gklearn.kernels.treeletKernel¶
@author: linlin
@references:
[1] Gaüzère B, Brun L, Villemin D. Two new graphs kernels in chemoinformatics. Pattern Recognition Letters. 2012 Nov 1;33(15):2038-47.
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find_all_paths(G, length, is_directed)[source]¶ Find all paths with a certain length in a graph. A recursive depth first search is applied.
- G : NetworkX graphs
- The graph in which paths are searched.
- length : integer
- The length of paths.
- path : list of list
- List of paths retrieved, where each path is represented by a list of nodes.
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find_paths(G, source_node, length)[source]¶ Find all paths with a certain length those start from a source node. A recursive depth first search is applied.
- G : NetworkX graphs
- The graph in which paths are searched.
- source_node : integer
- The number of the node from where all paths start.
- length : integer
- The length of paths.
- path : list of list
- List of paths retrieved, where each path is represented by a list of nodes.
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get_canonkeys(G, node_label, edge_label, labeled, is_directed)[source]¶ Generate canonical keys of all treelets in a graph.
- G : NetworkX graphs
- The graph in which keys are generated.
- node_label : string
- node attribute used as label. The default node label is atom.
- edge_label : string
- edge attribute used as label. The default edge label is bond_type.
- labeled : boolean
- Whether the graphs are labeled. The default is True.
- canonkey/canonkey_l : dict
- For unlabeled graphs, canonkey is a dictionary which records amount of every tree pattern. For labeled graphs, canonkey_l is one which keeps track of amount of every treelet.
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treeletkernel(*args, sub_kernel, node_label='atom', edge_label='bond_type', parallel='imap_unordered', n_jobs=None, verbose=True)[source]¶ Calculate treelet graph kernels between graphs.
- Gn : List of NetworkX graph
- List of graphs between which the kernels are calculated.
- G1, G2 : NetworkX graphs
- Two graphs between which the kernel is calculated.
- sub_kernel : function
- The sub-kernel between 2 real number vectors. Each vector counts the numbers of isomorphic treelets in a graph.
- node_label : string
- Node attribute used as label. The default node label is atom.
- edge_label : string
- Edge attribute used as label. The default edge label is bond_type.
- parallel : string/None
Which paralleliztion method is applied to compute the kernel. The Following choices are available:
‘imap_unordered’: use Python’s multiprocessing.Pool.imap_unordered method.
None: no parallelization is applied.
- n_jobs : int
- Number of jobs for parallelization. The default is to use all computational cores. This argument is only valid when one of the parallelization method is applied.
- Kmatrix : Numpy matrix
- Kernel matrix, each element of which is the treelet kernel between 2 praphs.