1. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Neural Network training Morten Nielsen, CBS, BioCentrum, DTU

2. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Neural network programs How –Classification neural network Howlin –Real value neural network Nnlinplayer –Neural network player i.e. no training

3. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU How2doit How and howlin clumsy but very fast and efficient Fortran programs Three important files –Parameter file; howlin.dathowlin.dat –Data fileData file –Synaps (weight) fileSynaps

4. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Output Format of output fileoutput file Plotting training and test performance –howlinplot fileout

5. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Neural networks Neural networks can learn higher order correlations! –What does this mean? 0 0 => 0 0 1 => 1 1 0 => 1 1 1 => 0 No linear function can learn this pattern

6. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Neural networks w 11 w 12 v1v1 w 21 w 22 v2v2 w 11 =1, w 12 =-1 w 21 =1 w 22 =-1 V 1 = 0.5 v 2 = -0.5

7. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU nnlinplayer Use weight file(s) to generate neural network predictions Format –nnlinplayer synapsfilelist inputfilesynapsfilelistinputfile Makes consensus prediction over N neural networks Input file must be generated separately –seq2inp data Using pipes –seq2inp data | nnlinplayet synlist --

8. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU how Classification network Generates input data directly from sequence –RIISSIEQKEENKGGEDKLKMIREYRQMVE Input is how fileshow files

9. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Useful programs fasta2pep seq2inp ranlines splitfile balanceset xycorr Examples fasta2pep ex.fsa | grep -v # | seq2inp -- | grep -v # | ranlines -- | grep -v # | splitfile -nc 4 -- seq2inp data | nnlinplayer synlist -- | grep -v # | args 1,3 | xycorr

10. CENTER FOR BIOLOGICAL SEQUENCE ANALYSISTECHNICAL UNIVERSITY OF DENMARK DTU Exercises Copy all files from –/usr/opt/www/pub/CBS/researchgroups/immunology/intro/NeuralNet works/exercise/* to some directory Open the file doit –What does the program do? –Run the program and save the output to a file named datafile –Make a howlin neural network training Set the number of hidden neurons in the howlin2002.dat file to 0 Run the training typing –howlin2002 output Plot the training/test performance using the howlinplot program Redo the training using 2 hidden neurons –Check the synaps file. What are the weight values? Do the prediction of T cell epitopes exercise www.cbs.dtu.dk/courses/27485.imm/exercise5/index.php