2-training-inference/2.2-aml-interpretability/1-simple-feature-transformations-explain-local.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
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   "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/NotebookVM/how-to-use-azureml/explain-model/tabular-data/simple-feature-transformations-explain-local.png)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Explain binary classification model predictions with raw feature transformations\n",
    "_**This notebook showcases how to use the Azure Machine Learning Interpretability SDK to explain and visualize a binary classification model that uses one to one and one to many feature transformations.**_\n",
    "\n",
    "\n",
    "## Table of Contents\n",
    "\n",
    "1. [Introduction](#Introduction)\n",
    "1. [Run model explainer locally at training time](#Explain)\n",
    "    1. Apply feature transformations\n",
    "    1. Train a binary classification model\n",
    "    1. Explain the model on raw features\n",
    "        1. Generate global explanations\n",
    "        1. Generate local explanations\n",
    "1. [Visualize results](#Visualize)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Introduction\n",
    "\n",
    "This notebook illustrates creating explanations for a binary classification model, IBM employee attrition classification, that uses one to one and one to many feature transformations from raw data to engineered features. The one to many feature transformations include one hot encoding on categorical features. The one to one feature transformations apply standard scaling on numeric features. Our tabular data explainer is then used to get raw feature importances.\n",
    "\n",
    "\n",
    "We will showcase raw feature transformations with three tabular data explainers: TabularExplainer (SHAP), MimicExplainer (global surrogate), and PFIExplainer.\n",
    "\n",
    "| ![Interpretability Toolkit Architecture](./img/interpretability-architecture.png) |\n",
    "|:--:|\n",
    "| *Interpretability Toolkit Architecture* |\n",
    "\n",
    "Problem: IBM employee attrition classification with scikit-learn (run model explainer locally)\n",
    "\n",
    "1. Transform raw features to engineered features\n",
    "2. Train a SVC classification model using Scikit-learn\n",
    "3. Run 'explain_model' globally and locally with full dataset in local mode, which doesn't contact any Azure services.\n",
    "4. Visualize the global and local explanations with the visualization dashboard.\n",
    "---\n",
    "\n"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Explain\n",
    "\n",
    "### Run model explainer locally at training time"
   ]
  },
  {
   "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.svm import SVC\n",
    "import pandas as pd\n",
    "import numpy as np\n",
    "from azureml.core import Workspace, Dataset\n",
    "\n",
    "# Explainers:\n",
    "# 1. SHAP Tabular Explainer\n",
    "from interpret.ext.blackbox import TabularExplainer\n",
    "\n",
    "# OR\n",
    "\n",
    "# 2. Mimic Explainer\n",
    "from interpret.ext.blackbox import MimicExplainer\n",
    "# You can use one of the following four interpretable models as a global surrogate to the black box model\n",
    "from interpret.ext.glassbox import LGBMExplainableModel\n",
    "from interpret.ext.glassbox import LinearExplainableModel\n",
    "from interpret.ext.glassbox import SGDExplainableModel\n",
    "from interpret.ext.glassbox import DecisionTreeExplainableModel\n",
    "\n",
    "# OR\n",
    "\n",
    "# 3. PFI Explainer\n",
    "from interpret.ext.blackbox import PFIExplainer "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Load the IBM employee attrition data created before\n",
    "\n",
    "Note: as you are now accessing the workspace, the Notebook VM needs to be authenticated for access through device authentication. Hence, you will be prompted with a device login like so: \n",
    "\n",
    "    Performing interactive authentication. Please follow the instructions on the terminal.\n",
    "    To sign in, use a web browser to open the page https://microsoft.com/devicelogin and enter the code ARQPFR4B4 to authenticate.\n",
    "    \n",
    "Please follow these instructions in a new browser tab."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# get the IBM employee attrition dataset from the workspace\n",
    "ws = Workspace.from_config()\n",
    "attritionData = ws.datasets['IBM-Employee-Attrition'].to_pandas_dataframe()\n",
    "attritionData.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# or, if you did not create the dataset in the first part of the workshop, you can just create it now\n",
    "web_path ='https://raw.githubusercontent.com/danielsc/azureml-workshop-2019/master/data/IBM-Employee-Attrition.csv'\n",
    "attritionDataSet = Dataset.Tabular.from_delimited_files(path=web_path)\n",
    "attritionDataSet.register(ws, name='IBM-Employee-Attrition')\n",
    "attritionData = attritionDataSet.to_pandas_dataframe()\n",
    "attritionData.head()"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Dropping Employee count as all values are 1 and hence attrition is independent of this feature\n",
    "attritionData = attritionData.drop(['EmployeeCount'], axis=1)\n",
    "# Dropping Employee Number since it is merely an identifier\n",
    "attritionData = attritionData.drop(['EmployeeNumber'], axis=1)\n",
    "\n",
    "attritionData = attritionData.drop(['Over18'], axis=1)\n",
    "\n",
    "# Since all values are 80\n",
    "attritionData = attritionData.drop(['StandardHours'], axis=1)\n",
    "target = attritionData[\"Attrition\"]\n",
    "\n",
    "attritionXData = attritionData.drop(['Attrition'], axis=1)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Split data into train and test\n",
    "from sklearn.model_selection import train_test_split\n",
    "x_train, x_test, y_train, y_test = train_test_split(attritionXData, \n",
    "                                                    target, \n",
    "                                                    test_size = 0.2,\n",
    "                                                    random_state=0,\n",
    "                                                    stratify=target)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# collect the categorical and numerical column names in separate lists\n",
    "categorical = []\n",
    "for col, value in attritionXData.iteritems():\n",
    "    if value.dtype == 'object':\n",
    "        categorical.append(col)\n",
    "        \n",
    "numerical = attritionXData.columns.difference(categorical)        "
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Transform raw features"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "We can explain raw features by either using a `sklearn.compose.ColumnTransformer` or a list of fitted transformer tuples. The cell below uses `sklearn.compose.ColumnTransformer`. In case you want to run the example with the list of fitted transformer tuples, comment the cell below and uncomment the cell that follows after. "
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from sklearn.compose import ColumnTransformer\n",
    "\n",
    "# We create the preprocessing pipelines for both numeric and categorical data.\n",
    "numeric_transformer = Pipeline(steps=[\n",
    "    ('imputer', SimpleImputer(strategy='median')),\n",
    "    ('scaler', StandardScaler())])\n",
    "\n",
    "categorical_transformer = Pipeline(steps=[\n",
    "    ('imputer', SimpleImputer(strategy='constant', fill_value='missing')),\n",
    "    ('onehot', OneHotEncoder(handle_unknown='ignore'))])\n",
    "\n",
    "transformations = ColumnTransformer(\n",
    "    transformers=[\n",
    "        ('num', numeric_transformer, numerical),\n",
    "        ('cat', categorical_transformer, categorical)])\n",
    "\n",
    "# Append classifier to preprocessing pipeline.\n",
    "# Now we have a full prediction pipeline.\n",
    "clf = Pipeline(steps=[('preprocessor', transformations),\n",
    "                      ('classifier', SVC(kernel='linear', C = 1.0, probability=True))])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Train a SVM classification 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": [
    "# 1. Using SHAP TabularExplainer\n",
    "# clf.steps[-1][1] returns the trained classification model\n",
    "explainer = TabularExplainer(clf.steps[-1][1], \n",
    "                             initialization_examples=x_train, \n",
    "                             features=attritionXData.columns, \n",
    "                             classes=[\"Not leaving\", \"leaving\"], \n",
    "                             transformations=transformations)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "# 2. Using MimicExplainer\n",
    "# augment_data is optional and if true, oversamples the initialization examples to improve surrogate model accuracy to fit original model.  Useful for high-dimensional data where the number of rows is less than the number of columns. \n",
    "# max_num_of_augmentations is optional and defines max number of times we can increase the input data size.\n",
    "# LGBMExplainableModel can be replaced with LinearExplainableModel, SGDExplainableModel, or DecisionTreeExplainableModel\n",
    "# explainer = MimicExplainer(clf.steps[-1][1], \n",
    "#                            x_train, \n",
    "#                            LGBMExplainableModel, \n",
    "#                            augment_data=True, \n",
    "#                            max_num_of_augmentations=10, \n",
    "#                            features=attritionXData.columns, \n",
    "#                            classes=[\"Not leaving\", \"leaving\"], \n",
    "#                            transformations=transformations)\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "\n",
    "# 3. Using PFIExplainer\n",
    "\n",
    "# Use the parameter \"metric\" to pass a metric name or function to evaluate the permutation. \n",
    "# Note that if a metric function is provided a higher value must be better.\n",
    "# Otherwise, take the negative of the function or set the parameter \"is_error_metric\" to True.\n",
    "# Default metrics: \n",
    "# F1 Score for binary classification, F1 Score with micro average for multiclass classification and\n",
    "# Mean absolute error for regression\n",
    "\n",
    "# explainer = PFIExplainer(clf.steps[-1][1], \n",
    "#                          features=x_train.columns, \n",
    "#                          transformations=transformations,\n",
    "#                          classes=[\"Not leaving\", \"leaving\"])"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generate global explanations\n",
    "Explain overall model predictions (global explanation)"
   ]
  },
  {
   "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 = explainer.explain_global(x_test)\n",
    "\n",
    "# Note: if you used the PFIExplainer in the previous step, use the next line of code instead\n",
    "# global_explanation = explainer.explain_global(x_test, true_labels=y_test)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Sorted SHAP values\n",
    "print('ranked global importance values: {}'.format(global_explanation.get_ranked_global_values()))\n",
    "# Corresponding feature names\n",
    "print('ranked global importance names: {}'.format(global_explanation.get_ranked_global_names()))\n",
    "# Feature ranks (based on original order of features)\n",
    "print('global importance rank: {}'.format(global_explanation.global_importance_rank))\n",
    "\n",
    "# Note: PFIExplainer does not support per class explanations\n",
    "# Per class feature names\n",
    "print('ranked per class feature names: {}'.format(global_explanation.get_ranked_per_class_names()))\n",
    "# Per class feature importance values\n",
    "print('ranked per class feature values: {}'.format(global_explanation.get_ranked_per_class_values()))"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Print out a dictionary that holds the sorted feature importance names and values\n",
    "# print('global importance rank: {}'.format(global_explanation.get_feature_importance_dict()))"
   ]
  },
  {
   "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": [
    "# feature shap values for all features and all data points in the training data\n",
    "#print('local importance values: {}'.format(global_explanation.local_importance_values))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "### Generate local explanations\n",
    "Explain local data points (individual instances)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Note: PFIExplainer does not support local explanations\n",
    "# You can pass a specific data point or a group of data points to the explain_local function\n",
    "\n",
    "# E.g., Explain the first data point in the test set\n",
    "instance_num = 1\n",
    "local_explanation = explainer.explain_local(x_test[:instance_num])"
   ]
  },
  {
   "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)[instance_num]\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",
    "print('local importance values: {}'.format(sorted_local_importance_values))\n",
    "print('local importance names: {}'.format(sorted_local_importance_names))"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "## Visualize\n",
    "Load the visualization dashboard"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "from azureml.contrib.interpret.visualize import ExplanationDashboard"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": [
    "ExplanationDashboard(global_explanation, model, x_test)"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
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