MachineLearningNotebooks/how-to-use-azureml/automated-machine-learning/sparse-data-train-test-split/auto-ml-sparse-data-train-test-split.ipynb

{
  "cells": [
    {
      "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/automated-machine-learning/sparse-data-train-test-split/auto-ml-sparse-data-train-test-split.png)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "# Automated Machine Learning\n",
        "_**Train Test Split and Handling Sparse Data**_\n",
        "\n",
        "## Contents\n",
        "1. [Introduction](#Introduction)\n",
        "1. [Setup](#Setup)\n",
        "1. [Data](#Data)\n",
        "1. [Train](#Train)\n",
        "1. [Results](#Results)\n",
        "1. [Test](#Test)\n"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Introduction\n",
        "In this example we use the scikit-learn's [20newsgroup](http://scikit-learn.org/stable/modules/generated/sklearn.datasets.fetch_20newsgroups.html) to showcase how you can use AutoML for handling sparse data and how to specify custom cross validations splits.\n",
        "Make sure you have executed the [configuration](../../../configuration.ipynb) before running this notebook.\n",
        "\n",
        "In this notebook you will learn how to:\n",
        "1. Create an `Experiment` in an existing `Workspace`.\n",
        "2. Configure AutoML using `AutoMLConfig`.\n",
        "4. Train the model.\n",
        "5. Explore the results.\n",
        "6. Test the best fitted model.\n",
        "\n",
        "In addition this notebook showcases the following features\n",
        "- Explicit train test splits \n",
        "- Handling **sparse data** in the input"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Setup\n",
        "\n",
        "As part of the setup you have already created an Azure ML `Workspace` object. For AutoML you will need to create an `Experiment` object, which is a named object in a `Workspace` used to run experiments."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "import logging\n",
        "\n",
        "import pandas as pd\n",
        "\n",
        "import azureml.core\n",
        "from azureml.core.experiment import Experiment\n",
        "from azureml.core.workspace import Workspace\n",
        "from azureml.train.automl import AutoMLConfig"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "ws = Workspace.from_config()\n",
        "\n",
        "# choose a name for the experiment\n",
        "experiment_name = 'sparse-data-train-test-split'\n",
        "\n",
        "experiment = Experiment(ws, experiment_name)\n",
        "\n",
        "output = {}\n",
        "output['SDK version'] = azureml.core.VERSION\n",
        "output['Subscription ID'] = ws.subscription_id\n",
        "output['Workspace'] = ws.name\n",
        "output['Resource Group'] = ws.resource_group\n",
        "output['Location'] = ws.location\n",
        "output['Experiment Name'] = experiment.name\n",
        "pd.set_option('display.max_colwidth', -1)\n",
        "outputDf = pd.DataFrame(data = output, index = [''])\n",
        "outputDf.T"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Data"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from sklearn.datasets import fetch_20newsgroups\n",
        "from sklearn.feature_extraction.text import HashingVectorizer\n",
        "from sklearn.model_selection import train_test_split\n",
        "\n",
        "remove = ('headers', 'footers', 'quotes')\n",
        "categories = [\n",
        "    'alt.atheism',\n",
        "    'talk.religion.misc',\n",
        "    'comp.graphics',\n",
        "    'sci.space',\n",
        "]\n",
        "data_train = fetch_20newsgroups(subset = 'train', categories = categories,\n",
        "                                shuffle = True, random_state = 42,\n",
        "                                remove = remove)\n",
        "\n",
        "X_train, X_valid, y_train, y_valid = train_test_split(data_train.data, data_train.target, test_size = 0.33, random_state = 42)\n",
        "\n",
        "\n",
        "vectorizer = HashingVectorizer(stop_words = 'english', alternate_sign = False,\n",
        "                               n_features = 2**16)\n",
        "X_train = vectorizer.transform(X_train)\n",
        "X_valid = vectorizer.transform(X_valid)\n",
        "\n",
        "summary_df = pd.DataFrame(index = ['No of Samples', 'No of Features'])\n",
        "summary_df['Train Set'] = [X_train.shape[0], X_train.shape[1]]\n",
        "summary_df['Validation Set'] = [X_valid.shape[0], X_valid.shape[1]]\n",
        "summary_df"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Train\n",
        "\n",
        "Instantiate an `AutoMLConfig` object to specify the settings and data used to run the experiment.\n",
        "\n",
        "|Property|Description|\n",
        "|-|-|\n",
        "|**task**|classification or regression|\n",
        "|**primary_metric**|This is the metric that you want to optimize. Classification supports the following primary metrics: <br><i>accuracy</i><br><i>AUC_weighted</i><br><i>average_precision_score_weighted</i><br><i>norm_macro_recall</i><br><i>precision_score_weighted</i>|\n",
        "|**iteration_timeout_minutes**|Time limit in minutes for each iteration.|\n",
        "|**iterations**|Number of iterations. In each iteration AutoML trains a specific pipeline with the data.|\n",
        "|**preprocess**|Setting this to *True* enables AutoML to perform preprocessing on the input to handle *missing data*, and to perform some common *feature extraction*.<br>**Note:** If input data is sparse, you cannot use *True*.|\n",
        "|**X**|(sparse) array-like, shape = [n_samples, n_features]|\n",
        "|**y**|(sparse) array-like, shape = [n_samples, ], Multi-class targets.|\n",
        "|**X_valid**|(sparse) array-like, shape = [n_samples, n_features] for the custom validation set.|\n",
        "|**y_valid**|(sparse) array-like, shape = [n_samples, ], Multi-class targets.|"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "automl_config = AutoMLConfig(task = 'classification',\n",
        "                             debug_log = 'automl_errors.log',\n",
        "                             primary_metric = 'AUC_weighted',\n",
        "                             iteration_timeout_minutes = 60,\n",
        "                             iterations = 5,\n",
        "                             preprocess = False,\n",
        "                             verbosity = logging.INFO,\n",
        "                             X = X_train, \n",
        "                             y = y_train,\n",
        "                             X_valid = X_valid, \n",
        "                             y_valid = y_valid)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "Call the `submit` method on the experiment object and pass the run configuration. Execution of local runs is synchronous. Depending on the data and the number of iterations this can run for a while.\n",
        "In this example, we specify `show_output = True` to print currently running iterations to the console."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "local_run = experiment.submit(automl_config, show_output=True)"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "local_run"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Results"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "#### Widget for Monitoring Runs\n",
        "\n",
        "The widget will first report a \"loading\" status while running the first iteration. After completing the first iteration, an auto-updating graph and table will be shown. The widget will refresh once per minute, so you should see the graph update as child runs complete.\n",
        "\n",
        "**Note:** The widget displays a link at the bottom. Use this link to open a web interface to explore the individual run details."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "from azureml.widgets import RunDetails\n",
        "RunDetails(local_run).show() "
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "\n",
        "#### Retrieve All Child Runs\n",
        "You can also use SDK methods to fetch all the child runs and see individual metrics that we log."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "children = list(local_run.get_children())\n",
        "metricslist = {}\n",
        "for run in children:\n",
        "    properties = run.get_properties()\n",
        "    metrics = {k: v for k, v in run.get_metrics().items() if isinstance(v, float)}\n",
        "    metricslist[int(properties['iteration'])] = metrics\n",
        "    \n",
        "rundata = pd.DataFrame(metricslist).sort_index(1)\n",
        "rundata"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "### Retrieve the Best Model\n",
        "\n",
        "Below we select the best pipeline from our iterations. The `get_output` method returns the best run and the fitted model. The Model includes the pipeline and any pre-processing.  Overloads on `get_output` allow you to retrieve the best run and fitted model for *any* logged metric or for a particular *iteration*."
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "best_run, fitted_model = local_run.get_output()"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "#### Best Model Based on Any Other Metric\n",
        "Show the run and the model which has the smallest `accuracy` value:"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# lookup_metric = \"accuracy\"\n",
        "# best_run, fitted_model = local_run.get_output(metric = lookup_metric)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "#### Model from a Specific Iteration\n",
        "Show the run and the model from the third iteration:"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# iteration = 3\n",
        "# best_run, fitted_model = local_run.get_output(iteration = iteration)"
      ]
    },
    {
      "cell_type": "markdown",
      "metadata": {},
      "source": [
        "## Test"
      ]
    },
    {
      "cell_type": "code",
      "execution_count": null,
      "metadata": {},
      "outputs": [],
      "source": [
        "# Load test data.\n",
        "from pandas_ml import ConfusionMatrix\n",
        "\n",
        "data_test = fetch_20newsgroups(subset = 'test', categories = categories,\n",
        "                               shuffle = True, random_state = 42,\n",
        "                               remove = remove)\n",
        "\n",
        "X_test = vectorizer.transform(data_test.data)\n",
        "y_test = data_test.target\n",
        "\n",
        "# Test our best pipeline.\n",
        "\n",
        "y_pred = fitted_model.predict(X_test)\n",
        "y_pred_strings = [data_test.target_names[i] for i in y_pred]\n",
        "y_test_strings = [data_test.target_names[i] for i in y_test]\n",
        "\n",
        "cm = ConfusionMatrix(y_test_strings, y_pred_strings)\n",
        "print(cm)\n",
        "cm.plot()"
      ]
    }
  ],
  "metadata": {
    "authors": [
      {
        "name": "savitam"
      }
    ],
    "kernelspec": {
      "display_name": "Python 3.6",
      "language": "python",
      "name": "python36"
    },
    "language_info": {
      "codemirror_mode": {
        "name": "ipython",
        "version": 3
      },
      "file_extension": ".py",
      "mimetype": "text/x-python",
      "name": "python",
      "nbconvert_exporter": "python",
      "pygments_lexer": "ipython3",
      "version": "3.6.6"
    }
  },
  "nbformat": 4,
  "nbformat_minor": 2
}