Skip to content

Instantly share code, notes, and snippets.

@mdfarragher
Created Jul 22, 2020
Embed
What would you like to do?

Assignment: Predict heart disease risk

In this assignment you're going to build an app that can predict the heart disease risk in a group of patients.

The first thing you will need for your app is a data file with patients, their medical info, and their heart disease risk assessment. We're going to use the famous UCI Heart Disease Dataset which has real-life data from 303 patients.

Download the Processed Cleveland Data file and save it as processed.cleveland.data.csv.

The data file looks like this:

Processed Cleveland Data

It’s a CSV file with 14 columns of information:

  • Age
  • Sex: 1 = male, 0 = female
  • Chest Pain Type: 1 = typical angina, 2 = atypical angina , 3 = non-anginal pain, 4 = asymptomatic
  • Resting blood pressure in mm Hg on admission to the hospital
  • Serum cholesterol in mg/dl
  • Fasting blood sugar > 120 mg/dl: 1 = true; 0 = false
  • Resting EKG results: 0 = normal, 1 = having ST-T wave abnormality, 2 = showing probable or definite left ventricular hypertrophy by Estes’ criteria
  • Maximum heart rate achieved
  • Exercise induced angina: 1 = yes; 0 = no
  • ST depression induced by exercise relative to rest
  • Slope of the peak exercise ST segment: 1 = up-sloping, 2 = flat, 3 = down-sloping
  • Number of major vessels (0–3) colored by fluoroscopy
  • Thallium heart scan results: 3 = normal, 6 = fixed defect, 7 = reversible defect
  • Diagnosis of heart disease: 0 = normal risk, 1-4 = elevated risk

The first 13 columns are patient diagnostic information, and the last column is the diagnosis: 0 means a healthy patient, and values 1-4 mean an elevated risk of heart disease.

You are going to build a binary classification machine learning model that reads in all 13 columns of patient information, and then makes a prediction for the heart disease risk.

Let’s get started. You need to build a new application from scratch by opening a terminal and creating a new NET Core console project:

https://gist.github.com/42b033a0eaa2d974c6a889b64994bf67

Now install the following ML.NET packages:

https://gist.github.com/e79ddad3ad8a98f1ad5fb0318d56974d

Now you are ready to add some types. You’ll need one to hold patient info, and one to hold your model predictions.

Replace the contents of the Program.fs file with this:

https://gist.github.com/e2f39403546071ea12e4a0bea16d2f10

The HeartData class holds one single patient record. Note how each field is tagged with a LoadColumn attribute that tells the CSV data loading code which column to import data from.

There's also a HeartPrediction class which will hold a single heart disease prediction. There's a boolean Prediction, a Probability value, and the Score the model will assign to the prediction.

Note the CLIMutable attribute that tells F# that we want a 'C#-style' class implementation with a default constructor and setter functions for every property. Without this attribute the compiler would generate an F#-style immutable class with read-only properties and no default constructor. The ML.NET library cannot handle immutable classes.

Now look at the final Diagnosis column in the data file. Our label is an integer value between 0-4, with 0 meaning 'no risk' and 1-4 meaning 'elevated risk'.

But you're building a Binary Classifier which means your model needs to be trained on boolean labels.

So you'll have to somehow convert the 'raw' numeric label (stored in the Diagnosis field) to a boolean value.

To set that up, you'll need a helper type:

https://gist.github.com/4afd6ed75afe4c7779abbd2a7d093552

The ToLabel type contains the label converted to a boolean value. We'll set up that conversion in a minute.

Also note the mutable keyword. By default F# types are immutable and the compiler will prevent us from assigning to any property after the type has been instantiated. The mutable keyword tells the compiler to create a mutable type instead and allow property assignments after construction.

Now you're going to load the training data in memory:

https://gist.github.com/b8de6eae29d9a530ac8bb3c390a5569f

This code uses the method LoadFromTextFile to load the CSV data directly into memory. The field annotations we set up earlier tell the function how to store the loaded data in the HeartData class.

The TrainTestSplit function then splits the data into a training partition with 80% of the data and a test partition with 20% of the data.

Now you’re ready to start building the machine learning model:

https://gist.github.com/a3315286e9c987fe02968727b2d20ede

Machine learning models in ML.NET are built with pipelines, which are sequences of data-loading, transformation, and learning components.

This pipeline has the following components:

  • A CustomMapping that transforms the numeric label to a boolean value. We define 0 values as healthy, and anything above 0 as an elevated risk.
  • Concatenate which combines all input data columns into a single column called 'Features'. This is a required step because ML.NET can only train on a single input column.
  • A FastTree classification learner which will train the model to make accurate predictions.

The FastTreeBinaryClassificationTrainer is a very nice training algorithm that uses gradient boosting, a machine learning technique for classification problems.

With the pipeline fully assembled, we can train the model by piping the TrainSet into the Fit function.

You now have a fully- trained model. So now it's time to take the test partition, predict the diagnosis for each patient, and calculate the accuracy metrics of the model:

https://gist.github.com/7f6ca2af491b1c46ff2ddf7f2e55b0ae

This code pipes the TestSet into model.Transform to set up a prediction for every patient in the set, and then pipes the predictions into Evaluate to compare these predictions to the ground truth and automatically calculate all evaluation metrics:

  • Accuracy: this is the number of correct predictions divided by the total number of predictions.
  • AreaUnderRocCurve: a metric that indicates how accurate the model is: 0 = the model is wrong all the time, 0.5 = the model produces random output, 1 = the model is correct all the time. An AUC of 0.8 or higher is considered good.
  • AreaUnderPrecisionRecallCurve: an alternate AUC metric that performs better for heavily imbalanced datasets with many more negative results than positive.
  • F1Score: this is a metric that strikes a balance between Precision and Recall. It’s useful for imbalanced datasets with many more negative results than positive.
  • LogLoss: this is a metric that expresses the size of the error in the predictions the model is making. A logloss of zero means every prediction is correct, and the loss value rises as the model makes more and more mistakes.
  • LogLossReduction: this metric is also called the Reduction in Information Gain (RIG). It expresses the probability that the model’s predictions are better than random chance.
  • PositivePrecision: also called ‘Precision’, this is the fraction of positive predictions that are correct. This is a good metric to use when the cost of a false positive prediction is high.
  • PositiveRecall: also called ‘Recall’, this is the fraction of positive predictions out of all positive cases. This is a good metric to use when the cost of a false negative is high.
  • NegativePrecision: this is the fraction of negative predictions that are correct.
  • NegativeRecall: this is the fraction of negative predictions out of all negative cases.

When monitoring heart disease, you definitely want to avoid false negatives because you don’t want to be sending high-risk patients home and telling them everything is okay.

You also want to avoid false positives, but they are a lot better than a false negative because later tests would probably discover that the patient is healthy after all.

To wrap up, You’re going to create a new patient record and ask the model to make a prediction:

https://gist.github.com/81ad719d8142c3fb3e90c10a4c6af821

This code uses the CreatePredictionEngine method to set up a prediction engine, and then creates a new patient record for a 36-year old male with asymptomatic chest pain and a bunch of other medical info.

We then pipe the patient record into the Predict function and display the diagnosis.

What’s the model going to predict?

Time to find out. Go to your terminal and run your code:

https://gist.github.com/599e9666b30a629db8e5b4d438bf6112

What results do you get? What is your accuracy, precision, recall, AUC, AUCPRC, and F1 value?

Is this dataset balanced? Which metrics should you use to evaluate your model? And what do the values say about the accuracy of your model?

And what about our patient? What did your model predict?

Think about the code in this assignment. How could you improve the accuracy of the model? What are your best AUC and AUCPRC values?

Share your results in our group!

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment