Introduction
During the last couple of weeks we learned about how to read data, do exploratory data analysis (EDA) and prepare data for training. The next step in a typical machine learning pipeline is to train the model and to investigate the results.
Objective
Continue to familiarise with Python and other ML packages
Learn to train a model for regression and complete the introduction to model development pipeline.
Learn to investigate the predictions and the developed model.
Dataset
We examine two regression datasets in this lab. The first one is to do with house prices, some factors associated with the prices and trying to predict house prices. The second dataset is predicting the amount of share bikes hired every day in Washington D.C., USA, based on time of the year, day of the week and weather factors. These datasets are available in housing.data.csv and bikeShareDay.csv in the code repository.
First, ensure the two data files are located within the Jupyter workspace.
If you are on the local machine copy the two data data directories (BostonHousingPrice,Bike-Sharing-Dataset) to your current folder.
If you are on AWS you can upload the data to the notebook instance by clicking the upload files icon on the left sidebar.
Problem Formulation
The first step in developing a model is to formulate the problem in a way that we can apply machine learning. To reiterate, the task in the Boston house price dataset is to predict the house price (MEDV), using some attributes of the house and neighbourhood.
� Observe the data and see if there is a pattern that would allow us to predict the house price using the attributes given? You can use the observations from the EDA for this.
� What category does the task belong to?
✔ Task category:
supervised, multivariate regression
Given that the attributes and the target is available to us (if not we have to source them), the next item is to establish the performance measure.
� What would be a suitable performance measure for this problem?
✔ Performance measures: We will cover the performance measures in lecture 4. For this we will select:
R^2 error: It is intuitive compared to MSE - computes how good our regression model as compared to a very simple model that just predicts the mean value of target from the train set as predictions
We should use the insights gained from observing the data (EDA) in selecting the performance measure. e.g. are there outliers in target?,
Load the dataset and pre-process
Use the knowledge obtained in the last couple of weeks to load the Boston house price data set and pre-process the data (feature scaling, data splitting).
import pandas as pd
import matplotlib.pyplot as plt
import numpy as np
bostonHouseFrame = pd.read_csv('./BostonHousingPrice/housing.data.csv', delimiter='\s+')
bostonHouseFrame.head()
We can now separate the target and the attributes
bostonHouse_X = bostonHouseFrame.drop(['MEDV'], axis=1)
bostonHouse_y = bostonHouseFrame['MEDV']
bostonHouse_y.head()Out:
0 24.0 1 21.6 2 34.7 3 33.4 4 36.2 Name: MEDV, dtype: float64
Hold out some data for validation
Split DataSet
from sklearn.model_selection import train_test_split
with pd.option_context('mode.chained_assignment', None):
bostonHouse_X_train, bostonHouse_X_test, bostonHouse_y_train, bostonHouse_y_test = train_test_split(bostonHouse_X, bostonHouse_y, test_size=0.2, shuffle=True)Do feature scaling
from sklearn.preprocessing import MinMaxScaler
from sklearn.preprocessing import PowerTransformer
logNorm_attributes = ['CRIM','NOX','AGE','DIS','LSTAT']
minmax_attributes = list(set(bostonHouse_X.columns).difference(set(logNorm_attributes)))
bostonHouse_X_train_scaled = bostonHouse_X_train.copy()
bostonHouse_X_test_scaled = bostonHouse_X_test.copy()
minmaxscaler = MinMaxScaler().fit(bostonHouse_X_train_scaled.loc[:, minmax_attributes])
bostonHouse_X_train_scaled.loc[:, minmax_attributes] = minmaxscaler.transform(bostonHouse_X_train_scaled.loc[:, minmax_attributes])
bostonHouse_X_test_scaled.loc[:, minmax_attributes] = minmaxscaler.transform(bostonHouse_X_test_scaled.loc[:, minmax_attributes])
powertransformer = PowerTransformer(method='yeo-johnson', standardize=False).fit(bostonHouse_X_train.loc[:, logNorm_attributes])
bostonHouse_X_train_scaled.loc[:, logNorm_attributes] = powertransformer.transform(bostonHouse_X_train.loc[:, logNorm_attributes])
bostonHouse_X_test_scaled.loc[:, logNorm_attributes] = powertransformer.transform(bostonHouse_X_test.loc[:, logNorm_attributes])
minmaxscaler_pt = MinMaxScaler().fit(bostonHouse_X_train_scaled.loc[:, logNorm_attributes])
bostonHouse_X_train_scaled.loc[:, logNorm_attributes] = minmaxscaler_pt.transform(bostonHouse_X_train_scaled.loc[:, logNorm_attributes])
bostonHouse_X_test_scaled.loc[:, logNorm_attributes] = minmaxscaler_pt.transform(bostonHouse_X_test_scaled.loc[:, logNorm_attributes])Plot features to see if everthing is in order.
plt.figure(figsize=(20,20))
for i, col in enumerate(bostonHouse_X_train_scaled.columns):
plt.subplot(4,5,i+1)
plt.hist(bostonHouse_X_train_scaled[col], alpha=0.3, color='b', density=True)
plt.hist(bostonHouse_X_test_scaled[col], alpha=0.3, color='r', density=True)
plt.title(col)
plt.xticks(rotation='vertical')Out:
Now we have prepared our dataset and are ready to build models.
Building a regression model We have already established that the task is regression and R^2 as the performance measure. When developing a model we would first want to establish a reasonable baseline model.
� What would be a reasonable baseline for this problem?
✔ Baseline model: We can select a linear regression model as a baseline model.
During the EDA we observed that some attributes (e.g. 'RM') have a linear relationship with the target value.
Linear model is a simple model that is intuitive.
Lets fit (train) a linear regression model to our scaled training data using the LinearRegression in scikit-learn. Read the documentation of LinearRegression to understand all the parameters.
from sklearn.linear_model import LinearRegression
model_lr = LinearRegression().fit(bostonHouse_X_train_scaled, bostonHouse_y_train)
The function LinearRegression.fit() does all the optimizations (training) we discussed in the lecture under the hood and produces the optimal model (parameters or weights). We can print the parameter of the fitted model.
print("Parameter of the Linear model: ", model_lr.coef_)
print("Intercept of the Linear model: ", model_lr.intercept_)Out:
Parameter of the Linear model: [ 2.78627393 0.30884166 -1.15763694 1.90802381 -9.8273479 16.3848238 1.00503503 -15.45475849 3.86309064 -6.53550453 -6.31709437 4.60227559 -27.37496673] Intercept of the Linear model: 39.68739436763477
We can now use the trained model to obtain predictions to unseen data. This process is called prediction.
bostonHouse_y_test_pred = model_lr.predict(bostonHouse_X_test_scaled)Array bostonHouse_y_test_pred contains the predictions made by the model. How does it compare with the "actual" house prices for the test set. Lets first visually observe.
fig, ax = plt.subplots()
ax.scatter(bostonHouse_y_test, bostonHouse_y_test_pred, s=25, cmap=plt.cm.coolwarm, zorder=10)
lims = [
np.min([ax.get_xlim(), ax.get_ylim()]), # min of both axes
np.max([ax.get_xlim(), ax.get_ylim()]), # max of both axes
]
ax.plot(lims, lims, 'k--', alpha=0.75, zorder=0)
ax.plot(lims, [np.mean(bostonHouse_y_train),]*2, 'r--', alpha=0.75, zorder=0)
ax.set_aspect('equal')
ax.set_xlim(lims)
ax.set_ylim(lims)
plt.xlabel('Actual House Price')
plt.ylabel('Predicted House Price')
plt.show()
Out:
� What observations did you make?
✔ Observations:
The model has been able to reasonably predict the house price of unseen examples.
It performs better that a simple model that just predicts the mean value of target (red line)
Let's obtain quantitative values of performance.
R2 Score
from sklearn.metrics import r2_score
r2_lr = r2_score(bostonHouse_y_test, bostonHouse_y_test_pred)
print('The R^2 score for the linier regression model is: {:.3f}'.format(r2_lr))
Out:
The R^2 score for the linier regression model is: 0.737
� How would you interpret the results?
Discuss this with the tutor.
� Is there an advantage of using feature scaling? Let's do a simple experiment by fitting a regression model to un-scaled data.
model_us_lr = LinearRegression().fit(bostonHouse_X_train, bostonHouse_y_train)
bostonHouse_y_test_us_pred = model_us_lr.predict(bostonHouse_X_test)
r2_us_lr = r2_score(bostonHouse_y_test, bostonHouse_y_test_us_pred)
print('The R^2 score for the linier regression model (without feature scaling) is: {:.3f}'.format(r2_us_lr))out:
The R^2 score for the linier regression model (without feature scaling) is: 0.693
Next week we will explore more of the model building phase. For now let's assume that we are happy with the performance of the linear regression model.
Explanatory Model Analysis We now have a model that can predict the house prices reasonably. However at the moment it is a black box: "We feed in the attributes and it will provide a prediction". The test set measurements have provided us some empirical evidence that the model performs reasonably well on unseen examples.
Is this empirical evidence adequate to trust the model? Do you think the model has picked up a pattern in data that is reasonable and generalizable or has it picked up some accidental property in the dataset which enables it to do well on the data we have collected so far? To answer such questions we need to investigate the model closely. Unfortunately we are not yet ready (theoretically) to explore all the options in terms of understanding a model. Let's see a few basic techniques that we can use to investigate a model.
Residual plots We have already used one technique (prediction vs actual plot). Another common tool that can be used to explore a model is to plot the residuals (deviation from the actual value).
fig, ax = plt.subplots()
ax.scatter(bostonHouse_y_test, bostonHouse_y_test-bostonHouse_y_test_pred, s=25, cmap=plt.cm.coolwarm, zorder=10)
xlims = ax.get_xlim()
ax.plot(xlims, [0.0,]*2, 'k--', alpha=0.75, zorder=0)
ax.set_xlim(xlims)
plt.xlabel('Actual House Price')
plt.ylabel('Residual')
plt.show()Out:
âš Warning: The test set should be used for this analysis. Train set may be over-fitted to data
� What observations did you make?
✔ Observations: For most models, residuals should express a random behavior with certain properties (like, e.g., being concentrated around 0). If we find any systematic deviations from the expected behavior, they may signal an issue with a model (e.g. plot shows a nonlinear pattern, residual in some parts of the plot is much larger/smaller to others).
There are several other types of residual plots
☞ Additional Reference: Familiarize yourself with model residual based diagnostic plots .
Understanding Diagnostic Plots for Linear Regression Analysis
Creating Diagnostic Plots in Python: uses statsmodel, see if you convert them to scikit learn models
Feature importance Another key technique used to investigate simple models is feature importance. Here we estimate how much each feature contributed towards the final prediction value. For linear models this is straightforward. We can simply look at the model coefficients.
coefs = pd.DataFrame(
model_lr.coef_ * bostonHouse_X_train_scaled.std(axis=0),
columns=['Coefficient importance'], index=bostonHouse_X_train_scaled.columns
)
coefs.sort_values(by=['Coefficient importance']).plot(kind='barh', figsize=(9, 7))
plt.title('Ridge model, small regularization')
plt.axvline(x=0, color='.5')
plt.subplots_adjust(left=.3)Out:
Looking at the coefficient plot to gauge feature importance can be misleading as some of them vary on a small scale, while others (if unscaled).
âš Warning: Coefficients must be scaled to the same unit of measure to retrieve feature importance. Scaling them with the standard-deviation of the feature is a useful proxy.
âš Warning: Correlated features induce instabilities in the coefficients of linear models and their effects cannot be well teased apart.
� What observations did you make?
✔ Observations:
Number of rooms and accessibility to highways are highly important towards increasing the predicted price.
lower status of the population, distances to employment centres, nitric oxides concentration, property-tax rate tend to decrease the predicted price.
the relationship between property-tax rate and house price is of concern (not what we expect). This is because in the dataset there are many industrial areas with high TAX. If we are to do feature selection, we would have dropped this feature on the evidence we have.
ZN and INDUS are not very important for house price prediction.
...
Another parallel technique in scikit-learn for model inspection is Permutation feature importance: a model inspection technique that can be used for any fitted estimator when the data is tabular. More details are provided in scikit-learn documentation
from sklearn.inspection import permutation_importance
r = permutation_importance(model_lr, bostonHouse_X_test_scaled, bostonHouse_y_test, n_repeats=30)
inx = np.argsort(r.importances_mean)
plt.barh(bostonHouse_X_test_scaled.columns[inx], r.importances_mean[inx])
plt.xticks(rotation='vertical')
plt.show()Plot Data:
� Is permutation importance same as plotting regression coefficients?
There are many other techniques to inspect models. We will learn more during the course.
Exercise: Analyse the Bike Share Data ☞ Task: Develop a linear regression model the Bike Share Data. Now you see how to do this task for the house price dataset. Repeat the same process for the Daily Bike Share rental data.
Answer the following questions and discuss this with your lab demonstrator. Please do attempt this, and don’t wait to see if solutions are released (they will not be!)
What are the appropriate performance measure for this task?
What is a suitable baseline model?
What is the performance of the baseline model and is it adequate?
Can you trust your model?
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