MachineLearningNotebooks/how-to-use-azureml/explain-model/explain-tabular-data-raw-features/explain-sklearn-raw-features.ipynb

{
  "cells": [
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# Summary\n",
        "From raw data that is a mixture of categoricals and numeric, featurize the categoricals using one hot encoding. Use tabular explainer to get explain object and then get raw feature importances"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Copyright (c) Microsoft Corporation. All rights reserved.\n",
        "\n",
        "Licensed under the MIT License."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "![Impressions](https://PixelServer20190423114238.azurewebsites.net/api/impressions/MachineLearningNotebooks/how-to-use-azureml/explain-model/explain-tabular-data-raw-features/explain-sklearn-raw-features.png)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Explain a model with the AML explain-model package on raw features\n",
        "\n",
        "1. Train a Logistic Regression model using Scikit-learn\n",
        "2. Run 'explain_model' with full dataset in local mode, which doesn't contact any Azure services.\n",
        "3. Run 'explain_model' with summarized dataset in local mode, which doesn't contact any Azure services.\n",
        "4. Visualize the global and local explanations with the visualization dashboard."
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "This example needs sklearn-pandas. If it is not installed, uncomment and run the following line."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "#!pip install sklearn-pandas"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from sklearn.pipeline import Pipeline\n",
        "from sklearn.impute import SimpleImputer\n",
        "from sklearn.preprocessing import StandardScaler, OneHotEncoder\n",
        "from sklearn.linear_model import LogisticRegression\n",
        "from azureml.explain.model.tabular_explainer import TabularExplainer\n",
        "from sklearn_pandas import DataFrameMapper\n",
        "import pandas as pd\n",
        "import numpy as np"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "titanic_url = ('https://raw.githubusercontent.com/amueller/'\n",
        "               'scipy-2017-sklearn/091d371/notebooks/datasets/titanic3.csv')\n",
        "data = pd.read_csv(titanic_url)\n",
        "# fill missing values\n",
        "data = data.fillna(method=\"ffill\")\n",
        "data = data.fillna(method=\"bfill\")"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# 1. Run model explainer locally with full data"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Similar to example [here](https://scikit-learn.org/stable/auto_examples/compose/plot_column_transformer_mixed_types.html#sphx-glr-auto-examples-compose-plot-column-transformer-mixed-types-py), use a subset of columns"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from sklearn.model_selection import train_test_split\n",
        "\n",
        "numeric_features = ['age', 'fare']\n",
        "categorical_features = ['embarked', 'sex', 'pclass']\n",
        "\n",
        "y = data['survived'].values\n",
        "X = data[categorical_features + numeric_features]\n",
        "\n",
        "x_train, x_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from sklearn.pipeline import Pipeline\n",
        "from sklearn.impute import SimpleImputer\n",
        "from sklearn.preprocessing import StandardScaler, OneHotEncoder\n",
        "from sklearn_pandas import DataFrameMapper\n",
        "\n",
        "# Impute, standardize the numeric features and one-hot encode the categorical features.    \n",
        "\n",
        "transformations = [\n",
        "    ([\"age\", \"fare\"], Pipeline(steps=[\n",
        "        ('imputer', SimpleImputer(strategy='median')),\n",
        "        ('scaler', StandardScaler())\n",
        "    ])),\n",
        "    ([\"embarked\"], Pipeline(steps=[\n",
        "        (\"imputer\", SimpleImputer(strategy='constant', fill_value='missing')), \n",
        "        (\"encoder\", OneHotEncoder(sparse=False))])),\n",
        "    ([\"sex\", \"pclass\"], OneHotEncoder(sparse=False))    \n",
        "]\n",
        "\n",
        "\n",
        "# Append classifier to preprocessing pipeline.\n",
        "# Now we have a full prediction pipeline.\n",
        "clf = Pipeline(steps=[('preprocessor', DataFrameMapper(transformations)),\n",
        "                      ('classifier', LogisticRegression(solver='lbfgs'))])"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Train a Logistic Regression model, which you want to explain"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "model = clf.fit(x_train, y_train)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Explain predictions on your local machine"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "tabular_explainer = TabularExplainer(clf.steps[-1][1], initialization_examples=x_train, features=x_train.columns, transformations=transformations)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# Passing in test dataset for evaluation examples - note it must be a representative sample of the original data\n",
        "# x_train can be passed as well, but with more examples explanations will take longer although they may be more accurate\n",
        "global_explanation = tabular_explainer.explain_global(x_test)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "sorted_global_importance_values = global_explanation.get_ranked_global_values()\n",
        "sorted_global_importance_names = global_explanation.get_ranked_global_names()\n",
        "dict(zip(sorted_global_importance_names, sorted_global_importance_values))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Explain overall model predictions as a collection of local (instance-level) explanations"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# explain the first member of the test set\n",
        "local_explanation = tabular_explainer.explain_local(x_test[:1])"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# get the prediction for the first member of the test set and explain why model made that prediction\n",
        "prediction_value = clf.predict(x_test)[0]\n",
        "\n",
        "sorted_local_importance_values = local_explanation.get_ranked_local_values()[prediction_value]\n",
        "sorted_local_importance_names = local_explanation.get_ranked_local_names()[prediction_value]\n",
        "\n",
        "# Sorted local SHAP values\n",
        "print('ranked local importance values: {}'.format(sorted_local_importance_values))\n",
        "# Corresponding feature names\n",
        "print('ranked local importance names: {}'.format(sorted_local_importance_names))"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# 2. Load visualization dashboard"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# Note you will need to have extensions enabled prior to jupyter kernel starting\n",
        "!jupyter nbextension install --py --sys-prefix azureml.contrib.explain.model.visualize\n",
        "!jupyter nbextension enable --py --sys-prefix azureml.contrib.explain.model.visualize\n",
        "# Or, in Jupyter Labs, uncomment below\n",
        "# jupyter labextension install @jupyter-widgets/jupyterlab-manager\n",
        "# jupyter labextension install microsoft-mli-widget"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from azureml.contrib.explain.model.visualize import ExplanationDashboard"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "ExplanationDashboard(global_explanation, model, x_test)"
      ]
    }
  ],
  "metadata": {
    "authors": [
      {
        "name": "mesameki"
      }
    ],
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