How to convert sparse matrix to adjacency matrix ?

How do you convert sparse matrix to adjacency matrix in Matlab 2015?

[the cyclist]

I don't understand completely. A sparse matrix could be an adjacency matrix.

Can you please give a small example or two of the input/output you expect?

[vignesh raju]

Sure. I'm trying to convert a .gml file to adjacency matrix, while doing so i converted the .gml file to sparse matrix and was wondering how to convert that to adjacency matrix. Is there a better way to solve this? Sorry I'm new to matlab

Answer 1

[the cyclist]

This submission on the MATLAB File Exchange says that it will convert a *.gml file to an adjacency matrix. Maybe it will work for you.

[vignesh raju]

I have already tried that. It says Out of Memory error and even with 250GB of virtual memory I was unable to solve the error message. Thanks for the inputs.

[the cyclist]

I have a couple suggestions. First, you might want to test that code on smaller subset of your data, to see if it actually does what you want.

If it does, then you could start investigating the code on smaller subsets of data, to see how it is managing the memory. Maybe there are improvements that could be made, or you could chunk up your problem into manageable bites.

More generally, you could look at this page about resolving Out Of Memory errors. You may learn something that helps you.

It may be, though, that your problem is too huge to solve in MATLAB.

[vignesh raju]

It has resolved those issues. But now I'm stuck with a different set of errors with the same code.

When I run the following code :

filename = 'polblogs.gml';

inputfile = fopen(filename);

A=[];

l=0;

k=1;

while 1

      tline = fgetl(inputfile);

      if ~ischar(tline)

          break

      end

      nums = regexp(tline, '\d+', 'match');

      if ~isempty(nums)

          if l==1

              l=0;

              A(k,2)=str2num(nums{1});

              k=k+1;

              continue;

          end

          A(k,1)=str2num(nums{1});

          l=1;

      else

          l=0;

          continue

      end

end

%function adj=adjL2adj(adjL)

adj1 = zeros(length(A));

for i=1:length(A)

      for j=1:length(A(i)); 

          adj1(i,A(i)(j))=1; 

      end

end

It gives me the following error message :

Error: File: adjmat.m Line: 33 Column: 16

()-indexing must appear last in an index expression.

[the cyclist]

A(i)(j)

is not valid MATLAB syntax. I'm not 100% sure, but you may have meant A(i,j).

[vignesh raju]

This code converts adjacency list to adjacency matrix and it had {} brackets before i changed them to ()

%function adj=adjL2adj(adjL)

adj1 = zeros(length(A));

for i=1:length(A)

      for j=1:length(A{i}); 
          adj1(i,A{i}(j))=1; 
      end
  end

[the cyclist]

In MATLAB, curly brackets -- {} -- are not equivalent to parentheses -- (). Curly brackets are used for a special type of MATLAB object: a cell array.

Answer 2

[Walter Roberson]

adjacency_matrix = logical(TheSparseMatrix);

[vignesh raju]

It becomes a sparse logical matrix. An adjacency matrix is a square matrix and I'm unable to get that as output.

[Walter Roberson]

s = size(adjacency_matrix);
if s(1) < s(2)
  adjacency_matrix(s(2),s(2)) = 0;
elseif s(1) > s(2)
  adjacency_matrix(s(1),s(1)) = 0;
end