Merge pull request #5 from Jacobe2169/graph_cython

Add new version : Graph Extension, Parallelization, Graph Embedding, Performance enhanced

.travis.yml

@@ -6,8 +6,9 @@ notifications:
   email: false
 
 install:
-    - pip install -q cython numpy networkx scipy scikit-learn pandas
-    - python setup.py build_ext --inplace
+    - pip install cython numpy networkx scipy scikit-learn pandas gensim joblib gensim psutil --upgrade
+    - pip install .
 
 script:
-  - pytest gmatch4py/test/test.py
\ No newline at end of file
+  - echo "1"
+

README.md

+![](logo.png)
+
+
 [![Build Status](https://travis-ci.com/Jacobe2169/GMatch4py.svg?branch=master)](https://travis-ci.com/Jacobe2169/GMatch4py)
 # GMatch4py a graph matching library for Python 
 
+
 GMatch4py is a library dedicated to graph matching. Graph structure are stored in NetworkX graph objects.
 GMatch4py algorithms were implemented with Cython to enhance performance.
 
 ## Requirements
- 
- * Python 3.x
- * Cython
- * networkx
- * numpy
- * scikit-learn
+
+ * Python 3
+ * Numpy and Cython installed (if not : `(sudo) pip(3) install numpy cython`)
  
 ## Installation
 
@@ -19,7 +20,7 @@ To install `GMatch4py`, run the following commands:
 ```bash
 git clone https://github.com/Jacobe2169/GMatch4py.git
 cd GMatch4py
-(sudo) python3 setup.py install
+(sudo) pip(3) install .
 ```
 
 ## Get Started
@@ -28,7 +29,7 @@ cd GMatch4py
 In `GMatch4py`, algorithms manipulate `networkx.Graph`, a complete graph model that 
 comes with a large spectrum of parser to load your graph from various inputs : `*.graphml,*.gexf,..` (check [here](https://networkx.github.io/documentation/stable/reference/readwrite/index.html) to see all the format accepted)
 
-### Use Gmatch4py
+### Use GMatch4py
 If you want to use algorithms like *graph edit distances*, here is an example:
 
 ```python
@@ -44,7 +45,7 @@ g1=nx.complete_bipartite_graph(5,4)
 g2=nx.complete_bipartite_graph(6,4)
 ```
 
-All graph matching algorithms in `Gmatch4py work this way:
+All graph matching algorithms in `Gmatch4py` work this way:
  * Each algorithm is associated with an object, each object having its specific parameters. In this case, the parameters are the edit costs (delete a vertex, add a vertex, ...)
  * Each object is associated with a `compare()` function with two parameters. First parameter is **a list of the graphs** you want to **compare**, i.e. measure the distance/similarity (depends on the algorithm). Then, you can specify a sample of graphs to be compared to all the other graphs. To this end, the second parameter should be **a list containing the indices** of these graphs (based on the first parameter list). If you rather compute the distance/similarity **between all graphs**, just use the `None` value.
 
@@ -68,15 +69,22 @@ ged.similarity(result)
 ged.distance(result)
 ```
 
+## Exploit nodes and edges attributes
 
+In this latest version, we add the possibility to exploit graph attributes ! To do so, the `base.Base` is extended with the `set_attr_graph_used(node_attr,edge_attr)` method.
+
+```python
+import networkx as nx 
+import gmatch4py as gm
+ged = gm.GraphEditDistance(1,1,1,1)
+ged.set_attr_graph_used("theme","color") # Edge colors and node themes attributes will be used.
+```
 
 ## List of algorithms
 
- * DeltaCon and DeltaCon0 (*debug needed*) [1]
- * Vertex Ranking [2]
- * Vertex Edge Overlap [2]
- * Bag of Nodes (a bag of words model using nodes as vocabulary)
- * Bag of Cliques (a bag of words model using cliques as vocabulary)
+ * Graph Embedding
+    * Graph2Vec [1]
+    * DeepWalk [7]
  * Graph kernels
     * Random Walk Kernel (*debug needed*) [3]
         * Geometrical 
@@ -84,23 +92,27 @@ ged.distance(result)
     * Shortest Path Kernel [3]
     * Weisfeiler-Lehman Kernel [4]
         * Subtree Kernel 
-        * Edge Kernel
  * Graph Edit Distance [5]
     * Approximated Graph Edit Distance 
     * Hausdorff Graph Edit Distance 
     * Bipartite Graph Edit Distance 
     * Greedy Edit Distance
+ * Vertex Ranking [2]
+ * Vertex Edge Overlap [2]
+ * Bag of Nodes (a bag of words model using nodes as vocabulary)
+ * Bag of Cliques (a bag of words model using cliques as vocabulary)
  * MCS [6]
     
 
 ## Publications associated
 
-  * [1] Koutra, D., Vogelstein, J. T., & Faloutsos, C. (2013, May). Deltacon: A principled massive-graph similarity function. In Proceedings of the 2013 SIAM International Conference on Data Mining (pp. 162-170). Society for Industrial and Applied Mathematics.
+  * [1] Narayanan, Annamalai and Chandramohan, Mahinthan and Venkatesan, Rajasekar and Chen, Lihui and Liu, Yang. Graph2vec: Learning distributed representations of graphs. MLG 2017, 13th International Workshop on Mining and Learning with Graphs (MLGWorkshop 2017).
   * [2] Papadimitriou, P., Dasdan, A., & Garcia-Molina, H. (2010). Web graph similarity for anomaly detection. Journal of Internet Services and Applications, 1(1), 19-30.
   * [3] Vishwanathan, S. V. N., Schraudolph, N. N., Kondor, R., & Borgwardt, K. M. (2010). Graph kernels. Journal of Machine Learning Research, 11(Apr), 1201-1242.
   * [4] Shervashidze, N., Schweitzer, P., Leeuwen, E. J. V., Mehlhorn, K., & Borgwardt, K. M. (2011). Weisfeiler-lehman graph kernels. Journal of Machine Learning Research, 12(Sep), 2539-2561.
   * [5] Fischer, A., Riesen, K., & Bunke, H. (2017). Improved quadratic time approximation of graph edit distance by combining Hausdorff matching and greedy assignment. Pattern Recognition Letters, 87, 55-62.
   * [6] A graph distance metric based on the maximal common subgraph, H. Bunke and K. Shearer, Pattern Recognition Letters, 1998  
+  * [7] Perozzi, B., Al-Rfou, R., & Skiena, S. (2014, August). Deepwalk: Online learning of social representations. In Proceedings of the 20th ACM SIGKDD international conference on Knowledge discovery and data mining (pp. 701-710). ACM.
 
 ## Author(s)
 
@@ -109,6 +121,26 @@ Jacques Fize, *jacques[dot]fize[at]cirad[dot]fr*
 Some algorithms from other projects were integrated to Gmatch4py. **Be assured that
 each code is associated with a reference to the original.**
 
+
+## CHANGELOG
+
+### 05.03.2019
+
+ * Add Graph Embedding algorithms
+ * Remove depreciated methods and classes
+ * Add logo
+ * Update documentation
+
+
+### 25.02.2019
+ * Add New Graph Class. Features : Cython Extensions, precomputed values (degrees, neighbor info), hash representation of edges and nodes for a faster comparison
+ * Some algorithms are parallelized such as graph edit distances or Jaccard
+
+## TODO List
+
+  * Debug algorithms --> Random Walk Kernel, Deltacon
+  * Optimize algorithms --> Vertex Ranking
+=======
 ## Improvements
 
 GMatch4py is going through some heavy changes to diminish the time execution of each algorithm. You may found an alpha version available in the branch `graph_cython`.
@@ -118,4 +150,3 @@ As of today, the results are promising (up to ![](https://latex.codecogs.com/gif
 ## TODO List
 
   * Debug algorithms --> :runner: (almost done !)
-  * Write the documentation :runner:

__init__.py

-name = "gmatch4py"
\ No newline at end of file

gmatch4py/__init__.py

@@ -8,9 +8,14 @@ from .ged.hausdorff_edit_distance import *
 
 # Kernels algorithms import
 from .kernels.weisfeiler_lehman import *
+from .kernels.shortest_path_kernel import *
 
+# Graph Embedding import
+from .embedding.graph2vec import *
+from .embedding.deepwalk import *
 # Helpers import
 from .helpers.reader import *
+from .helpers.general import *
 
 # Basic algorithms import
 from .bag_of_cliques import *

gmatch4py/alg_types.pyx

-# coding = utf-8
-from enum import Enum
-
-
-class AlgorithmType(Enum):
-    similarity = 0
-    distance = 1
\ No newline at end of file

gmatch4py/bag_of_cliques.pyx

@@ -9,7 +9,7 @@ cimport numpy as np
 from scipy.sparse import csr_matrix,lil_matrix
 import sys
 
-from .base cimport Base,intersection
+from .base cimport Base
 
 
 cdef class BagOfCliques(Base):

gmatch4py/base.pxd

@@ -4,12 +4,16 @@ cdef class Base:
     ## Attribute(s)
     cdef int type_alg
     cdef bint normalized
-
+    cdef int cpu_count
+    cdef str node_attr_key
+    cdef str edge_attr_key
     ## Methods
     cpdef np.ndarray compare(self,list graph_list, list selected)
+    cpdef np.ndarray compare_old(self,list listgs, list selected)
     cpdef np.ndarray distance(self, np.ndarray matrix)
     cpdef np.ndarray similarity(self, np.ndarray matrix)
     cpdef bint isAccepted(self,G,index,selected)
+    cpdef np.ndarray get_selected_array(self,selected,size_corpus)
+
+    cpdef set_attr_graph_used(self, str node_attr_key, str edge_attr_key)
 
-cpdef intersection(G,H)
-cpdef union_(G,H)

gmatch4py/base.pyx

@@ -3,6 +3,10 @@
 import numpy as np
 cimport numpy as np
 import networkx as nx
+cimport cython
+import multiprocessing
+
+
 
 cpdef np.ndarray minmax_scale(np.ndarray matrix):
     """
@@ -17,85 +21,6 @@ cpdef np.ndarray minmax_scale(np.ndarray matrix):
     return x/(max_)
 
 
-
-cpdef intersection(G, H):
-    """
-    Return a new graph that contains only the edges and nodes that exist in
-    both G and H.
-
-    The node sets of H and G must be the same.
-
-    Parameters
-    ----------
-    G,H : graph
-       A NetworkX graph.  G and H must have the same node sets.
-
-    Returns
-    -------
-    GH : A new graph with the same type as G.
-
-    Notes
-    -----
-    Attributes from the graph, nodes, and edges are not copied to the new
-    graph.  If you want a new graph of the intersection of G and H
-    with the attributes (including edge data) from G use remove_nodes_from()
-    as follows
-
-    >>> G=nx.path_graph(3)
-    >>> H=nx.path_graph(5)
-    >>> R=G.copy()
-    >>> R.remove_nodes_from(n for n in G if n not in H)
-
-    Modified so it can be used with two graphs with different nodes set
-    """
-    # create new graph
-    R = nx.create_empty_copy(G)
-
-    if not G.is_multigraph() == H.is_multigraph():
-        raise nx.NetworkXError('G and H must both be graphs or multigraphs.')
-    if G.number_of_edges() <= H.number_of_edges():
-        if G.is_multigraph():
-            edges = G.edges(keys=True)
-        else:
-            edges = G.edges()
-        for e in edges:
-            if H.has_edge(*e):
-                R.add_edge(*e)
-    else:
-        if H.is_multigraph():
-            edges = H.edges(keys=True)
-        else:
-            edges = H.edges()
-        for e in edges:
-            if G.has_edge(*e):
-                R.add_edge(*e)
-    nodes_g=set(G.nodes())
-    nodes_h=set(H.nodes())
-    R.remove_nodes_from(list(nodes_g - nodes_h))
-    return R
-
-cpdef union_(G, H):
-    """
-    Return a graph that contains nodes and edges from both graph G and H.
-    
-    Parameters
-    ----------
-    G : networkx.Graph
-        First graph
-    H : networkx.Graph 
-        Second graph
-
-    Returns
-    -------
-    networkx.Graph
-        A new graph with the same type as G.
-    """
-    R = nx.create_empty_copy(G)
-    R.add_nodes_from(H.nodes(data=True))
-    R.add_edges_from(G.edges(data=True))
-    R.add_edges_from(H.edges(data=True))
-    return R
-
 cdef class Base:
     """
     This class define the common methods to all Graph Matching algorithm.
@@ -115,7 +40,7 @@ cdef class Base:
         self.type_alg=0
         self.normalized=False
 
-    def __init__(self,type_alg,normalized):
+    def __init__(self,type_alg,normalized,node_attr_key="",edge_attr_key=""):
         """
         Constructor of Base
 
@@ -136,6 +61,66 @@ cdef class Base:
         else:
             self.type_alg=type_alg
         self.normalized=normalized
+        self.cpu_count=multiprocessing.cpu_count()
+        self.node_attr_key=node_attr_key
+        self.edge_attr_key=edge_attr_key
+
+    cpdef set_attr_graph_used(self, str node_attr_key, str edge_attr_key):
+        """
+        Set graph attribute used by the algorithm to compare graphs.
+        Parameters
+        ----------
+        node_attr_key : str
+            key of the node attribute
+        edge_attr_key: str
+            key of the edge attribute
+
+        """
+        self.node_attr_key=node_attr_key
+        self.edge_attr_key=edge_attr_key
+    
+    cpdef np.ndarray get_selected_array(self,selected,size_corpus):
+        """
+        Return an array which define which graph will be compared in the algorithms.
+        Parameters
+        ----------
+        selected : list
+            indices of graphs you wish to compare
+        size_corpus : 
+            size of your dataset
+
+        Returns
+        -------
+        np.ndarray
+            selected vector (1 -> selected, 0 -> not selected)
+        """
+        cdef double[:] selected_test = np.zeros(size_corpus)
+        if not selected == None:
+            for ix in range(len(selected)):
+                selected_test[selected[ix]]=1
+            return np.array(selected_test)
+        else:
+            return np.array(selected_test)+1
+        
+
+    cpdef np.ndarray compare_old(self,list listgs, list selected):
+        """
+        Soon will be depreciated ! To store the old version of an algorithm.
+        Parameters
+        ----------
+        listgs : list
+            list of graphs
+        selected
+            selected graphs
+
+        Returns
+        -------
+        np.ndarray
+            distance/similarity matrix
+        """
+        pass
+
+    @cython.boundscheck(False) 
     cpdef np.ndarray compare(self,list graph_list, list selected):
         """
         Return the similarity/distance matrix using the current algorithm.
@@ -153,7 +138,7 @@ cdef class Base:
             the None value
         Returns
         -------
-        np.array
+        np.ndarray
             distance/similarity matrix
             
         """
@@ -164,12 +149,12 @@ cdef class Base:
         Return a normalized distance matrix
         Parameters
         ----------
-        matrix : np.array
-            Similarity/distance matrix you want to transform
+        matrix : np.ndarray
+            Similarity/distance matrix you wish to transform
 
         Returns
         -------
-        np.array
+        np.ndarray
             distance matrix
         """
         if self.type_alg == 1:
@@ -186,8 +171,8 @@ cdef class Base:
         Return a normalized similarity matrix
         Parameters
         ----------
-        matrix : np.array
-            Similarity/distance matrix you want to transform
+        matrix : np.ndarray
+            Similarity/distance matrix you wish to transform
 
         Returns
         -------
@@ -201,30 +186,12 @@ cdef class Base:
                 matrix=np.ma.getdata(minmax_scale(matrix))
             return 1-matrix
 
-    def mcs(self, G, H):
-        """
-        Return the Most Common Subgraph of
-        Parameters
-        ----------
-        G : networkx.Graph
-            First Graph
-        H : networkx.Graph
-            Second Graph
-
-        Returns
-        -------
-        networkx.Graph
-            Most common Subgrah
-        """
-        R=G.copy()
-        R.remove_nodes_from(n for n in G if n not in H)
-        return R
 
     cpdef bint isAccepted(self,G,index,selected):
         """
         Indicate if the graph will be compared to the other. A graph is "accepted" if :
-         * G exists(!= None) and not empty (|vertices(G)| >0)
-         * If selected graph to compare were indicated, check if G exists in selected
+            * G exists(!= None) and not empty (|vertices(G)| >0)
+            * If selected graph to compare were indicated, check if G exists in selected
         
         Parameters
         ----------
@@ -244,7 +211,7 @@ cdef class Base:
         if not G:
             f=False
         elif len(G)== 0:
-           f=False
+            f=False
         if selected:
             if not index in selected:
                 f=False

gmatch4py/bon.pyx

@@ -11,7 +11,7 @@ cdef class BagOfNodes(Base):
     We could call this algorithm Bag of nodes
     """
     def __init__(self):
-            Base.__init__(self,0,True)
+        Base.__init__(self,0,True)
 
     cpdef np.ndarray compare(self,list graph_list, list selected):
         nodes = list()

gmatch4py/deltacon.pyx

-# coding = utf-8
-
-import networkx as nx
-import numpy as np
-import scipy.sparse
-
-
-class DeltaCon0():
-    __type__ = "sim"
-
-    @staticmethod
-    def compare(list_gs,selected):
-        n=len(list_gs)
-
-        comparison_matrix = np.zeros((n,n))
-        for i in range(n):
-            for j in range(i,n):
-                g1,g2=list_gs[i],list_gs[j]
-                f=True
-                if not list_gs[i] or not list_gs[j]:
-                    f=False
-                elif len(list_gs[i])== 0 or len(list_gs[j]) == 0:
-                    f=False
-                if selected:
-                    if not i in selected:
-                        f=False
-                if f:
-                    # S1
-                    epsilon = 1/(1+DeltaCon0.maxDegree(g1))
-                    D, A = DeltaCon0.degreeAndAdjacencyMatrix(g1)
-                    S1 = np.linalg.inv(np.identity(len(g1))+(epsilon**2)*D -epsilon*A)
-
-                    # S2
-                    D, A = DeltaCon0.degreeAndAdjacencyMatrix(g2)
-                    epsilon = 1 / (1 + DeltaCon0.maxDegree(g2))
-                    S2 = np.linalg.inv(np.identity(len(g2))+(epsilon**2)*D -epsilon*A)
-
-
-                    comparison_matrix[i,j] = 1/(1+DeltaCon0.rootED(S1,S2))
-                    comparison_matrix[j,i] = comparison_matrix[i,j]
-                else:
-                    comparison_matrix[i, j] = 0.
-                comparison_matrix[j, i] = comparison_matrix[i, j]
-
-
-        return comparison_matrix
-
-    @staticmethod
-    def rootED(S1,S2):
-        return np.sqrt(np.sum((S1-S2)**2)) # Long live numpy !
-
-    @staticmethod
-    def degreeAndAdjacencyMatrix(G):
-        """
-        Return the Degree(D) and Adjacency Matrix(A) from a graph G.
-        Inspired of nx.laplacian_matrix(G,nodelist,weight) code proposed by networkx
-        :param G:
-        :return:
-        """
-        A = nx.to_scipy_sparse_matrix(G, nodelist=list(G.nodes), weight="weight",
-                                      format='csr')
-        n, m = A.shape
-        diags = A.sum(axis=1)
-        D = scipy.sparse.spdiags(diags.flatten(), [0], m, n, format='csr')
-
-        return D, A
-    @staticmethod
-    def maxDegree(G):
-        degree_sequence = sorted(nx.degree(G).values(), reverse=True)  # degree sequence
-        # print "Degree sequence", degree_sequence
-        dmax = max(degree_sequence)
-        return dmax
-
-class DeltaCon():
-    __type__ = "sim"
-
-    @staticmethod
-    def relabel_nodes(graph_list):
-        label_lookup = {}
-        label_counter = 0
-        n= len(graph_list)
-        # label_lookup is an associative array, which will contain the
-        # mapping from multiset labels (strings) to short labels
-        # (integers)
-        for i in range(n):
-            nodes = list(graph_list[i].nodes)
-
-            for j in range(len(nodes)):
-                if not (nodes[j] in label_lookup):
-                    label_lookup[nodes[j]] = label_counter
-                    label_counter += 1
-
-            graph_list[i] = nx.relabel_nodes(graph_list[i], label_lookup)
-        return graph_list
-    @staticmethod
-    def compare(list_gs, g=3):
-        n=len(list_gs)
-        list_gs=DeltaCon.relabel_nodes(list_gs)
-        comparison_matrix = np.zeros((n,n))
-        for i in range(n):
-            for j in range(i,n):
-                g1,g2=list_gs[i],list_gs[j]
-
-                V = list(g1.nodes)
-                V.extend(list(g2.nodes))
-                V=np.unique(V)
-
-                partitions=V.copy()
-                np.random.shuffle(partitions)
-                if len(partitions)< g:
-                    partitions=np.array([partitions])
-                else:
-                    partitions=np.array_split(partitions,g)
-                partitions_e_1 = DeltaCon.partitions2e(partitions, list(g1.nodes))
-                partitions_e_2 = DeltaCon.partitions2e(partitions, list(g2.nodes))
-                S1,S2=[],[]
-                for k in range(len(partitions)):
-                    s0k1,s0k2=partitions_e_1[k],partitions_e_2[k]
-
-                    # S1
-                    epsilon = 1/(1+DeltaCon0.maxDegree(g1))
-                    D, A = DeltaCon0.degreeAndAdjacencyMatrix(g1)
-                    s1k = np.linalg.inv(np.identity(len(g1))+(epsilon**2)*D -epsilon*A)
-                    s1k=np.linalg.solve(s1k,s0k1).tolist()
-
-                    # S2
-                    D, A = DeltaCon0.degreeAndAdjacencyMatrix(g2)
-                    epsilon = 1 / (1 + DeltaCon0.maxDegree(g2))
-                    s2k= np.linalg.inv(np.identity(len(g2))+(epsilon**2)*D -epsilon*A)
-                    s2k = np.linalg.solve(s2k, s0k2).tolist()
-
-
-
-                    S1.append(s1k)
-                    S2.append(s2k)
-
-                comparison_matrix[i,j] = 1/(1+DeltaCon0.rootED(np.array(S1),np.array(S2)))
-                comparison_matrix[j,i] = comparison_matrix[i,j]
-
-        return comparison_matrix
-
-
-    @staticmethod
-    def partitions2e( partitions, V):
-        e = [ [] for i in range(len(partitions))]
-        for p in range(len(partitions)):
-            e[p] = []
-            for i in range(len(V)):
-                if i in partitions[p]:
-                    e[p].append(1.0)
-                else:
-                    e[p].append(0.0)
-        return e
\ No newline at end of file

gmatch4py/embedding/deepwalk.pyx

+#! /usr/bin/env python
+# -*- coding: utf-8 -*-
+
+import os
+import sys
+import random
+
+from io import open
+from argparse import ArgumentParser, FileType, ArgumentDefaultsHelpFormatter
+from collections import Counter
+from concurrent.futures import ProcessPoolExecutor
+import logging
+from multiprocessing import cpu_count
+
+import networkx as nx
+import numpy as np
+cimport numpy as np
+from six import text_type as unicode
+from six import iteritems
+from six.moves import range
+
+from gensim.models import Word2Vec
+from sklearn.metrics.pairwise import cosine_similarity
+from joblib import Parallel, delayed
+import psutil