Graph theoretic concepts Devika Subramanian Comp 140 Fall 2008

The small world phenomenon 

The phenomenon is surprising because  

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Size of graph is very large (> 6 billion for the planet). Graph is sparse in the sense that each person is connected to at most k other people (k about a 1000). Graph is decentralized; there is no dominant central vertex to which other vertices are directly connected. Graph is highly clustered, in that most friendship circles are strongly overlapping

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(c) Devika Subramanian, 2008

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History of research 

Karinthy (1929) 

Hungarian novelist: “Chains” (5 degrees of separation)

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Solomonoff and Rapoport (1951) 

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Erdos and Renyi (1960) 

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Theoretical biology: random graphs, phase transition in connectedness Pure mathematics: founders of random graph theory (giant components)

Milgram and Travers (1967): 

Sociology and Psychology: acquaintance network, six degrees of separaration

Leskovec 10/14/2008 

and Horvitz (2008) (c) Devika Subramanian, 2008

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Models for small world? 

Erdos-Renyi model 

n nodes, each node has a probability p of being connected. k = average degree

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(c) Devika Subramanian, 2008

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Erdos-Renyi model 

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Average degree k < 1 in ER(n,p) graph 

Small, isolated clusters

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Small diameters

Average degree k = 1 in ER(n,p) graph 

A giant component appears

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Diameter peaks

Average degree k > 1 in ER(n,p) graph 

Almost all nodes connected

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Diameter shrinks (c) Devika Subramanian, 2008

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Erdos-Renyi model

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(c) Devika Subramanian, 2008

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“Giant component” property 

In many real-world networks, we see  

Small diameter Few connected components: often just one giant component that emerges at a threshold probability 

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Tipping points of Malcolm Gladwell

Degree distribution follows a power law

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(c) Devika Subramanian, 2008

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Power law 

Power law: y = f(x) = x^{-a}

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(c) Devika Subramanian, 2008

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Degree distributions of real-world networks

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(c) Devika Subramanian, 2008

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Barabasi-Albert model 

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Graph not static, but grows with time. Preferential attachment: 

The probability that a new vertex will be connected to vertex i depends proportionally on its degree ki over the sum of all degrees in the graph

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(c) Devika Subramanian, 2008

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BA graph generation 

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Start with a small fully connected graph Add vertex one by one, attaching m edges from new vertex to other vertices probabilistically in proportion to number of edges that vertex already has

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(c) Devika Subramanian, 2008

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Properties of BA model 

Small diameters

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Threshold phenomena

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Degree distribution follows power law

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Explains formation of many graphs in the real world: WWW, collaboration networks, power networks, protein networks, citation networks, etc. networkx has a barabasi_albert() function to generate such graphs.

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(c) Devika Subramanian, 2008

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Graph representations Devika Subramanian Comp 140 Fall 2008

Adjacency matrix representation 

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For a graph with n vertices, represent edges by n x n array If there is an edge between vertex i and vertex j, position (i,j) in array is a 1, otherwise it is a 0.

Can extend this representation to weighted graphs by replacing 1s and 0s by other numbers. 10/14/2008 (c) Devika Subramanian, 2008 

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Adjacency list representation 

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For each vertex in a graph, associate a list of adjacent vertices. For weighted graphs, associate a list of tuples (vertex,weight) representing adjacent vertices and their edge weights/costs.

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(c) Devika Subramanian, 2008

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Graph representations 0 1

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(c) Devika Subramanian, 2008

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Graph representations 0 1

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Weighted graph representation 0

210 1 203

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Weighted graph representations 0

210 1 203

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[(1,210),(3,440)]

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[(0,210),(2,203),(3.314)]

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[(1,203),(3,260),(4,270)]

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[(0,440),(1,314),(2,260)]

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[(2,270)]

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(c) Devika Subramanian, 2008

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networkx graph representation 

Graphs packaged as objects 

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An object is some data together with a set of methods for accessing and manipulating the data. Noun-oriented programming (Guzdial), “ask, don’t touch” philosophy(Kay)

An abstraction that hides implementation details and exposes a clean interface to you.

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(c) Devika Subramanian, 2008

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networkx Interface 

import networkx as nx

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G = nx.Graph()

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G is an instance of a Graph

for i in range(10): G.add_edge(i,i+1)

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nx.diameter(G)

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nx.connected_component_subgraphs(G)

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G = nx.binomial_graph(100,0.05) 10/14/2008 (c) Devika Subramanian, 2008

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Python classes 

A class is a blueprint for an object  

Defines how to create an object Defines the interface to interact with the object class

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instance

(c) Devika Subramanian, 2008

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networkx graph class 

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Constructor

https://networkx.lanl.gov/reference/ networkx/ Class Graph(object): def __init__(self,data=None,name=‘’): self.adj={} if data is not None: convert.from_whatever(data.create_using=self) self.name=name def nodes(self): return self.adj.keys() Accessor self refers to the object itself

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(c) Devika Subramanian, 2008

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Graph class 

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Defines variables adj and name which are local to the graph object Instead of passing adjacency lists, node lists, we encapsulate the data in an object and pass the object; much cleaner! Can change underlying representation of graph object, without having package users change their code.

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(c) Devika Subramanian, 2008

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networkx graph constructor def __init__(self,data=None,name=‘’): self.adj = {} if data is not None: convert.from_whatever(data.create_using=self) self.name = name

https://networkx.lanl.gov/reference/networkx/ 10/14/2008

(c) Devika Subramanian, 2008

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networkx graph representation def add_node(self,n): if n not in self.adj: self.adj[n] = {} def nodes(self): return self.adj.keys() def neighbors(self,n): return self.adj[n].keys()

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def add_edge(self,u,v=None): if v is None: (u,v) = u if u not in self.adj: self.adj[u] = {} if v not in self.adj: self.adj[v] = {} if u == v: return self.adj[u][v] = None self.adj[v][u] = None

(c) Devika Subramanian, 2008

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Dictionary of dictionaries 1

None

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None

(c) Devika Subramanian, 2008

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Special graphs: digraphs 

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https://networkx.lanl.gov/reference/ networkx/ Inheritance 

Basic functions are inherited

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New methods specific to digraphs are added

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Some functions are over-ridden.

Advantage: code reuse

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(c) Devika Subramanian, 2008

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Public and private data 

G = nx.Graph()

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G.adj can be set to anything we like

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Convention: anything with two leading underscores is private. Encapsulation or data hiding, so people access data via functions, rather than directly manipulate the internal structures. 

G.add_node()

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G.add_edge()

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G.nodes()

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G.edges()

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(c) Devika Subramanian, 2008

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Advantages of encapsulation 

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By defining a specific interface you can keep other modules from doing anything incorrect to your data By limiting the functions you are going to support, you leave yourself free to change the internal data without messing up your users 

Makes code more modular, since you can change large parts of your classes without affecting other parts of the program, so long as they only use your public functions

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