The morning sessions will consist of lectures and small
practical exercises introducing the different algorithms, and the afternoon sessions
will consist of programming exercises where
the algorithms will be implemented.
The main programming language will be Python
and all program templates provided in the course will be written in Python.
Prior detailed knowlegde of Python programming is NOT required. However, basic programming skills are required to follow the course.
BACKGROUND TEXTS
- 9.00 - 10.30
- Some more on Deep Learning (Jonas Birkelund Nilsson) [PDF]
- 10.30 - 11.10
- What goes on inside a CNN? (Morten Nielsen) [PDF]
- 11.10 - 11.30
- Doing things in C
- 11.30 - 12.00
- Selection of projects, formation of project groups and start of project work Document for project signup.
- 12.00 - 13.00
- Lunch
- 13.00 - 14.00
- Cont - Selection of projects, formation of project groups and start of project work Document for project signup.
Wednesday 15. - Tuesday 21. June. Project work
- No lectures. Project work
- Projects must be submitted (in PDF format) via campusnet Tuesday 21. of June 11.59
Wedensday, 22. June, Exam
The written exam will be available at the course page
Wedensday 22th of June at 8.59, and need to be handed in
via DTU Learn Wedensday 22th of June before 11.00. The exam is open
book, meaning that you can seek information at the internet. You however
cannot consult anyone, and plagiarism is
seriously condemned. The exam will take place in the usual class room building 321 class room 033.
exam.ipynb (NoteBook)
exam.html (HTML)
Wednesday 22. June (afternoon) and Thursday, 23. June
Project evaluation
Each group has 20 minutes to present their project including 5 minutes for
questions. Note, only the group will be present for the presentation of
the individual projects. The project presentations will take place in the
usual class room building 321 class room 033.
Wednesday 22nd of June
13.00 - 13.20
Group 9
Comparative study of PSSM, ANN, SMM for MHC peptide binding
Lasse Rene, Helene Wegener, Jonathan Møller, Alberte Estad
13.20 - 13.40
Group 6
Gene expression profiling as a tool for cell type prediction
Laura Machado, Jonas Dalsberg Joergensen, Fredrik Junghus
13.40 - 14.00
Group 3
Gibbs sampler approach to the prediction of MHC class II binding motifs including pseudo counts and sequences weighting clustering (Hobohm) techniques
Angeliki Kallia Spentza, Javiera Laing Carmona, Klara Alicja Kotkowska, Mads Cort Nielsen
14.10 - 14.30
Group 15
Comparison of "fake" versus "true" cross-validation
Inigo Miguelez Goyeneche, Sergio Esteban Echeverra, Niels Jakob Larsen, Jake Pham
14.30 - 14.50
Group 1
Method evaluation using cross validation (Comparison between "fake" and "true" CV)
Casper Rasmussen, Line Sandvad Nielsen, Bogdan Capsa
14.50 - 15.10
Group 14
Peptide MHC binding predictions using position specific scoring matrices including pseudo counts and sequences weighting clustering (Hobohm) techniques
Karolina Krzesinska, Dave Rojas, Mads Hartmann, Myeonghyun Jonathan Yoou
15.10 - 15.25
Break
15.25 - 15.45
Group 2
Prediction of transcript factor binding sites in Escherichia coli based on iModulons
Viktor Hesselberg-Thomsen, Jorge Carrasco, Shannara Taylor Parkins, Mikkel Anbo
15.45 - 16.05
Group 4
Comparison of fake versus true cross-validation
Eskild Fisker Angen, Esben Vestergaard Ayan, Chen Chen, Yi Huang
16.05 - 16.25
Group 5
Comparative study of PSSM, ANN, SMM for peptide MHC binding
Chatpakorn Christiansen, Aleksander Moldt Haack, Camilla Reiter Elbæk, Yat-Tsai Richie Wan
Thursday 23rd of June
9.00 - 9.20
Group 7
Comparative study of PSSM, ANN, SMM for MHC peptide binding
Prince Ravi Leow, Adikrishna Murali Mohan, Baris Kara
9.20 - 9.40
Group 8
Comparative study of PSSM, ANN, SMM for MHC peptide binding
Siddhi Jain, Dimitrios Loukas, Christopher Sonne Hansen, Lasse Schnell Danielsen
9.40 - 10.00
Group 11
Gibbs sampler approach to the prediction of MHC class II binding motifs including pseudo counts and sequences weighting clustering (Hobohm) techniques
Maurice Kappelmeyer, Jonathan Funk, Alem Gusinac, Eric Bautista
10.10 - 10.30
Group 12
Comparative study of PSSM, ANN, SMM for MHC peptide binding
Enrique Martinez Diez, Aldis Helga Bjorgvinsdottir, Bernat Godayol Farran
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