From ecec0a598d877b593cc6aafb33c1e6e9dfdf1ac5 Mon Sep 17 00:00:00 2001 From: Cunliang Geng Date: Fri, 5 Feb 2021 18:13:26 +0100 Subject: [PATCH] add walk or maxlen option to bin commands --- bin/iScore.predict | 10 ++++++++-- bin/iScore.predict.mpi | 10 ++++++++-- bin/iScore.svm | 2 +- bin/iScore.train | 9 ++++++--- bin/iScore.train.mpi | 9 ++++++--- 5 files changed, 29 insertions(+), 11 deletions(-) diff --git a/bin/iScore.predict b/bin/iScore.predict index 1239b12..ff94d11 100755 --- 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 index 63d1b12..88c2136 100755 --- 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 index 1f98a0c..35530cc 100755 --- 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 index f1b8c83..72ad1af 100755 --- 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 index e526849..560d9ff 100755 --- 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)