Add examples by shuo-zhou · Pull Request #15 · pykale/kale-linear

shuo-zhou · 2026-06-07T19:30:47Z

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Copilot

Pull request overview

This PR adds a set of runnable examples (scripts, configs, and Jupyter notebooks) demonstrating domain adaptation workflows and related utilities, and wires up example dependencies in setup.py so users can install the extra packages needed to run tutorials.

Changes:

Add new example packages for toy domain adaptation, multi-site neuroimaging adaptation, cardiac MRI MPCA, and brain lateralization (with supporting utilities/configs/notebooks).
Add pykale to the example extras in setup.py to support example imports from the kale namespace.
Introduce compatibility wrapper modules in examples/brain_lateralization/utils/ (e.g., io_.py, plot.py) to consolidate imports.

Reviewed changes

Copilot reviewed 31 out of 36 changed files in this pull request and generated 12 comments.

Show a summary per file

File	Description
setup.py	Adds `pykale` to example extras (but example deps still missing items needed by new examples).
examples/toy_domain_adaptation/tutorial.ipynb	New notebook tutorial for toy domain adaptation.
examples/toy_domain_adaptation/README.md	New README describing the toy domain adaptation example.
examples/toy_domain_adaptation/main.py	New runnable script version of the toy domain adaptation demo.
examples/toy_domain_adaptation/init.py	Package marker for the toy domain adaptation example.
examples/multisite_neuroimg_adapt/tutorial.ipynb	New notebook tutorial for multi-site neuroimaging domain adaptation.
examples/multisite_neuroimg_adapt/README.md	New README describing the multi-site neuroimaging example.
examples/multisite_neuroimg_adapt/main.py	New runnable script for the multi-site neuroimaging workflow.
examples/multisite_neuroimg_adapt/configs/tutorial.yaml	New YAML config for the multi-site neuroimaging tutorial.
examples/multisite_neuroimg_adapt/configs/README.md	README for the multi-site example configuration folder.
examples/multisite_neuroimg_adapt/config.py	Default YACS config for the multi-site neuroimaging example.
examples/multisite_neuroimg_adapt/init.py	Package marker for the multi-site neuroimaging example.
examples/cmri_mpca/tutorial.ipynb	New notebook tutorial for cardiac MRI MPCA pipeline.
examples/cmri_mpca/README.md	New README describing the cardiac MRI MPCA example.
examples/cmri_mpca/main.py	New runnable script for the cardiac MRI MPCA pipeline.
examples/cmri_mpca/configs/tutorial_svc.yaml	New tutorial config for SVC classifier.
examples/cmri_mpca/configs/tutorial_lr.yaml	New tutorial config for logistic regression classifier.
examples/cmri_mpca/configs/README.md	README for the cardiac MRI example configuration folder.
examples/cmri_mpca/config.py	Default YACS config for the cardiac MRI example.
examples/cmri_mpca/init.py	Package marker for the cardiac MRI example.
examples/brain_lateralization/utils/stats.py	New stats helpers (including compatibility wrappers).
examples/brain_lateralization/utils/results.py	New result loading/saving helpers for the brain lateralization example.
examples/brain_lateralization/utils/plotting.py	New plotting utilities for the brain lateralization example.
examples/brain_lateralization/utils/plot.py	Compatibility wrapper for plotting utilities.
examples/brain_lateralization/utils/neuro_io.py	Neuroimaging I/O helpers (gifti/nifti).
examples/brain_lateralization/utils/io_.py	Compatibility import aggregator for brain lateralization utilities.
examples/brain_lateralization/utils/half_brain.py	Data download/loading + half-brain splitting utilities.
examples/brain_lateralization/utils/experiment.py	Main experiment runner for GSDA lateralization.
examples/brain_lateralization/utils/data_io.py	General data I/O helpers used by the brain lateralization pipeline.
examples/brain_lateralization/utils/init.py	Package marker for brain lateralization utils.
examples/brain_lateralization/tutorial.ipynb	New notebook demo for brain lateralization GSDA workflow.
examples/brain_lateralization/configs/test.yaml	New test config for brain lateralization.
examples/brain_lateralization/configs/demo-hcp.yaml	Demo config for HCP dataset.
examples/brain_lateralization/configs/demo-gsp.yaml	Demo config for GSP dataset.
examples/brain_lateralization/configs/default_cfg.py	Default config for brain lateralization example.
examples/brain_lateralization/configs/init.py	Package marker for brain lateralization configs.
examples/brain_lateralization/utils/init.py	Package marker for brain lateralization utilities (duplicate entry).

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+    {
+      "metadata": {},
+      "source": [
+        "estimator = CoIRLS(kernel=cfg.MODEL.KERNEL, lambda_=cfg.MODEL.LAMBDA_, alpha=cfg.MODEL.ALPHA)\n",


+        "#@title Import required modules\n",
+        "import os\n",
+        "from configs.default_cfg import get_cfg_defaults\n",
+        "from utils.experiment import run_experiment\n",
+        "\n",
+        "from utils.io_ import load_result, reformat_results\n",
+        "from utils import plot"
+      ],


+      "source": [
+        "### Configurations\n",
+        "\n",
+        "The customized configuration used in this demo is stored in `configs/demoh-cp.yaml`, this file overwrites defaults in `default_cfg.py` where a value is specified. Change the configuration file path to `cfg_path = \"configs/demo-gsp.yaml\"` for running the demo with GSP data."


shuo-zhou · 2026-06-08T22:30:45Z

+DATASET:
+  ROOT: "D:/ShareFolder/BNA/Proc"
+  NUM_REPEAT: 5
+SOLVER:
+  SEED: 2022
+OUTPUT:
+  ROOT: 'D:/ShareFolder/BNA/Result'


changed dir

shuo-zhou · 2026-06-08T22:28:47Z

+_C.DATASET.BASE_DIR = "SA_64x64_v2.0"
+_C.DATASET.FILE_FORAMT = "zip"
+_C.DATASET.LANDMARK_FILE = "landmarks.csv"


Copilot

Pull request overview

Copilot reviewed 31 out of 36 changed files in this pull request and generated 10 comments.

+        "if 'google.colab' in str(get_ipython()):\n",
+        "    print('Running on CoLab')\n",
+        "    !pip uninstall --yes imgaug && pip uninstall --yes albumentations && pip install git+https://github.com/aleju/imgaug.git\n",
+        "    !pip install numpy>=2.0.0\n",
+        "    !pip install git+https://github.com/pykale/pykale.git\n",
+        "    !git clone https://github.com/pykale/pykale.git\n",
+        "    %cd pykale/examples/toy_domain_adaptation\n",
+        "else:\n",
+        "    print('Not running on CoLab')"


+        "if 'google.colab' in str(get_ipython()):\n",
+        "    print('Running on CoLab')\n",
+        "    !pip uninstall --yes imgaug && pip uninstall --yes albumentations && pip install git+https://github.com/aleju/imgaug.git\n",
+        "    !git clone https://github.com/pykale/pykale.git\n",
+        "    %cd pykale\n",
+        "    !pip install .[image,example]\n",
+        "    %cd examples/multisite_neuroimg_adapt\n",
+        "else:\n",
+        "    print('Not running on CoLab')"


+        "if 'google.colab' in str(get_ipython()):\n",
+        "    print('Running on CoLab')\n",
+        "    !pip uninstall --yes imgaug && pip uninstall --yes albumentations && pip install git+https://github.com/aleju/imgaug.git\n",
+        "    !git clone https://github.com/pykale/pykale.git\n",
+        "    %cd pykale\n",
+        "    !pip install .[image,example] \n",
+        "    %cd examples/cmri_mpca\n",
+        "else:\n",
+        "    print('Not running on CoLab')"


+        "# Group-Specific Discriminant Analysis for sex-specific lateralization Running Demo\n",
+        "\n",
+        "[Open in Colab](https://colab.research.google.com/github/shuo-zhou/GSDA-Lateralization/blob/main/gsda_demo.ipynb)  (click `Runtime`\u2006\u2192\u2006`Run all (Ctrl+F9)`)"


Copilot

Pull request overview

Copilot reviewed 31 out of 36 changed files in this pull request and generated 13 comments.

+        "    !pip install git+https://github.com/pykale/kale-linear.git\n",
+        "    !git clone https://github.com/pykale/kale-linear.git\n",
+        "    %cd kalelinear/examples/toy_domain_adaptation\n",
+        "else:\n",


+      "source": [
+        "# Group-Specific Discriminant Analysis for sex-specific lateralization Running Demo\n",
+        "\n",
+        "[Open in Colab](https://colab.research.google.com/github/pykale/kale-linear/blob/main/examples/brain_lateralization/gsda_demo.ipynb)  (click `Runtime`\u2006\u2192\u2006`Run all (Ctrl+F9)`)"


+        "    - [Construct brain networks](#Extracting-Brain-Networks-Features)\n",
+        "- Machine learning pipeline:\n",
+        "    - [Baseline: Ridge classifier](#Baseline-Model)\n",
+        "    - [Domain adaptation](#Domain-Adaptation)\n",


+def load_weight_plot_corr(dataset, base_dir, sessions, seed_start, fontsize=14):
+    control_weights = fetch_weights(base_dir, "mix", "0_group_mix", dataset, sessions=sessions, seed_=seed_start)
+    n_control_weights = control_weights.shape[0]
+


+            weights = fetch_weights(
+                base_dir,
+                group,
+                int(lambda_),
+                dataset,
+                sessions=sessions,
+                seed_=seed_start,
+            )
+            corr_matrix = np.corrcoef(control_weights, weights)[n_control_weights:, :n_control_weights]
+            corrs["mean"].append(np.mean(corr_matrix))
+            corrs["sd"].append(np.std(corr_matrix))


+    return df.loc[index1, df_column_name].to_numpy()
+
+
+def load_result(dataset, root_dir, lambdas, seed_start, test_size=0.0):


+            res_fname = "results_%s_L%s_test_size0%s_Fisherz_%s.csv" % (
+                dataset,
+                lambda_str,
+                test_size_str,
+                random_state,
+            )


+    for lambda_ in lambdas:
+        res_dict[lambda_] = pd.concat(res_dict[lambda_])
+
+    res_df_all = pd.concat(res_list)
+    res_df_all = res_df_all.reset_index(drop=True)
+
+    return res_df_all


+    plt.xlabel(r"$\lambda$", fontsize=fontsize)
+    plt.rcParams["text.usetex"] = False
+
+    plt.savefig("figures/%s_corr.svg" % dataset, format="svg", bbox_inches="tight")


+    plt.savefig(
+        "figures/corr_annot_%s_%s.svg" % (dataset, group_dict[group_label]),
+        format="svg",
+        bbox_inches="tight",
+    )


shuo-zhou added 4 commits June 3, 2026 21:30

init examples

c85e016

init gsda exmaple

dbde43d

update gsda exmaple

55127b7

refactor gsda example

c3a306e

shuo-zhou requested a review from Copilot June 7, 2026 19:31

Copilot started reviewing on behalf of shuo-zhou June 7, 2026 19:31 View session

Copilot AI reviewed Jun 7, 2026

View reviewed changes

Fix import issues and typos in exmaples

61f838e

shuo-zhou requested a review from Copilot June 8, 2026 22:34

Copilot started reviewing on behalf of shuo-zhou June 8, 2026 22:34 View session

Copilot AI reviewed Jun 8, 2026

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Fix colab links and install in example notebooks

ff413af

shuo-zhou requested a review from Copilot June 9, 2026 10:57

Copilot started reviewing on behalf of shuo-zhou June 9, 2026 10:57 View session

Copilot AI reviewed Jun 9, 2026

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		return df.loc[index1, df_column_name].to_numpy()


		def load_result(dataset, root_dir, lambdas, seed_start, test_size=0.0):

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