change default max walk length to 3

bin/iScore.kernel

@@ -31,7 +31,7 @@ parser.add_argument('--test',action='store_true',help='Only test the functions o
 
 # parameter of the calculations
 parser.add_argument('--lamb',type=float,default=1,help='Lambda parameter in the Kernel calculations. Default: 1')
-parser.add_argument('--walk',type=int,default=4,help='Max walk length in the Kernel calculations. Default: 4')
+parser.add_argument('--walk',type=int,default=3,help='Max walk length in the Kernel calculations. Default: 3')
 parser.add_argument('--method',type=str,default='vect',help="Method used in the calculation: 'vect'(default), 'combvec', 'iter'")
 
 # cuda parameters

bin/iScore.kernel.mpi

@@ -32,7 +32,7 @@ parser.add_argument('--test',action='store_true',help='Only test the functions o
 
 # parameter of the calculations
 parser.add_argument('--lamb',type=float,default=1,help='Lambda parameter in the Kernel calculations. Default: 1')
-parser.add_argument('--walk',type=int,default=4,help='Max walk length in the Kernel calculations. Default: 4')
+parser.add_argument('--walk',type=int,default=3,help='Max walk length in the Kernel calculations. Default: 3')
 parser.add_argument('--method',type=str,default='vect',help="Method used in the calculation: 'vect'(default), 'combvec', 'iter'")
 
 

bin/iScore.train

@@ -24,7 +24,7 @@ parser.add_argument('--graph',default='./graph/',type=str,help='Graph pickle fil
 parser.add_argument('--arc',default='training_set.tar.gz', type = str, help='name of the achive')
 
 # maximum walk length
-parser.add_argument('--walk',default=4, type=int, help='maximum walk length')
+parser.add_argument('--walk',default=3, type=int, help='maximum walk length')
 
 # get the args
 args = parser.parse_args()

bin/iScore.train.mpi

@@ -24,7 +24,7 @@ parser.add_argument('--graph',default='./graph/',type=str,help='Graph pickle fil
 parser.add_argument('--archive',default='training_set.tar.gz', type = str, help='name of the achive')
 
 # maximum walk length
-parser.add_argument('--walk',default=4, type=int, help='maximum walk length')
+parser.add_argument('--walk',default=3, type=int, help='maximum walk length')
 
 # get the args
 args = parser.parse_args()

iScore/graphrank/kernel.py

@@ -58,7 +58,7 @@ def __init__(self,testIDs='testID.lst',trainIDs='trainID.lst',
         >>># get the path of the check file
         >>>checkfile = ker.get_check_file()
         >>># run the calculations
-        >>>ker.run(lamb=1.0,walk=4,check=checkfile)
+        >>>ker.run(lamb=1.0,walk=3,check=checkfile)
 
 
         Args:
@@ -351,7 +351,7 @@ def run(self,lamb,walk,outfile='kernel.pkl',cuda=False,gpu_block=(8,8,1),check=N
     #
     ##############################################################
 
-    def compute_K(self,lamb=1,walk=4):
+    def compute_K(self,lamb=1,walk=3):
         """Compute random walk graph kernel
 
         Notes:
@@ -966,7 +966,7 @@ def iscore_kernel(testID=None,trainID=None,
                   test_graph='./graph', train_graph='./graph',\
                   train_archive=None,
                   check=None, outfile='kernel.pkl',test=False,
-                  lamb=1, walk=4, method='vect',
+                  lamb=1, walk=3, method='vect',
                   tune_kernel=False,func='all',cuda=False, gpu_block=[8,8,1]):
 
     # init and load the data
@@ -997,7 +997,7 @@ def iscore_kernel_mpi(testID=None,trainID=None,
                       test_graph='./graph', train_graph='./graph',
                       train_archive=None,
                       check=None, outfile='kernel.pkl',test=False,
-                      lamb=1, walk=4, method='vect',rank=0,size=1):
+                      lamb=1, walk=3, method='vect',rank=0,size=1):
 
     # init and load the data
     ker = Kernel(testIDs=testID,test_graph = test_graph,