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SyntheticNetwork.py
608 lines (571 loc) · 29.9 KB
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SyntheticNetwork.py
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import networkx as nx
import operator
import random
import numpy as np
import math
class SyntheticNetwork:
def __init__(self, nodeCount, graph=1, corePercent=0.0935, communities=37, mean=6.0143885, actual=105):
self.graph = nx.Graph()
self.nodeDict = {}
self.zeroNodes = []
self.percentOfCore = corePercent
self.numOfCommunities = communities
self.meanValue = mean
self.actualNodeCount = actual
self.degreeDistr = []
self.unusedEdges = 0
self.graphType = graph
self.nodeCount = nodeCount
for num in range(0,self.nodeCount):
self.graph.add_node(num)
self.nodeDict[num] = 0
self.assignDegreeDistribution()
# self.designateDegrees()
self.buildGraph()
def assignDegreeDistribution(self):
if self.graphType == 1: # This is trust
self.calculateDegreeDistribution(0, self.meanValue) # 6.0143885
if self.graphType == 2: # This is LOC
self.calculateDegreeDistribution(0, 0.4)
if self.graphType == 3: # This is Knowledge
self.calculateDegreeDistribution(24.978829, 1.7784218)
def calculateDegreeDistribution(self, shape, other=float(0)):
for node in range(0, self.nodeCount):
if self.graphType == 1:
degree = abs(int(random.expovariate(1/other)))
elif self.graphType == 2:
degree = abs(int(random.expovariate(1/other)))
elif self.graphType == 3:
degree = abs(int(random.weibullvariate(shape, other)))
print "Node: Degree ", node, degree
self.nodeDict[node] = degree
if (degree == 0) or (degree == 1):
self.zeroNodes.append(node)
# if self.graphType == 3:
# sortedDict = sorted(self.nodeDict.items(), key=operator.itemgetter(1), reverse=False)
# print "Sorted Dict", sortedDict
# for node in range(0, int(self.nodeCount * .27338129)): # .27338129 is the percentage of nodes with 0 or 1 in real graph
# key = sortedDict[node][0]
# value = random.random()
# if value <= .86842015:
# self.nodeDict[key] = 0
# else:
# self.nodeDict[key] = 1
for node in self.zeroNodes:
chance = random.uniform(0,1)
if chance <= 0.50:
self.nodeDict[node] = 2
else:
self.nodeDict[node] = 3
print "New NodeDict items", sorted(self.nodeDict.items(), key=operator.itemgetter(1), reverse=False)
def designateDegrees(self):
'''Used when manually entering degrees in a list.'''
# choose which nodes are going to be what degree
counter = 0
for tple in self.degreeDistr:
for num in range(0, tple[0]):
self.nodeDict[counter] = tple[1]
counter += 1
def determineIfEnoughNodesForCore(self, coreSize):
minimumDegreeCount = coreSize
counter = 0
for node in self.nodeDict:
if (self.nodeDict[node]) > minimumDegreeCount:
counter += 1
if counter >= coreSize:
return (True, counter)
else:
return (False, counter)
def modifyNodeDictToAccomodateFullCore(self,coreSize, currentCoreSize):
nodesNeededToBeIncreased = coreSize - currentCoreSize
for node in range(0,nodesNeededToBeIncreased):
randNum = random.randint(0, (self.nodeCount))
if (self.nodeDict[randNum]) < coreSize:
self.nodeDict[randNum] = coreSize + 1
def buildCore(self, srtList):
sizeOfCore = self.findCoreSize() # .1799 is the % of nodes in the core of dataset
# determine if there are enough nodes to construct a core
enoughToFillNode = self.determineIfEnoughNodesForCore(sizeOfCore)
# If there aren't enough nodes to build a core, modify nodes at random to fill it in.
if enoughToFillNode[0] == False:
self.modifyNodeDictToAccomodateFullCore(sizeOfCore, enoughToFillNode[1])
# print "Size of core is: ", sizeOfCore
returnList = []
# returnList.append(srtList[0][0]) # this adds largest to core, we don't want that
while len(returnList) != sizeOfCore:
# print " len of return list: len of core: ", len(returnList), sizeOfCore
#print "Finding randNum"
randNum = (random.randint(1,(self.nodeCount))) -1
# print "Found randNum and it's value is", randNum, self.nodeDict[randNum]
if ((self.nodeDict[randNum]) >= sizeOfCore) and (randNum not in returnList) and (randNum > 0):
#print "Entered if statement"
returnList.append(randNum)
#print "len of return list and core is: ", len(returnList), sizeOfCore
'''If it is stuck in the while loop, most likely there aren't enough nodes with degrees large enough
to fill it'''
return returnList # returns a list made up of single elements representing nodes
def findCoreSize(self):
if self.graphType == 1:
coreSize = int(self.percentOfCore * len(self.nodeDict)) # where .0935 is % of nodes seen in core from dataset
if self.graphType == 2:
coreSize = int(.0719 * len(self.nodeDict))
if (self.graphType == 3) or (self.graphType == 4):
coreSize = int(.1799 * len(self.nodeDict))
return coreSize
def findLeaders(self, communities, sortedDict):
leaderList = []
# pull out the top nodes and place into leader list
for node in range(0,communities):
leaderList.append(sortedDict[node])
# now permute the leader list and return it
permutedLeaders = np.random.permutation(leaderList)
return permutedLeaders
def updateSortedList(self, sortedList, core):
newSort = sortedList
for node in core:
nodeLocation = [x for x, y in enumerate(newSort) if y[0] == node] # finding node in the tuple and its index
del newSort[nodeLocation[0]]
return newSort
def buildCommunityStructure(self, sortedDict, coreNodes):
returnList = []
numOfCommunities = self.findNumOfCommunites()
for comm in range(0, numOfCommunities):
community = []
returnList.append(community)
updatedSortedList = self.updateSortedList(sortedDict, coreNodes)
leaders = self.findLeaders(numOfCommunities, updatedSortedList)
leaderList = []
for leader in leaders:
leaderList.append(leader[0])
pogList = self.updateSortedList(updatedSortedList, leaderList)
permutedPogList = np.random.permutation(pogList)
pogs = []
for pog in permutedPogList:
pogs.append(pog[0])
# at this point the core, leaders, and POGs have been separated.
for comm in returnList:
# First assign a leader to each community and remove from list of available leaders
comm.append(leaderList[0])
del leaderList[0]
# Now choose 9 other pogs to add to the community
if len(pogs) >= 19:
for node in range(0, 19):
comm.append(pogs[0])
del pogs[0]
else:
nodesLeft = len(pogs)
for node in range(0, nodesLeft):
comm.append(pogs[0])
del pogs[0]
return returnList # returns list of lists. The lists are nodes, they are single elements
def findNumOfCommunites(self):
if self.graphType == 1:
numCommunities = int((self.nodeCount * self.numOfCommunities) / self.actualNodeCount)
elif self.graphType == 2:
numCommunities = int((self.nodeCount * 25) / 105)
elif self.graphType == 3:
numCommunities = int((self.nodeCount * 39) / 105)
return numCommunities
def buildGraph(self):
hasEdgesAddedToGraph = set()
sortedDict = sorted(self.nodeDict.items(), key=operator.itemgetter(1), reverse=True)
coreNodes = self.buildCore(sortedDict)
print coreNodes
communityList = self.buildCommunityStructure(sortedDict, coreNodes)
core = self.connectCore(coreNodes)
for node in core:
hasEdgesAddedToGraph.add(node)
counter = 0
counter1 = 0
for comm in communityList:
# if it's the first community, it's going to try and attach to the core.
if counter == 0:
if self.graphType == 3:
graphAdditions = self.connectCommunity3(comm, core, core)
else:
graphAdditions = self.connectCommunity(comm, core, core)
for node in graphAdditions:
hasEdgesAddedToGraph.add(node)
# For subsequent communities, look at the nodes and attach leader to the greatest node count or core.
if counter >= 1:
if self.graphType == 3:
graphAdditions = self.connectCommunity3(comm, core, core)
else:
graphAdditions = self.connectCommunity(comm, hasEdgesAddedToGraph, core)
for node in graphAdditions:
hasEdgesAddedToGraph.add(node)
counter1 += 1
print "Completed community: ", counter1
print "Printed all communites"
# Now add the rest of the edges to the graph
self.assignRest(coreNodes, (self.pullLeadersFromCommunityList(communityList)))
def pullLeadersFromCommunityList(self, communities):
leaders = []
for community in communities:
leaders.append(community[0])
return leaders # returns list of leaders of all communities
def connectCommunityConnectionStatus(self, comparison, actual):
count = 0
for node in comparison:
for partner in actual:
if (self.graph.has_edge(node, partner) == False) and (node != partner):
count += 1
return count
def findMaxValueNode(self, nodesWithEdgesInGraph):
maxValNode = (0,0)
for node in nodesWithEdgesInGraph:
if node in self.nodeDict:
if self.nodeDict[node] >= maxValNode[1]:
maxValNode = (node, self.nodeDict[node])
return maxValNode
def connectCommunity(self, community, nodesWithEdgesInGraph, core):
# First find the person the community is going to connect to.
addedEdgesToGraph = set()
# maxValueNode = (0, 0)
communityLength = len(community)
connectionDict = {}
maxValueNode = self.findMaxValueNode(nodesWithEdgesInGraph)
# for node in nodesWithEdgesInGraph:
# if self.nodeDict[node] >= maxValueNode[1]:
# maxValueNode = (node, self.nodeDict[node])
# Per node, figure out how many people to connect to within community
for node in community:
availableEdges = self.nodeDict[node]
# max edges to use is a clique, min edges is 0
if availableEdges >= communityLength:
randomNum = random.randint((int(.8 * communityLength)), communityLength) - 1
connectionDict[node] = randomNum
elif availableEdges == 0:
connectionDict[node] = 0
elif availableEdges <= communityLength:
randomNum = random.randint((int(.8 * availableEdges)), availableEdges)
connectionDict[node] = randomNum
# Now, connect people to the community
totalEdges = self.findTotalEdges(connectionDict) # Finds total edges available to community members
nodesInGraph = community
while totalEdges > 0:
for node in nodesInGraph:
partner = random.choice(nodesInGraph)
if self.nodeDict[node] == 0:
del self.nodeDict[node]
nodesInGraph.remove(node)
else:
if self.graph.has_edge(node, partner) == False:
if node in self.nodeDict and partner in self.nodeDict:
if ((self.nodeDict[node]) > 0) and ((self.nodeDict[partner]) > 0) and (node != partner):
self.graph.add_edge(node, partner)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[partner] = (self.nodeDict[partner]) - 1
connectionDict[node] = (connectionDict[node]) - 1
connectionDict[partner] = (connectionDict[partner]) - 1
totalEdges = self.findTotalEdges(connectionDict)
# print "Total Edges in while statement: ", totalEdges
addedEdgesToGraph.add(node)
addedEdgesToGraph.add(partner)
# Now connect leader
if self.graph.has_edge(community[0], maxValueNode[0]) == False:
if ((self.nodeDict[community[0]]) > 0) and ((self.nodeDict[maxValueNode[0]]) > 0) and (
community[0] != maxValueNode[0]):
self.graph.add_edge(community[0], maxValueNode[0])
self.nodeDict[community[0]] = (self.nodeDict[community[0]]) - 1
self.nodeDict[maxValueNode[0]] = (self.nodeDict[maxValueNode[0]]) - 1
addedEdgesToGraph.add(community[0])
addedEdgesToGraph.add(maxValueNode[0])
# Now connect two more
# sortedCommunity = sorted(connectionDict.items(), key=operator.itemgetter(1), reverse=True)
# coreMembers = list(core)
# if len(sortedCommunity) >= 2 :
# for num in range(0,2):
# sortedNode = sortedCommunity[num]
# maxValueNode = self.findMaxValueNode(nodesWithEdgesInGraph)
# coreMember = random.choice(coreMembers)
# probability = random.uniform(0,1)
# probToForm = random.uniform(0,1)
# if probToForm <= 0.80:
# if probability <= 0.70:
# self.connectToLeader(sortedNode[0], maxValueNode[0])
# addedEdgesToGraph.add(sortedNode[0])
# addedEdgesToGraph.add(maxValueNode[0])
# else:
# self.connectToLeader(sortedNode[0], coreMember)
# addedEdgesToGraph.add(sortedNode[0])
# addedEdgesToGraph.add(coreMember)
self.closeTriangles(connectionDict)
# IF there aren't many common neighbors, then create some triangles
self.createTriangles(connectionDict)
return addedEdgesToGraph
def connectToLeader(self, node, maxNode):
if self.graph.has_edge(node, maxNode) == False:
if ((self.nodeDict[node]) > 0) and ((self.nodeDict[maxNode]) > 0) and (node != maxNode):
self.graph.add_edge(node, maxNode)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[maxNode] = (self.nodeDict[maxNode]) - 1
def createTriangles(self, connections):
trianglesCreated = 0
for node in connections:
if (self.graph.has_node(node) == True) and (node not in self.zeroNodes) :
neighborlist = self.graph.neighbors(node)
for neighbor in neighborlist:
if (self.graph.has_node(neighbor) == True) and (neighbor not in self.zeroNodes):
neighborsNeighbors = self.graph.neighbors(neighbor)
# choose a rand number to set prob of creating a triangle between node, neighbor, and closer
rand = random.uniform(0,1)
closer = random.choice(neighborsNeighbors)
counter = 0
if node not in self.nodeDict:
self.nodeDict[node] = 0
if neighbor not in self.nodeDict:
self.nodeDict[neighbor] = 0
if closer not in self.zeroNodes:
if closer not in self.nodeDict:
self.nodeDict[closer] = 0
if (rand <= 0.95) and (closer != node):
if self.graph.has_edge(node, closer) == False:
print "Triangle not complete from node"
self.nodeDict[node] = (self.nodeDict[node]) + 1
self.nodeDict[closer] = (self.nodeDict[closer]) + 1
self.graph.add_edge(node, closer)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[closer] = self.nodeDict[closer] - 1
if self.nodeDict[node] <= 0:
del self.nodeDict[node]
if self.nodeDict[closer] <= 0:
del self.nodeDict[closer]
counter += 1
if self.graph.has_edge(neighbor, closer) == False:
"Triangle not complete from neighbor"
self.nodeDict[neighbor] = (self.nodeDict[neighbor]) + 1
self.nodeDict[closer] = (self.nodeDict[closer]) + 1
self.graph.add_edge(neighbor, closer)
self.nodeDict[neighbor] = (self.nodeDict[neighbor]) - 1
self.nodeDict[closer] = (self.nodeDict[closer]) - 1
if self.nodeDict[node] <= 0:
del self.nodeDict[node]
if self.nodeDict[closer] <= 0:
del self.nodeDict[closer]
counter += 1
if counter > 0:
trianglesCreated += 1
counter = 0
print "Triangles Created: ", trianglesCreated
def closeTriangles(self, connections):
trianglesClosed = 0
for node in connections:
if self.graph.has_node(node) == True:
neighborList = self.graph.neighbors(node)
for neighbor in neighborList:
if self.graph.has_node(neighbor) == True:
neighborsNeighbors = self.graph.neighbors(neighbor)
# now we have two neighbor lists. Find the intersection of the lists and those are the common nodes
intersectionList = [nb for nb in neighborList if nb in neighborsNeighbors]
# now for each node in the intersection, check if the edges to that node exist from node and neighbor nd add it
if len(intersectionList) > 0:
counter = 0
for closer in intersectionList:
if self.graph.has_edge(node, closer) == False:
print "Triangle not complete from node"
self.nodeDict[node] = (self.nodeDict[node]) + 1
self.nodeDict[closer] = (self.nodeDict[closer]) + 1
self.graph.add_edge(node, closer)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[closer] = (self.nodeDict[closer]) - 1
counter += 1
if self.graph.has_edge(neighbor, closer) == False:
"Triangle not complete from neighbor"
self.nodeDict[neighbor] = (self.nodeDict[neighbor]) + 1
self.nodeDict[closer] = (self.nodeDict[closer]) + 1
self.graph.add_edge(neighbor, closer)
self.nodeDict[neighbor] = (self.nodeDict[neighbor]) - 1
self.nodeDict[closer] = (self.nodeDict[closer]) - 1
counter += 1
if counter > 0:
trianglesClosed += 1
counter = 0
print "Triangles closed in this community: ", trianglesClosed
def connectCommunity3(self, community, nodesWithEdgesInGraph, core):
# First find the person the community is going to connect to.
addedEdgesToGraph = set()
maxValueNode = (0,0)
# communityLength = len(community)
connectionDict = {}
for node in nodesWithEdgesInGraph:
if self.nodeDict[node] >= maxValueNode[1]:
maxValueNode = (node, self.nodeDict[node])
# First populate the connectionDictionary with the members of that dictionary.
for node in community:
connectionDict[node] = self.nodeDict[node]
# put nodes in a list to use in next loop
actualCommunity = []
for node in connectionDict:
actualCommunity.append(node)
# Then take out all of the zero nodes to see how many people will actually connect in the community
for node in actualCommunity:
if connectionDict[node] == 0:
del connectionDict[node]
# New community length is the length of the connectionDict at tbis point.
communityLength = len(connectionDict)
actualCommunity = []
for node in connectionDict:
actualCommunity.append(node)
# Per node, figure out how many people to connect to within community
for node in actualCommunity:
availableEdges = self.nodeDict[node]
# max edges to use is a clique, min edges
if availableEdges >= communityLength:
randomNum = random.randint(1, communityLength)
connectionDict[node] = randomNum
elif availableEdges == 0:
connectionDict[node] = 0
elif availableEdges <= communityLength:
randomNum = random.randint(1, availableEdges)
connectionDict[node] = randomNum
# Now, connect people to the community
totalEdges = self.findTotalEdges(connectionDict) # Finds total edges available to community members
nodesInGraph = actualCommunity
switch = False
while switch == False :
if len(connectionDict) == 1:
break
comparisonDict = connectionDict
for node in nodesInGraph:
partner = random.choice(nodesInGraph)
if connectionDict[node] == 0:
del connectionDict[node]
nodesInGraph.remove(node)
continue
else:
# print "Entered else statement"
if self.graph.has_edge(node, partner) == False:
if node in self.nodeDict and partner in self.nodeDict:
if ((connectionDict[node]) > 0) and ((connectionDict[partner]) > 0) and (node != partner):
self.graph.add_edge(node, partner)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[partner] = (self.nodeDict[partner]) - 1
connectionDict[node] = (connectionDict[node]) - 1
connectionDict[partner] = (connectionDict[partner]) - 1
totalEdges = self.findTotalEdges(connectionDict)
# print "Total Edges in while statement: ", totalEdges
addedEdgesToGraph.add(node)
addedEdgesToGraph.add(partner)
else:
print "comparison", comparisonDict
print "actual", connectionDict
allConnectionsMadeStatus = self.connectCommunityConnectionStatus(comparisonDict, connectionDict)
print "all connection status", allConnectionsMadeStatus
if (totalEdges == 0) or (allConnectionsMadeStatus == 0) or (len(connectionDict) == 1):
switch = True
# Now connect leader
if self.graph.has_edge(community[0], maxValueNode[0]) == False:
if ((self.nodeDict[community[0]]) > 0) and ((self.nodeDict[maxValueNode[0]]) > 0) and (community[0] != maxValueNode[0]):
self.graph.add_edge(community[0], maxValueNode[0])
self.nodeDict[community[0]] = (self.nodeDict[community[0]]) - 1
self.nodeDict[maxValueNode[0]] = (self.nodeDict[maxValueNode[0]]) - 1
addedEdgesToGraph.add(community[0])
addedEdgesToGraph.add(maxValueNode[0])
print "added a leader"
self.closeTriangles(connectionDict)
self.createTriangles(connectionDict)
return addedEdgesToGraph
def addNode(self, node, partner):
if self.graph.has_edge(node, partner) == False:
if node in self.nodeDict and partner in self.nodeDict:
if ((self.nodeDict[node]) > 0) and ((self.nodeDict[partner]) > 0) and (node != partner):
self.graph.add_edge(node, partner)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[partner] = (self.nodeDict[partner]) - 1
def assignRest(self, core, leaders):
availableMembers = self.findAvailableMembers()
garbage = []
switch = False
while switch == False:
comparisonDict = self.nodeDict
allConnectionsStatus = self.determineIfAllConnectionsMade(comparisonDict)
# print "enter while loop"
if (len(self.nodeDict) == 0) or (allConnectionsStatus == 0):
self.unusedEdges = self.determineUnusedEdges()
switch = True
break
for node in availableMembers:
if self.nodeDict[node] == 0:
del self.nodeDict[node]
garbage.append(node)
availableMembers.remove(node)
else:
if self.nodeDict[node] > 0:
if node in core:
chanceToConnectToLeader = random.random()
if chanceToConnectToLeader >= float(.3):
partner = random.choice(leaders)
self.addNode(node, partner)
else:
partner = random.choice(availableMembers)
self.addNode(node, partner)
elif node in leaders:
chanceToConnectToCore = random.random()
if chanceToConnectToCore >= float(.3):
partner = random.choice(core)
self.addNode(node, partner)
else:
partner = random.choice(availableMembers)
self.addNode(node, partner)
else:
partner = random.choice(availableMembers)
self.addNode(node, partner)
for node in garbage:
if node in availableMembers:
availableMembers.remove(node)
# print "nodeDict is :", self.nodeDict
def determineIfAllConnectionsMade(self, comparison):
count = 0
for node in comparison:
for partner in self.nodeDict:
if (self.graph.has_edge(node, partner) == False) and (node != partner):
count += 1
return count
def determineUnusedEdges(self):
unusedEdges = 0
for node in self.nodeDict:
unusedEdges += self.nodeDict[node]
return unusedEdges
def findAvailableMembers(self):
members = []
for node in self.nodeDict:
members.append(node)
return members
def findTotalEdges(self, community):
totalEdges = 0
for node in community:
totalEdges += community[node]
return totalEdges
def connectCore(self, core):
addedEdgesToGraph = set()
for node in core:
if self.nodeDict[node] != 0:
for partner in core:
if self.nodeDict[partner] != 0:
if node != partner:
if self.graph.has_edge(node, partner) == False:
self.graph.add_edge(node, partner)
self.nodeDict[node] = (self.nodeDict[node]) - 1
self.nodeDict[partner] = (self.nodeDict[partner]) - 1
addedEdgesToGraph.add(node)
addedEdgesToGraph.add(partner)
return addedEdgesToGraph
############# Main ################
# network1 = SyntheticNetwork(139)
# print network1.graph.edges()
# print "Unused edges in network 1 total to: ", network1.unusedEdges
# nx.write_gexf(network1.graph, "trustSynthetic4.gexf")
# #
# network2 = SyntheticNetwork(139, 2)
# print network2.graph.edges()
# print "Unused edges in network 2 total to: ", network2.unusedEdges
# nx.write_gexf(network2.graph, "LOCSynthetic4.gexf")
# network3 = SyntheticNetwork(139, 3)
# print network3.graph.edges()
# print "Unused edges in network 3 total to: ", network3.unusedEdges
# nx.write_gexf(network3.graph, "KnowledgeSynthetic4.gexf")
# network4 = SyntheticNetwork(139, 4)
# print network4.graph.edges()
# print "Unused edges in network 4 total to: ", network4.unusedEdges
# nx.write_gexf(network4.graph, "MonoplexSynthetic2.gexf")