MOfinder: A Novel Algorithm for Detecting Overlapping Modules from Protein-Protein Interaction Network

Algorithm 1

Input: The PPI network 𝐺=(𝑉,𝐸);

   Cluster coefficient threshold CC;

   Sliding window 𝑠.

   Output: modules.

   (1)𝑀= zeros(𝑉,𝑉); // initialization of network matrix

   (2) for each 𝑒∈𝐸  do

   (3)     𝑀(𝑒1,𝑒2)=1; // build sparse matrix, 𝑒1∈𝑉,𝑒2∈𝑉

   (4) end for

   (5) Mg = global AMD(𝑀);

   (6) While 𝑎+𝑠⩽𝑉  do //𝑎=1, as start

   (7)    mg = Mg(𝑎∶𝑎+𝑠,𝑎∶𝑎+𝑠);

   (8)    ml = local AMD(mg);

   (9)    if cc (ml)⩾CC do

(10)       insert ml to modules;

(11)    end if

(12)    𝑎=𝑎+1;

(13) end while

(14) for each module𝐴 in modules do

(15)    if module𝐴∈ module𝐵 do // module𝐵 in modules and module𝐴≠ module𝐵

(16)       discard module𝐴 from modules; // delete redundancy

(17)    end if

(18) end for