space-graph 1.0.0

Pure Python SPACE: sparse partial correlation estimation

space-graph

Discover which variables in your dataset are directly related to each other, even after accounting for all other variables. Given a data matrix, SPACE estimates a sparse network of partial correlations -- connections that remain after removing indirect effects. Designed for settings where the number of variables can far exceed the number of samples (e.g. genomics).

Pure Python implementation of SPACE (Sparse Partial Correlation Estimation) from Peng et al. (2009), with no R or C dependencies.

Paper: Sparse Partial Correlation Estimation for High-Dimensional Data

Install

pip install space-graph

Optional Numba (faster inner jsrm loop):

pip install 'space-graph[numba]'

From GitHub:

pip install git+https://github.com/shahrozeabbas/space-graph.git

Usage

import numpy as np
from space_graph import SPACE

X = np.random.randn(20, 5)

model = SPACE(
    alpha=0.7,
    max_outer_iter=2,
    max_inner_iter=500,
    tol=1e-6,
    weight='uniform',
)

model.fit(X)

print(model.partial_correlation_)

Choosing alpha

Use SPACE.select_alpha(X, alphas) to pick the regularization strength by BIC (Peng et al. 2009, Sec. 2.4). It fits across the grid and returns the alpha minimizing sum_i [n * log(RSS_i) + log(n) * k_i], where k_i is the number of neighbors of variable i.

import numpy as np
from space_graph import SPACE

template = SPACE(max_outer_iter=3)
alphas = np.geomspace(0.005, 1.0, 15)
best_alpha = template.select_alpha(X, alphas)

model = SPACE(alpha=best_alpha, max_outer_iter=3).fit(X)

Pass return_curve=True to also get the per-alpha BIC vector for plotting. The template is not mutated — reuse or discard it.

Penalty

• alpha: overall regularization strength (like sklearn).
• gamma (γ) in [0, 1]: mix between L1 and L2 terms.
  • lam1 = alpha * gamma (L1 / sparsity)
  • lam2 = alpha * (1 - gamma) (L2 / ridge)
  • Default gamma=1 matches R space::space.joint default lam2 = 0.

Options

• tol (default 1e-6): inner solver convergence + active-set threshold, same scale as the reference C code.
• weight: default uniform (equivalently equal, unit weights). Other modes:
  • sig — reweight each variable by its residual variance (updates each outer iteration).
  • degree — reweight by node connectivity (updates each outer iteration).
  • custom ndarray of length p — internally normalized to mean 1, so alpha's scale stays comparable to the other modes.
• backend (default auto): inner joint sparse regression (JSRM) solver. numpy always uses pure NumPy. auto uses Numba when installed (lazy on first fit), otherwise NumPy. numba requires Numba and raises ImportError if it is missing. The first fit with auto or numba pays a one-time compile cost.

Tests

pytest

Optional: build libjsrm_test.so from ../space/src/JSRM.c to run the ctypes cross-check in tests/test_space.py.

License

GPL-3.0-or-later (same family as the original space R package).