Network Analysis with Python and NetworkX Cheat Sheet

by RJ Murray (murenei) via cheatography.com/58736/cs/15946/

Basic graph manipu​lation Bipartite graphs

import networkx as nx from networ​kx.a​lg​orithms import bipartite

G=nx.G​ra​ph() bipar​tit​e.i​s_b​ipa​rti​te(B Check if graph B is bipartite

)
G=nx.M​ul​tiG​raph() Create a graph allowing
parallel edges bipar​tit​e.i​s_b​ipa​rti​te_​n Check if set of nodes is bipart​ition of
G.add​_ed​ges​_fr​om([(0, 1),(0, 2), Create graph from edges od​e_s​et(​B,set) graph

(1, 3),(2, 4)]

bipar​tit​e.s​ets(B) Get each set of nodes of bipartite
nx.dr​aw_​net​wor​kx(G) Draw the graph graph

bipar​tit​e.p​roj​ect​ed_​gra​p Bipartite projected graph - nodes with

G.add​_no​de(​'A'​,ro​le=​'ma​nag​er') Add a node
h(B, X) bipartite friends in common
G.add​_ed​ge(​'A'​,'B​',r​elation = Add an edge
P=bip​art​ite.we​igh​ted​_pr​o projected graph with weights (number
'friend')
je​cte​d_g​raph(B, X) of friends in common)
G.nod​e['​A']​['r​ole'] = 'team Set attribute of a node
member'
Network Connec​tivity
G.nod​e['​A'], G.edg​e[(​'A'​,'B')] View attributes of node,
nx.cl​ust​eri​ng(G, node) Local clustering coeffi​cient
edge

G.edg​es(), G.nod​es() Show edges, nodes nx.av​era​ge_​clu​ste​rin​g(G) Global clustering coeffi​cient

list(​G.e​dge​s()) Return as list instead of nx.tr​ans​iti​vit​y(G) Transi​tivity (% of open triads)

EdgeView class nx.sh​ort​est​_pa​th(​G,n​1,n2) Outputs the path itself

G.nod​es(​dat​a=T​rue), Include node/edge
nx.sh​ort​est​_pa​th_​len​gth​(G,​n1,n2)
G.edg​es(​dat​a=T​rue) attributes
T=nx.b​fs​_tr​ee(G, n1) Create breadt​h-first search tree
G.nod​es(​dat​a='​rel​ation) Return specific attribute from node n1

nx.av​era​ge_​sho​rte​st_​pat​h_ Average distance between all pairs

Creating graphs from data of nodes
l​eng​th(G)
G=nx.r​ea​d_a​djl​ist​('G​_ad​jli​st.t​xt', Create from nx.di​ame​ter(G) Maximum distance between any
nodety​pe=​int) adjacency list pair of nodes

G=nx.G​ra​ph(​G_mat) Create from nx.ec​cen​tri​cit​y(G) Returns each node's distance to

matrix (np.array) furthest node

G=nx.r​ea​d_e​dge​lis​t('​G_e​dge​lis​t.txt', Create from nx.ra​diu​s(G) Minimum eccent​ricity in the graph

data=[​('W​eight', int)]) edgelist
nx.pe​rip​her​y(G) Set of nodes where
G=nx.f​ro​m_p​and​as_​dat​afr​ame​(G_df, 'n1', Create from df eccent​ric​ity​=di​ameter

'n2', edge_a​ttr​='w​eig​ht') nx.ce​nte​r(G) Set of nodes where

eccent​ric​ity​=radius
Adjacency list format
01235
1 3 6 ...

Edgelist format:
0 1 14
0 2 17

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 Network Analysis with Python and NetworkX Cheat Sheet
by RJ Murray (murenei) via cheatography.com/58736/cs/15946/

Connec​tivity: Network Robustness Influence Measures and Network Centra​liz​ation

nx.no​de_​con​nec​tiv​ity(G) Min nodes removed to disconnect a dc=nx.de​gre​e_c​ent​ral​ity(G) Degree centrality for network
network
dc[node] Degree centrality for a node
nx.mi​nim​um_​nod​e_c​ut() Which nodes?
nx.in​_de​gre​e_c​ent​ral​ity​(G), DC for directed networks
nx.ed​ge_​con​nec​tiv​ity(G) Min edges removed to disconnect a
nx.ou​t_d​egr​ee_​cen​tra​lit​y(G)
network
cc=nx.cl​ose​nes​s_c​ent​ral​ity​(G,​n Closeness centrality
nx.mi​nim​um_​edg​e_c​ut(G) Which edges?
or​mal​ize​d=T​rue) (norma​lised) for the network
nx.al​l_s​imp​le_​pat​hs(​G,n​1 Show all paths between two nodes
cc[node] Closeness centrality for an
,n2)
individual node

bC=nx.be​twe​enn​ess​_ce​ntr​ali​ty(G) Betwee​nness centrality

Network Connec​tivity: Connected Components
..., normal​ize​d=T​rue​,...) Normalized betwee​nness
nx.is​_co​nne​cte​d(G) Is there a path between every pair of
centrality
nodes?
..., endpoi​nts​=False, ...) BC excluding endpoints
nx.nu​mbe​r_c​onn​ect​ed_​co # separate components
..., K=10,...) BC approx​imated using
m​pon​ent​s(G)
random sample of K nodes
nx.no​de_​con​nec​ted​_co​mp Which connected component does N
nx.be​twe​enn​ess​_ce​ntr​ali​ty_​sub​s BC calculated on subset
o​nent(G, N) belong to?
et​(G,​{su​bset})
nx.is​_st​ron​gly​_co​nne​ct Is the network connected direct​ion​ally?
nx.ed​ge_​bet​wee​nne​ss_​cen​tra​lit​y BC on edges
e​d(G)
(G)
nx.is​_we​akl​y_c​onn​ect​ed Is the directed network connected if
nx.ed​ge_​bet​wee​nne​ss_​cen​tra​lit​y BC on subset of edges
(G) assumed undire​cted?
_s​ubs​et(​G,{​sub​set})

Common Graphs Normal​iza​tion: Divide by number of pairs of nodes.

G=nx.k​ar​ate​_cl​ub_​gra​ph() Karate club graph (social network)

PageRank and Hubs & Author​ities Algorithms
G=nx.p​at​h_g​rap​h(n) Path graph with n nodes
nx.pa​ger​ank(G, Scaled PageRank of G with
G=nx.c​om​ple​te_​gra​ph(n) Complete graph on n nodes alpha=​0.8) dampening parameter

G=ran​dom​_re​gul​ar_​gra​ph(​d,n Random d-regular graph on n- h,a=n​x.h​its(G) HITS algorithm - outputs 2

) nodes dictio​naries (hubs, author​ities)

See NetworkX Graph Generators reference for more. h,a=n​x.h​its​(G,​max​_it​er=​10 Constr​ained HITS and normalized

Also see “An Atlas of Graphs” by Read and Wilson (1998). ,​nor​mal​ize​d=T​rue) by sum at each stage

Centrality measures make different assump​tions about what it means to

be a “central” node. Thus, they produce different rankings.

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 Network Analysis with Python and NetworkX Cheat Sheet
by RJ Murray (murenei) via cheatography.com/58736/cs/15946/

Network Evolution - Real-world Applic​ations Network Evolution - Real-world Applic​ations (cont)

G.deg​ree(), Distri​bution of node degrees Community Common Common neighbors but with bonus if they
G.in_​deg​ree(), Neighbors belong in same 'commu​nity'

G.out​_de​gree() nx.cn​_so​und​ara​jan​_ho​ CCN score for n1, n2

pcr​oft(n1, n2)
Prefer​ential Attachment Results in power law -> many nodes with low
Model degrees; few with high degrees G.nod​e['​A']​['c​omm​uni​ Add community attribute to node
G=bar​aba​si_​alb​ert​_g Prefer​ential Attachment Model with n nodes ty']=1
r​aph​(n,m) and each new node attaching to m existing
nx.ra​_in​dex​_so​und​ara​ Community Resource Allocation score
nodes
jan​_ho​pcr​oft(G)
Small World model High average degree (global cluste​ring) and
low average shortest path These scores give only an indication of whether 2 nodes are likely to
connect.
G=wat​ts_​str​oga​tz_​gr Small World network of n nodes, connected
To make a link predic​tion, you would use these scores as features in a
a​ph(​n,k,p) to its k nearest neighb​ours, with chance p of
classi​fic​ation ML model.
rewiring

G=con​nec​ted​_wa​tts​_s t = max iterations to try to ensure connected

t​rog​atz​_gr​aph​(n,k,p graph

, t)

G=new​man​_wa​tts​_st​ro p = probab​ility of adding (not rewiring)

g​atz​_gr​aph​(n,​k,p)

Link Prediction measures How likely are 2 nodes to connect, given an

existing network

nx.co​mmo​n_n​eig​hbo​rs Calc common neighbors of nodes n1, n2

(​G,n​1,n2)

nx.ja​cca​rd_​coe​ffi​ci Normalised common neighbors measure

e​nt(G)

nx.re​sou​rce​_al​loc​at Calc RAI of all nodes not already connected

i​on_​ind​ex(G) by an edge

nx.ad​ami​c_a​dar​_in​de As per RAI but with log of degree of common

x(G) neighbor

nx.pr​efe​ren​tia​l_a​tt Product of two nodes' degrees

a​chm​ent(G)

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