.. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: .. "auto_examples/04-interpolation-based/05-run_ismi_covariate_example.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html .. note:: :class: sphx-glr-download-link-note :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title .. _sphx_glr_auto_examples_04-interpolation-based_05-run_ismi_covariate_example.py: Using Inter-Site Matched Interpolation (ISMI) with matching covariates ====================================================================== This notebook demonstrates the use of :class:`.InterSiteMatchedInterpolation` for harmonizing multi-site data using matching covariates. .. GENERATED FROM PYTHON SOURCE LINES 9-36 .. rst-class:: sphx-glr-script-out .. code-block:: none 2026-06-10 10:54:19 [debug ] Total Samples to generate 3000 2026-06-10 10:54:19 [debug ] Total Samples to generate per site [1000 1000 1000] 2026-06-10 10:54:19 [info ] Using balanced classes: [[0.5, 0.5], [0.5, 0.5], [0.5, 0.5]] 2026-06-10 10:54:19 [info ] `balance_per_site` is: [[0.5, 0.5], [0.5, 0.5], [0.5, 0.5]] 2026-06-10 10:54:19 [info ] Overall class balance across sites: [0.5 0.5] 2026-06-10 10:54:19 [debug ] locs: [50, 50, 50] and probs: None 2026-06-10 10:54:19 [debug ] locs: None and probs: [[0.5, 0.5], [0.5, 0.5], [0.5, 0.5]] 2026-06-10 10:54:19 [debug ] Covariates requested: ['age', 'sex'] 2026-06-10 10:54:19 [info ] For site 0 2026-06-10 10:54:19 [info ] Generating 1000 samples 2026-06-10 10:54:19 [debug ] Balance [0.5, 0.5] for site 0 2026-06-10 10:54:19 [debug ] Site 0 — covariate 'age': mean=50.893 2026-06-10 10:54:19 [debug ] Site 0 — covariate 'sex': mean=0.524 2026-06-10 10:54:19 [debug ] Site 0, site effect strength [3.0, 3.0, 3.0] 2026-06-10 10:54:19 [info ] For site 1 2026-06-10 10:54:19 [info ] Generating 1000 samples 2026-06-10 10:54:19 [debug ] Balance [0.5, 0.5] for site 1 2026-06-10 10:54:19 [debug ] Site 1 — covariate 'age': mean=49.223 2026-06-10 10:54:19 [debug ] Site 1 — covariate 'sex': mean=0.508 2026-06-10 10:54:19 [debug ] Site 1, site effect strength [3.0, 3.0, 3.0] 2026-06-10 10:54:19 [info ] For site 2 2026-06-10 10:54:19 [info ] Generating 1000 samples 2026-06-10 10:54:19 [debug ] Balance [0.5, 0.5] for site 2 2026-06-10 10:54:19 [debug ] Site 2 — covariate 'age': mean=49.728 2026-06-10 10:54:19 [debug ] Site 2 — covariate 'sex': mean=0.519 2026-06-10 10:54:19 [debug ] Site 2, site effect strength [3.0, 3.0, 3.0] 2026-06-10 10:54:19 [info ] Generated 3000 samples across 3 sites 2026-06-10 10:54:19 [info ] Class distribution: [1500 1500] 2026-06-10 10:54:19 [info ] Site distribution: [1000 1000 1000] 2026-06-10 10:54:19 [debug ] Using 1 categorical covariates 2026-06-10 10:54:19 [debug ] Using 1 continuous covariates with tolerance: [5.] 2026-06-10 10:54:19 [info ] [ISMI] Mode: pairwise 2026-06-10 10:54:19 [info ] [ISMI] Sites: [0 1 2] (3 sites, 3 pairs) 2026-06-10 10:54:19 [info ] [ISMI] Alpha: uniform[0.2, 0.4] 2026-06-10 10:54:19 [info ] [ISMI] Behavior: k=2 matches per sample 2026-06-10 10:54:19 [info ] [ISMI] Target tolerance: None 2026-06-10 10:54:19 [info ] [ISMI] Categorical covariates: 1 2026-06-10 10:54:19 [info ] [ISMI] Continuous covariates: 1 (tol: [5.]) 2026-06-10 10:54:19 [info ] [ISMI] Processing 3 pairs 2026-06-10 10:54:19 [info ] [ISMI] Pair: 0 (1000) ↔ 1 (1000) /home/runner/work/UniHarmony/UniHarmony/src/uniharmony/interpolation/_inter_site_matched.py:469: UserWarning: Sample has 1 matches but k=2 requested, using all X_synth_1, y_synth_1, n_un_1 = self._interpolate(X1, y1, X2, y2, matches_1to2, self.alpha_min_, self.alpha_max_) /home/runner/work/UniHarmony/UniHarmony/src/uniharmony/interpolation/_inter_site_matched.py:475: UserWarning: Sample has 1 matches but k=2 requested, using all X_synth_2, y_synth_2, n_un_2 = self._interpolate(X2, y2, X1, y1, matches_2to1, rev_min, rev_max) 2026-06-10 10:54:20 [info ] [ISMI] Generated 3970 samples (8 unmatched) 2026-06-10 10:54:20 [info ] [ISMI] Pair: 0 (1000) ↔ 2 (1000) 2026-06-10 10:54:20 [info ] [ISMI] Generated 3978 samples (4 unmatched) 2026-06-10 10:54:20 [info ] [ISMI] Pair: 1 (1000) ↔ 2 (1000) 2026-06-10 10:54:20 [info ] [ISMI] Generated 3970 samples (8 unmatched) 2026-06-10 10:54:20 [info ] [ISMI] Complete: 3000 original + 11918 synthetic = 14918 total (397.3% increase), 20 unmatched {(np.int64(0), np.int64(1)): 6, (np.int64(1), np.int64(0)): 2, (np.int64(0), np.int64(2)): 2, (np.int64(2), np.int64(0)): 2, (np.int64(1), np.int64(2)): 4, (np.int64(2), np.int64(1)): 4} | .. code-block:: Python import numpy as np from uniharmony.interpolation import InterSiteMatchedInterpolation from uniharmony.datasets import make_multisite_classification # Generate sample data with 3 sites X, y, sites, covars = make_multisite_classification(n_samples=3000, n_sites=3, covariates=["age", "sex"]) # Define covariates for matching categorical_covariate = covars["sex"].reshape(-1,1) continuous_covariate = covars["age"].reshape(-1,1) covariate_tolerance = np.array([5.0]) # ±5 years tolerance # Create interpolator with pairwise mode and k=2 matches ismi = InterSiteMatchedInterpolation(alpha=(0.2, 0.4), covariate_tolerance=covariate_tolerance, k=2, mode="pairwise", random_state=42) # Generate harmonized dataset X_res, y_res = ismi.fit_resample(X, y, sites, categorical_covariate=categorical_covariate, continuous_covariate=continuous_covariate) # Check unmatched samples print(ismi.unmatched_samples_) .. rst-class:: sphx-glr-timing **Total running time of the script:** (0 minutes 2.091 seconds) .. _sphx_glr_download_auto_examples_04-interpolation-based_05-run_ismi_covariate_example.py: .. only:: html .. container:: sphx-glr-footer sphx-glr-footer-example .. container:: sphx-glr-download sphx-glr-download-jupyter :download:`Download Jupyter notebook: 05-run_ismi_covariate_example.ipynb <05-run_ismi_covariate_example.ipynb>` .. container:: sphx-glr-download sphx-glr-download-python :download:`Download Python source code: 05-run_ismi_covariate_example.py <05-run_ismi_covariate_example.py>` .. container:: sphx-glr-download sphx-glr-download-zip :download:`Download zipped: 05-run_ismi_covariate_example.zip <05-run_ismi_covariate_example.zip>` .. only:: html .. rst-class:: sphx-glr-signature `Gallery generated by Sphinx-Gallery `_