Máster en Bioinformática Aplicada a Medicina Personalizada y Salud (Curso 2022-2023)
- Day 1 (01.03.2023):
- 1/2 Theory
- 1/2 Practice: Setting up the environment for the Hands-On practice sessions
- Day 2 (02.03.2022):
- 1/2 Theory
- 1/2 Theory: presentation of a real case-study (the PolyDeep project)
- Day 3 (03.03.2022):
- 1/2 Theory
- 1/2 Project: Session I (project presentation and creation of work groups)
- Day 4 (13.03.2023):
- Practice: Hands-On (Machine Learning Basics in Python with scikit-learn Part I)
- Day 5 (14.03.2023):
- Practice: Hands-On (Machine Learning Basics in Python with scikit-learn Part II)
- Day 6 (15.03.2023):
- 1/2 Theory
- 1/2 Project: Session II (with problem and dataset presentation)
- Day 7 (16.03.2023):
- Project: Session III
- Day 8 (17.03.2023):
- Project Session: IV (with results presentation)
The theory slides are available here.
Follow the steps in the official page to install Docker https://docs.docker.com/engine/install/ubuntu/
Make sure the docker user group exists.
sudo groupadd docker
Add your user to the docker group.
sudo usermod -aG docker $USER
Reboot the system and the changes will be applied.
Run the following comands to pull the Docker image for the hands-on practice sessions:
docker pull singgroup/jupyter-machine-learning:2022-2023
During the hands-on sessions (Machine Learning Basics in Python with scikit-learn), we are going to use the Breast Cancer Data
available at the UCI Machine Learning Repository. More information about this dataset can be found here and here.
Go to an empty folder and run the following commands to download the data:
mkdir data
wget https://archive.ics.uci.edu/ml/machine-learning-databases/breast-cancer-wisconsin/wdbc.data -O data/wdbc.data
sed -i '1iid,diagnosis,radius_mean,texture_mean,perimeter_mean,area_mean,smoothness_mean,compactness_mean,concavity_mean,concave points_mean,symmetry_mean,fractal_dimension_mean,radius_se,texture_se,perimeter_se,area_se,smoothness_se,compactness_se,concavity_se,concave_points_se,symmetry_se,fractal_dimension_se,radius_worst,texture_worst,perimeter_worst,area_worst,smoothness_worst,compactness_worst,concavity_worst,concave points_worst,symmetry_worst,fractal_dimension_worst' data/wdbc.data
Alternatively, the file is also available here.
Clone or download this repository and then run the following command (from the local repository) to use the Docker image to start a Jupyter notebook with the required libraries already installed:
docker run --rm -p 8888:8888 -v "$(pwd)":"$(pwd)" -w "$(pwd)" singgroup/jupyter-machine-learning:2022-2023
The resources/notebook-ml-1.ipynb
file contains the notebook to develop during these sessions.
The information about the project is available here.
- Practical Statistics for Data Scientists: 50 Essential Concepts
- Hands-On Machine Learning with Scikit-Learn, Keras, and TensorFlow, 2nd Edition
- Ten quick tips for machine learning in computational biology [10.1186/s13040-017-0155-3]
- LIBSVM -- A Library for Support Vector Machines
- scikit-learn: machine learning in Python