Recently, I am trying to use the OrthoClust R package for multiple species network clustering. I did not found the control parameters in annealing process as described in your paper: "Standard simulated annealing was employed. Spin values were randomly assigned initially, and updated via a heat bath algorithm. The initial temperature was chosen in a way such that the flipping rate (the probability that a node changes its spin state) was higher than 1 – 1/q. The temperature was gradually decreased with a cooling factor 0.9, until the flipping rate was less than 1%." I did also not found the simulation annealing algorithm in the matlab file OrthoClustN.m (represented by a greedy algorithm). Please help me solve this problem. Thank you for your time.
The annealing procedure is very slow for practical problems. in the revision stage of our manuscript, we discovered the greedy algorithm (Louvain algorithm) and therefore wrapped up the matlab code, and implemented in R too. it’s a very well regard algorithm, and we strongly encourage you to try the matlab code for your purpose.