gklearn.kernels.untilHPathKernel¶
@author: linlin
@references:
[1] Liva Ralaivola, Sanjay J Swamidass, Hiroto Saigo, and Pierre Baldi. Graph kernels for chemical informatics. Neural networks, 18(8):1093–1110, 2005.
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find_all_paths_until_length(G, length, ds_attrs, node_label='atom', edge_label='bond_type', tolabelseqs=True)[source]¶ Find all paths no longer than a certain maximum length in a graph. A recursive depth first search is applied.
- G : NetworkX graphs
- The graph in which paths are searched.
- length : integer
- The maximum length of paths.
- ds_attrs: dict
- Dataset attributes.
- 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.
- path : list
- List of paths retrieved, where for unlabeled graphs, each path is represented by a list of nodes; while for labeled graphs, each path is represented by a list of strings consists of labels of nodes and/or edges on that path.
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untilhpathkernel(*args, node_label='atom', edge_label='bond_type', depth=10, k_func='MinMax', compute_method='trie', parallel='imap_unordered', n_jobs=None, verbose=True)[source]¶ Calculate path graph kernels up to depth/hight h 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.
- 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.
- depth : integer
- Depth of search. Longest length of paths.
- k_func : function
A kernel function applied using different notions of fingerprint similarity, defining the type of feature map and normalization method applied for the graph kernel. The Following choices are available:
‘MinMax’: use the MiniMax kernel and counting feature map.
‘tanimoto’: use the Tanimoto kernel and binary feature map.
None: no sub-kernel is used, the kernel is computed directly.
- compute_method : string
Computation method to store paths and compute the graph kernel. The Following choices are available:
‘trie’: store paths as tries.
‘naive’: store paths to lists.
- n_jobs : int
- Number of jobs for parallelization.
- Kmatrix : Numpy matrix
- Kernel matrix, each element of which is the path kernel up to h between 2 praphs.