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Bioinformatics with Python Cookbook

You're reading from   Bioinformatics with Python Cookbook Learn how to use modern Python bioinformatics libraries and applications to do cutting-edge research in computational biology

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Product type Hardcover
Published in Sep 2022
Publisher
ISBN-13 9781803236421
Length 360 pages
Edition 1st Edition
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Author (1):
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Tiago Antao Tiago Antao
Author Profile Icon Tiago Antao
Tiago Antao
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Toc

Table of Contents (15) Chapters Close

Preface 1. Chapter 1: Python and the Surrounding Software Ecology 2. Chapter 2: Getting to Know NumPy, pandas, Arrow, and Matplotlib FREE CHAPTER 3. Chapter 3: Next-Generation Sequencing 4. Chapter 4: Advanced NGS Data Processing 5. Chapter 5: Working with Genomes 6. Chapter 6: Population Genetics 7. Chapter 7: Phylogenetics 8. Chapter 8: Using the Protein Data Bank 9. Chapter 9: Bioinformatics Pipelines 10. Chapter 10: Machine Learning for Bioinformatics 11. Chapter 11: Parallel Processing with Dask and Zarr 12. Chapter 12: Functional Programming for Bioinformatics 13. Index 14. Other Books You May Enjoy

Predicting breast cancer outcomes using Random Forests

We are now going to predict the outcomes for some patients using Random Forests. A random forest is an ensemble method (it will use several instances of other machine learning algorithms) that uses many decision trees to arrive at robust conclusions about the data. We are going to use the same example as in the previous recipe: breast cancer traits and outcomes.

This recipe has two main goals: to introduce you to random forests and issues regarding the training of machine learning algorithms.

Getting ready

The code for this recipe can be found in Chapter10/Random_Forest.py.

How to do it…

Take a look at the code:

  1. We start, as in the previous recipe, by getting rid of samples with missing information:
    import pandas as pd
    import numpy as np
    import pandas as pd
    from sklearn.ensemble import RandomForestClassifier
    from sklearn.model_selection import train_test_split
    from sklearn.tree import export_graphviz...
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