Neural Network training

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19 Οκτ 2013 (πριν από 3 χρόνια και 11 μήνες)

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CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

Neural Network training

Morten Nielsen,

CBS, BioCentrum,

DTU

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

Neural network programs


How


Classification neural network


Howlin


Real value neural network


Nnlinplayer


Neural network player i.e. no training



CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

How2doit


How and howlin clumsy but very fast
and efficient Fortran programs


Three important files


Parameter file;
howlin.dat


Data file


Synaps

(weight) file

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

Output


Format of
output file


Plotting training and test
performance


howlinplot

fileout

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL 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

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

Neural networks

w
11

w
12

v
1

w
21

w
22

v
2

w
11
=1, w
12
=
-
1 w
21
=1 w
22
=
-
1

V
1

= 0.5 v
2
=
-
0.5

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

nnlinplayer


Use weight file(s) to generate neural network
predictions


Format


nnlinplayer
synapsfilelist

inputfile


Makes consensus prediction over N neural
networks


Input file must be generated separately


seq2inp

data


Using pipes


seq2inp data | nnlinplayet synlist
--

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL UNIVERSITY OF DENMARK DTU

how


Classification network


Generates input data directly from
sequence


RIISSIEQKEENKGGEDKLKMIREYRQMVE


Input is
how files

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL 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

CENTER FOR BIOLOGICAL SEQUENCE ANALYSIS

TECHNICAL 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 < howlin2002.dat > 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