README for dataset PROTEINS


=== Usage ===

This folder contains the following comma separated text files 
(replace DS by the name of the dataset):

n = total number of nodes
m = total number of edges
N = number of graphs

(1) 	DS_A.txt (m lines) 
	sparse (block diagonal) adjacency matrix for all graphs,
	each line corresponds to (row, col) resp. (node_id, node_id)

(2) 	DS_graph_indicator.txt (n lines)
	column vector of graph identifiers for all nodes of all graphs,
	the value in the i-th line is the graph_id of the node with node_id i

(3) 	DS_graph_labels.txt (N lines) 
	class labels for all graphs in the dataset,
	the value in the i-th line is the class label of the graph with graph_id i

(4) 	DS_node_labels.txt (n lines)
	column vector of node labels,
	the value in the i-th line corresponds to the node with node_id i

There are OPTIONAL files if the respective information is available:

(5) 	DS_edge_labels.txt (m lines; same size as DS_A_sparse.txt)
	labels for the edges in DS_A_sparse.txt 

(6) 	DS_edge_attributes.txt (m lines; same size as DS_A.txt)
	attributes for the edges in DS_A.txt 

(7) 	DS_node_attributes.txt (n lines) 
	matrix of node attributes,
	the comma seperated values in the i-th line is the attribute vector of the node with node_id i

(8) 	DS_graph_attributes.txt (N lines) 
	regression values for all graphs in the dataset,
	the value in the i-th line is the attribute of the graph with graph_id i


=== Previous Use of the Dataset ===

Feragen, A., Kasenburg, N., Petersen, J., de Bruijne, M., Borgwardt, K.M.: Scalable
kernels for graphs with continuous attributes. In: C.J.C. Burges, L. Bottou, Z. Ghahra-
mani, K.Q. Weinberger (eds.) NIPS, pp. 216-224 (2013)

Neumann, M., Garnett R., Bauckhage Ch., Kersting K.: Propagation Kernels: Efficient Graph 
Kernels from Propagated Information. Under review at MLJ.


=== References ===

K. M. Borgwardt, C. S. Ong, S. Schoenauer, S. V. N. Vishwanathan, A. J. Smola, and H. P. 
Kriegel. Protein function prediction via graph kernels. Bioinformatics, 21(Suppl 1):i47–i56, 
Jun 2005.

I. Schomburg, A. Chang, C. Ebeling, M. Gremse, C. Heldt, G. Huhn, and D. Schomburg. Brenda, 
the enzyme database: updates and major new developments. Nucleic Acids Research, 32D:431–433, 2004.


