     1.0  0.054
num_0    numeric       NaN                   0.200     1.0  0.051

Two columns of pure noise command 49 % of the distance, while each informative numeric column gets ~5 %. Equal weights equalise the nominal weight, not the contribution — and contribution is what the clustering actually sees. The mechanism is arithmetic, not bad luck: a balanced nominal column with K levels has expected dissimilarity 1 − 1/K (0.97 at 30 levels), while a range-scaled numeric column tops out at 1/3 and is usually nearer 0.2.

weights="balanced" sets w_k ∝ 1 / E[d_k], so every column contributes the same expected distance:

MixedMetric(weights="balanced").fit(X).column_report()["share"]
# every column ≈ 0.143

Measured over 5 seeds (800 rows, 3 clusters):

weights	kNN purity (k=10)	ARI (KMeans on transform)	ARI s.d.
"equal" (Gower 1971)	0.905	0.827	0.083
"type_balanced"	0.910	0.846	0.062
"balanced"	0.937	0.894	0.024

kNN purity — the fraction of a point's 10 nearest neighbours sharing its true cluster — is reported because it measures the metric with no clustering algorithm in the way. Note also the collapse in variance: balanced is not just better on average, it is three times more stable across seeds.

(Reproduce with python examples/weighting_matters.py.)

---

Quick start

from mixdist import MixedMetric

metric = MixedMetric(weights="balanced").fit(df)

D = metric.pairwise(df)                        # full distance matrix
dist, idx = metric.kneighbors(n_neighbors=10)  # exact kNN, never builds n×n
Z = metric.transform(df)                       # ||Z_i − Z_j||² == Gower distance

metric.column_report()      # which variables own the distance
metric.explain(df, 3, 17)   # why rows 3 and 17 are similar, column by column

Column typing

Types are inferred (object/category/bool → nominal, ordered Categorical → ordinal, low-cardinality integers → nominal), and you override what matters:

MixedMetric(
    categorical=["plan_tier", "region"],
    ordinal=["satisfaction"],
    numeric_range="robust",   # inner-quantile scaling; one outlier can't flatten a column
)

Missing values are handled the way Gower intended — the column drops out of that pair's denominator, not the whole dataset.

---

Scaling

Distances accumulate one column at a time into a bounded block, so no (n, m, p) intermediate is ever built. Measured on this machine (7 columns; python examples/scaling.py):

n	kneighbors	peak	pairwise	peak	reference gower	peak
2,000	0.09 s	164 MB	0.06 s	196 MB	11.4 s	18 MB
5,000	0.52 s	329 MB	0.33 s	528 MB	71.1 s	106 MB
10,000	2.04 s	330 MB	1.31 s	1,128 MB	285.6 s	412 MB
20,000	7.96 s	331 MB	—	—	—	—

Two things to read off it. Speed: ~200× faster than the reference implementation at n = 10,000. Memory: kneighbors is flat in n — the matrix is never materialised — while pairwise necessarily grows as n² because the matrix is the output. (mixdist computes in float64 and gower in float32, which accounts for the 2× in the pairwise column.)

So on anything large, don't ask for the matrix:

# Top-k directly — O(n·k) memory, exact, no approximation
dist, idx = metric.kneighbors(query_df, reference_df, n_neighbors=20)

# Or stream the matrix in blocks
for start, stop, block in metric.iter_pairwise(df):
    ...

Results agree with the reference gower package to 4e-8 (float32 precision) — see tests/test_reference_gower.py, which is run against it directly.

---

Euclidean embedding (the interesting part)

Gower's distance is a non-negatively weighted average of |u − v| on range-scaled numerics and 1[u ≠ v] on nominals. Both are metrics of negative type, and negative type is closed under non-negative combination — so √d_Gower embeds isometrically in ℓ₂, and the map can be written down explicitly rather than recovered by MDS.

transform() builds it: thermometer features for numeric columns, scaled one-hot for nominal ones, amplitudes chosen so that

‖transform(X)[i] − transform(X)[j]‖²  ==  pairwise(X)[i, j]

exactly, up to 1/n_bins quantisation per numeric column.

import faiss, numpy as np

Z = metric.transform(df, n_components=256)     # optional JL projection
index = faiss.IndexFlatL2(Z.shape[1])
index.add(np.ascontiguousarray(Z))
index.search(Z[:5], 10)                        # Gower nearest neighbours, at FAISS speed

The same trick makes sklearn.cluster.KMeans, HDBSCAN and UMAP operate on Gower geometry without modification.

---

Clustering

Two algorithms, chosen because they attack the weighting problem from opposite directions.

KPrototypes — Huang (1997)

from mixdist import KPrototypes

km = KPrototypes(n_clusters=4, gamma="modha-spangler", random_state=0).fit(df)
km.labels_, km.gamma_, km.cluster_centers_

gamma="auto" uses Huang's rule of thumb. gamma="modha-spangler" searches the balance by minimising the product of the numeric and categorical within-cluster distortions (Modha & Spangler, 2003) — no labels, no tuning, one run per grid point.

KAMILA — Foss et al. (2016)

from mixdist import KAMILA

km = KAMILA(n_clusters=4, random_state=0).fit(df)
km.cluster_centers_
km.level_probabilities_["plan_tier"]   # per-cluster level probabilities

KAMILA has no gamma. It models the continuous block as a spherical cluster with a KDE-estimated radial density and the categorical block as per-cluster multinomials, then compares log-densities — quantities already on a common scale. The balance comes from the data.

This is the first Python implementation; the reference implementation is the R package kamila. It is written from the published description, not ported, so behaviour agrees but numbers need not match bit for bit.

Explaining clusters

metric.explain_clusters(df, km.labels_)

          num_0   num_1   num_2   cat_0   cat_1  noise_0  noise_1
cluster
0        0.0110  0.0285  0.0219  0.0353  0.0338   0.0001   0.0001
1        0.0106  0.0258  0.0232  0.0314  0.0295   0.0002   0.0001
2        0.0135  0.0269  0.0241  0.0345  0.0307   0.0002   0.0002

Entry (g, k) is the weighted dispersion reduction of column k inside cluster g: how much tighter the column gets once you condition on the cluster, on the Gower scale. The noise columns score ~0.0002 against ~0.03 for the informative ones, and they do so even though they sit far from the global centre — which is the trap this measure is built to avoid. Negative entries mean the cluster is more heterogeneous than the data at large. No surrogate model is involved.

---

Design notes

• No scikit-learn dependency, but estimators implement get_params/set_params, so they drop into Pipeline and GridSearchCV when scikit-learn is present.
• gower_matrix(X) is provided as a one-line drop-in for the common gower.gower_matrix idiom, defaulting to weights="equal" for exact compatibility.
• Constant columns are dropped with a warning. They contribute no distance but do enter Gower's denominator, silently rescaling everything.

Limitations

• transform() cannot represent missing values exactly — Gower's pair-dependent denominator has no single feature map. The default imputes and warns; pass on_missing="error" to refuse instead.
• KAMILA's continuous model assumes spherical clusters, as in the original paper.
• gamma="modha-spangler" costs one full clustering per grid point.

References

• Gower, J. C. (1971). A general coefficient of similarity and some of its properties. Biometrics 27(4).
• Huang, Z. (1997). Clustering large data sets with mixed numeric and categorical values. PAKDD.
• Modha, D. S. & Spangler, W. S. (2003). Feature weighting in k-means clustering. Machine Learning 52(3).
• Foss, A., Markatou, M., Ray, B. & Heching, A. (2016). A semiparametric method for clustering mixed data. Machine Learning 105(3).
• Schoenberg, I. J. (1938). Metric spaces and positive definite functions. TAMS 44(3) — the negative-type result behind transform().

License

BSD 3-Clause.