add walk or maxlen option to bin commands

DeepRank · Feb 5, 2021 · ecec0a5 · ecec0a5
1 parent 917b57d
commit ecec0a5
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Showing 5 changed files with 29 additions and 11 deletions.
diff --git a/bin/iScore.predict b/bin/iScore.predict
@@ -25,6 +25,12 @@ parser = argparse.ArgumentParser(description=' iScore - Predict the class of new
 # where the kernels are stored
 parser.add_argument('-gt', '--ground_truth',default=None,type=str,help='File containing the ground truth')
 
+# walk length for kernel
+parser.add_argument('--walk',default=3, type=int, help='walk length for creating kernel')
+
+# max walk length to use in svm
+parser.add_argument('--maxlen', type=int, default=None, help='max walk length of the kernel. Default max len possible with the kernel file')
+
 # where the kernels are stored
 parser.add_argument('--kernel',default='./kernel/',type=str,help='Kernel pickle file to use')
 
@@ -54,12 +60,12 @@ else:
 if not os.path.isdir(args.kernel):
     os.mkdir(args.kernel)
     kfile = os.path.join(args.kernel,'kernel.pckl')
-    iscore_kernel(test_graph=args.graph,train_archive=args.archive,outfile=kfile)
+    iscore_kernel(test_graph=args.graph,walk=args.walk,train_archive=args.archive,outfile=kfile)
 else:
     print('Reusing kernels in %s' %(args.kernel))
 
 # grahrank score
-iscore_svm(load_model=None,package_name=args.archive,testID=args.ground_truth)
+iscore_svm(load_model=None,package_name=args.archive,maxlen=args.maxlen,testID=args.ground_truth)
 
 # add energy terms
 iscore_energy(method=args.energy)

diff --git a/bin/iScore.predict.mpi b/bin/iScore.predict.mpi
@@ -28,6 +28,12 @@ parser = argparse.ArgumentParser(description=' iScore - Predict the class of new
 # where the kernels are stored
 parser.add_argument('-gt', '--ground_truth',default=None,type=str,help='File containing the ground truth')
 
+# walk length for kernel
+parser.add_argument('--walk',default=3, type=int, help='walk length for creating kernel')
+
+# max walk length to use in svm
+parser.add_argument('--maxlen', type=int, default=None, help='max walk length of the kernel. Default max len possible with the kernel file')
+
 # where the kernels are stored
 parser.add_argument('--kernel',default='./kernel/',type=str,help='Kernel pickle file to use')
 
@@ -77,13 +83,13 @@ comm.Barrier()
 
 if gen_kernel:
 	kfile = os.path.join(args.kernel,'kernel.pckl')
-	iscore_kernel_mpi(test_graph=args.graph,train_archive=args.archive,outfile=kfile,rank=rank,size=size)
+	iscore_kernel_mpi(test_graph=args.graph,walk=args.walk,train_archive=args.archive,outfile=kfile,rank=rank,size=size)
 comm.Barrier()
 
 # predcit the model
 if rank == 0:
 
-	iscore_svm(load_model=None,package_name=args.archive,testID=args.ground_truth)
+	iscore_svm(load_model=None,maxlen=args.maxlen,package_name=args.archive,testID=args.ground_truth)
 
 	# add energy terms
 	iscore_energy(method=args.energy)

diff --git a/bin/iScore.svm b/bin/iScore.svm
@@ -28,7 +28,7 @@ parser.add_argument('--package_name',type=str,default='training_set.tar.gz',help
 parser.add_argument('--graph',default='./graph/',type=str,help='Graph pickle file to use')
 parser.add_argument('--include_kernel',action='store_true',help='include the kernel in the packaged model')
 
-# max walk len
+# max walk length to use in svm
 parser.add_argument('--maxlen', type=int, default=None,help='max walk length of the kernel. Default max len possible with the kernel file')
 
 

diff --git a/bin/iScore.train b/bin/iScore.train
@@ -23,8 +23,11 @@ parser.add_argument('--graph',default='./graph/',type=str,help='Graph pickle fil
 #name of the archive to save
 parser.add_argument('--arc',default='training_set.tar.gz', type = str, help='name of the achive')
 
-# maximum walk length
-parser.add_argument('--walk',default=3, type=int, help='maximum walk length')
+# walk length for kernel
+parser.add_argument('--walk',default=3, type=int, help='walk length for creating kernel')
+
+# max walk length to use in svm
+parser.add_argument('--maxlen', type=int, default=None, help='max walk length of the kernel. Default max len possible with the kernel file')
 
 # get the args
 args = parser.parse_args()
@@ -46,4 +49,4 @@ else:
 	print("Reuse the kernels in  %s" %args.kernel)
 
 # train the model
-iscore_svm(train=True,package_model=True,package_name=args.arc,maxlen=args.walk)
+iscore_svm(train=True,package_model=True,package_name=args.arc,maxlen=args.maxlen)
diff --git a/bin/iScore.train.mpi b/bin/iScore.train.mpi
@@ -23,8 +23,11 @@ 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=3, type=int, help='maximum walk length')
+# walk length for kernel
+parser.add_argument('--walk',default=3, type=int, help='walk length for creating kernel')
+
+# max walk length to use in svm
+parser.add_argument('--maxlen', type=int, default=None, help='max walk length of the kernel. Default max len possible with the kernel file')
 
 # get the args
 args = parser.parse_args()
@@ -58,4 +61,4 @@ comm.Barrier()
 
 # train the model
 if rank == 0:
-	iscore_svm(train=True,package_model=True,package_name=args.archive)
+	iscore_svm(train=True, package_model=True, maxlen=args.maxlen, package_name=args.archive)