Improvement of Network Deconvolution algorithm through non-linear attenuation

• Network Deconvolution

We used the original code from 'Network deconvolution as a general method to distinguish direct dependencies in networks' which is availabe at http://compbio.mit.edu/nd/code/ND_regulatory.m



• Non-linear attenuation version of Network Deconvolution

The main part of the code is the same as the original code; however, the code is modified in the Network Deconvolution loop as follow (lines 185-190 of ND_regulatory.m):

%network deconvolution

for i = 1:size(D,1)
    D(i,i) = (D(i,i))/(m+(D(i,i)^(1/τ)));
end

mat_new1 = U*D*inv(U);