How to formulate this expression - matlab

I am new to MATLAB and I want to formulate the following lease square expression in Matlab. I have some codes that I am typing here. But the optimization problem solution seems not to be correct. Does anyone has an idea why?
First, I want to solve the heat equation
$$T_t(x,t) = - L_x . T(x,t) + F(x,t)$$
where L_x is Laplacian matrix of the graph.
then find y from the following least square.
$$ \min_y \sum_{j} \sum_{i} (\hat{T}_j(t_i) - T_j(t_i, y))^2$$
Thanks in advance!!
Here is my code:
%++++++++++++++++ main ++++++++++++++++++++
% incidence matrix for original graph
C_hat = [ 1 -1 0 0 0 0;...
0 1 -1 0 0 -1;...
0 0 0 0 -1 1;...
0 0 0 1 1 0;...
-1 0 1 -1 0 0];
% initial temperature for each vertex in original graph
T_hat_0 = [0 7 1 9 4];
[M_bar,n,m_bar,T_hat_heat,T_hat_temp] = simulate_temp(T_hat_0,C_hat);
C = [ 1 1 -1 -1 0 0 0 0 0 0;...
0 -1 0 0 1 -1 1 0 0 0;...
0 0 1 0 0 1 0 -1 -1 0;...
0 0 0 1 0 0 -1 0 1 -1;...
-1 0 0 0 -1 0 0 1 0 1];
%
% initial temperature for each vertex in original graph
T_0 = [0 7 1 9 4];
%
% initial temperature simulation
[l,n,m,T_heat,T_temp] = simulate_temp(T_0,C);
%
% bounds for variables
lb = zeros(m,1);
ub = ones(m,1);
%
% initial edge weights
w0 = ones(m,1);
% optimization problem
% w = fmincon(#fun, w0, [], [], [], [], lb, ub);
%++++++++++++++++++++ function++++++++++++++++++++++++++++
function [i,n,m,T_heat,T_temp] = simulate_temp(T,C)
%
% initial conditions
delta_t = 0.1;
M = 20; %% number of time steps
t = 1;
[n,m] = size(C);
I = eye(n);
L_w = C * C';
T_ini = T';
Temp = zeros(n,1);
% Computing Temperature
%
for i=1:M
K = 2*I + L_w * delta_t;
H = 2*I - L_w * delta_t;
%
if i == 1
T_heat = (K \ H) * T_ini;
%
t = t + delta_t;
else
T_heat = (K \ H) * Temp;
%
t = t + delta_t;
end
% replacing column of T_final with each node temperature in each
% iteration. It adds one column to the matrix in each step
T_temp(:,i) = T_heat;
%
Temp = T_heat;
end
end
%++++++++++++++++++ function+++++++++++++++++++++++++++++++++++++++++
function w_i = fun(w);
%
for r=1:n
for s=1:M_bar
w_i = (T_hat_temp(r,s) - T_temp(r,s)).^2;
end
end

To give a more clear answer, I need more information about what form you have the functions F_j and E_j in.
I've assumed that you feed each F_j a value, x_i, and get back a number. I've also assumed that you feed E_j a value x_i, and another value (or vector) y, and get back a value.
I've also assumed that by 'i' and 'j' you mean the indices of the columns and rows respectively, and that they're finite.
All I can suggest without knowing more info is to do this:
Pre-calculate the values of the functions F_j for each x_i, to give a matrix F - where element F(i,j) gives you the value F_j(x_i).
Do the same thing for E_j, giving a matrix E - where E(i,j) corresponds to E_j(x_i,y).
Perform (F-E).^2 to subtract each element of F and E, then square them element-wise.
Take sum( (F-E).^2**, 2)**. sum(M,2) will sum across index i of matrix M, returning a column vector.
Finally, take sum( sum( (F-E).^2, 2), 1) to sum across index j, the columns, this will finally give you a scalar.

Related

How to vary the values in the matrix according to z axis value in matlab

I created random connectivity information matrix. From that I have plotted x,y and z axis points in 3D graph .Now I just want to apply the zaxis values in the corresponding connectivity such that where ever 1 is present in connectivity it should be multiplied by corresponding zaxis values (eg: if in conn matrix (1,3)place =1 then it should take particular zaxis values and multiply). But I getting the same values for all the places. Suggestions.
%Conncectivity Matrix
success = 0;
n = input('Enter the No. of Nodes'); %size of matrix
k = input('Enter the max connectivity'); %maximal number of 1s
p = 0.5;
Result_Matrix = zeros(n,n);
while (success == 0)
Result_Matrix = (rand(n,n) < p);
Result_Matrix(logical(eye(n))) = 0;
Result_Matrix = max(Result_Matrix, Result_Matrix');
s = sum(Result_Matrix,1);
success = 1;
if min(s) == 0
success = 0; p = p*2; % too few 1s, increase p
end
if max(s) > k
success = 0; p = p/2; % too many 1s, decrease p
end
end
m=Result_Matrix;
conn_mat=m;
disp('connection matrix');
disp(m);
[r,c] = find(m);
A = [r,c]
%3D-GRAPH
PlotSizex=100;
PlotSizey=100;
PlotSizez=-100;
x=PlotSizex*rand(1,n)
y=PlotSizey*rand(1,n)
z=PlotSizez*rand(1,n)
plot3(x(A).', y(A).',z(A).', 'O-')
%Zaxis values multiply with Connectivity
d=zeros(n,n);
z % values of zaxis
for i=1:n
for j=i+1:n
d(i,j)= z(i);
d(j,i)=d(i,j);
end
end
New matrix= d.*m %d is zaxis values and m is connectivity matrix.
I do obtain different values in new_matrix:
new_matrix =
0 -63.4303 -63.4303 0 0
-63.4303 0 0 -23.9408 0
-63.4303 0 0 -24.5725 0
0 -23.9408 -24.5725 0 -76.5436
0 0 0 -76.5436 0
My connection matrix is:
connection matrix
0 1 1 0 0
1 0 0 1 0
1 0 0 1 0
0 1 1 0 1
0 0 0 1 0
and z values are:
z =
-63.4303 -23.9408 -24.5725 -76.5436 -86.3677
I find it strange to multiply the elements in your connection matrix with a single z value, because each element in the connection matrix is related to two points in space (and thus two z values). So, it would make more sense to use the following:
for i=1:n
for j=i:n
d(i,j)= z(i)*z(j); % or another combination of z(i) and z(j)
d(j,i)=d(i,j);
end
end

Quick Assembly of sparse matrix

I have indices
I = [nGrid x 9] matrix % mesh on fine grid (9 point rectangle)
J = [nGrid x 4] matrix % mesh on coarse grid (4 point rectangle)
Here, nGrid is large number depending on the mesh (e.g. 1.e05)
Then I want to do like
R_ref = [4 x 9] matrix % reference restriction matrix from fine to coarse
P_ref = [9 x 4] matrix % reference prolongation matrix from coarse to fine
R = sparse(size) % n_Coarse x n_Fine
P = sparse(size) % n_Fine x n_Coarse
for k = 1 : nGrid % number of elements on coarse grid
R(I(k,:),J(k,:)) = R_ref;
P(J(k,:),I(k,:)) = P_ref;
end
size is predetermined number.
Note that even if there is same index in (I,J), I do not want to accumulate. I just want to put stencils Rref and Pref at each indices respectively.
I know that this is very slow due to the data structure of sparse.
Usually, I use
sparse(row,col,entry,n_row,n_col)
I can use this by manipulate I, J, R_ref, P_ref by bsxfun and repmat.
However, this cannot be done because of the accumulation of sparse function
(if there exists (i,j) such that [row(i),col(i)]==[row(j),col(j)], then R(row(i),row(j)) = entry(i)+entry(j))
Is there any suggestion for this kind of assembly procedure?
Sample code
%% INPUTS
% N and M could be much larger
N = 2^5+1; % number of fine grid in x direction
M = 2^5+1; % number of fine grid in y direction
% [nOx * nOy] == nGrid
nOx = floor((M)/2)+1; % number of coarse grid on x direction
nOy = floor((N)/2)+1; % number of coarse grid on y direction
Rref = [4 4 -1 4 -2 0 -1 0 0
-1 -1 -2 4 4 4 -1 4 4
-1 -1 4 -2 4 -2 4 4 -1
0 4 4 0 0 4 -1 -2 -1]/8;
Pref = [2 1 0 1 0 0 0 0 0
0 0 0 1 1 1 0 1 2
0 0 1 0 1 0 2 1 0
0 2 1 0 0 1 0 0 0]'/2;
%% INDEX GENERATION
tri_ref = reshape(bsxfun(#plus,[0,1,2]',[0,N,2*N]),[],1)';
TRI_ref = reshape(bsxfun(#plus,[0,1]',[0,nOy]),[],1)';
I = reshape(bsxfun(#plus,(1:2:N-2)',0:2*N:(M-2)*N),[],1);
J = reshape(bsxfun(#plus,(1:nOy-1)',0:nOy:(nOx-2)*nOy),[],1);
I = bsxfun(#plus,I,tri_ref);
J = bsxfun(#plus,J,TRI_ref);
%% THIS PART IS WHAT I WANT TO CHANGE
R = sparse(nOx*nOy,N*M);
P = R';
for k = 1 : size(I,1)
R(J(k,:),I(k,:)) = Rref;
P(I(k,:),J(k,:)) = Pref;
end

Writing an adjacency matrix for a graph [duplicate]

Consider a set of points arranged on a grid of size N-by-M.
I am trying to build the adjacency matrix such that
neighboring points are connected.
For example, in a 3x3 grid with a graph:
1-2-3
| | |
4-5-6
| | |
7-8-9
We should have the corresponding adjacency matrix:
+---+------------------------------------------------------+
| | 1 2 3 4 5 6 7 8 9 |
+---+------------------------------------------------------+
| 1 | 0 1 0 1 0 0 0 0 0 |
| 2 | 1 0 1 0 1 0 0 0 0 |
| 3 | 0 1 0 0 0 1 0 0 0 |
| 4 | 1 0 0 0 1 0 1 0 0 |
| 5 | 0 1 0 1 0 1 0 1 0 |
| 6 | 0 0 1 0 1 0 0 0 1 |
| 7 | 0 0 0 1 0 0 0 1 0 |
| 8 | 0 0 0 0 1 0 1 0 1 |
| 9 | 0 0 0 0 0 1 0 1 0 |
+---+------------------------------------------------------+
As a bonus, the solution should work for both 4- and 8-connected neighboring points, that is:
o o o o
o X o vs. o X o
o o o o
This the code that I have so far:
N = 3; M = 3;
adj = zeros(N*M);
for i=1:N
for j=1:M
k = sub2ind([N M],i,j);
if i>1
ii=i-1; jj=j;
adj(k,sub2ind([N M],ii,jj)) = 1;
end
if i<N
ii=i+1; jj=j;
adj(k,sub2ind([N M],ii,jj)) = 1;
end
if j>1
ii=i; jj=j-1;
adj(k,sub2ind([N M],ii,jj)) = 1;
end
if j<M
ii=i; jj=j+1;
adj(k,sub2ind([N M],ii,jj)) = 1;
end
end
end
How can this improved to avoid all the looping?
If you notice, there is a distinct pattern to the adjacency matrices you are creating. Specifically, they are symmetric and banded. You can take advantage of this fact to easily create your matrices using the diag function (or the spdiags function if you want to make a sparse matrix). Here is how you can create the adjacency matrix for each case, using your sample matrix above as an example:
4-connected neighbors:
mat = [1 2 3; 4 5 6; 7 8 9]; % Sample matrix
[r, c] = size(mat); % Get the matrix size
diagVec1 = repmat([ones(c-1, 1); 0], r, 1); % Make the first diagonal vector
% (for horizontal connections)
diagVec1 = diagVec1(1:end-1); % Remove the last value
diagVec2 = ones(c*(r-1), 1); % Make the second diagonal vector
% (for vertical connections)
adj = diag(diagVec1, 1)+diag(diagVec2, c); % Add the diagonals to a zero matrix
adj = adj+adj.'; % Add the matrix to a transposed copy of
% itself to make it symmetric
And you'll get the following matrix:
adj =
0 1 0 1 0 0 0 0 0
1 0 1 0 1 0 0 0 0
0 1 0 0 0 1 0 0 0
1 0 0 0 1 0 1 0 0
0 1 0 1 0 1 0 1 0
0 0 1 0 1 0 0 0 1
0 0 0 1 0 0 0 1 0
0 0 0 0 1 0 1 0 1
0 0 0 0 0 1 0 1 0
8-connected neighbors:
mat = [1 2 3; 4 5 6; 7 8 9]; % Sample matrix
[r, c] = size(mat); % Get the matrix size
diagVec1 = repmat([ones(c-1, 1); 0], r, 1); % Make the first diagonal vector
% (for horizontal connections)
diagVec1 = diagVec1(1:end-1); % Remove the last value
diagVec2 = [0; diagVec1(1:(c*(r-1)))]; % Make the second diagonal vector
% (for anti-diagonal connections)
diagVec3 = ones(c*(r-1), 1); % Make the third diagonal vector
% (for vertical connections)
diagVec4 = diagVec2(2:end-1); % Make the fourth diagonal vector
% (for diagonal connections)
adj = diag(diagVec1, 1)+... % Add the diagonals to a zero matrix
diag(diagVec2, c-1)+...
diag(diagVec3, c)+...
diag(diagVec4, c+1);
adj = adj+adj.'; % Add the matrix to a transposed copy of
% itself to make it symmetric
And you'll get the following matrix:
adj =
0 1 0 1 1 0 0 0 0
1 0 1 1 1 1 0 0 0
0 1 0 0 1 1 0 0 0
1 1 0 0 1 0 1 1 0
1 1 1 1 0 1 1 1 1
0 1 1 0 1 0 0 1 1
0 0 0 1 1 0 0 1 0
0 0 0 1 1 1 1 0 1
0 0 0 0 1 1 0 1 0
Just for fun, here's a solution to construct the adjacency matrix by computing the distance between all pairs of points on the grid (not the most efficient way obviously)
N = 3; M = 3; %# grid size
CONNECTED = 8; %# 4-/8- connected points
%# which distance function
if CONNECTED == 4, distFunc = 'cityblock';
elseif CONNECTED == 8, distFunc = 'chebychev'; end
%# compute adjacency matrix
[X Y] = meshgrid(1:N,1:M);
X = X(:); Y = Y(:);
adj = squareform( pdist([X Y], distFunc) == 1 );
And here's some code to visualize the adjacency matrix and the graph of connected points:
%# plot adjacency matrix
subplot(121), spy(adj)
%# plot connected points on grid
[xx yy] = gplot(adj, [X Y]);
subplot(122), plot(xx, yy, 'ks-', 'MarkerFaceColor','r')
axis([0 N+1 0 M+1])
%# add labels
[X Y] = meshgrid(1:N,1:M);
X = reshape(X',[],1) + 0.1; Y = reshape(Y',[],1) + 0.1;
text(X, Y(end:-1:1), cellstr(num2str((1:N*M)')) )
I just found this question when searching for the same problem. However, none of the provided solutions worked for me because of the problem size which required the use of sparse matrix types. Here is my solution which works on large scale instances:
function W = getAdjacencyMatrix(I)
[m, n] = size(I);
I_size = m*n;
% 1-off diagonal elements
V = repmat([ones(m-1,1); 0],n, 1);
V = V(1:end-1); % remove last zero
% n-off diagonal elements
U = ones(m*(n-1), 1);
% get the upper triangular part of the matrix
W = sparse(1:(I_size-1), 2:I_size, V, I_size, I_size)...
+ sparse(1:(I_size-m),(m+1):I_size, U, I_size, I_size);
% finally make W symmetric
W = W + W';
Just came across this question. I have a nice working m-function (link: sparse_adj_matrix.m) that is quite general.
It can handle 4-connect grid (radius 1 according to L1 norm), 8-connect grid (radius 1 according to L_infty norm).
It can also support 3D (and arbitrarily higher domensional grids).
The function can also connect nodes further than radius = 1.
Here's the signiture of the function:
% Construct sparse adjacency matrix (provides ii and jj indices into the
% matrix)
%
% Usage:
% [ii jj] = sparse_adj_matrix(sz, r, p)
%
% inputs:
% sz - grid size (determine the number of variables n=prod(sz), and the
% geometry/dimensionality)
% r - the radius around each point for which edges are formed
% p - in what p-norm to measure the r-ball, can be 1,2 or 'inf'
%
% outputs
% ii, jj - linear indices into adjacency matrix (for each pair (m,n)
% there is also the pair (n,m))
%
% How to construct the adjacency matrix?
% >> A = sparse(ii, jj, ones(1,numel(ii)), prod(sz), prod(sz));
%
%
% Example:
% >> [ii jj] = sparse_adj_matrix([10 20], 1, inf);
% construct indices for 200x200 adjacency matrix for 8-connect graph over a
% grid of 10x20 nodes.
% To visualize the graph:
% >> [r c]=ndgrid(1:10,1:20);
% >> A = sparse(ii, jj, 1, 200, 200);;
% >> gplot(A, [r(:) c(:)]);
Your current code doesn't seem so bad. One way or another you need to iterate over all neighbor pairs. If you really need to optimize the code, I would suggest:
loop over node indices i, where 1 <= i <= (N*M)
don't use sub2ind() for efficiency, the neighbors of node i are simpy [i-M, i+1, i+M, i-1] in clockwise order
Notice that to get all neighbor pairs of nodes:
you only have to compute the "right" neighbors (i.e. horizontal edges) for nodes i % M != 0 (since Matlab isn't 0-based but 1-based)
you only have to compute "above" neighbors (i.e. vertical edges) for nodes i > M
there is a similar rule for diagonal edges
This would leed to a single loop (but same number of N*M iterations), doesn't call sub2ind(), and has only two if statements in the loop.
For each node in the graph add a connection to the right and one downwards. Check that you don't overreach your grid. Consider the following function that builds the adjacency matrix.
function adj = AdjMatrixLattice4( N, M )
% Size of adjacency matrix
MN = M*N;
adj = zeros(MN,MN);
% number nodes as such
% [1]---[2]-- .. --[M]
% | | |
% [M+1]-[M+2]- .. -[2*M]
% : : :
% [] [] .. [M*N]
for i=1:N
for j=1:N
A = M*(i-1)+j; %Node # for (i,j) node
if(j<N)
B = M*(i-1)+j+1; %Node # for node to the right
adj(A,B) = 1;
adj(B,A) = 1;
end
if(i<M)
B = M*i+j; %Node # for node below
adj(A,B) = 1;
adj(B,A) = 1;
end
end
end
end
Example as above AdjMatrixLattice4(3,3)=
0 1 0 1 0 0 0 0 0
1 0 1 0 1 0 0 0 0
0 1 0 0 0 1 0 0 0
1 0 0 0 1 0 1 0 0
0 1 0 1 0 1 0 1 0
0 0 1 0 1 0 0 0 1
0 0 0 1 0 0 0 1 0
0 0 0 0 1 0 1 0 1
0 0 0 0 0 1 0 1 0

matlab: praticle state simulation

Lets say I want to simulate a particle state, which can be normal (0) or excited (1) in given frame. The particle is in excited state f % of time. If the particle is in excited state, it lasts for ~L frames (with poisson distribution). I want to simulate that state for N time points. So the input is for example:
N = 1000;
f = 0.3;
L = 5;
and the result will be something like
state(1:N) = [0 0 1 1 1 1 0 0 0 0 1 1 1 0 0 0 0 0 0 0 0 0 1 1 1 1 1 0 0 0 0 0 ... and so on]
with sum(state)/N close to 0.3
How to do that?
Thanks!
%% parameters
f = 0.3; % probability of state 1
L1 = 5; % average time in state 1
N = 1e4;
s0 = 1; % init. state
%% run simulation
L0 = L1 * (1 / f - 1); % average time state 0 lasts
p01 = 1 / L0; % probability to switch from 0 to 1
p10 = 1 / L1; % probability to switch from 1 to 0
p00 = 1 - p01;
p11 = 1 - p10;
sm = [p00, p01; p10, p11]; % build stochastic matrix (state machine)
bins = [0, 1]; % possible states
states = zeros(N, 1);
assert(all(sum(sm, 2) == 1), 'not a stochastic matrix');
smc = cumsum(sm, 2); % cummulative matrix
xi = find(bins == s0);
for k = 1 : N
yi = find(smc(xi, :) > rand, 1, 'first');
states(k) = bins(yi);
xi = yi;
end
%% check result
ds = [states(1); diff(states)];
idx_begin = find(ds == 1 & states == 1);
idx_end = find(ds == -1 & states == 0);
if idx_end(end) < idx_begin(end)
idx_end = [idx_end; N + 1];
end
df = idx_end - idx_begin;
fprintf('prob(state = 1) = %g; avg. time(state = 1) = %g\n', sum(states) / N, mean(df));
The average length of the excited state is 5. The average length of the normal state, should thus be around 12 to obtain.
The strategy can be something like this.
Start in state 0
Draw a random number a from a Poisson distribution with mean L*(1-f)/f
Fill the state array with a zeroes
Draw a random number b from a Poission distribution with mean L
Fill the state array witb b ones.
Repeat
Another option would be to think in terms of switching probabilities, where the 0->1 and 1->0 probabilities are unequal.

MATLAB matrix not formatting correctly

I have some code below, and I cant seem to get the matrices formatted correctly. I have been trying to get the matrices to look more professional (close together) with \t and fprintf, but cant seem to do so. I am also having some trouble putting titles for each columns of the matrix. Any help would be much appreciated!
clear all
clc
format('bank')
% input file values %
A = [4 6 5 1 0 0 0 0 0; 7 8 4 0 1 0 0 0 0; 6 5 9 0 0 1 0 0 0; 1 0 0 0 0 0 -1 0 0; 0 1 0 0 0 0 0 -1 0; 0 0 1 0 0 0 0 0 -1];
b = [480; 600; 480; 24; 20; 25];
c = [3000 4000 4000 0 0 0 0 0 0];
% Starting xb %
xb = [1 2 3 4 5 6]
% Starting xn %
xn = [7 8 9]
cb = c(xb)
cn = c(xn)
% Get B from A %
B = A(:,xb)
% Get N from A %
N = A(:,xn)
% Calculate z %
z = ((cb*(inv(B))*A)-c)
% Calculate B^(-1) %
Binv = inv(B)
% Calculate RHS of row 0 %
RHS0 = cb*Binv*b
% Calculates A %
A = Binv*A
%STARTING Tableau%
ST = [z RHS0;A b]
for j=1:A
fprintf(1,'\tz%d',j)
end
q = 0
while q == 0
m = input('what is the index value of the ENTERING variable? ')
n = input('what is the index value of the LEAVING variable? ')
xn(xn==m)= n
xb(xb==n) = m
cb = c(xb)
cn = c(xn)
B = A(:,xb)
N = A(:,xn)
Tableuz = (c-(cb*(B^(-1))*A))
RHS0 = (cb*(B^(-1))*b)
TableuA = ((B^(-1))*A)
Tableub = ((B^(-1))*b)
CT = [Tableuz RHS0; TableuA Tableub];
disp(CT)
q = input('Is the tableau optimal? Y-1, N-0')
end
I didn't dig into what you are doing really deeply, but a few pointers:
* Put semicolons at the end of lines you don't want printing to the screen--it makes it easier to see what is happening elsewhere.
* Your for j=1:A loop only prints j. I think what you want is more like this:
for row = 1:size(A,1)
for column = 1:size(A,2)
fprintf('%10.2f', A(row,column));
end
fprintf('\n');
end
If you haven't used the Matlab debugger yet, give it a try; it makes a lot of these problems easier to spot. All you have to do to start it is to add a breakpoint to the file by clicking on the dash(-) next to the line numbers and starting the script. Quick web searches can turn up the solution very quickly too--someone else has usually already had any problem you're going to run into.
Good luck.
Try using num2str with a format argument of your desired precision. It's meant for converting matrices to strings. (note: this is different than mat2str which serializes matrices so they can be deserialized with eval)