Course is held online at zoom

Contact: claudio.mirabello@scilifelab.se; bengt.sennblad@scilifelab.se

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Schedule

Monday 2020-12-07

09:00 - 10.00 Introduction gh / html (Bengt, Claudio, Olga)
gwd path: session_introduction/session_introduction.ipynb

10:00 - 11:00 Setting up: Conda environment and GitHub repository. (Claudio, Bengt, Olga)
Instructions on HackMD

11.00 - 12.00 ANN building blocks 1 gh / html (Bengt, Claudio, Olga)
gwd path: session_annBuildingBlocks/session_annBuildingBlocks_1.ipynb

12:00 - 13:00 lunch

13.00 - 14.00 ANN building blocks 2 gh / html (Bengt, Claudio, Olga)
gwd path: session_annBuildingBlocks/session_annBuildingBlocks_2.ipynb

14.00 - 15.00 ANN building blocks 3 gh / html (Bengt, Claudio, Olga)
gwd path: session_annBuildingBlocks/session_annBuildingBlocks_1.ipynb

15.00 - 17.00 ANN building blocks Lab keras gh (Claudio, Bengt, Olga)
gwd path: session_annBuildingBlocks/lab_keras/introduction_to_keras.ipynb

Tuesday 2020-12-08

9.00 - 12.00 ANN building blocks Lab keras cntd. gh (Claudio, Bengt, Olga)
gwd path: session_annBuildingBlocks/lab_keras/introduction_to_keras.ipynb

12:00 - 13:00 lunch

13.00 - 14.00 Convolutional Neural Networks 1 gh html (Christophe, Claudio, Bengt)
gwd path: session_convolutionalNeuralNetworks/Lecture/CNN_lecture_1_classification.ipynb

14.00 - 15.30 Convolutional Neural Networks 1 gh (Christophe, Claudio, Bengt)
gwd path: session_convolutionalNeuralNetworks/Labs/CNN_Keras_lab_1.ipynb

15.30 - 16.00 Convolutional Neural Networks 2 gh html (Christophe, Claudio, Bengt)
gwd path: session_convolutionalNeuralNetworks/Lecture/CNN_lecture_2_segmentation.ipynb

16.00 - 17.00 Convolutional Neural Networks 2 gh (Christophe, Claudio, Bengt)
gwd path: session_convolutionalNeuralNetworks/Labs/CNN_Keras_lab_2.ipynb

Wednesday 2020-12-09

9.00 - 10.00 Keras in R – autoencoders Lecture lecture html
lab html
(Marcin, Claudio, Bengt)
lecture gwd path: session_rAutoencoders/lecture_autoencoders_r/lecture_autoencoders.html lecture gwd path: session_rAutoencoders/lab_autoencoder_hapmap.html

10.00 - 12.00 Keras in R – autoencoders Lab1 html
(Marcin, Claudio, Bengt)
gwd path: session_rAutoencoders/lab_autoencoder_hapmap.html

12:00 - 13:00 lunch

13.00 - 15.00 Recurrent Neural Networks 1 gh (Dan, Per, Claudio, Bengt)
gwd path: session_recurrentNeuralNetworks/lecture-and-exercises.ipynb

15.00 - 17.00 Recurrent Neural Networks 2 Lab Introduction gh
Lab gh

(Per, Dan, Claudio, Bengt)
gwd path Introduction: session_recurrentNeuralNetworks/lab_recombination_rate/slides.ipynb
gwd path Lab: session_recurrentNeuralNetworks/lab_recombination_rate/recrate_exercise.ipynb

Thursday 2020-12-10

9.00 - 12.00 Good practices of project design lecture lecture gh
Lab on Train/Validation splitting gh
(Claudio, Bengt, Eva)
lecture gwd path: session_goodPracticesDatasetDesign/good_practices_project_design.ipynb gwd path: session_goodPracticesDatasetDesign/lab_validation/rigorous_train_validation_splitting.ipynb

12:00 - 13:00 lunch

13.00 - 15.00 Good practices of project design: Lab on target leakage gh (Claudio, Bengt, Eva)
gwd path: session_goodPracticesDatasetDesign/lab_targetLeakage/investigating_target_leakage.ipynb

15.00 - 17.00 Good practices of project design: Lab on transfer learning gh (Claudio, Bengt, Eva)
gwd path: session_goodPracticesDatasetDesign/lab_transferLearning/transfer_learning.ipynb

Friday 2020-12-11

9.00 - 10.00 Bayesian Neural Networks (Nikolay, Claudio, Bengt)

Main lecture file:

html DeepLearningForLifeSciences_Oskolkov gwd path: session_BNN/DeepLearningForLifeSciences_Oskolkov.ppt

Cited notebooks:

html BayesianDeepLearning gwd path: session_BNN/BayesianDeepLearning.ipynb
html CIFAR10_Bayesian gwd path: session_BNN/CIFAR10_Bayesian.ipynb
html DeepLearningAncientDNA gwd path:session_BNN/DeepLearningAncientDNA.ipynb
html DeepLearningDataIntegration gwd path: session_BNN/DeepLearningDataIntegration.ipynb
html DeepLearningMetagenomics gwd path:session_BNN/DeepLearningMetagenomics.ipynb
html DeepLearningNeanderthalIntrogression gwd path: session_BNN/DeepLearningNeanderthalIntrogression.ipynb
html DeepLearningSingleCellipynb gwd_path: session_BNN/DeepLearningSingleCellipynb
html HumanProteinAtlas
gwd path: session_BNN/HumanProteinAtlas.ipynb
html MO_Melander_DeepLearning
gwd path: session_BNN/MO_Melander_DeepLearning.ipynb
html segmentation_maskrcnn gwd path: session_BNN/segmentation_maskrcnn.ipynb

10.00 - 11.00 convolutional Autoencoders gh html (Carl, Claudio, Bengt)

11.00 - 12.00 Buffert time/Extra lab time (Claudio, Bengt,…)

12:00 - 13:00 lunch

13.00 - 14.00 Feedback session (HackMD documetn will be posted on the course slack channel) (Claudio, Bengt, …)

14.00 - 15.00 Extra lab time (Claudio, Bengt,…)