pymcmm 0.3.0

Mixed-Copula Mixture Model for clustering mixed-type data

pymcmm

Mixed-Copula Mixture Model (MCMM) for clustering datasets with mixed continuous, categorical, and ordinal data types.

Features

• Mixed Data Types: Handle continuous, categorical, and ordinal variables simultaneously
• Gaussian Copula: Capture complex dependencies between variables
• Missing Values: Native support for missing data
• Student-t Marginals: Robust to outliers with automatic degree of freedom estimation
• Speedy Mode: Efficient computation for large datasets using sparse MST/KNN graphs
• Cython Acceleration: Optional speedup (up to 35x) with Cython

Installation

From GitHub (Recommended)

pip install git+https://github.com/YuZhao20/pymcmm.git

From PyPI (Coming Soon)

pip install pymcmm

With Cython Acceleration

pip install git+https://github.com/YuZhao20/pymcmm.git
pip install cython
cd /path/to/pymcmm
python setup.py build_ext --inplace

Verify acceleration:

import mcmm
mcmm.check_acceleration()

Quick Start

import pandas as pd
from mcmm import MCMMGaussianCopulaSpeedy

df = pd.DataFrame({
    'income': [50000, 60000, 75000, 80000],
    'age': [25, 35, 45, 55],
    'gender': ['M', 'F', 'M', 'F'],
    'satisfaction': [1, 2, 3, 4],
})

model = MCMMGaussianCopulaSpeedy(
    n_components=2,
    cont_marginal='student_t',
    copula_likelihood='full',
    verbose=1
)

model.fit(
    df,
    cont_cols=['income', 'age'],
    cat_cols=['gender'],
    ord_cols=['satisfaction']
)

clusters = model.predict(df)
probabilities = model.predict_proba(df)

print(f"BIC: {model.bic_:.2f}")
print(f"Log-likelihood: {model.loglik_:.2f}")

Cython Acceleration

Overview

pymcmm includes optional Cython-accelerated implementations that provide significant speedups for computationally intensive operations. Cython is not required - the package automatically falls back to pure Python implementations if Cython modules are not available.

What Gets Accelerated

Component	Pure Python	Cython	Speedup
Normal CDF/PPF	scipy.stats	Custom C implementation	up to 10x
Student-t CDF	scipy.stats	Incomplete beta function	up to 15x
Bivariate copula density	numpy/scipy	Optimized C loops	up to 20x
E-step (batch)	Python loops	Parallel Cython	up to 35x
M-step (marginals)	Python loops	Vectorized Cython	up to 25x
Weighted correlation	numpy	Optimized pairwise	up to 10x

Performance Benchmark

Typical speedup for a dataset with n=500, p=13, K=3:

Mode	Pure Python	Cython	Speedup
MCMMGaussianCopula	~65s	~1.9s	up to 35x
MCMMGaussianCopulaSpeedy	~45s	~1.5s	up to 30x

Note: Actual speedup varies depending on hardware and dataset characteristics.

Building Cython Extensions

Prerequisites:

• C compiler (gcc, clang, or MSVC)
• Cython >= 0.29
• NumPy development headers

macOS:

xcode-select --install
brew install libomp  # Optional: for parallel processing
pip install cython
python setup.py build_ext --inplace

Linux:

sudo apt-get install build-essential python3-dev
pip install cython
python setup.py build_ext --inplace

Windows:

pip install cython
python setup.py build_ext --inplace

Verification and Benchmarking

import mcmm

# Check if Cython is enabled
mcmm.check_acceleration()

# Run performance benchmark
mcmm.run_benchmark()

Troubleshooting

If Cython compilation fails:

1. Missing compiler: Install build tools for your platform
2. NumPy headers not found: Reinstall NumPy with pip install --force-reinstall numpy
3. OpenMP errors on macOS: The library works without OpenMP; parallel loops will be sequential

The package will always work without Cython - just slower.

Model Classes

MCMMGaussianCopula

Full copula model with O(p^2) pairwise dependencies.

from mcmm import MCMMGaussianCopula

model = MCMMGaussianCopula(
    n_components=3,
    cont_marginal='student_t',
    copula_likelihood='full',
    max_iter=100,
    verbose=1
)

MCMMGaussianCopulaSpeedy

Optimized for large datasets using sparse graph approximation.

from mcmm import MCMMGaussianCopulaSpeedy

model = MCMMGaussianCopulaSpeedy(
    n_components=3,
    cont_marginal='student_t',
    speedy_graph='mst',
    corr_subsample=3000,
    n_jobs=-1,
    verbose=1
)

Parameters

Parameter	Default	Description
n_components	3	Number of clusters
cont_marginal	'student_t'	Marginal for continuous vars: 'gaussian' or 'student_t'
t_nu	5.0	Initial degrees of freedom for Student-t
estimate_nu	True	Estimate nu from data
ord_marginal	'cumlogit'	Ordinal marginal: 'cumlogit' or 'freq'
copula_likelihood	'full'	Copula type: 'full' or 'pairwise'
pairwise_weight	'abs_rho'	Pairwise weight: 'abs_rho' or 'uniform'
dt_mode	'mid'	Discretization mode: 'mid' or 'random'
shrink_lambda	0.05	Correlation matrix shrinkage
max_iter	100	Maximum EM iterations
tol	1e-4	Convergence tolerance
n_jobs	1	Number of parallel jobs (-1 for all cores)
random_state	None	Random seed for reproducibility
verbose	0	Verbosity level

Speedy Mode Additional Parameters

Parameter	Default	Description
speedy_graph	'mst'	Graph type: 'mst' or 'knn'
speedy_k_per_node	3	K for KNN graph
corr_subsample	3000	Subsample size for correlation estimation
e_step_batch	4096	Batch size for E-step

Methods

Fitting

model.fit(df, cont_cols=None, cat_cols=None, ord_cols=None)

Prediction

clusters = model.predict(df)
proba = model.predict_proba(df)
log_lik = model.score_samples(df)

Outlier Detection

is_outlier, scores, threshold = model.detect_outliers(df, q=1.0)

Attributes (after fitting)

Attribute	Description
pi_	Cluster mixing proportions (K,)
mu_	Cluster means for continuous vars (K, p_cont)
sig_	Cluster stds for continuous vars (K, p_cont)
R_	Correlation matrices (K, p, p)
fitted_nu_	Estimated degrees of freedom
loglik_	Final log-likelihood
bic_	Bayesian Information Criterion
history_	Log-likelihood history

Example: Customer Segmentation

import pandas as pd
from mcmm import MCMMGaussianCopulaSpeedy

df = pd.read_csv('customers.csv')

results = []
for k in range(2, 8):
    model = MCMMGaussianCopulaSpeedy(
        n_components=k,
        random_state=42,
        verbose=0
    )
    model.fit(df, 
              cont_cols=['income', 'age', 'spending'],
              cat_cols=['region', 'gender'],
              ord_cols=['satisfaction'])
    results.append({'k': k, 'bic': model.bic_, 'loglik': model.loglik_})

best = min(results, key=lambda x: x['bic'])
print(f"Best K: {best['k']} (BIC: {best['bic']:.2f})")

Scalability Guidelines

Dataset Size	Recommended Mode	Cython
n < 1,000	MCMMGaussianCopula	Optional
n < 10,000	MCMMGaussianCopulaSpeedy	Recommended
n > 10,000	MCMMGaussianCopulaSpeedy + n_jobs=-1	Recommended

Citation

If you use this package in your research, please cite:

@software{pymcmm,
  author = {Yu Zhao},
  title = {pymcmm: Mixed-Copula Mixture Model for Python},
  institution = {Tokyo University of Science},
  url = {https://github.com/YuZhao20/pymcmm},
  version = {0.3.0},
  year = {2025}
}

License

MIT License

Contributing

Contributions are welcome! Please feel free to submit a Pull Request.