RecRWR: A Recursive Random Walk Method for Improved Identification of Diseases

Algorithm 1

Pseudocode for the RecRWR method.

Algorithm Recursive Random Walk with Restarts

Input : Adjancecy matrix A  of size N  ×  N;

    Vector of size N  with n seed proteins p0;

    Restart probability r

Output : Sorted list of candidate diseases

(1) Let m1,   …,  mk  be the binary vectors of length N

(2) Let W  be a column normalized of the A matrix of size  N  ×  N

(3)

(4) Let p  ≔  p0;

(5) Let i  ≔  1,  j  ≔  1;

(6)

(7) While ((m1^' * |p  −  pt  −  1|)  >=  rho)

(8)    Process (i,  j,  p)

(9)

(10) Let  x  ≔  top(p  *  diag(m1));

(11) Output x;

(12)

(13)

(14) Process (i,  j,  p)

(15)    If (i  ==  j)

(16)       While (j  <=  k)

(17)          p  ≔  Process  (i,  j,  p);

(18)

(19)    If (i  !=  j)

(20)       p  ≔  Process (j,  j,  p)

(21)

(22)    p  ≔  p^'  *  Wmij;

(23)    Wmij  ≔  diag(mi)  *  W  *  diag(mj)

(24)    While  ((mi^'  *  (delta(p))  >  ro)

(25)       p  ≔  (r  *  p0  +  (1  −  r)Wij  *  p);

(26)

(27)    p  ≔  p^'  *  Wmij;

(28)    p  ≔  SelectTop(p,  n);

(29)

(30)    return  p;