Category: machine learning

Comparing Machine Learning Methods

When working with data and modeling, its sometimes hard to determine what model you should use for a particular modeling project.  A quick way to find an algorithm that might work better than others is to run through an algorithm comparison loop to see how various models work against your data. In this post, I’ll be comparing machine learning methods using a few different sklearn algorithms.  As always, you can find a jupyter notebook for this article on my github here and find other articles on this topic here.

I’ve used Jason Brownlee’s article from 2016 as the basis for this article…I wanted to expand a bit on what he did as well as use a different dataset. In this article, we’ll be using the Indian Liver Disease dataset (found here).

From the dataset page:

This data set contains 416 liver patient records and 167 non liver patient records collected from North East of Andhra Pradesh, India. The “Dataset” column is a class label used to divide groups into liver patient (liver disease) or not (no disease). This data set contains 441 male patient records and 142 female patient records.

Let’s get started by setting up our imports that we’ll use.

import pandas as pd
import matplotlib.pyplot as plt
plt.rcParams["figure.figsize"] = (20,10)

from sklearn import model_selection
from sklearn.linear_model import LogisticRegression
from sklearn.svm import SVC
from sklearn.neighbors import KNeighborsClassifier
from sklearn.tree import DecisionTreeClassifier
from sklearn.naive_bayes import GaussianNB
from sklearn.discriminant_analysis import LinearDiscriminantAnalysis


Next, we’ll read in the data from the CSV file located in the local directory.

#read in the data
data = pd.read_csv('indian_liver_patient.csv')

If you do a head() of the dataframe, you’ll get a good feeling for the dataset.

Indian Liver Disease Data

We’ll use all columns except Gender for this tutorial. We could use gender by converting the gender to a numeric value (e.g., 0 for Male, 1 for Female) but for the purposes of this post, we’ll just skip this column.

data_to_use = data
del data_to_use['Gender']
data_to_use.dropna(inplace=True)

The ‘Dataset’ column is the value we are trying to predict…whether the user has liver disease or not so we’ll that as our “Y” and the other columns for our “X” array.

values = data_to_use.values

Y = values[:,9]
X = values[:,0:9]

Before we run our machine learning models, we need to set a random number to use to seed them. This can be any random number that you’d like it to be. Some people like to use a random number generator but for the purposes of this, I’ll just set it to 12 (it could just as easily be 1 or 3 or 1023 or any other number).

random_seed = 12

Now we need to set up our models that we’ll be testing out. We’ll set up a list of the models and give them each a name. Additionally, I’m going to set up the blank arrays/lists for the outcomes and the names of the models to use for comparison.

outcome = []
model_names = []
models = [('LogReg', LogisticRegression()), 
          ('SVM', SVC()), 
          ('DecTree', DecisionTreeClassifier()),
          ('KNN', KNeighborsClassifier()),
          ('LinDisc', LinearDiscriminantAnalysis()),
          ('GaussianNB', GaussianNB())]

We are going to use a k-fold validation to evaluate each algorithm and will run through each model with a for loop, running the analysis and then storing the outcomes into the lists we created above. We’ll use a 10-fold cross validation.

for model_name, model in models:
    k_fold_validation = model_selection.KFold(n_splits=10, random_state=random_seed)
    results = model_selection.cross_val_score(model, X, Y, cv=k_fold_validation, scoring='accuracy')
    outcome.append(results)
    model_names.append(model_name)
    output_message = "%s| Mean=%f STD=%f" % (model_name, results.mean(), results.std())
    print(output_message)

The output from this loop is:

LogReg| Mean=0.718633 STD=0.058744
SVM| Mean=0.715124 STD=0.058962
DecTree| Mean=0.637568 STD=0.108805
KNN| Mean=0.651301 STD=0.079872
LinDisc| Mean=0.716878 STD=0.050734
GaussianNB| Mean=0.554719 STD=0.081961

From the above, it looks like the Logistic Regression, Support Vector Machine and Linear Discrimination Analysis methods are providing the best results (based on the ‘mean’ values). Taking Jason’s lead, we can take a look at a box plot to see what the accuracy is for each cross validation fold, we can see just how good each does relative to each other and their means.

fig = plt.figure()
fig.suptitle('Machine Learning Model Comparison')
ax = fig.add_subplot(111)
plt.boxplot(outcome)
ax.set_xticklabels(model_names)
plt.show()

Machine Learning Comparison

From the box plot, when it is easy to see the three mentioned machine learning methods (Logistic Regression, Support Vector Machine and Linear Discrimination Analysis) are providing better accuracies. From this outcome, we can then take this data and start working with these three models to see how we might be able to optimize the modeling process to see if one model works a bit better than others.

Forecasting with Random Forests

When it comes to forecasting data (time series or other types of series), people look to things like basic regression, ARIMA, ARMA, GARCH, or even Prophet but don’t discount the use of Random Forests for forecasting data.

Random Forests are generally considered a classification technique but regression is definitely something that Random Forests can handle.

For this post, I am going to use a dataset found here called Sales Prices of Houses in the City of Windsor (CSV here, description here).  For the purposes of this post, I’ll only use the price and lotsize columns. Note: In a future post, I’m planning to resist this data and perform multivariate regression with Random Forests.

To get started, let’s import all the necessary libraries to get started. As always, you can grab a jupyter notebook to run through this analysis yourself here.

import pandas as pd
import matplotlib.pyplot as plt

# lets set the figure size and color scheme for plots
# personal preference and not needed).
plt.rcParams['figure.figsize']=(20,10)
plt.style.use('ggplot')

Now, lets load the data:

df = pd.read_csv('../examples/Housing.csv')
df = df[['price', 'lotsize']]

Again, we are only using two columns from the data set – price and lotsize. Let’s plot this data to take a look at it visually to see if it makes sense to use lotsize as a predictor of price.

df.plot(subplots=True)

Housing Data Visualization

Looking at the data, it looks like a decent guess to think lotsize might forecast price.

Now, lets set up our dataset to get our training and testing data ready.

X = (dataset['lotsize'])
y = (dataset['price'])
    
X_train = X[X.index < 400]
y_train = y[y.index < 400]              
    
X_test = X[X.index >= 400]    
y_test = y[y.index >= 400]

In the above, we set X and y for the random forest regressor and then set our training and test data. For training data, we are going to take the first 400 data points to train the random forest and then test it on the last 146 data points.

Now, let’s run our random forest regression model.  First, we need to import the Random Forest Regressor from sklearn:

from sklearn.ensemble.forest import RandomForestRegressor

And now….let’s run our Random Forest Regression and see what we get.

# build our RF model
RF_Model = RandomForestRegressor(n_estimators=100,
                                 max_features=1, oob_score=True)

# let's get the labels and features in order to run our 
# model fitting
labels = y_train#[:, None]
features = X_train[:, None]

# Fit the RF model with features and labels.
rgr=RF_Model.fit(features, labels)

# Now that we've run our models and fit it, let's create
# dataframes to look at the results
X_test_predict=pd.DataFrame(
    rgr.predict(X_test[:, None])).rename(
    columns={0:'predicted_price'}).set_index('predicted_price')
X_train_predict=pd.DataFrame(
    rgr.predict(X_train[:, None])).rename(
    columns={0:'predicted_price'}).set_index('predicted_price')

# combine the training and testing dataframes to visualize
# and compare.
RF_predict = X_train_predict.append(X_test_predict)

Let’s visualize the price and the predicted_price.

df[['price', 'predicted_price']].plot()

price vs predicted price

That’s really not a bad outcome for a wild guess that lotsize predicts price. Visually, it looks pretty good (although there are definitely errors).

Let’s look at the base level error. First, a quick plot of the ‘difference’ between the two.

df['diff']=df.predicted_price - df.price
df['diff'].plot(kind='bar')

Price vs Predicted Difference

There are some very large errors in there.  Let’s look at some values like R-Squared and Mean Squared Error. First, lets import the appropriate functions from sklearn.

from sklearn.metrics import r2_score

Now, lets look at R-Squared:

RSquared = r2_score(y_train[:, None], X_train_predict.reset_index().values)

R-Squared is 0.6976…or basically 0.7.  That’s not great but not terribly bad either for a random guess. A value of 0.7 (or 70%) tells you that roughly 70% of the variation of the ‘signal’ is explained by the variable used as a predictor.  That’s really not bad in the grand scheme of things.

I could go on with other calculations for error but the point of this post isn’t to show ‘accuracy’ but to show ‘process’ on how how to use Random Forest for forecasting.

Looks for more posts on using random forests for forecasting.


If you want a very good deep-dive into using Random Forest and other statistical methods for prediction, take a look at The Elements of Statistical Learning: Data Mining, Inference, and Prediction, Second Edition (Amazon Affiliate link)

Book Review – Machine Learning With Random Forests And Decision Trees by Scott Hartshorn

Machine Learning With Random Forests And Decision Trees: A Mostly Intuitive Guide, But Also Some PythonI just finished reading Machine Learning With Random Forests And Decision Trees: A Mostly Intuitive Guide, But Also Some Python (amazon affiliate link).

The short review

This is a great introductory book for anyone looking to learn more about Random Forests and Decision Trees. You won’t be an expert after reading this book, but you’ll understand the basic theory and and how to implement random forests in python.

The long(ish) review

This is a short book – only 76 pages. But…those 76 pages are full of good, introductory information on Random Forests and Decision Trees.  Even though I’ve been using random forests and other machine learning approaches in python for years, I can easily see value for people that are just starting out with machine learning and/or random forests. That said, there were a few things in the book that I had either forgotten or didn’t know (Entropy Criteria for example).

While the entire book is excellent, the section on Feature Importance is the best in the book.  This section provides a very good description of the ‘why’ and the ‘how’ of feature importance (and therefore, feature selection) for use in random forests and decision trees.  There are some very good points made in this section regarding how to get started with feature selection and cross validation.

Additionally, the book provides a decent overview of the idea of ‘out-of-sample’ (or ‘Out-of-bag’) data.  I’m a huge believer in keeping some data out of your initial training data set to use for validation after you’ve built your models.

If you’re looking for a good introductory book on random forests and decision trees, pick this one up ( (amazon affiliate link)) …its only $2.99 for the kindle version.  Like I mentioned earlier, this book won’t make you an expert but it will provide a solid grounding to get started on the topic of random forests, decision trees and machine learning.

One negative comment I have on this book is that there is very little python in the book. The book isn’t marketed as strictly a python book, but I would have expected a bit more python in the book to help drive home some of the theory with runnable code. That said, this is a very small negative to the book overall.