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 but will make following the course very much easier. However, basic programming skills are required to follow the course.
PROGRAMS AND TOOLS
Each group has 15 minutes to present their project including 5 minutes for questions. Note, only the group will be present for the presentation of the individual projects. After the present, each member of the group is evaluated in a oral exam covering the complete course curriculum.
The exam will take place in the usual class room, building 210, room 042/048
Wednesday June 25th 8.00 - 8.50 Group 1 Gibbs sampler approach to the prediction of SGBP binding sites including pseudo counts and sequences weighting clustering (Hobohm) techniques Natalia (s250668), Maria (s250352), Xiaopeng (s194408) 8.50 - 9.25 Group 2 Comparation of FFNN and NNAlign for MHC binding prediction Marco (s243116), Martina (s243118) 9.25 - 10.10 Group 3 Comparative study of PSSM, ANN, SMM for peptide MHC binding Nicoline (s203530), Mathilde (s215063), Alberte (s215067) and Kristine (s215098) 10.20 - 11.05 Group 4 Compare PSSM, ANN, and SMM - predict MHC binding Annekatrine (s225074), Bunia (s215085), Emma (s215090) 11.05 - 11.50 Group 5 Comparative study using ANN with different sequence encoding schemes Magnus (s204581), Oliver (s204692), Johanna (s204657), 12.45 - 13.40 Group 6 Comparative study of PSSM, ANN, SMM for peptide MHC binding Xavi (s243360), Luis (s243302), Miguel (s243284) and Natalia (s243547) 13.40 - 14.35 Group 7 Comparative study of ANN with sparse, blosum and BERT encoding Astrid (s193254), Jui-Tse (s244401), Dinis (s212484), Sebastian (s233425) 14.35 - 14.50 Karolina Tudelska (s212846) 14.50 - 15.05 Saxe í Dali Wagner (s204559) Thursday June 26th 9.00 - 9.55 Group 8 Comparative study of ANN with different peptide encodings Pablo (s243357), Victor (s243634), Antonio (s243171), Elena (s243312) 9.55 - 10.40 Group 9 HOBOHM-1 redundancy filtering of MHC class I binders in training data Tobias (s215105), Asbjørn (s215045), and Henrik (s215065) 10.40 - 11.25 Group 10 Implementation of a Baum-Welsh algorithm and/or Gibbs-sampling method for training of an HMM Maximo (s247270), Tomas (s250441), Mikkel (s184240) 11.25 - 12.20 Group 11 Comparative study of FFNN and NNAlign for peptide MHC binding Mei Lin (s194685), Magnus (s224188), Suru (s233406), Anne Sofie (s244028)