Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB Tutorial – CCN Course 2012

How to code a neural network simulation

Malte J. Rasch

National Key Laboratory of Cognitive Neuroscience and Learning

Beijing Normal University
China

July 17, 2012

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Overview

Basic introduction to Matlab

Learn to code a neural network simulation
Further exercises with solutions
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Why MATLAB ?
Pro:
Matrix-like numerical operations very fast and easy to use
Good plotting capabilities
Script language for programming small to medium sized
problems in applied mathematics (rapid prototyping)
Widely used in the neuroscience community for data analysis
as well as computational projects
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Why MATLAB ?
Pro:
Matrix-like numerical operations very fast and easy to use
Good plotting capabilities
Script language for programming small to medium sized
problems in applied mathematics (rapid prototyping)
Widely used in the neuroscience community for data analysis
as well as computational projects
Contra:
Support of symbolic/analytic expressions less advanced
Mathematica, Maple
Often not flexible/ fast enough for big projects
e.g. Python much more versatile
specialized software for detailed/large neural network
simulations
(NEURON, PCSIM, NEST, GENESIS, ...)
Very expensive, especially when using on a cluster
free alternative: (scientific) python
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Starting MATLAB

Easy: Just click on MATLAB symbol...

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Scalar expressions
Binary operations: work as expected, use = + - * / ^.
a2 x
Example (compute y = 2+a + b)
>> a = 2;
>> b = 1;
>> x = 0.5;
>> y = a^2*x/(2+a) + b;
>> y
y =
1.500
Unary operations: called as functions with (), eg.
sin cos tan atan sqrt log gamma
√
sin x
Example ( compute y = ln x )
>> x = 0.5;
>> y = sqrt(sin(x))/log(x);
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB == MATrix LABoratory

Not suprisingly, in MATLAB everything is about matrices.

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB == MATrix LABoratory

Not suprisingly, in MATLAB everything is about matrices.

However, the matrix-like datastructure in MATLAB is better called

a n-dimensional array, because it can be manipulated in
non-algebraic ways.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB == MATrix LABoratory

Not suprisingly, in MATLAB everything is about matrices.

However, the matrix-like datastructure in MATLAB is better called

a n-dimensional array, because it can be manipulated in
non-algebraic ways.

(Almost) all functions will work on arrays as well

usually element-wise
Many MATLAB functions will produce arrays as output
Array operations much faster than for-looped element-wise
operation
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Arrays: Overview

How to initialize arrays

Indexing
Calculating with arrays
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Calculating with arrays is

straight-forward
however, carefully check
the size of matrices
if element-wise or matrix-like operations are intended
which matrix dimension to operate on
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Calculating with arrays is

straight-forward
however, carefully check
the size of matrices
if element-wise or matrix-like operations are intended
which matrix dimension to operate on

Example (compute yi = Axi + b with b, xi ∈ R2 )

>> A = [1,0.2;0.4,1]; >> N = 5;

>> b = [1;2] + 0.1; % same as b = [b,b,b,b,b]
>> x = 2*randn(2,1); >> bi = repmat(b,[1,N]);
>> y = A * x + b >> xi = 2*randn(2,N);
y = >> xi(:,1) = x;
4.5535 >> yi = A * xi + bi
1.4856 yi =
4.5535 2.3126 [..] -0.9021
1.4856 6.8091 [..] -0.1080
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays

1 Implicitly, using function returning an array

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays

1 Implicitly, using function returning an array

2 By explicit concatenation
Concatenation of columns of arrays
[ arr1, arr2, ... , arrn]
Concatenation of rows of arrays
[ arr1; arr2; ... ; arrn]
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays

1 Implicitly, using function returning an array

2 By explicit concatenation
Concatenation of columns of arrays
[ arr1, arr2, ... , arrn]
Concatenation of rows of arrays
[ arr1; arr2; ... ; arrn]
Note: an scalar is also regarded as an array (of size [1,1]).
Note 2: arrays must have matching sizes.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays

1 Implicitly, using function returning an array

2 By explicit concatenation
Concatenation of columns of arrays
[ arr1, arr2, ... , arrn]
Concatenation of rows of arrays
[ arr1; arr2; ... ; arrn]
Note: an scalar is also regarded as an array (of size [1,1]).
Note 2: arrays must have matching sizes.
Example (Concatenation)

>> A = [1,2;3,4] >> C = [A;A]

A = C =
1 2 1 2
3 4 3 4
>> B = [A,A] 1 2
B = 3 4
1 2 1 2
3 4 3 4
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays: implicitly

Functions that pre-allocate memory and set each array element to

an initial value:
zeros – all zero ND-arrays
ones – all one ND-arrays
rand – random ND-arrays (equally in [0, 1])
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays: implicitly

Functions that pre-allocate memory and set each array element to

an initial value:
zeros – all zero ND-arrays
ones – all one ND-arrays
rand – random ND-arrays (equally in [0, 1])
colon (:) – for linear sequences, syntax:
istart:[step:]iend
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays: implicitly

Functions that pre-allocate memory and set each array element to

an initial value:
zeros – all zero ND-arrays
ones – all one ND-arrays
rand – random ND-arrays (equally in [0, 1])
colon (:) – for linear sequences, syntax:
istart:[step:]iend
– many others, for details type: help command
randn, linspace, logspace, ndgrid, repmat,...
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Syntax for initializing arrays: implicitly

Functions that pre-allocate memory and set each array element to

an initial value:
zeros – all zero ND-arrays
ones – all one ND-arrays
rand – random ND-arrays (equally in [0, 1])
colon (:) – for linear sequences, syntax:
istart:[step:]iend
– many others, for details type: help command
randn, linspace, logspace, ndgrid, repmat,...
Example (Functions initializing arrays)
>> A = zeros(3,3); >> x = 3:-0.5:1
>> A = ones(4,4,4); x =
>> size(A) 3.0 2.5 2.0 1.5 1.0
ans = >> A = ones(2)
4 4 4 1 1
1 1
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Indexing arrays
1 Subscript of a matrix:
access the (i, j)-th element of a 2D-matrix A of dimension (m, n)
>> A(i,j)

Note: The first index is always 1 (not 0 as in most other languages)

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Indexing arrays
1 Subscript of a matrix:
access the (i, j)-th element of a 2D-matrix A of dimension (m, n)
>> A(i,j)

Note: The first index is always 1 (not 0 as in most other languages)

2 Linear index of a matrix:
access the (i, j)th element of the 2D-matrix A of dimension (m, n)
>> linearidx = i + (j-1)*m;
>> A(linearidx)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Indexing arrays
1 Subscript of a matrix:
access the (i, j)-th element of a 2D-matrix A of dimension (m, n)
>> A(i,j)

Note: The first index is always 1 (not 0 as in most other languages)

2 Linear index of a matrix:
access the (i, j)th element of the 2D-matrix A of dimension (m, n)
>> linearidx = i + (j-1)*m;
>> A(linearidx)
3 “Slice” indexing with “:”
access the i-th row and jth column in A, respectively
>> A(i,:)
>> A(:,j)

get all elements as a cocatenated column vector

>> A(:)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Indexing arrays (2)

4 Multiple indices
vectors of linear indices can be used

>> A([1, 4, 5 ,6])

access the 1st to 4th rows of the 2D-matrix A of dimension (m, n)

>> A(1:4,:)

access the 2nd (m,n)-slice of a 3D-matrix B of dimension (m, n, p)

>> B(:,:,2)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Indexing arrays (2)

4 Multiple indices
vectors of linear indices can be used

>> A([1, 4, 5 ,6])

access the 1st to 4th rows of the 2D-matrix A of dimension (m, n)

>> A(1:4,:)

access the 2nd (m,n)-slice of a 3D-matrix B of dimension (m, n, p)

>> B(:,:,2)

5 Logical indexing
logical matrices of the same size as A can be used as indices

>> A(A>0)
>> A(find(A>0))
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Calculating with arrays

1 Element-wise interpretation
For instance, sin cos log etc.
Reserved symbols, .* ./ .^
2 “true” matrix interpretation (with dot product)
Symbols * / ^ etc.
3 Operations on one specified dimensions of the matrix
For instance, sum mean max etc.
4 Array manipulations
eg. reshape repmat permute circshift tril

Example (element-wise product and dot product)

>> A = ones(2,2); >> A*A

>> A.*A ans =
ans = 2 2
1 1 2 2
1 1
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Useful operations on specified dimensions

Often used functions on array elements include
size – number of elements in a dimension
sum – sum of elements along an array dimension
prod – product of elements
all, any – logical AND or OR, respectively
mean – mean of elements
max – maximal element of an array dimension
– and many more, eg. min var std median diff

Functions are usually called as

res = func(arr,dim);

Note: max and min are exceptions! Here: res = max(arr,[],dim);

For details type: help func
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB is a script language

Scripts are blocks of code which can be called within MATLAB or

within another script.
They are text-files with extensions “.m”.
They should contain all commands associated with a scientific
project.
(at least to easily reproduce and the calculations)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

MATLAB is a script language

Scripts are blocks of code which can be called within MATLAB or

within another script.
They are text-files with extensions “.m”.
They should contain all commands associated with a scientific
project.
(at least to easily reproduce and the calculations)

There are basically two types of m-files

1 m-file script
A squential list of MATLAB commands
The variable scope is that of the caller.
2 m-file function
m-file functions accept input parameters and deliver outputs.
The variable scope is different from that of the caller.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided
with MATLAB
>> edit myscript
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided
with MATLAB
>> edit myscript
2 Write all your calculations in a text-file with extension “.m”
(here myscript.m)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided
with MATLAB
>> edit myscript
2 Write all your calculations in a text-file with extension “.m”
(here myscript.m)
3 Save file in the current working directory
(or addpath to search path )
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided
with MATLAB
>> edit myscript
2 Write all your calculations in a text-file with extension “.m”
(here myscript.m)
3 Save file in the current working directory
(or addpath to search path )
4 Call your script by calling it from the “Command Window”
>> myscript;
(no compilation needed)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided
with MATLAB
>> edit myscript
2 Write all your calculations in a text-file with extension “.m”
(here myscript.m)
3 Save file in the current working directory
(or addpath to search path )
4 Call your script by calling it from the “Command Window”
>> myscript;
(no compilation needed)
5 Note: The variable scope is that of the caller. This means that
the variables of the script are now present in the workspace
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file scripts

Excercise #1 (How to write an m-file script)

Write an m-file computing the Stirling approximation
√  n n
n! ≈ 2πn
e
Hint: π is defined in MATLAB as pi, and e x as exp(x).
Solution #1

Reminder:
1 Open a text-editor

>> edit myscript

2 Write calculations in text-file with extension “.m”
3 Save file into current working directory
4 Call your script

>> myscript;
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);

Call the function with

>> result = myfun(p1,p2,...);
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);

Call the function with

>> result = myfun(p1,p2,...);

Note: The variable scope is different from that of the caller. That
means, that variables defined in the function body are NOT
present in the workspace after calling the function
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);

Call the function with

>> result = myfun(p1,p2,...);

Note: The variable scope is different from that of the caller. That
means, that variables defined in the function body are NOT
present in the workspace after calling the function
Note 2: Input arguments are always referenced by value
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

How to write an m-file function?

Identical to writing an m-file script, except:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);

Call the function with

>> result = myfun(p1,p2,...);

Note: The variable scope is different from that of the caller. That
means, that variables defined in the function body are NOT
present in the workspace after calling the function
Note 2: Input arguments are always referenced by value
Note 3: When called the m-file file name is used.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

m-file functions

Excercise #2 (writing a m-file function)

Write an m-file function computing the Stirling approximation
√  n n
n! ≈ 2πn
e
for a given n
Solution #2

Reminder:
In the first line input and output arguments are defined:
function outarg = myfun(inarg1,inarg2,...);
Call the function with
>> result = myfun(p1,p2,...);
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Basic syntax

The basic syntax is similar to other script languages, eg. “python”.

MATLAB has the usual flow control structures, namely

if .. else for decisions
for-loop
while-loop
switch .. case for multiple if-else decisions
try .. catch for handling errors
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Basic syntax: flow control (1)

if-else block syntax:
1 if scalar condition
2 expressions
3 else
4 expressions
5 end

Relational operators, eg.: == (equals), || (or), && (and), ~ (not)

for details type: help relop
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Basic syntax: flow control (1)

if-else block syntax:
1 if scalar condition
2 expressions
3 else
4 expressions
5 end

Relational operators, eg.: == (equals), || (or), && (and), ~ (not)

for details type: help relop

Example (if-else)

a = rand ( 1 ) ;
i f a == 0 . 5
f p r i n t f ( ’ you a r e v e r y l u c k y ! ’ ) ;
end
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Programming: basic flow control (2)

for-loop block syntax:
1 for i = array
2 % i==a r r a y ( j ) i n t h e j −t h l o o p
3 expressions
4 end

(one can also use break and continue keywords)

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Programming: basic flow control (2)

for-loop block syntax:
1 for i = array
2 % i==a r r a y ( j ) i n t h e j −t h l o o p
3 expressions
4 end

(one can also use break and continue keywords)

Example (for loop)

a =0;
for i = 1:100
a = a+i ;
end
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Plotting with MATLAB

Very flexible plotting tools

Many functions for a variety of plot types and graphics
drawing

A Stimulus Simple cell response Response profile

2
RF filter 〈 |⋅|2 〉
x,y,t

Avg. response
K
θ,ρ,ω (+ phase invariance) 1.5

1
θ
2
y

y
0.5
θ3 0
t vary θ t
0° 90° 180°
:
x x

B Static C Low speed D High speed E Low speed High speed

Horz. RF

Vert. RF
→ Movement dir. →

→ Movement dir. →

10

5
TF [Hz]

−5
Response

2
−10 0
2 0 −2
−2
SF [cyc/deg] SF [cyc/deg]
° ° ° ° ° ° ° ° °
0 90 180 0 90 180 0 90 180
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Overview

Just two most useful plotting commands

plot – plots all kinds of lines, dots, markers in 2D
imagesc – plots an 2-D pseudo image
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Overview

Just two most useful plotting commands

plot – plots all kinds of lines, dots, markers in 2D
imagesc – plots an 2-D pseudo image

Note: For an overview of 2D plotting commands: help graph2d

Note 2: For fancy graphs see: help specgraph
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

How to plot
How to plot:
1 Open a figure (window) with
>> figure;
2 Create an axes object with
>> axes;
3 Type the plotting command of your choice
>> plot(x,y,’b--’,’LineWidth’,2);
Note: graphics commands draw into the current axes (gca) on the current
figure (gcf). They automatically create a new figure and axes if necessary.

4 Make the plot nicer by adding labels and setting limits, eg:
>> xlabel(’Time [s]’);
>> ylabel(’Response [spks/sec]’);
>> xlim([-1,1]); ylim([-2,2]);
>> title(’Simulation’)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

plot command
Basic syntax:
handle = plot(X,Y,linespec,optname1,val1,...);

X,Y – x- and y-values to plot. If Y is a 2-D array, all columns are

plotted as different lines
linespec – a string with a short hand for color and line style and
marker type. See help plot for an overview. Eg,
linespec = ’:ko’
plots dotted (:) black line (k) with a circle at each given
coordinate (xi , yi )
optname1 – a string specifing the option name, eg. ’LineWidth’
val1 – a corresponding value.
handle – graphics handle for later reference, eg. with
>> set(handle,optname1,val1)
Tip: To get an overview over all possible options, try get(handle)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Plotting example: empirical PDF of Gaussian

1 figure ;
2
3 % p l o t G a u s s i a n PDF
4 x = −4:0.01:4; 0.45
5 y = exp ( −0.5∗ x . ˆ 2 ) / s q r t ( 2 ∗ p i ) ; 0.4
true PDF
empirical PDF

6 p l o t ( x , y , ’−k ’ , ’ L i n e w i d t h ’ , 2 ) ;
0.35
7
0.3
8 % e m p i r i c a l pdf

Probability density
0.25
9 % h i s t o g r a m o f 1000 random v a l u e s
10 [ N, z ]= h i s t ( r a n d n ( 1 0 0 0 , 1 ) ) ; 0.2

11 %n o r m a l i z a t i o n 0.15

12 p = N/sum (N) / ( z (2) − z ( 1 ) ) ; 0.1

13 0.05

14 h o l d on ; %a d d s a l l f o l l o w i n g g r a p h s 0
−4 −3 −2 −1 0 1 2 3 4
Random variable x
15 %t o t h e c u r r e n t a x e s
16 plot ( z , p , ’ rx ’ , ’ MarkerSize ’ ,10);
17 hold o f f ;
18
19 x l a b e l ( ’ Random v a r i a b l e x ’ )
20 ylabel ( ’ Probability density ’ )
21 l e g e n d ( ’ t r u e PDF ’ , ’ e m p i r i c a l PDF ’ )
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Goal of tutorial

We will program a neural network simulation together.

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

We will practice on the way:

Writing scripts
Usage of array notation
How to integrate ODEs
How to plot results
How to simulate neurons and synapses
How to program a quite realistic network simulation
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Network model simulation

What has to be done in principle:

n neurons, excitatory and inhibitory, are inter-connected with
synapses.
The each neuron and synapse follows a particular dynamic
over time.
The simulation calculates the dynamic and spiking activity of
each neuron for each t.
The network gets some input and reacts in a certain and the
response of the network is plotted.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

We will proceed in 4 successive steps

1 Simulate a single neuron with current step input

2 Simulate a single neuron with Poisson input
3 Simulate 1000 neurons (no recurrent connections)
4 Simulate complete network (conductance based)
Network activity
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Which neuron model to use?

Biophysical model (i.e. Hodgkin-Huxley model)

dVm 1 X
Cm =− (Vm − VL ) − gi (t)(Vm − Ei ) + Isyn + Iapp
dt Rm
i

Including non-linear dynamics of many channels in gi (t)

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Which neuron model to use?

Biophysical model (i.e. Hodgkin-Huxley model)

dVm 1 X
Cm =− (Vm − VL ) − gi (t)(Vm − Ei ) + Isyn + Iapp
dt Rm
i

Including non-linear dynamics of many channels in gi (t)

Mathematical simplification (Izhikevich, book chapter 8)

X
v̇ = (0.04v + 5) v + 150 − u − wj gj (v − Ej ) + Iapp
j
u̇ = a (b v − u)
v ← c, u ← u + d, if v ≥ 35

with g˙j = −gj /τg and gj ← gj + 1 if vj ≥ 35. It is b = 0.2, c = −65, and

d = 8, a = 0.02 for exc. neurons and d = 2, a = 0.1 for inh. neurons.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Neuron model
peak 30 mV
RZ RS
v'= 0.04v 2+5v +140 - u + I LTS,TC
8

parameter d
0.25

parameter b
u'= a(bv - u)
reset c IB
RS,IB,CH FS 4
v(t) 0.2
if v = 30 mV, de
cay FS,LTS,RZ CH
reset d with r 2
then v c, u u + d ate a
0.05 TC
u(t)
sensitivity b 0 0.02 0.1 -65 -55 -50
parameter a parameter c

regular spiking (RS) intrinsically bursting (IB) chattering (CH) fast spiking (FS)

v(t)

I(t)

thalamo-cortical (TC) thalamo-cortical (TC) resonator (RZ) low-threshold spiking (LTS)

20 mV

40 ms

-63 mV

-87 mV
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1: Simulate a single neuron with injected current

Exercise 1
Simulate the neuron model for 1000ms and plot the resulting
voltage trace. Apply a current step (Iapp = 7pA) between time
200ms and 700ms.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1: Simulate a single neuron with injected current

Exercise 1
Simulate the neuron model for 1000ms and plot the resulting
voltage trace. Apply a current step (Iapp = 7pA) between time
200ms and 700ms.

Neuron model:
v̇ = (0.04v + 5) v + 140 − u + Iapp
u̇ = a (b v − u)
v ← c, u ← u + d, if v ≥ 35

with d = 8, a = 0.02, b = 0.2,

c = −65 for an excitatory neuron.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
3 Loop over T − 1 time steps and do for each step t HowTo
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
3 Loop over T − 1 time steps and do for each step t HowTo
1 set Iapp ← 7 if t∆t is between 200 and 700 (otherwise 0)
HowTo
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
3 Loop over T − 1 time steps and do for each step t HowTo
1 set Iapp ← 7 if t∆t is between 200 and 700 (otherwise 0)
HowTo

2 if vt < 35: update element t + 1 HowTo of v and u

according to HowTo
vt+1 ← vt + ∆t {(0.04 vt + 5) vt − ut + 140 + Iapp }
ut+1 ← ut + ∆t a (b vt − ut )
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
3 Loop over T − 1 time steps and do for each step t HowTo
1 set Iapp ← 7 if t∆t is between 200 and 700 (otherwise 0)
HowTo

2 if vt < 35: update element t + 1 HowTo of v and u

according to HowTo
vt+1 ← vt + ∆t {(0.04 vt + 5) vt − ut + 140 + Iapp }
ut+1 ← ut + ∆t a (b vt − ut )
3 if vt ≥ 35: set vt+1 ← c and ut+1 ← ut + d (and optional
vt ← 35)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 1 in detail:
Open MATLAB HowTo and create a new file (script) that will simulate the neuron
HowTo . If you do not know how to use a command get some help HowTo

Proceed as follows:
1 Initialize parameter values (∆t = 0.5ms, a = 0.02, d = 8, · · · )
HowTo

2 Reserve memory for voltage trace v and u (of length T = 1000/∆t)

HowTo and set first element to −70 and −14, respectively.
3 Loop over T − 1 time steps and do for each step t HowTo
1 set Iapp ← 7 if t∆t is between 200 and 700 (otherwise 0)
HowTo

2 if vt < 35: update element t + 1 HowTo of v and u

according to HowTo
vt+1 ← vt + ∆t {(0.04 vt + 5) vt − ut + 140 + Iapp }
ut+1 ← ut + ∆t a (b vt − ut )
3 if vt ≥ 35: set vt+1 ← c and ut+1 ← ut + d (and optional
vt ← 35)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2: Single neuron with synaptic input

Exercise 2
Simulate the neuron model for 1000ms and plot the resulting
voltage trace. Assume that 100 synapses are attached to the
neuron, with each pre-synaptic neuron firing with a Poisson
process of rate frate = 2 Hz between time 200ms and 700ms.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2: Single neuron with synaptic input

Exercise 2
Simulate the neuron model for 1000ms and plot the resulting
voltage trace. Assume that 100 synapses are attached to the
neuron, with each pre-synaptic neuron firing with a Poisson
process of rate frate = 2 Hz between time 200ms and 700ms.

Synaptic input model:

X
Isyn = wjin gjin (t)(Ejin − v (t))
j

ġjin = gjin /τg

gjin ← gjin + 1, if rj (t) < frate ∆t

with τg = 10ms, weights wjin = 0.07,

Ej = 0, rj (t) ∈ [0, 1] uniform
random numbers drawn for each
step t, and j = 1 . . . 100.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2 in detail:
Use the last script, save it under a new file name, and add the necessary lines.

Proceed as follows:
1 Initialize new parameter values (τg = 10, frate = 0.002ms−1 )
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2 in detail:
Use the last script, save it under a new file name, and add the necessary lines.

Proceed as follows:
1 Initialize new parameter values (τg = 10, frate = 0.002ms−1 )
2 Reserve memory and initialize gin = (gjin ), win = (wjin ), and
E = (Ej ) (vectors of length nin = 100) with constant elements
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2 in detail:
Use the last script, save it under a new file name, and add the necessary lines.

Proceed as follows:
1 Initialize new parameter values (τg = 10, frate = 0.002ms−1 )
2 Reserve memory and initialize gin = (gjin ), win = (wjin ), and
E = (Ej ) (vectors of length nin = 100) with constant elements
3 Inside the for-loop change/add the following:
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2 in detail:
Use the last script, save it under a new file name, and add the necessary lines.

Proceed as follows:
1 Initialize new parameter values (τg = 10, frate = 0.002ms−1 )
2 Reserve memory and initialize gin = (gjin ), win = (wjin ), and
E = (Ej ) (vectors of length nin = 100) with constant elements
3 Inside the for-loop change/add the following:
1 set pj = 1 if r ≤ frate ∆t (otherwise 0) in the case when i∆t is
between 200 and 700 (otherwise 0). r = (rj ) is a vector of
uniform random numbers of length nin
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 2 in detail:
Use the last script, save it under a new file name, and add the necessary lines.

Proceed as follows:
1 Initialize new parameter values (τg = 10, frate = 0.002ms−1 )
2 Reserve memory and initialize gin = (gjin ), win = (wjin ), and
E = (Ej ) (vectors of length nin = 100) with constant elements
3 Inside the for-loop change/add the following:
1 set pj = 1 if r ≤ frate ∆t (otherwise 0) in the case when i∆t is
between 200 and 700 (otherwise 0). r = (rj ) is a vector of
uniform random numbers of length nin
2 before the vt update: implement the conductance dynamics g
and set Iapp (using array notation HowTo carefully HowTo ):
gjin ← gjin + pj
win · gin ⊙ Ein − win · gin ⊙ vt



Iapp ←
gjin ← (1 − ∆t/τg ) gjin
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3: Simulate 1000 neurons (not inter-connected)

Exercise 3
Simulate 1000 neurons for 1000 ms and plot the resulting spikes.
Assume that each neuron receives (random) 10% of the 100
Poisson spike trains of rate frate = 2 Hz between time 200 ms and
700 ms. Note that the neurons are not yet inter-connected.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3: Simulate 1000 neurons (not inter-connected)

Exercise 3
Simulate 1000 neurons for 1000 ms and plot the resulting spikes.
Assume that each neuron receives (random) 10% of the 100
Poisson spike trains of rate frate = 2 Hz between time 200 ms and
700 ms. Note that the neurons are not yet inter-connected.

Excitatory and inhibitory neurons:

A neuron is, with probability pI = 0.2,
a (fast-spiking) inhibitory neuron
(a = 0.1, d = 2), others are (regular
spiking) excitatory neurons (a = 0.02
and d = 8). Weights of the input
synapse j to inhibitory neuron i is
w in = 0.07 if connected (otherwise 0).
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
2 Initialize 2 logical vectors (for indexing HowTo ) kinh and kexc of
length n, where kinh has a 1 in element i with probability p = 0.2
(marking an inhibitory neuron) and 0 otherwise. kexc = ¬kinh .
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
2 Initialize 2 logical vectors (for indexing HowTo ) kinh and kexc of
length n, where kinh has a 1 in element i with probability p = 0.2
(marking an inhibitory neuron) and 0 otherwise. kexc = ¬kinh .
3 Reserve memory and initialize vij , uij (now being n × T matrices).
Set parameters ai and di according to kexc and kinh .
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
2 Initialize 2 logical vectors (for indexing HowTo ) kinh and kexc of
length n, where kinh has a 1 in element i with probability p = 0.2
(marking an inhibitory neuron) and 0 otherwise. kexc = ¬kinh .
3 Reserve memory and initialize vij , uij (now being n × T matrices).
Set parameters ai and di according to kexc and kinh .
4 The weights wijin = 0.07 now form a n × nin matrix. Set 90 %
random elements to 0 to account for the connection probability.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
2 Initialize 2 logical vectors (for indexing HowTo ) kinh and kexc of
length n, where kinh has a 1 in element i with probability p = 0.2
(marking an inhibitory neuron) and 0 otherwise. kexc = ¬kinh .
3 Reserve memory and initialize vij , uij (now being n × T matrices).
Set parameters ai and di according to kexc and kinh .
4 The weights wijin = 0.07 now form a n × nin matrix. Set 90 %
random elements to 0 to account for the connection probability.
5 Inside the for-loop change/add the following:
1 Same update equations (for vi,t+1 and ui,t+1 ) but use array
notation to update all i neurons simultaneously.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 3 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize new parameter values (n = 1000)
2 Initialize 2 logical vectors (for indexing HowTo ) kinh and kexc of
length n, where kinh has a 1 in element i with probability p = 0.2
(marking an inhibitory neuron) and 0 otherwise. kexc = ¬kinh .
3 Reserve memory and initialize vij , uij (now being n × T matrices).
Set parameters ai and di according to kexc and kinh .
4 The weights wijin = 0.07 now form a n × nin matrix. Set 90 %
random elements to 0 to account for the connection probability.
5 Inside the for-loop change/add the following:
1 Same update equations (for vi,t+1 and ui,t+1 ) but use array
notation to update all i neurons simultaneously.
6 Plot the spike raster. Plot black dots at {(t, i)|vit ≥ 35} for
excitatory neuron i. Use red dots for inhibitory neurons.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4: Simulate recurrent network

Exercise 4
Simulate 1000 neurons as before but with added recurrent
connections.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4: Simulate recurrent network

Exercise 4
Simulate 1000 neurons as before but with added recurrent
connections.

Recurrent synaptic activations

A neuron i is sparsely (with probability
prc = 0.1) connected to a neuron j.
Thus neuron i receives an additional
current Iisyn of the form:
n
X
Iisyn = wij gj (t) (Ej − vi (t))
j=1

Weights are Gamma distributed (scale

0.003, shape 2). Inh. to exc.
connections are twice as strong.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
2 Reserve memory and initialize weights W = (wij ) to zero.
Randomly choose 10% of the matrix elements.
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
2 Reserve memory and initialize weights W = (wij ) to zero.
Randomly choose 10% of the matrix elements.
3 Set the chosen weight matrix elements to values drawn from a
Gamma distribution of scale 0.003 and shape 2 HowTo
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
2 Reserve memory and initialize weights W = (wij ) to zero.
Randomly choose 10% of the matrix elements.
3 Set the chosen weight matrix elements to values drawn from a
Gamma distribution of scale 0.003 and shape 2 HowTo
4 Make the weight matrix “sparse” HowTo
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
2 Reserve memory and initialize weights W = (wij ) to zero.
Randomly choose 10% of the matrix elements.
3 Set the chosen weight matrix elements to values drawn from a
Gamma distribution of scale 0.003 and shape 2 HowTo
4 Make the weight matrix “sparse” HowTo

5 Scale weights from inh. to exc. neurons by the factor of 2

Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Step 4 in detail:
Modify the last script (after saving it under new name).

Proceed as follows:
1 Initialize and allocate memory for the new variables ( g = (gj ), Ej ).
Set Ej = −85 if j is an inhibitory neuron (otherwise 0).
2 Reserve memory and initialize weights W = (wij ) to zero.
Randomly choose 10% of the matrix elements.
3 Set the chosen weight matrix elements to values drawn from a
Gamma distribution of scale 0.003 and shape 2 HowTo
4 Make the weight matrix “sparse” HowTo

5 Scale weights from inh. to exc. neurons by the factor of 2

6 Inside the for-loop change/add the following:
1 add the equations for recurrent conductances gj

gj ← gj + 1, if vj (t − 1) ≥ 35
syn
I ← W · (g ⊙ E) − (W · g) ⊙ v
gj ← (1 − ∆t/τg ) gj
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Congratulation !

You have just coded and simulated a

quite realistic network model !
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Optional exercises
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises

Exercise (p-series)
Calculate the p-series (generalization of the Harmonic Series) for a
given p up to a given m
m
X 1
µm =
np
i=1

Use array notation.

Advise: Use array notation and avoid for-loops whereever you can!
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises

Exercise (blob movie)

1 Generate a two arrays with, x and y , ranging from -2 to 2
(and about 100 elements)
2 Generate two 100 by 100 grid-matrices, X and Y using
meshgrid with x and y as input (look at X and Y to
understand what meshgrid is doing).
3 calculate a matrix Z of the same size as X and Y where each
2 2
element is given by zi = e −(xi +yi ) .
4 write a loop with t ranging from 0 to 1000 where you
1 plot the matrix Z (using imagesc)
2 circular shift the matrix Z by 1 element (using circshift)
3 force the plot to be drawn (using drawnow)
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises

Exercise (Logical indexing and basic plotting)

1 Generate a 100 by 2 matrix M of Gaussian random values
2 Plot a point cloud (first vs. second column of M) using blue
circles
3 Calculate how many values of M are positive
4 Erase all rows in M which have at least one negative value
5 Plot the points of the modified array M using red crosses in
the same graph as above.
6 Set both axes limits to −3 to 3 and plot dotted gray lines on
the coordinate axes (where y = 0 or x = 0).
7 Label the axes and write a legend
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises

Exercise (Poisson spike trains)

Write a function that generates a homogeneous Poisson spike train
of rate λ having exactly N spikes. Use array notations (cumsum).
Hint: Poisson spike intervals t are exponentially distributed. They
can be generated by inverse transform sampling: Given uniform
random variables u in 0 to 1 valid inter-spike intervals can be
calculated as
log u
t=−
λ

Advise: Use array notation and avoid for-loops whereever you can!
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises

Exercise (More on spike trains)

Generate a long Poisson spike train (with the function from the
last exercise). Compute the mean and standard deviation of the
inter-spike interval distribution.
Further, write a function that counts the number of spike times
falling into time-bins of length ∆t.
Hint: Use diff to get the intervals from spike times.
Hint 2: Use histc to bin the spike-times
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Exercises
Exercise (Plot 2-D Gaussian point cloud)
Write a function which plots a point cloud of n random
samples drawn from a 2D Normal distribution (with 0 5
mean) and variance Σ = (RD)T (RD), where the
0
rotation matrix is defined as
  -5
cos θ − sin θ
R=
sin θ cos θ -5 0 5

and D is a diagonal matrix of the standard deviation in

the principal directions
 
σ1 0
D=
0 σ2

The function should accept parameters σ1 , σ2 , and θ.

Hint: use randn to produce independent Normal-distributed random vectors xi

and transform them according to yi = RDxi .
Introduction Arrays Coding Plotting Network model: Step 1 Step 2 Step 3 Step 4 Exercises

Advanced exercise

Exercise (Optimizing Matlab code)

Optimize “bad” Matlab code for generating self-organizing maps.

See provided code and description in som_exercise.zip.
Howtos

How to start Matlab

Easy: Just click on Matlab symbol...

back
Howtos

How to get help

Each Matlab function has

a header which describes its
usage
Just type:
>> help command
or
>> doc command

Alternatively:
http://www.mathworks.com/access/helpdesk/help/techdoc/
back
Howtos

How to plot in general

How to plot:
1 Open a figure (window) with
>> figure;

2 Issue plotting command of your choice

>> plot(x,y,’b--’,’LineWidth’,2);
HowTo Note: graphics commands draw into the current axes (gca) on the
current figure (gcf). They automatically create a new figure and axes if
necessary.

3 Make the plot nicer by adding labels and setting limits, eg:

>> xlabel(’Time [s]’);

>> ylabel(’Response [spks/sec]’);
>> xlim([-1,1]); ylim([-2,2]);
>> title(’Simulation’)
back
Howtos

How to use the plot command

Basic syntax:
handle = plot(X,Y,linespec,optname1,val1,...);

X,Y – x- and y-values to plot. If Y is a 2-D array, all columns are

plotted as different lines
linespec – a string with a short hand for color and line style and
marker type. See help plot for an overview. Eg,
linespec = ’:ko’
plots dotted (:) black line (k) with a circle at each given
coordinate (xi , yi )
optname1 – a string specifing the option name, eg. ’LineWidth’
val1 – a corresponding value.
handle – graphics handle for later reference, eg. with
>> set(handle,optname1,val1)
Tip: To get an overview over all possible options, try get(handle)
back
Howtos

How to initialize parameters

Just use the syntax

>> parname = value;

Example
>> a = 2;
>> vreset = 0;
>> tau = 0.02
tau =
0.02
back
Howtos

How to use scalar expressions

Binary operations: work as expected, use = + - * / ^
a2 x
Example (compute y = 2+a + b)
>> a = 2;
>> b = 1;
>> x = 0.5;
>> y = a^2*x/(2+a) + b;
>> y
y =
1.500
back
Howtos

How to initialize arrays

1 Implicitly, using function returning an array

2 By explicit concatenation
Concatenation of columns of arrays
[ arr1, arr2, ... , arrn]
Concatenation of rows of arrays
[ arr1; arr2; ... ; arrn]
Note: an scalar is also regarded as an array (of size [1,1]).
Note 2: arrays must have matching sizes.
Example (Concatenation)

>> A = [1,2;3,4] >> C = [A;A]

A = C =
1 2 1 2
3 4 3 4
>> B = [A,A] 1 2
B = 3 4
1 2 1 2
3 4 3 4
Howtos

How to pre-allocate memory

Functions for pre-allocating memory include:

colon (:) – for linear sequences
zeros – all zero array of given size
ones – all one array of given size
rand – random array of given size (equally in [0, 1])
To improve performance arrays should always be pre-allocated!
Example (Functions initializing arrays)
>> A = zeros(3,3); >> x = 3:-0.5:1
>> A = ones(4,4,4); x =
>> size(A) 3.0 2.5 2.0 1.5 1.0
ans = >> A = ones(2)
4 4 4 1 1
1 1
back
Howtos

How to write an m-file script?

1 open a text-editor of your choice or use the editor provided

with Matlab
>> edit myscript
2 Write all your calculations in a text-file with extension “.m”
(here myscript.m)
3 Save file in the current working directory
(or addpath to search path )
4 Call your script by calling it from the “Command Window”
>> myscript;

Example (myscript.m)

1 %t h i s i s my f i r s t s c r i p t . I t d i s p l a y s a random number
2 random number = rand ( 1 ) ;
3 f p r i n t f ( ’A random number : %1.4 f : \ n ’ , random number ) ;

back
Howtos

How to use basic syntax: if-clause

if-else block syntax:
1 if scalar condition
2 expressions
3 else
4 expressions
5 end

Relational operators, eg.: == (equals), || (or), && (and), ~ (not)

for details type: help relop
Example (if-else)

a = rand ( 1 ) ;
i f a == 0 . 5
f p r i n t f ( ’ you a r e v e r y l u c k y ! ’ ) ;
end

back
Howtos

How to use a for-loop

for-loop block syntax:
1 for i = array
2 % i==a r r a y ( j ) i n t h e j −t h l o o p
3 expressions
4 end

(one can also use break and continue keywords)

Example (for loop)

a =0;
for i = 1:100
a = a+i ;
end

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Howtos

How to index arrays

1 Subscript of a matrix:
access the (i, j)-th element of a 2D-matrix W of dimension (m, n)
>> W(i,j) = 1
Note: The first index is always 1 (not 0 as in most other languages)
2 Linear index of a matrix:
access the (i, j)th element of the 2D-matrix W of dimension (m, n)
>> linearidx = i + (j-1)*m;
>> W(linearidx)
3 “Slice” indexing with “:”
access the i-th row and jth column in W , respectively
>> wi = W(i,:)
>> wj = W(:,j)
get all elements as a concatenated column vector
>> W(:)
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Howtos

How to index arrays (2)

4 Multiple indices
vectors of linear indices can be used
>> W([1, 4, 5 ,6])
access the 1st to 4th rows of the 2D-matrix W of dimension (m, n)
>> W(1:4,:)
access the 2nd (m,n)-slice of a 3D-matrix V of dimension (m, n, p)
>> W(:,:,2)
5 Logical indexing
logical matrices of the same size as W can be used as index (very
useful)
>> W(W>0)
>> W(find(W>0)) = 1
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Howtos

Calculating with arrays

1 Element-wise interpretation
For instance, sin cos log etc.
Reserved symbols, .* ./ .^
2 “true” matrix interpretation (with dot product)
Symbols * / ^ etc.
3 Operations on one specified dimensions of the matrix
For instance, sum mean max etc.
4 Array manipulations
eg. reshape repmat permute circshift tril

Example (element-wise product and dot product)

>> A = ones(2,2); >> A*A

>> A.*A ans =
ans = 2 2
1 1 2 2
1 1
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Howtos

Calculating with arrays is

straightforward
however, carefully check
the size of matrices
if element-wise or matrix-like operations are intended
which matrix dimension to operate on

Example (compute yi = W xi + b with b, xi ∈ R2 )

>> W = [1,0.2;0.4,1]; >> N = 5;

>> b = [1;2] + 0.1; % same as b = [b,b,b,b,b]
>> x = 2*randn(2,1); >> bi = repmat(b,[1,N]);
>> y = W * x + b >> xi = 2*randn(2,N);
y = >> xi(:,1) = x;
4.5535 >> yi = W * xi + bi
1.4856 yi =
4.5535 2.3126 [..] -0.9021
1.4856 6.8091 [..] -0.1080

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Howtos

Gamma distribution

The Gamma probability density function is defined as

1 x
p(x|k, θ) = k
x k−1 e − θ
Γ(k)θ

with shape k and scale θ and x ∈ [0, ∞).

Example (Gamma random numbers)

>> shape = 2;
>> scale = 0.003;
>> n = 1e7;
>> r = gamrnd(shape,scale,n,1);
>> size(r)
ans =
1000000 1
>> hist(r,1000)

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Howtos

How to use sparse matrices

In Matlab it is often more efficient (faster) to use sparse matrices

instead of regular matrices if the majority of matrix elements are 0.
To generate a sparse matrix:

>> W = sparse(W);

In general, the syntax for using sparse matrices is the same as for
regular matrices.
Example (Sparse matrix)
>> W = double(rand(100,100)>0.9);
>> Ws = sparse(W);
>> y = Ws*x; % the same as y=W*x but faster

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Howtos

Solution to Excercise #1

1 %compute t h e S t i r l i n g Formula
2
3 n = 50;
4
5 n f a c t o r i a l = s q r t ( 2 ∗ p i ∗n ) ∗ ( n/ exp ( 1 ) ) ˆ n
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Howtos

Solution to Excercise #2

1 function n f a c t o r i a l = s t i r f a c (n ) ;
2 %compute t h e S t i r l i n g Formula
3

4 n f a c t o r i a l = s q r t ( 2 ∗ p i ∗n ) ∗ ( n/ exp ( 1 ) ) ˆ n ;
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