OpenI
/
graphkit-learn

"""
@author: linlin
@references: Liva Ralaivola, Sanjay J Swamidass, Hiroto Saigo, and Pierre Baldi. Graph kernels for chemical informatics. Neural networks, 18(8):1093–1110, 2005.
"""

import sys
import pathlib
sys.path.insert(0, "../")
import time

import networkx as nx
import numpy as np


def untildpathkernel(*args, node_label = 'atom', edge_label = 'bond_type', labeled = True, depth = 10, k_func = 'tanimoto'):
    """Calculate path graph kernels up to depth d between graphs.
    Parameters
    ----------
    Gn : List of NetworkX graph
        List of graphs between which the kernels are calculated.
    /
    G1, G2 : NetworkX graphs
        2 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.
    labeled : boolean
        Whether the graphs are labeled. The default is True.
    depth : integer
        Depth of search. Longest length of paths.
    k_func : function
        A kernel function used using different notions of fingerprint similarity.

    Return
    ------
    Kmatrix : Numpy matrix
        Kernel matrix, each element of which is the path kernel up to d between 2 praphs.
    """
    depth = int(depth)
    if len(args) == 1: # for a list of graphs
        Gn = args[0]
        Kmatrix = np.zeros((len(Gn), len(Gn)))

        start_time = time.time()

        # get all paths of all graphs before calculating kernels to save time, but this may cost a lot of memory for large dataset.
        all_paths = [ find_all_paths_until_length(Gn[i], depth, node_label = node_label, edge_label = edge_label, labeled = labeled) for i in range(0, len(Gn)) ]

        for i in range(0, len(Gn)):
            for j in range(i, len(Gn)):
                Kmatrix[i][j] = _untildpathkernel_do(all_paths[i], all_paths[j], k_func, node_label = node_label, edge_label = edge_label, labeled = labeled)
                Kmatrix[j][i] = Kmatrix[i][j]

        run_time = time.time() - start_time
        print("\n --- kernel matrix of path kernel up to %d of size %d built in %s seconds ---" % (depth, len(Gn), run_time))

        return Kmatrix, run_time

    else: # for only 2 graphs

        start_time = time.time()

        all_paths1 = find_all_paths_until_length(args[0], depth, node_label = node_label, edge_label = edge_label, labeled = labeled)
        all_paths2 = find_all_paths_until_length(args[1], depth, node_label = node_label, edge_label = edge_label, labeled = labeled)

        kernel = _untildpathkernel_do(all_paths1, all_paths2, k_func, node_label = node_label, edge_label = edge_label, labeled = labeled)

        run_time = time.time() - start_time
        print("\n --- path kernel up to %d built in %s seconds ---" % (depth, run_time))

        return kernel, run_time


def _untildpathkernel_do(paths1, paths2, k_func, node_label = 'atom', edge_label = 'bond_type', labeled = True):
    """Calculate path graph kernels up to depth d between 2 graphs.

    Parameters
    ----------
    paths1, paths2 : list
        List of paths in 2 graphs, where for unlabeled graphs, each path is represented by a list of nodes; while for labeled graphs, each path is represented by a string consists of labels of nodes and edges on that path.
    k_func : function
        A kernel function used using different notions of fingerprint similarity.
    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.

    Return
    ------
    kernel : float
        Treelet Kernel between 2 graphs.
    """
    all_paths = list(set(paths1 + paths2))

    if k_func == 'tanimoto':
        vector1 = [ (1 if path in paths1 else 0) for path in all_paths ]
        vector2 = [ (1 if path in paths2 else 0) for path in all_paths ]
        kernel_uv = np.dot(vector1, vector2)
        kernel = kernel_uv / (len(set(paths1)) + len(set(paths2)) - kernel_uv)

    else: # MinMax kernel
        path_count1 = Counter(paths1)
        path_count2 = Counter(paths2)
        vector1 = [ (path_count1[key] if (key in path_count1.keys()) else 0) for key in all_paths ]
        vector2 = [ (path_count2[key] if (key in path_count2.keys()) else 0) for key in all_paths ]
        kernel = np.sum(np.minimum(vector1, vector2)) / np.sum(np.maximum(vector1, vector2))

    return kernel

# this method find paths repetively, it could be faster.
def find_all_paths_until_length(G, length, node_label = 'atom', edge_label = 'bond_type', labeled = True):
    """Find all paths with a certain maximum length in a graph. A recursive depth first search is applied.

    Parameters
    ----------
    G : NetworkX graphs
        The graph in which paths are searched.
    length : integer
        The maximum length of paths.
    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.

    Return
    ------
    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 string consists of labels of nodes and edges on that path.
    """
    all_paths = []
    for i in range(0, length + 1):
        new_paths = find_all_paths(G, i)
        if new_paths == []:
            break
        all_paths.extend(new_paths)

    if labeled == True: # convert paths to strings
        path_strs = []
        for path in all_paths:
            strlist = [ G.node[node][node_label] + G[node][path[path.index(node) + 1]][edge_label] for node in path[:-1] ]
            path_strs.append(''.join(strlist) + G.node[path[-1]][node_label])

        return path_strs

    return all_paths


def find_paths(G, source_node, length):
    """Find all paths with a certain length those start from a source node. A recursive depth first search is applied.

    Parameters
    ----------
    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.

    Return
    ------
    path : list of list
        List of paths retrieved, where each path is represented by a list of nodes.
    """
    return [[source_node]] if length == 0 else \
        [ [source_node] + path for neighbor in G[source_node] \
        for path in find_paths(G, neighbor, length - 1) if source_node not in path ]


def find_all_paths(G, length):
    """Find all paths with a certain length in a graph. A recursive depth first search is applied.

    Parameters
    ----------
    G : NetworkX graphs
        The graph in which paths are searched.
    length : integer
        The length of paths.

    Return
    ------
    path : list of list
        List of paths retrieved, where each path is represented by a list of nodes.
    """
    all_paths = []
    for node in G:
        all_paths.extend(find_paths(G, node, length))

    ### The following process is not carried out according to the original article
    # all_paths_r = [ path[::-1] for path in all_paths ]


    # # For each path, two presentation are retrieved from its two extremities. Remove one of them.
    # for idx, path in enumerate(all_paths[:-1]):
    #     for path2 in all_paths_r[idx+1::]:
    #         if path == path2:
    #             all_paths[idx] = []
    #             break

    # return list(filter(lambda a: a != [], all_paths))
    return all_paths