Machine Learning for Biologists (Mumbai, 2018-05-09)

Introduction

• A one day workshop that offers a basic introduction into Machine Learning methods with a focus on biological applications. In a practical part the participants will learn how to apply the gained theoretical knowledge using Python and the scikit-learn library.

Topics

• General instroduction
• Feauture
• Supervised Learning
  • Linear Models
  • Suport Vector Machines
  • k Nearest Neighbors
  • Decision trees / Random forests / Boosting
  • Naive Bayes Classifiers
  • Neural Networks and Deep Learning
• Unsupervised Learning
  • Clustering
  • Dimension reduction with PCA and t-SNE
• Reinforcement Learning

Audience / Requirements

You should have basic Python programming skills and know how to use Jupyter notebook. Furthermore you need to bring a laptop with the software installation described below.

Reading recommendations

• TBA

Installation instruction

Python is a popular language for research computing, and great for general-purpose programming as well. Installing all of its research packages individually can be a bit difficult, so we recommend Anaconda, an all-in-one installer.

Regardless of how you choose to install it, please make sure you install Python version 3.x (e.g., 3.6 is fine). Additionally you need an installation of scikit-learn and matplotlib (the recommended Anaconda installation contains these libraries).

We will teach Python using the Jupyter notebook, a programming environment that runs in a web browser. For this to work you will need a reasonably up-to-date browser. The current versions of the Chrome, Safari and Firefox browsers are all supported (some older browsers, including Internet Explorer version 9 and below, are not).

Windows

• Video Tutorial

1. Open https://www.anaconda.com/download/#windows with your web browser.
2. Download the Python 3 installer for Windows.
3. Install Python 3 using all of the defaults for installation except make sure to check Make Anaconda the default Python.

macOS

• Video Tutorial

1. Open https://www.anaconda.com/download/#macos with your web browser.
2. Download the Python 3 installer for OS X.
3. Install Python 3 using all of the defaults for installation.

Linux

1. Open https://www.anaconda.com/download/#linux with your web browser.
2. Download the Python 3 installer for Linux. (The installation requires using the shell. If you aren't comfortable doing the installation yourself stop here and request help at the workshop.)
3. Open a terminal window.
4. Type

bash Anaconda3-

and then press tab. The name of the file you just downloaded should appear. If it does not, navigate to the folder where you downloaded the file, for example with:

cd Downloads

Then, try again.

5. Press enter. You will follow the text-only prompts. To move through the text, press the space key. Type yes and press enter to approve the license. Press enter to approve the default location for the files. Type yes and press enter to prepend Anaconda to your PATH (this makes the Anaconda distribution the default Python).

6. Close the terminal window.

Reuse of this content

CC-BY Konrad Förstner and Till Sauerwein