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Algorithms in Bioinformatics - #27625

Information for participants

GENERAL SCHEDULE
Lectures will be in the morning from 9.00 - 12.00, and exercises in the afternoon from 13.00 - 17.00.

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 C, and all program templates provided in the course will be written in C. Prior knowlegde of C programming is NOT required. However, basic programming skills are required to follow the course.

LITERATURE: The course curriculum consists of review paper and selected chapters from Immunological Bioinformatics, Lund et al., MIT Press, 2005. All course material will be made available online during the course. All course material is available here Course material.

PROGRAMS AND TOOLS


Course Programme
Please note that the programme is updated on a regular basis - click the 'refresh' button once in a while to make sure that you have the most updated information

LITERATURE:

O Monday, 2. January

Introduction to course, UNIX and C-programming crash course 101
Morten Nielsen

  • BACKGROUND TEXTS
    9.00 - 9.15
    Introduction to course
    Introduction to course. [PDF] .
    9.15 - 9.35
    Introduction to the immune system
    Introduction to the immune system. [PDF] .
    9.35 - 9.45
    Performance measures
    Performance measures. [PDF] .
    9.45 - 10.00
    Coffe break
    10.00 - 12.00
    Unix crash course
    A UNIX/Linux crash course
    Answers to part 3 (gawk)
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Doing it on your local machine
    C-programming crash course 101 - first part (loops, data-structure, sub-routines, variables, input/output)
    C-programming crash course, part 1
    C-programming crash course 101 - second part (Linked lists, dynamic memory allocation, pointers)
    C-programming crash course, part 2.
    Answers to C-programming exercises part 1 and 2


    O Tuesday, 3. January
    Your first C program, Weight matrix (PSSM) construction, and Psi-Blast
    Morten Nielsen

  • BACKGROUND TEXTS
    9.00 - 9.15
    Questions to yesterdays lectures/exercise
    A few notes on sequence alignment
    Some notes on sequence alignment [PDF] .
    9.15 - 10.30
    Some notes on command line parsing. [PDF].
    The development of the first c-program working using command line parsing.
    C-programming - Part 3. Your first c program.
    Answers to C-programming exercise - Part 2.
    10.30 - 10.45
    Blosum scoring matrices [PDF] .
    10.45 - 12.00
    Weight matrix construction. [PDF].
    Handout. Estimation of pseudo counts
    Answer
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Implementation of PSSM construction from pre-aligned sequences including pseudo count correction for low counts and sequence clustering
    PSSM construction and evaluation
    PSSM answers


    O Wednesday, 4. January

    Sequence alignment and Dynamic programming
    Morten Nielsen

    BACKGROUND TEXTS
    9.00 - 9.15
    Questions to yesterdays lectures/exercises
    9.15 - 11.00
    Sequence alignment [PDF] .
    Handout (O3)
    Handout (O2)
    Handout answers
    11.00 - 12.00
    Blast alignment heuristics, Psi-Blast, and sequence profiles [PDF] .
    Psi-Blast handout.
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Implementation of the Smith-Waterman Dynamic programming algorithm
    Matrix dumps from alignment programs (to be used for debugging)
    Answers to sequence alignment exercise

    O Thursday, 5. January
    Data redundancy reduction algortihms
    Optimizations methods
    Gibbs sampling
    Morten Nielsen

    BACKGROUND TEXTS
    9.00 - 9.15
    Questions to yesterdays lectures
    9.15 - 10.00
    Data redundancy reduction algorithms (Hobohm1 and Hobohm2). [ PDF].
    10.00 - 10.45
    Optimization procedures - Gradient decent, Monte Carlo
    Optimization procedures [PDF]
    GD handout
    10.45 - 11.00
    Break
    11.00 - 12.00
    Gibbs sampling and Gibbs clustering
    Gibbs sampling. [PDF] .
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Hobohm redundancy reduction algorithms
    Answers to Hobohm programming exercise
    Implementating of a Gibbs sampling algorithm for prediction of MHC class II binding
    Answers

    O Friday, 6. January
    Hidden Markov Models
    Morten Nielsen

  • BACKGROUND TEXTS
    9.00 - 9.15
    Questions to yesterdays lectures
    9.15 - 11.00
    Hidden Markov models (with a break around 10.30)
    Viterbi decoding, Forward/Backward algorithm, Posterior decoding, Baum-Welsh learning
    HMM slides [ PDF].
    Viterbi Handout
    Answers
    Forward Handout
    Answers
    11.00 - 12.00
    Profile Hidden Markov Models.
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Implementation of Viterbi and posterior decoding.
    Hidden Markov exercises
    Answer to Hidden Markov exercises

    O Monday, 9. January
    Cross validation and training of data driven prediction methods. Stabilization matrix method (SMM)
    Morten Nielsen

  • BACKGROUND TEXTS
    9.00 - 9.15
    Questions to yesterdays lectures/exercise
    9.15 - 9.45
    Cross validation and training of data driven prediction methods
    Cross-validation, overfitting and method evaluation. [PDF] .
    9.45 - 10.15
    Stabilization matrix method (SMM) background
    SMM background. [PDF] .
    SMM handout
    10.15 - 10.30
    Break
    10.30 - 12.00
    Implementing and evaluating SMM algorithms using cross-validation
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Continuation of exercise
    Answers

    O Tuesday, 10. January
    Artificial neural networks - I. Sequence encoding and feedforward algorithm
    Morten Nielsen

  • BACKGROUND TEXTS
    • Immunological Bioinformatics. MIT Press. Chapter 4.
    • Background
    • Sequence encoding
    • Feed forward algorithm
    • Back-propagation and neural network training
    9.00 - 9.15
    Questions to yesterdays lectures/exercise
    9.15 - 10.30
    Artificial neural networks. [PDF] .
    Handout
    10.30 - 10.40
    Break
    10.40 - 12.00
    Network training - backpropagation
    Training of artificial neural networks.. [PDF] .
    Handout
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Implementation of sequence encoding and feed forward algorithm
    Network part I answers
    Implementation of Implementation of back-propagation and neural network training
    Network part 2 answers

    O Wednesday, 11. January
    Project work and an introduction to the Theano artificial neural network library
    Morten Nielsen

  • BACKGROUND TEXTS
    • Immunological Bioinformatics. MIT Press. Chapter 4.
    9.00 - 9.15
    Questions to yesterdays lectures/exercise
    9.15 - 10.00
    Description of potential projects and formation of groups
    Project suggestions, and descriptions.
    10.00 - 11.00
    NNAlign, alignment using ANN's [PDF]
    Trick for ANN training [PDF.
    11.00 - 12.00
    The Lasagne artificial neural network library (Vanessa Jurtz)
    [PDF].
    12.00 - 13.00
    Lunch
    13.00 - 17.00
    Using the Lasagne python library to construct ANN models (Vanessa Jurtz)
    Exercise.
    Google doc to share hyperparameters.


    O Thursday 12. - Wednesday 18. January. Project work
    No lectures. Project work
    Projects must be submitted (in PDF format) via campusnet Wednesday 18. of January 23.59 at the latest.

    O Friday, 20. January. 8.30-17.50

    Project evaluation and Exam (in building 208 room 062, where we had the classes)
    Program exam
    7.55 - 8.30
    s161282 Arnór Ingi Sigurdsson
    s161363 Quoc Tien Au

    8.30 - 9.15
    s170357 Christian Brinch Mollerup
    s123134 Sara Eiriksdottir Andersen
    s101577 Frederik Duus Møller

    9.15 - 9.50
    s112835 Mathias Blicher Bjerregård
    s143849 Asbjørn Eller Skaarup

    9.50 - 10.35
    s123496 Carina Skaarup
    s103495 Rikke Linnemann Nielsen
    s151038 Judit Szarvas

    10.35 - 11.20
    s072198 Sandra Christine Andersen
    s122868 Line Meyhoff Aastrup
    s123343 Thanh Thien Nguyen

    11.20 - 11.55
    s143829 Marianne Helenius
    s143846 Mikkel Ammentorp Storm

    Lunch 11.55 - 12.45

    12.45 - 13.20
    s123122 Christian Kronborg Cantalapiedra
    Loan Vulliard

    13.20 - 14.05
    s134891 Christina Bligaard Pedersen
    s134888 Camilla Koldbæk Lemvigh
    s134921 Rosa Lundbye Allesøe

    14.05 - 14.50
    s134915 Ulrika Boulund
    s134901 Malene Revsbech Christiansen
    s134903 Mette Simone Aae Madsen

    14.50 - 15.25
    s146261 Arun Kumar Somavarapu
    s161946 Takahiro Shinoda

    15.25 - 16.00
    s103025 Søren Norge Andreassen
    s133507 Rasmus Villebro

    16.00 - 16.45
    s134885 Helle Rus Povlsen
    s102240 Emma Christine Jappe
    s110719 Joachim Johansen

    16.45 - 17.20
    s161197 Rasa Audange Muktupavela
    s151164 Adrian Gabriel Zucco

    17.20 - 17.40
    S151202 Baosheng Hou


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