Added cosine knn function

cosineknn.m

@@ -0,0 +1,94 @@
+function S = cosineknn(A,K)
+% COSINEKNN Compute k-nearest neighbors with a cosine distance metric
+% 
+% S = cosineknn(A,k) computes a cosine similarity metric between the
+% vertices of A or the upper half of a bipartite graph A
+%
+
+% David F. Gleich
+% Copyright, Stanford University, 2009
+
+% History
+% 2009-08-12: Initial version
+
+% TODO support struct input
+% TODO support other similarity functions
+% TODO allow option for diagonal similarity too
+% TODO allow option for triplet output
+
+
+if isstruct(A), 
+    error('cosineknn:notSupported','struct input is not supported yet');
+else
+    [rp ci ai]=sparse_to_csr(A); check=1;
+    [rpt cit ait]=sparse_to_csr(A'); 
+    [n,m] = size(A);
+end
+
+% compute a row norm (which means we accumlate the column indices of At)
+rn = accumarray(cit,ait.^2);
+rn = sqrt(rn);
+rn(rn>eps(1)) = 1./rn(rn>eps(1)); % do division once
+
+% the output is a n-by-n matrix, allocate storage for it
+si = zeros(n*K,1);
+sj = zeros(n*K,1);
+sv = zeros(n*K,1);
+nused = 0;
+
+dwork = zeros(n,1);
+iwork = zeros(n,1);
+iused = zeros(n,1);
+for i=1:n
+    % for each row of A, compute an inner product against all rows of A.
+    % to do this efficiently, we know that the inner-product will
+    % only be non-zero if two rows of A overlap in a column.  Thus, in
+    % row i of A, we look at all non-zero columns, and then look at all
+    % rows touched by those columns in the A' matrix.  We  compute
+    % the similarity metric, then sort and only store the top k.
+    
+    curused = 0; % track how many non-zeros we compute during this operation
+    
+    for ri=rp(i):rp(i+1)-1
+        % find all columns j in row i
+        j = ci(ri);
+        aij = ai(ri)*rn(i);
+        for rit=rpt(j):rpt(j+1)-1
+            % find all rows k in column j
+            k = cit(rit);
+            if k==i, continue; end % skip over the standard entries
+            akj = ait(rit)*rn(k);
+            if iwork(k)>0
+                % we already have a non-zero between row i and row k
+                dwork(iwork(k)) = dwork(iwork(k)) + aij*akj;
+            else
+                % we need to add a non-zero betwen row i and row k
+                curused = curused + 1;
+                iwork(k) = curused;
+                dwork(curused) = aij*akj;
+                iused(curused) = k;
+            end
+        end
+    end
+    % don't sort if fewer than K elements
+    if curused < K,
+        sperm = 1:curused;
+    else
+        [sdwork sperm] = sort(dwork(1:curused),1,'descend');
+    end
+    for k=1:min(K,length(sperm))
+        nused = nused + 1;
+        si(nused) = i;
+        sj(nused) = iused(sperm(k));
+        sv(nused) = dwork(sperm(k));
+    end
+    % reset the iwork array, no need to reset dwork, as it's just 
+    % overwritten
+    for k=1:curused
+        iwork(iused(k)) = 0;
+    end
+end
+si = si(1:nused);
+sj = sj(1:nused);
+sv = sv(1:nused);
+S = sparse(si,sj,sv,n,n);