261-5120-00L Machine Learning for Health Care (Spring 2020)

Abstract
The course will review the most relevant methods and applications of Machine Learning in Biomedicine, discuss the main challenges they present and their current technical problems.

Objective
During the last years, we have observed a rapid growth in the field of Machine Learning (ML), mainly due to improvements in ML algorithms, the increase of data availability and a reduction in computing costs. This growth is having a profound impact in biomedical applications, where the great variety of tasks and data types enables us to get benefit of ML algorithms in many different ways. In this course we will review the most relevant methods and applications of ML in biomedicine, discuss the main challenges they present and their current technical solutions.

Content
The course will consist of four topic clusters that will cover the most relevant applications of ML in Biomedicine:

1) Structured time series: Temporal time series of structured data often appear in biomedical datasets, presenting challenges as containing variables with different periodicities, being conditioned by static data, etc.
2) Medical notes: Vast amount of medical observations are stored in the form of free text, we will analyze stategies for extracting knowledge from them.
3) Medical images: Images are a fundamental piece of information in many medical disciplines. We will study how to train ML algorithms with them.
4) Genomics data: ML in genomics is still an emerging subfield, but given that genomics data are arguably the most extensive and complex datasets that can be found in biomedicine, it is expected that many relevant ML applications will arise in the near future. We will review and discuss current applications and challenges.

Prerequisites / Notice
Data Structures & Algorithms, Introduction to Machine Learning, Statistics/Probability, Programming in Python, Unix Command Line

Relation to Course 261-5100-00 Computational Biomedicine: This course is a continuation of the previous course with new topics related to medical data and machine learning. The format of Computational Biomedicine II will also be different. It is helpful but not essential to attend Computational Biomedicine before attending Computational Biomedicine II.

Location

The lecture will be held at ETH in ETF C 1.

Course Overview

Projects

Project 1: ECG time series
Deadline: 18.03.2020
Description: see slides of tutorial 2 (pp 31-44)
Data: download here
Codeshare: link to polybox (password sent by email)

Project 2: NLP tasks
Deadline: 09.04.2020
Project 2 description and data

Project 3: Image segmentation
Deadline: 29.04.2020
Project 3 description and data
Test Labels: download here

Project 4: Splice site prediction
Deadline: 20.05.2020
Project 4 description and data