- The course
- Before the course
- During the course
- Feature Importance
- Questions
June 11th, 2019
Outline
The Course: ML in Medical Bioinformatics
- Offered by MedBioInfo (The Swedish Research School in Medical Bioinformatics)
- Location: Linköping University, Sweden
- Access the course material here
- Easy to intermediate level
- Covers the most essential/practical ML for applications
- Excellent lecturers
- Manuela Zucknick (Statistician)
- Claudio Mirabello (NN expert)
- Almost non-medical … but I highly recommend it nonetheless!
Before the Course
Preparatory tasks (1 week)
- Most tasks were Python-based
- Use scikit-learn module for teaching ML
Reading
During the course
Practical Exercises
- Use jupyter-notebooks
- Discussion: R vs Python for ML (beginners vs advanced)
- Know your data, know your methods!
Applications in research and reproducibility (R)
Neural Networks and Deep Learning
Feature Importance
… or why John participated in the course!
Can ML help us find biomarkers?
Methods
- Variable selection
- Correlation plots between the features and the response
- Linear Regression Models with Regularization (LASSO, Elastic Nets)
- Random Forests (feature selection is embedded in decision trees)
- Use combination of methods!
- Neural Networks can also work but need a lot of engineering
Questions
