3 possible methods to this regularly asked question:
1. Using the sub2ind function
A = zeros(max(row_number), max(Column_number));
idx = sub2ind(size(A),row_number, Column_number);
A(idx) = Value;
2. Calculating the linear indices manually
A = zeros(max(row_number), max(Column_number));
idx = row_number(:,1) + (Column_number(:,2)-1)*size(A,1)
A(idx) = Value;
3. Use a sparse matrix
sparse(row_number, Column_number, Value)
And then call full on that if you want to convert it to a regular matrix
