Tag: Python

Scaffolding Azure Machine Learning Experiments

Microsoft has released the public preview of their newest data science service, Azure Machine Learning, that contains a collection of components to support the end-to-end machine learning solution. The Azure Machine Learning Workbench and the Azure Machine Learning Experimentation service are the two main components offered to machine learning practitioners to support them on exploratory data analysis, feature engineering and model selection and tuning.

This blog post describes how to conduct machine learning experiments with the supports of Azure Machine Learning Workbench and Azure Machine Learning Experimentation service. As the term “Experiment” implies, the process of building a machine learning model is not a waterfall process but instead an iterative process that involves multiple iteration of exploratory analysis, feature engineering, model selection and parameter tuning. To simplify the iterative experiment process and keep the experiment code in a neat structure, we can create some scaffolding code that takes care of the repeated operations for each iteration. Combining the scaffolding code and the job run history dashboard and version control feature offered by Azure Machine Learning, machine learning practitioners can conduct their experiments in a more organised style. There are many ways and patterns to construct the scaffolding code. This blog post will give an example and you can design your scaffolding code based on your own use cases.

Setup Azure Machine Learning environment

Firstly, we need to setup Azure Machine Learning environment, including creating experimentation accounts in Azure Machine Learning and installing required development tools on your computer. You can find the detailed guides from Microsoft official documentations here.

At the end of the setup, you should have the experimentation account created in your Azure tenant and installed Azure Machine Learning Workbench, Visual Studio Code Tools for AI, CLI tool and Python on your computer. In this blog post, I will use the Titanic survival dataset as the example that aims to predict the survival chance of a passenger based on a set of attributes of this passenger. You can find the dataset here.

Create Scaffolding Code and Make the Baseline (Iteration 0) Run

In this example, the following python files will be created to support the iterative experiment, including:

  • EDA & Preprocessing Jupyter notebook for EDA, data preprocessing and feature engineering
  • Experiment file for conducting the model evaluation, parameter tuning and output results to the job run dashboard
  • Individual model files to create the candidate model instance and the parameter options for tuning. In this example, three models are used as candidates, including Logistic Regression, Random Forest, and GBDT.

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EDA & Preprocessing.ipynb

In the scaffolding version of the EDA & Preprocessing notebook, we only include the minimum data handling that is just enough to support the baseline run. As you can see from the snapshot below, only one-hot encoding is conducted, and the null values are just simply dropped.

1t1

In this example, we will experiment on three models, logistic regression, random forest, and GBDT. We create a separate python file for each model with a single function getModel(). This function will return the model name, model object, the dictionary of parameter options for randomised search cross-validation, and the number of iteration of the random searches.

model_lr.py

from sklearn.linear_model import LogisticRegression
from scipy.stats import randint

def getModel():
    # create logistic regression classifier
    lr = LogisticRegression(random_state = 2)

    # create parameter distribution for parameter tuning
    param_dist = {'penalty': ['l1','l2'], 
                  'C': [0.001,0.01,0.1,1,10,100,1000]}

    # return model dict
    return {'name':"Logistic Regression", 'model':lr, 'param_dist':param_dist, 'n_iter': 10}

model_RF.py

from sklearn.ensemble import RandomForestClassifier
from scipy.stats import randint

def getModel():
    # create random forest classifer
    rf = RandomForestClassifier(n_estimators=20)

    # create parameter distribution for parameter tuning
    param_dist = {"max_depth": randint(6,9),
                  "max_features": ['auto', 12],
                  'n_estimators': [20, 50, 100, 150, 200],
                  "min_samples_split": randint(2, 10),
                  "min_samples_leaf": randint(2, 8),
                  "bootstrap": [True, False],
                  "criterion": ["gini", "entropy"]}

    # return model dict
    return {'name':"Random Forest", 'model':rf, 'param_dist':param_dist, 'n_iter': 20}

model_GBDT.py

import lightgbm as lgb
from scipy.stats import randint

def getModel():
    # create GBDT model
    gbm = lgb.LGBMClassifier(boosting_type='gbdt', objective='binary', is_unbalance=True, random_state=2, n_jobs=5)

    # create parameter distribution for parameter tuning
    param_dist = {
        'learning_rate': [0.005, 0.01, 0.1],
        'n_estimators': randint(50,300),
        'num_leaves': randint(20, 80),
        'feature_fraction':[0.5, 0.6, 0.7, 0.8],
        'bagging_fraction':[0.5, 0.6,0.7,0.8],
        'bagging_freq': randint(10,20)
    }

    # return model dict
    return {'name':"GBDT", 'model':gbm, 'param_dist':param_dist, 'n_iter': 20}

Optional – for each model file, you can also append the following code that enables you to perform the parameter tuning individually on each model through directly running of the individual python file.

import pandas as pd
import numpy as np
from sklearn.model_selection import RandomizedSearchCV, cross_val_score
from sklearn.metrics import accuracy_score, precision_score, recall_score

if __name__ == '__main__':
    # load preprocessed training dataset
    train = pd.read_csv('Data/train_processed.csv')

    # specify predictors and target columns
    target = "Survived"
    predictors =  [x for x in train.columns if x not in [target]]

    # fit model with random parameter search
    model = getModel()
    random_search = RandomizedSearchCV(model['model'], param_distributions=model['param_dist'], n_iter=model['n_iter'])
    random_search.fit(train[predictors], train[target])

    # Print top 5 scores and related param options
    results = random_search.cv_results_
    for i in range(1, 6):
        scores = np.flatnonzero(results['rank_test_score'] == i)
        for score in scores:
            print("Rank: {0}".format(i))
            print("score - mean: {0:.3f}, std: {1:.3f}".format(
                  results['mean_test_score'][score],
                  results['std_test_score'][score]))
            print("Parameters: {0}".format(results['params'][score]))

Experiment.py

The experiment file loads the data outputted from the EDA & Preprocessing notebook and fits into the models loaded from model_lr, model_RF, and model_GBDT files. RandomizedSearchCV is used to search the best parameters for each model (from the pre-defined parameter options). The best score for each model will then be logged into the job run history dashboard.

import pandas as pd
import numpy as np
from sklearn.model_selection import RandomizedSearchCV, cross_val_score
from sklearn.metrics import accuracy_score, precision_score, recall_score

from azureml.logging import get_azureml_logger
run_logger = get_azureml_logger()

import model_GBDT
import model_lr
import model_RF 

def runExperiment():
    # load preprocessed training dataset
    train = pd.read_csv('Data/train_processed.csv')

    # specify predictors and target columns
    target = "Survived"
    predictors =  [x for x in train.columns if x not in [target]]

    # get models from model files
    models = [model_GBDT.getModel(), model_lr.getModel(), model_RF.getModel()]

    # fit models with random parameter search and log the best score for each model to AML job run dashboard
    for model in models:
        random_search = RandomizedSearchCV(model['model'], param_distributions=model['param_dist'], n_iter=model['n_iter'])
        random_search.fit(train[predictors], train[target])
        results = random_search.cv_results_
        scores = np.flatnonzero(results['rank_test_score'] == 1)
        score = results['mean_test_score'][scores[0]]
        run_logger.log(model['name'], round(score, 3))


if __name__ == '__main__':
    runExperiment()

In the Azure Machine Learning Workbench, we can run the Experiment file. The job run history dashboard will show the results for each experiment iteration.  The snapshot below shows the results after the baseline (iteration 0) run.

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Experiment – Iteration 1…n

After the scaffolding code is in place and the baseline evaluation scores are available, we can start our formal experiment iterations to improve the model performances. For each iteration, we may conduct various operations on data preprocessing, feature engineering and parameters tuning, and we can then run the Experiment file to generate the result on the job run history dashboard.

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All the experiment iteration job run will be version controlled by the Azure Machine Learning Experimentation service. You can restore the code for any previous experiment iteration.

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IoT Machine Learning 5 – Evaluate Feature Importance using Tree-based Model

Tree-based model can be used to evaluate the importance of features. In this blog post I go through the steps of evaluating feature importance using the GBDT model in LightGBM. LightGBM is the gradient boosting framework released by Microsoft with high accuracy and speed (some test shows LightGBM can produce as accurate prediction as XGBoost but can reach 25x faster).

Firstly, we import the required packages: pandas for the data preprocessing, LightGBM for the GBDT model, and matplotlib for build the feature importance bar chart.

import pandas as pd
import matplotlib.pylab as plt
import lightgbm as lgb

Then, we need to load and preprocessing the training data. In this example, we use a predictive maintenance dataset.

# read data
train = pd.read_csv('E:\Data\predicitivemaintance_processed.csv')

# drop the columns that are not used for the model
train = train.drop(['Date', 'FailureDate'],axis=1)

# set the target column
target = 'FailNextWeek'

# One-hot encoding
feature_categorical = ['Model']
train = pd.get_dummies(train, columns=feature_categorical)

Next, we train the GBDT model with the training data

lgb_params = {
    'boosting_type': 'gbdt',
    'objective': 'binary',
    'num_leaves': 30,
    'num_round': 360,
    'max_depth':8,
    'learning_rate': 0.01,
    'feature_fraction': 0.5,
    'bagging_fraction': 0.8,
    'bagging_freq': 12
}
lgb_train = lgb.Dataset(train.drop(target, 1), train[target])
model = lgb.train(lgb_params, lgb_train)

After the model is trained, we can then call the plot_importance function of the trained model to get the importance of the features.

plt.figure(figsize=(12,6))
lgb.plot_importance(model, max_num_features=30)
plt.title("Feature importances")
plt.show()

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IoT Machine Learning 4 – Tuning Hyper-Parameters using Grid Search

Hyper-parameters tuning is one common but time-consuming task that aims to select the hyper-parameter values that maximise the accuracy of the model. Normally, cross validation is used to support hyper-parameters tuning that splits the data set to training set for learner training and the validation set to test the model. Python scikit-learn package provides the GridSearchCV class that can simplify the task for machine learning practitioners.

This blog post introduces how to use GridSeachCV class to tuning hyper-parameters using a predictive maintenance dataset as example.

Firstly, we need to import the required packages. Apart from the scikit-learn, we also need to import pandas for the data preprocessing, and LightGBM package for the GBDT model we are going to use as the model.

import pandas as pd
import lightgbm as lgb
from sklearn.model_selection import GridSearchCV

Then, we need to load and preprocessing the training data.

# read data
train = pd.read_csv('E:\Data\predicitivemaintance_processed.csv')

# preparing the predictor set and target set
train = train.drop(['Date', 'FailureDate'],axis=1)
target = 'FailNextWeek'
feature_categorical = ['Model']
train = pd.get_dummies(train, columns=feature_categorical)
X = train.drop(target, 1)
y = train[target]

Next, we create a GBDT model with a set of baseline parameters.

model = lgb.LGBMClassifier( 
    boosting_type="gbdt",
    is_unbalance=True, 
    random_state=10, 
    n_estimators=50,
    num_leaves=30, 
    max_depth=8,
    feature_fraction=0.5,  
    bagging_fraction=0.8, 
    bagging_freq=15, 
    learning_rate=0.01,    
)

Now, we move to the key part for the hyper-parameter tuning. In this example, we will tuning the hyper-parameters for ‘n_estimators’ and the ‘num_leaves’. We need to configure the range of parameter values we want to cover for each of them, and the grid search will cover a Cartesian product of those two set of parameter values.  For each parameter pair, in this example, 3-fold cross validation will be conducted with AUC used for scoring. In this example, 20 pairs of parameter will be evaluated and 3 fold for each of them. In total, 60 fits will be conducted.

params_opt = {'n_estimators':range(200, 600, 80), 'num_leaves':range(20,60,10)}
gridSearchCV = GridSearchCV(estimator = model, 
    param_grid = params_opt, 
    scoring='roc_auc',
    n_jobs=4,
    iid=False, 
    verbose=1,
    cv=3)
gridSearchCV.fit(X,y)
gridSearchCV.grid_scores_, gridSearchCV.best_params_, gridSearchCV.best_score_

After the code is run we can get the mean AUC value for each pair of parameter.

z1

As we can see the best hyper-parameter for ‘num_leaves’ is 30 and for ‘n_estimators’ is 360. We can then use those value to replace the baseline value used in the GBDT model and continue to tuning other hyper-parameters.

IoT Machine Learning 2 – Extracting Features from IoT Sensor Data using Python

The previous blog post discusses three common patterns for extracting feature from IoT sensor data:

  • Window-based descriptive statistics
  • Seasonal pattern
  • Trend pattern

This blog post introduces how to implement those three patterns in Python.

  1. Window-based descriptive statistics

There are three main types of descriptive statistics based on what they describe: distribution (e.g., skewness and kurtosis), central tendency (e.g., mean, median, and mode) and dispersion (e.g., standard deviation, variance, and Range). Python pandas package provides functions to a comprehensive list of descriptive statistics. You can find the reference to those functions here.

The descriptive statistics need to be calculated within a time window context, e.g., the last 12, 24, 72 hours. We can use the rolling method in pandas to get the rolling time window.

For example, we have the hourly reading data from sensor A:a1

We can get the rolling window sizing as 12, 24, 72 hours and calculate the mean, sd, and skew of each window size.

data['SensorA_mean_12h'] = data['SensorA'].rolling(12).mean()
data['SensorA_sd_12h'] = data['SensorA'].rolling(12).std()
data['SensorA_skew_12h'] = data['SensorA'].rolling(12).skew()
data['SensorA_mean_24h'] = data['SensorA'].rolling(24).mean()
data['SensorA_sd_24h'] = data['SensorA'].rolling(24).std()
data['SensorA_skew_24h'] = data['SensorA'].rolling(24).skew()
data['SensorA_mean_72h'] = data['SensorA'].rolling(72).mean()
data['SensorA_sd_72h'] = data['SensorA'].rolling(72).std()
data['SensorA_skew_72h'] = data['SensorA'].rolling(72).skew()
data.tails(5)

The python code above will generate the features as:

a1

  1. Seasonal pattern

As discussed in last blog post, the features representing seasonal pattern can be extracted from the timestamp of the IoT sensor data using the built-in Python datatime class, such as:

data['DayOfWeek']=data['DateTime'].dt.weekday
data['IsWeekend']=np.where(data['DateTime'].dt.weekday>4, 1, 0)
data['IsWorkingHour']=np.where((data['DateTime'].dt.hour>=9) & (data['DateTime'].dt.hour<=17), 1, 0)
data['Year']=data['DateTime'].dt.year
data['Month']=data['DateTime'].dt.month
data['DayOfMonth']=data['DateTime'].dt.day
data.tail(5)

We can get the output as:

a2

  1. Trend pattern

We can use shift function to extract the features for representing the trend pattern in a time-series dataset.

data['SensorA_lag_1h'] = data['SensorA'].shift(1)
data['SensorA_lag_2h'] = data['SensorA'].shift(2)
data['SensorA_lag_3h'] = data['SensorA'].shift(3)
data['SensorA_lag_4h'] = data['SensorA'].shift(4)
data['SensorA_lag_5h'] = data['SensorA'].shift(5)
data['SensorA_lag_6h'] = data['SensorA'].shift(6)
data['SensorA_lag_7h'] = data['SensorA'].shift(7)
data.tail(5)

We can the output as:
a3