diff --git a/docs/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/docs/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index 7c9ff31..e741989 100644 Binary files a/docs/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip and b/docs/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip differ diff --git a/docs/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/docs/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip index 9f4ffb2..e245e40 100644 Binary files a/docs/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip and b/docs/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip differ diff --git a/docs/_downloads/205fc01252fa85326bc85c58c2e96a08/plot_diabetesFeatures_importance_example.py b/docs/_downloads/6f624092537330c9f373c01828b2b9ae/plot_diabetes_variable_importance_example.py similarity index 94% rename from docs/_downloads/205fc01252fa85326bc85c58c2e96a08/plot_diabetesFeatures_importance_example.py rename to docs/_downloads/6f624092537330c9f373c01828b2b9ae/plot_diabetes_variable_importance_example.py index 8ba86de..29cf767 100644 --- a/docs/_downloads/205fc01252fa85326bc85c58c2e96a08/plot_diabetesFeatures_importance_example.py +++ b/docs/_downloads/6f624092537330c9f373c01828b2b9ae/plot_diabetes_variable_importance_example.py @@ -35,11 +35,11 @@ bbi_perm = BlockBasedImportance( estimator="RF", importance_estimator="Mod_RF", - do_hyper=True, - dict_hyper=None, + do_hypertuning=True, + dict_hypertuning=None, conditional=False, group_stacking=False, - prob_type="regression", + problem_type="regression", k_fold=k_fold, list_nominal=list_nominal, n_jobs=10, @@ -58,11 +58,11 @@ bbi_cond = BlockBasedImportance( estimator="RF", importance_estimator="Mod_RF", - do_hyper=True, - dict_hyper=None, + do_hypertuning=True, + dict_hypertuning=None, conditional=True, group_stacking=False, - prob_type="regression", + problem_type="regression", k_fold=k_fold, list_nominal=list_nominal, n_jobs=10, diff --git a/docs/_downloads/6352d1acfa60f2083a9b7a62b5203e91/plot_diabetesFeatures_importance_example.ipynb b/docs/_downloads/a70e28075a283d5e3fe675ced733c459/plot_diabetes_variable_importance_example.ipynb similarity index 78% rename from docs/_downloads/6352d1acfa60f2083a9b7a62b5203e91/plot_diabetesFeatures_importance_example.ipynb rename to docs/_downloads/a70e28075a283d5e3fe675ced733c459/plot_diabetes_variable_importance_example.ipynb index 8a0f7fc..7ba0b86 100644 --- a/docs/_downloads/6352d1acfa60f2083a9b7a62b5203e91/plot_diabetesFeatures_importance_example.ipynb +++ b/docs/_downloads/a70e28075a283d5e3fe675ced733c459/plot_diabetes_variable_importance_example.ipynb @@ -40,7 +40,7 @@ }, "outputs": [], "source": [ - "bbi_perm = BlockBasedImportance(\n estimator=\"RF\",\n importance_estimator=\"Mod_RF\",\n do_hyper=True,\n dict_hyper=None,\n conditional=False,\n group_stacking=False,\n prob_type=\"regression\",\n k_fold=k_fold,\n list_nominal=list_nominal,\n n_jobs=10,\n verbose=0,\n n_perm=100,\n)\nbbi_perm.fit(X, y)\nprint(\"Computing the importance scores with standard permutation\")\nresults_perm = bbi_perm.compute_importance()\npvals_perm = -np.log10(results_perm[\"pval\"] + 1e-10)" + "bbi_perm = BlockBasedImportance(\n estimator=\"RF\",\n importance_estimator=\"Mod_RF\",\n do_hypertuning=True,\n dict_hypertuning=None,\n conditional=False,\n group_stacking=False,\n problem_type=\"regression\",\n k_fold=k_fold,\n list_nominal=list_nominal,\n n_jobs=10,\n verbose=0,\n n_perm=100,\n)\nbbi_perm.fit(X, y)\nprint(\"Computing the importance scores with standard permutation\")\nresults_perm = bbi_perm.compute_importance()\npvals_perm = -np.log10(results_perm[\"pval\"] + 1e-10)" ] }, { @@ -58,7 +58,7 @@ }, "outputs": [], "source": [ - "bbi_cond = BlockBasedImportance(\n estimator=\"RF\",\n importance_estimator=\"Mod_RF\",\n do_hyper=True,\n dict_hyper=None,\n conditional=True,\n group_stacking=False,\n prob_type=\"regression\",\n k_fold=k_fold,\n list_nominal=list_nominal,\n n_jobs=10,\n verbose=0,\n n_perm=100,\n)\nbbi_cond.fit(X, y)\nprint(\"Computing the importance scores with conditional permutation\")\nresults_cond = bbi_cond.compute_importance()\npvals_cond = -np.log10(results_cond[\"pval\"] + 1e-5)" + "bbi_cond = BlockBasedImportance(\n estimator=\"RF\",\n importance_estimator=\"Mod_RF\",\n do_hypertuning=True,\n dict_hypertuning=None,\n conditional=True,\n group_stacking=False,\n problem_type=\"regression\",\n k_fold=k_fold,\n list_nominal=list_nominal,\n n_jobs=10,\n verbose=0,\n n_perm=100,\n)\nbbi_cond.fit(X, y)\nprint(\"Computing the importance scores with conditional permutation\")\nresults_cond = bbi_cond.compute_importance()\npvals_cond = -np.log10(results_cond[\"pval\"] + 1e-5)" ] }, { diff --git a/docs/_images/sphx_glr_plot_diabetesFeatures_importance_example_001.png b/docs/_images/sphx_glr_plot_diabetes_variable_importance_example_001.png similarity index 100% rename from docs/_images/sphx_glr_plot_diabetesFeatures_importance_example_001.png rename to docs/_images/sphx_glr_plot_diabetes_variable_importance_example_001.png diff --git a/docs/_images/sphx_glr_plot_diabetesFeatures_importance_example_thumb.png b/docs/_images/sphx_glr_plot_diabetes_variable_importance_example_thumb.png similarity index 100% rename from docs/_images/sphx_glr_plot_diabetesFeatures_importance_example_thumb.png rename to docs/_images/sphx_glr_plot_diabetes_variable_importance_example_thumb.png diff --git a/docs/_images/sphx_glr_plot_fmri_data_example_001.png b/docs/_images/sphx_glr_plot_fmri_data_example_001.png index 6881bc0..92ce6ea 100644 Binary files a/docs/_images/sphx_glr_plot_fmri_data_example_001.png and b/docs/_images/sphx_glr_plot_fmri_data_example_001.png differ diff --git a/docs/_images/sphx_glr_plot_fmri_data_example_thumb.png b/docs/_images/sphx_glr_plot_fmri_data_example_thumb.png index d24e4c2..822c0cd 100644 Binary files a/docs/_images/sphx_glr_plot_fmri_data_example_thumb.png and b/docs/_images/sphx_glr_plot_fmri_data_example_thumb.png differ diff --git a/docs/_sources/auto_examples/index.rst.txt b/docs/_sources/auto_examples/index.rst.txt index 99094c0..ebda58f 100644 --- a/docs/_sources/auto_examples/index.rst.txt +++ b/docs/_sources/auto_examples/index.rst.txt @@ -23,10 +23,10 @@ Examples Gallery .. only:: html - .. image:: /auto_examples/images/thumb/sphx_glr_plot_diabetesFeatures_importance_example_thumb.png + .. image:: /auto_examples/images/thumb/sphx_glr_plot_diabetes_variable_importance_example_thumb.png :alt: - :ref:`sphx_glr_auto_examples_plot_diabetesFeatures_importance_example.py` + :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` .. raw:: html @@ -78,7 +78,7 @@ Examples Gallery .. toctree:: :hidden: - /auto_examples/plot_diabetesFeatures_importance_example + /auto_examples/plot_diabetes_variable_importance_example /auto_examples/plot_2D_simulation_example /auto_examples/plot_fmri_data_example diff --git a/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt b/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt index cd5301a..cfaabbe 100644 --- a/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt +++ b/docs/_sources/auto_examples/plot_2D_simulation_example.rst.txt @@ -542,9 +542,9 @@ randomization. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (1 minutes 9.270 seconds) + **Total running time of the script:** (1 minutes 0.085 seconds) -**Estimated memory usage:** 101 MB +**Estimated memory usage:** 99 MB .. _sphx_glr_download_auto_examples_plot_2D_simulation_example.py: diff --git a/docs/_sources/auto_examples/plot_diabetesFeatures_importance_example.rst.txt b/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt similarity index 80% rename from docs/_sources/auto_examples/plot_diabetesFeatures_importance_example.rst.txt rename to docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt index 56d79a4..2e3a61c 100644 --- a/docs/_sources/auto_examples/plot_diabetesFeatures_importance_example.rst.txt +++ b/docs/_sources/auto_examples/plot_diabetes_variable_importance_example.rst.txt @@ -2,7 +2,7 @@ .. DO NOT EDIT. .. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY. .. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE: -.. "auto_examples/plot_diabetesFeatures_importance_example.py" +.. "auto_examples/plot_diabetes_variable_importance_example.py" .. LINE NUMBERS ARE GIVEN BELOW. .. only:: html @@ -10,12 +10,12 @@ .. note:: :class: sphx-glr-download-link-note - :ref:`Go to the end ` + :ref:`Go to the end ` to download the full example code. .. rst-class:: sphx-glr-example-title -.. _sphx_glr_auto_examples_plot_diabetesFeatures_importance_example.py: +.. _sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py: Variable Importance on diabetes dataset @@ -72,11 +72,11 @@ Standard Variable Importance bbi_perm = BlockBasedImportance( estimator="RF", importance_estimator="Mod_RF", - do_hyper=True, - dict_hyper=None, + do_hypertuning=True, + dict_hypertuning=None, conditional=False, group_stacking=False, - prob_type="regression", + problem_type="regression", k_fold=k_fold, list_nominal=list_nominal, n_jobs=10, @@ -116,11 +116,11 @@ Conditional Variable Importance bbi_cond = BlockBasedImportance( estimator="RF", importance_estimator="Mod_RF", - do_hyper=True, - dict_hyper=None, + do_hypertuning=True, + dict_hypertuning=None, conditional=True, group_stacking=False, - prob_type="regression", + problem_type="regression", k_fold=k_fold, list_nominal=list_nominal, n_jobs=10, @@ -182,9 +182,9 @@ Plotting the comparison -.. image-sg:: /auto_examples/images/sphx_glr_plot_diabetesFeatures_importance_example_001.png - :alt: plot diabetesFeatures importance example - :srcset: /auto_examples/images/sphx_glr_plot_diabetesFeatures_importance_example_001.png +.. image-sg:: /auto_examples/images/sphx_glr_plot_diabetes_variable_importance_example_001.png + :alt: plot diabetes variable importance example + :srcset: /auto_examples/images/sphx_glr_plot_diabetes_variable_importance_example_001.png :class: sphx-glr-single-img @@ -194,12 +194,12 @@ Plotting the comparison .. rst-class:: sphx-glr-timing - **Total running time of the script:** (0 minutes 47.285 seconds) + **Total running time of the script:** (0 minutes 46.171 seconds) -**Estimated memory usage:** 32 MB +**Estimated memory usage:** 28 MB -.. _sphx_glr_download_auto_examples_plot_diabetesFeatures_importance_example.py: +.. _sphx_glr_download_auto_examples_plot_diabetes_variable_importance_example.py: .. only:: html @@ -207,11 +207,11 @@ Plotting the comparison .. container:: sphx-glr-download sphx-glr-download-jupyter - :download:`Download Jupyter notebook: plot_diabetesFeatures_importance_example.ipynb ` + :download:`Download Jupyter notebook: plot_diabetes_variable_importance_example.ipynb ` .. container:: sphx-glr-download sphx-glr-download-python - :download:`Download Python source code: plot_diabetesFeatures_importance_example.py ` + :download:`Download Python source code: plot_diabetes_variable_importance_example.py ` .. only:: html diff --git a/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt b/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt index 3b29ecf..729f319 100644 --- a/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt +++ b/docs/_sources/auto_examples/plot_fmri_data_example.rst.txt @@ -184,7 +184,7 @@ You may choose a subject in [1, 2, 3, 4, 5, 6]. By default subject=2. Downloading data from http://data.pymvpa.org/datasets/haxby2001/MD5SUMS ... ...done. (0 seconds, 0 min) Downloading data from http://data.pymvpa.org/datasets/haxby2001/subj2-2010.01.14.tar.gz ... - Downloaded 107290624 of 291168628 bytes (36.8%, 1.7s remaining) Downloaded 238895104 of 291168628 bytes (82.0%, 0.4s remaining) ...done. (3 seconds, 0 min) + Downloaded 20447232 of 291168628 bytes (7.0%, 13.6s remaining) Downloaded 62308352 of 291168628 bytes (21.4%, 7.6s remaining) Downloaded 104996864 of 291168628 bytes (36.1%, 5.5s remaining) Downloaded 147136512 of 291168628 bytes (50.5%, 4.0s remaining) Downloaded 189079552 of 291168628 bytes (64.9%, 2.8s remaining) Downloaded 231620608 of 291168628 bytes (79.5%, 1.6s remaining) Downloaded 273883136 of 291168628 bytes (94.1%, 0.5s remaining) ...done. (8 seconds, 0 min) Extracting data from /home/runner/nilearn_data/haxby2001/def37a305edfda829916fa14c9ea08f8/subj2-2010.01.14.tar.gz..... done. @@ -361,7 +361,7 @@ However you might benefit from clustering randomization taking .. code-block:: none [Parallel(n_jobs=2)]: Using backend LokyBackend with 2 concurrent workers. - [Parallel(n_jobs=2)]: Done 5 out of 5 | elapsed: 32.6s finished + [Parallel(n_jobs=2)]: Done 5 out of 5 | elapsed: 31.3s finished @@ -599,9 +599,9 @@ spurious discoveries. .. rst-class:: sphx-glr-timing - **Total running time of the script:** (1 minutes 25.149 seconds) + **Total running time of the script:** (1 minutes 26.859 seconds) -**Estimated memory usage:** 2772 MB +**Estimated memory usage:** 2762 MB .. _sphx_glr_download_auto_examples_plot_fmri_data_example.py: diff --git a/docs/_sources/auto_examples/sg_execution_times.rst.txt b/docs/_sources/auto_examples/sg_execution_times.rst.txt index 10a1b8c..1d4dd20 100644 --- a/docs/_sources/auto_examples/sg_execution_times.rst.txt +++ b/docs/_sources/auto_examples/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**03:21.704** total execution time for 3 files **from auto_examples**: +**03:13.114** total execution time for 3 files **from auto_examples**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``plot_fmri_data_example.py``) - - 01:25.149 - - 2772.0 + - 01:26.859 + - 2762.1 * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``plot_2D_simulation_example.py``) - - 01:09.270 - - 100.8 - * - :ref:`sphx_glr_auto_examples_plot_diabetesFeatures_importance_example.py` (``plot_diabetesFeatures_importance_example.py``) - - 00:47.285 - - 31.5 + - 01:00.085 + - 98.6 + * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``plot_diabetes_variable_importance_example.py``) + - 00:46.171 + - 28.4 diff --git a/docs/_sources/sg_execution_times.rst.txt b/docs/_sources/sg_execution_times.rst.txt index 55c9bb2..2d28719 100644 --- a/docs/_sources/sg_execution_times.rst.txt +++ b/docs/_sources/sg_execution_times.rst.txt @@ -6,7 +6,7 @@ Computation times ================= -**03:21.704** total execution time for 3 files **from all galleries**: +**03:13.114** total execution time for 3 files **from all galleries**: .. container:: @@ -33,11 +33,11 @@ Computation times - Time - Mem (MB) * - :ref:`sphx_glr_auto_examples_plot_fmri_data_example.py` (``../examples/plot_fmri_data_example.py``) - - 01:25.149 - - 2772.0 + - 01:26.859 + - 2762.1 * - :ref:`sphx_glr_auto_examples_plot_2D_simulation_example.py` (``../examples/plot_2D_simulation_example.py``) - - 01:09.270 - - 100.8 - * - :ref:`sphx_glr_auto_examples_plot_diabetesFeatures_importance_example.py` (``../examples/plot_diabetesFeatures_importance_example.py``) - - 00:47.285 - - 31.5 + - 01:00.085 + - 98.6 + * - :ref:`sphx_glr_auto_examples_plot_diabetes_variable_importance_example.py` (``../examples/plot_diabetes_variable_importance_example.py``) + - 00:46.171 + - 28.4 diff --git a/docs/api.html b/docs/api.html index e284487..a80f874 100644 --- a/docs/api.html +++ b/docs/api.html @@ -5,7 +5,7 @@ - API Documentation — hidimstat 0.1.0 documentation + API Documentation — HiDimStat 0.1.0 documentation @@ -41,7 +41,7 @@ - hidimstat + HiDimStat 0.1.0 @@ -138,7 +138,7 @@

Functions

BlockBasedImportance([estimator, ...])

-

This class implements the Block Based Importance (BBI),

+

This class implements the Block-Based Importance (BBI), consisting of a learner block (first block) and an importance block (second block). For single-level see :footcite:t:`Chamma_NeurIPS2023` and for group-level see :footcite:t:`Chamma_AAAI2024`. Parameters ---------- estimator: scikit-learn compatible estimator, default=None The provided estimator for the prediction task (First block). The default estimator is the DNN learner. Other options are (1) RF for Random Forest. importance_estimator: {scikit-learn compatible estimator or string}, default=Mod_RF The provided estimator for the importance task (Second block). Using "Mod_RF" will apply the modified version of the Random Forest as the importance predictor. do_hypertuning: bool, default=True Tuning the hyperparameters of the provided estimator. dict_hypertuning: dict, default=None The dictionary of hyperparameters to tune. problem_type: str, default='regression' A classification or a regression problem. bootstrap: bool, default=True Application of bootstrap sampling for the training set. split_perc: float, default=0.8 The training/validation cut for the provided data. conditional: bool, default=True The permutation or the conditional sampling approach. list_nominal: dict, default=None The dictionary of binary, nominal and ordinal variables. Perm: bool, default=False The use of permutations or random sampling with CPI-DNN. n_perm: int, default=50 The number of permutations/random sampling for each column. n_jobs: int, default=1 The number of workers for parallel processing. verbose: int, default=0 If verbose > 0, the fitted iterations will be printed. groups: dict, default=None The knowledge-driven/data-driven grouping of the variables if provided. group_stacking: bool, default=False Apply the stacking-based method for the provided groups. prop_out_subLayers: int, default=0. If group_stacking is set to True, proportion of outputs for the linear sub-layers per group. index_i: int, default=None The index of the current processed iteration. random_state: int, default=2023 Fixing the seeds of the random generator. com_imp: boolean, default=True Compute or not the importance scores. group_label: list, default=None The list of group labels to perform GroupKFold Attributes ---------- ToDO.

clustered_inference(X_init, y, ward, n_clusters)

Clustered inference algorithm

diff --git a/docs/auto_examples/index.html b/docs/auto_examples/index.html index 465b9ca..401df9b 100644 --- a/docs/auto_examples/index.html +++ b/docs/auto_examples/index.html @@ -5,7 +5,7 @@ - Examples Gallery — hidimstat 0.1.0 documentation + Examples Gallery — HiDimStat 0.1.0 documentation @@ -39,7 +39,7 @@ - hidimstat + HiDimStat 0.1.0 @@ -110,8 +110,8 @@ @@ -458,8 +463,8 @@

Analysis of the results
show()
-

Total running time of the script: (1 minutes 25.149 seconds)

-

Estimated memory usage: 2772 MB

+

Total running time of the script: (1 minutes 26.859 seconds)

+

Estimated memory usage: 2762 MB