In [1]:

    

import networkx as nx
import numpy as np
import pandas as pd
import matplotlib.pyplot as plt
%matplotlib inline
import os
from glob import glob

pd.set_option('display.mpl_style', 'default') 
pd.set_option('display.width', 5000) 
pd.set_option('display.max_columns', 60)

# individual article network data files
#gml_files = glob('../output/network/*/*.gml')
#pos_files = glob('../output/network/positive/*.gml')
#neg_files = glob('../output/network/negative/*.gml')
#neu_files = glob('../output/network/neutral/*.gml')

def calculate_graph_inf(graph):
    graph.name = filename
    info = nx.info(graph)
    print info

def plot_graph(graph):
    info = nx.info(graph)
    print info
    plt.figure(figsize=(10,10))
    nx.draw_spring(graph, with_labels = True)


    

In [ ]:

    

# don't run
pos_graphs = []
pos_ugraphs = []
neg_graphs = []
neg_ugraphs = []
neu_graphs = []
neu_ugraphs = []

for graph_num, gml_graph in enumerate(pos_files):
    graph = nx.read_gml(gml_graph)
    ugraph = graph.to_undirected()
    U = graph.to_undirected(reciprocal=True)
    e = U.edges()
    ugraph.add_edges_from(e)
    (filepath, filename) = os.path.split(gml_graph)
    print('-' * 40)
    print(gml_graph)
    print(nx.info(graph))
    pos_graphs.append(graph)
    pos_ugraphs.append(ugraph)
    
for graph_num, gml_graph in enumerate(neg_files):
    graph = nx.read_gml(gml_graph)
    ugraph = graph.to_undirected()
    U = graph.to_undirected(reciprocal=True)
    e = U.edges()
    ugraph.add_edges_from(e)
    (filepath, filename) = os.path.split(gml_graph)
    print('-' * 40)
    print(gml_graph)
    print(nx.info(graph))
    neg_graphs.append(graph)
    neg_ugraphs.append(ugraph)
    
for graph_num, gml_graph in enumerate(neu_files):
    graph = nx.read_gml(gml_graph)
    ugraph = graph.to_undirected()
    U = graph.to_undirected(reciprocal=True)
    e = U.edges()
    ugraph.add_edges_from(e)
    (filepath, filename) = os.path.split(gml_graph)
    print('-' * 40)
    print(gml_graph)
    print(nx.info(graph))
    neu_graphs.append(graph)
    neu_ugraphs.append(ugraph)


    

In [ ]:

    

# don't run. this is for merging gml files into big graphs
# compose(G1, G2): combine graphs identifying nodes common to both
pos_all = nx.compose_all(pos_graphs)
pos_uall = nx.compose_all(pos_ugraphs)
neg_all = nx.compose_all(neg_graphs)
neg_uall = nx.compose_all(neg_ugraphs)
neu_all = nx.compose_all(neu_graphs)
neu_uall = nx.compose_all(neu_ugraphs)

# write to gml
nx.write_gml(pos_all, "../output/network/positive_all.gml")
nx.write_gml(pos_uall, "../output/network/positive_uall.gml")
nx.write_gml(neg_all, "../output/network/negative_all.gml")
nx.write_gml(neg_uall, "../output/network/negative_uall.gml")
nx.write_gml(neu_all, "../output/network/neutral_all.gml")
nx.write_gml(neu_uall, "../output/network/neutral_uall.gml")


    

In [2]:

    

#graph = nx.read_gml("../output/network/positive_all.gml")
#ugraph = nx.read_gml("../output/network/positive_uall.gml")

graph = nx.read_gml("../output/network/article_neg1.gml")
ugraph = graph.to_undirected()
U = graph.to_undirected(reciprocal=True)
e = U.edges()
ugraph.add_edges_from(e)


    

In [3]:

    

def drawIt(graph, what = 'graph'):
    nsize = graph.number_of_nodes()
    print "Drawing %s of size %s:" % (what, nsize)
    
    if nsize > 20:
        plt.figure(figsize=(10, 10))
        if nsize > 40:
            nx.draw_spring(graph, with_labels = True, node_size = 70, font_size = 12)
        else:
            nx.draw_spring(graph, with_labels = True)
    else:
        nx.draw_spring(graph, with_labels = True)
    plt.show()

def describeGraph(graph):
    components = sorted(nx.connected_components(graph), key = len, reverse = True)
    cc = [len(c) for c in components]
    subgraphs = list(nx.connected_component_subgraphs(graph))
    params = (graph.number_of_edges(),graph.number_of_nodes(),len(cc))
    print "Graph has %s nodes, %s edges, %s connected components\n" % params
    drawIt(graph)
    for sub in components:
        drawIt(graph.subgraph(sub), what = 'component')


    

In [4]:

    

# list of connected components (sets of nodes), starting with largest
print "List of connected components =", [len(c) for c in sorted(nx.connected_components(ugraph), key=len, reverse=True)]

# generate connected components as subgraphs; Gc is largest component
subgraphs = list(nx.connected_component_subgraphs(ugraph))


    

    




List of connected components = [1140, 7, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]

In [5]:

    

Gc = max(nx.connected_component_subgraphs(ugraph), key=len)
print "Size of greatest component =", len(Gc)


    

    




Size of greatest component = 1140

In [6]:

    

# returns all minimum k cutsets of an undirected graph
# i.e., the set(s) of nodes of cardinality equal to the node connectivity of G
# thus if removed, would break G into two or more connected components
cutsets = list(nx.all_node_cuts(Gc))
print "# of cutsets =", len(cutsets)


    

    




# of cutsets = 226

In [7]:

    

# returns a set of nodes or edges of minimum cardinality that disconnects G
print "Min node cut =", nx.minimum_node_cut(Gc, s='vaccines', t='autism')
print "Min edge cut =", nx.minimum_edge_cut(Gc)


    

    




Min node cut = set([u'mercury', u'toxic chemical ingredients', u'vaccine safety', u"alzheimer's", u'measles', u'CDC whistleblower', u'CDC', u'vaccine-injured children', u'thimerosal', u'vaccination', u'public', u'rates', u'encephalopathy', u'Vaccine Injury Compensation Program', u'MMR', u'studies', u'children', u'hepatitis B vaccine'])
Min edge cut = set([(u'influenza', u'childhood diseases')])

In [8]:

    

nx.minimum_node_cut(Gc, s='vaccines', t='autism')


    

    
Out[8]:





{u'CDC',
 u'CDC whistleblower',
 u'MMR',
 u'Vaccine Injury Compensation Program',
 u"alzheimer's",
 u'children',
 u'encephalopathy',
 u'hepatitis B vaccine',
 u'measles',
 u'mercury',
 u'public',
 u'rates',
 u'studies',
 u'thimerosal',
 u'toxic chemical ingredients',
 u'vaccination',
 u'vaccine safety',
 u'vaccine-injured children'}

In [9]:

    

a = nx.minimum_edge_cut(Gc, s='autism', t='vaccines')
a


    

    
Out[9]:





{(u'African American males', u'MMR'),
 (u'CDC whistleblower', u'mainstream media'),
 (u'autism', u'CDC'),
 (u'autism', u'MMR'),
 (u'autism', u'Ryan Mojabi'),
 (u'autism', u'Vaccine Injury Compensation Program'),
 (u'autism', u"alzheimer's"),
 (u'autism', u'children'),
 (u'autism', u'encephalopathy'),
 (u'autism', u'glutathione'),
 (u'autism', u'hepatitis B vaccine'),
 (u'autism', u'measles'),
 (u'autism', u'preservative'),
 (u'autism', u'public'),
 (u'autism', u'studies'),
 (u'autism', u'thimerosal'),
 (u'autism', u'toxic chemical ingredients'),
 (u'autism', u'vaccination'),
 (u'autism', u'vaccine safety'),
 (u'autism', u'vaccine-injured children'),
 (u'autism', u'vaccines'),
 (u'link', u'CDC'),
 (u'military records', u'measles decline'),
 (u'newborn boys', u'hepatitis B vaccine')}

In [10]:

    

labels = nx.get_edge_attributes(Gc,'edge')
edgelabels = {}
for e in labels.keys():
    e1 = e[0:2]
    edgelabels[e1]=labels[e]
edgelabels


    

    
Out[10]:





{(u'labor and delivery floor', u'parents'): u'walking into the',
 (u'public', u'autism'): u'wonders why they have',
 (u'Merck', u'lies'): u'exposed for',
 (u'patients', u'payment'): u'fight for',
 (u'holocaust',
  u'vaccine apologists'): u'relish in aiding and abetting a real-life',
 (u'Prevnar', u'vaccination'): u'added to childhood',
 (u'infectious diseases',
  u'people'): u'more than 500 million have died as a result of',
 (u'sicker children',
  u'vaccination'): u'dramatically increasing the number during the past 30 years led to',
 (u'chicken kidney cells',
  u'flu shots'): u'contain questionable ingredients such as',
 (u'newborns', u'hepatitis B vaccine'): u'routine use began 1992 for all',
 (u'government healthcare reform',
  u'mandatory vaccines'): u'may include trying to make',
 (u'safe', u'evidence'): u'may not prove the flu shot is',
 (u'drug companies',
  u'national vaccination policy'): u'astoundingly effective at manipulating',
 (u'higher doses', u'profits'): u'to maximize',
 (u'public health laws',
  u'informed consent'): u'stand up and fight to protect and expand in state level',
 (u'children', u'mandatory vaccines'): u'poison',
 (u'drugs', u'aspirin'): u'considered by many one of safest',
 (u'violation of basic human rights', u'vaccine court'): u'is',
 (u'prejudice', u'unvaccinated'): u'against the',
 (u'aspirin', u'serious problems'): u'if you take ten',
 (u'mainstream media',
  u'statistics'): u'about an occasional outbreak of a disease never seem to balance their accounts with readily available',
 (u'arthritis', u'bovine calf serum'): u'causes',
 (u'genetic predisposition', u'SB 277'): u'makes no mention of',
 (u'MMR', u'encephalopathy'): u'had caused the',
 (u'encephalitis', u'live-virus vaccine'): u'can cause',
 (u'trace amounts of thimerosal', u'children'): u'differently affect',
 (u'disabled children',
  u'over-vaccination'): u'may be chronically ill because of',
 (u'flu shots',
  u'flu-related deaths'): u'no studies have conclusively proven that flu shots prevent',
 (u'MRC-5 cells', u'shocking dangers'): u'of injecting',
 (u'human rights', u'SB 277'): u'is gross violation of',
 (u'seasonal flu shot',
  u'pandemic H1N1 swine flu vaccine'): u'2010/2011 contains',
 (u'bleeding during pregnancy',
  u'pregnant women'): u'were given thimerosal if there was any',
 (u'cover-up', u'censored medical news stories'): u'was one of the most',
 (u'children',
  u'brain damaged and autistic'): u'avoiding vaccinating will prevent from becoming',
 (u'vaccination', u'informed consent'): u'critical to',
 (u'practice of family center care',
  u'informed consent'): u'obtaining for a medical procedure under false pretenses is contrary to the',
 (u'Dr. Paul Offit', u'personal financial stake'): u'has big',
 (u'modern medicine', u'destructive nature'): u'has',
 (u'crazy approach', u'Jenny McCarthy'): u'used somewhat',
 (u'vaccines', u'aluminum'): u'contain',
 (u'consent for vaccines', u'parents'): u'do not receive truthful',
 (u'shingles vaccine', u'monosodium glutamate'): u'contains',
 (u'studies',
  u'safe'): u'funded by pharmaceutical companies proved influenza vaccine is',
 (u'vaccine damage', u'Big Pharma'): u'is used by',
 (u'measles outbreak', u'vaccinated children'): u'have something to fear from',
 (u'mutagen', u'thimerosal'): u'is a known',
 (u'highly susceptible',
  u'formula'): u'were Baby Boomers because they were almost exclusively fed',
 (u'children', u'normal life'): u'will never again lead',
 (u'diabetes deaths',
  u'high fructose corn syrup'): u"1.26 million each year yet they're still pushing in school lunches",
 (u'vaccines',
  u'more severe autism'): u'if we had not been diligent with their',
 (u'Dr. Paul Offit',
  u'vaccinations save lives'): u'is not just a doctor who believes that',
 (u'oil of oregano', u'essential oils'): u'is',
 (u'children with autism', u'special needs staff'): u'harmed by',
 (u'deaths', u'you'): u'please talk about it if suffered',
 (u'military records', u'great records'): u'kept',
 (u'MCR-5', u'Pro-Quad Hepatitis A'): u'used for',
 (u'marketing vaccines to children', u'unethical'): u'is',
 (u'pandemic H1N1 swine flu vaccine',
  u'United Kingdom'): u'damaged 800 children in',
 (u'prejudice', u'job'): u'could come soon when it comes to',
 (u'hydrolyzed porcine gelatin',
  u'synthetic growth hormones'): u'injecting poses risk of infection from',
 (u'Gardasil',
  u'lawsuit'): u'claims information comes from foreign countries for',
 (u'safe form of mercury',
  u'vaccine pushers'): u'is often ridiculously claimed by',
 (u'bribery', u'ethical track record'): u'full of',
 (u'Nichole Rolfe', u'solid marks'): u'earned',
 (u'skin reactions', u'bovine calf serum'): u'causes ',
 (u'mercury', u'glutathione levels'): u'is not the only toxin that can affect',
 (u'genetically-modified human albumin',
  u'vaccine ingredients'): u'disturbing like',
 (u'vaccine damage', u'medications'): u'is route to selling more',
 (u'toxic substances',
  u'infant death after vaccination'): u'was injected with multiple',
 (u'Dr. Paul Offit', u'For Profit Offit'): u'is also known as',
 (u'Jim Carrey', u'pro-vaccination'): u'claims to be',
 (u'measles cycle', u'Baby Boom'): u'did not happen after',
 (u'neurological damage', u'vaccinated children'): u'among',
 (u'unethical', u'vaccine bullying curriculum'): u'is',
 (u'outrageous',
  u'measles mortality'): u'given global population rate is not really',
 (u"alzheimer's", u'elderly'): u'is in',
 (u'ex-models', u'pharmaceutical companies'): u'hire',
 (u'National Vaccine Injury Compensation Program', u'litigious'): u'is',
 (u'vaccines',
  u'righteous anger'): u'after learning there is no way to scientifically prove',
 (u'Gardasil', u'seizures'): u'causes',
 (u'Octoxinol-9', u'vaccine ingredients'): u'is questionable',
 (u'Merck', u'shocking revelations'): u'have gone public with',
 (u'U.S. government', u'lead'): u'tells us is BAD',
 (u'exposures',
  u'autism'): u'we need to know what in combination mean to the health of children to turn around the tide of',
 (u'sanctions', u'health officials'): u'by',
 (u'misguided notion',
  u'health'): u'that more is always better when it comes to',
 (u'Pandemrix',
  u'European Medicines Agency'): u'warned in 2011 against using in under 20 years of age',
 (u'flu shots',
  u'monosodium glutamate'): u'contain questionable ingredients such as',
 (u'African-American children', u'vaccine-autism link'): u'in',
 (u'sick children', u'over-vaccination'): u'may be chronically ill because of',
 (u'vaccine injuries', u'heavy metals'): u'damage victims',
 (u'vaccine corruption', u'Jim Carrey'): u'shed light on',
 (u'preventable disease',
  u'vaccinated children'): u'are up to five times more likely than unvaccinated children to contract',
 (u'measles mortality',
  u'measles cases'): u'around 1 or 2 out of a thousand will become',
 (u'vaccine injuries',
  u'vaccine-injured families'): u'Surgeon General Vivek Murthy is rubbing salt in the wounds of',
 (u'safe level', u'thimerosal'): u'for humans no toxicologically established',
 (u'genetically susceptible children',
  u'vaccine damage'): u'are hyper-susceptible to',
 (u'toxins', u'healthy people'): u'might eliminate relatively quickly',
 (u'MRC-5 cells', u'lung tissue'): u'derived from',
 (u'doctors',
  u'ignorance of scientific facts'): u'who says the level of mercury in a vaccine is safe to inject into a child is only demonstrating their outrageous',
 (u'vaccines', u'antibiotics'): u'CDC openly admits still used in',
 (u'sanitation improvements', u'measles decline'): u'was due to',
 (u'patients', u'informed consent'): u'should be allowed',
 (u'vaccine reactions', u'you'): u'please talk about it if suffered serious',
 (u'hepatitis B vaccine',
  u'early intervention'): u'was associated with the receipt of',
 (u'vaccine corruption', u'CDC'): u'involved with',
 (u'vaccine story',
  u'public conversation'): u'only by sharing our perspective and what we know to be true about vaccination will the it open up',
 (u'mothers', u'social campaigns'): u'have shamed',
 (u'inflammatory adjuvant', u'aluminum'): u'used as',
 (u'truthful', u'consent for vaccines'): u'is not',
 (u'Supreme Court', u'vaccine court'): u'is higher power than',
 (u'African women',
  u'vaccines'): u'secretly laced with abortion chemicals were given to',
 (u'special care', u'vaccine-injured children'): u'require',
 (u'seasonal flu shot', u'thimerosal'): u'is present in nearly all',
 (u'high price', u'Prevnar'): u'added despite',
 (u'assault and battery',
  u'informed consent'): u'obtaining for a medical procedure under false pretenses is',
 (u'aluminum', u'human biology'): u'toxic when injected to',
 (u'shut your mouth and comply',
  u'you'): u'if question the vaccination issue, you will be told to',
 (u'vaccines', u'efficacy'): u'uncertainty surrounding',
 (u'vaccines', u'toxic chemical ingredients'): u'are used in',
 (u'vaccines', u'intelligent questions'): u'are not allowed to be asked about',
 (u'aluminum', u'mandatory vaccines'): u'poison children with',
 (u'effective', u'vaccines'): u'are not totally',
 (u'vaccines', u'pandemic H1N1 swine flu'): u'was highly reactive for',
 (u'Nichole Rolfe', u'proper protocol'): u'trying to abide by',
 (u'disability',
  u'vaccines'): u'more and more vaccines in early life setting some children up for',
 (u'epidemic proportions', u'measles'): u'was not at',
 (u'Freedom of Information Act',
  u'vaccine-autism link'): u'requests have resulted in copious evidence for',
 (u'vaccine doctrine', u'poisoning children'): u'has become',
 (u'NVIC', u'freedom of choice'): u'one of the top goals is preserving your',
 (u'health choices', u'right'): u'critical to make independent',
 (u'intelligent questions', u'censored'): u'are',
 (u'death from congenital malformation',
  u'measles mortality'): u'more likely than',
 (u'eye pain',
  u'adverse effects'): u'experienced after flu shot vaccines include',
 (u'vaccines', u'autism'): u'debate rages on',
 (u'rates', u'military records'): u'used actual',
 (u'cover-up', u'ethical track record'): u'full of',
 (u'Surgeon General Vivek Murthy',
  u'sell vaccines to minors'): u'uses Elmo to',
 (u'shingles vaccine', u'Zoster'): u'is branded',
 (u'vaccine supply', u'Congress'): u'pledged to protect',
 (u'cranial nerve paralysis',
  u'adverse effects'): u'experienced after flu shot vaccines include',
 (u'California Governor Jerry Brown',
  u'medical genocide'): u"will soon have to decide if he's going to commit",
 (u'pandemic H1N1 swine flu vaccine', u'cataplexy'): u'causes',
 (u'neurotoxin', u'aluminum'): u'are',
 (u'autism rise', u'genetic predisposition'): u'CDC claims due to',
 (u'vaccine additives', u'CDC'): u'admits',
 (u'brain inflammation', u'shingles'): u'can also lead to',
 (u'rational scientist',
  u'mercury'): u'cannot believe it is somehow safe injecting infants and children with',
 (u'thimerosal', u'reproductive toxin'): u'is a recognized',
 (u'modus operandi', u'harassment'): u'is becoming',
 (u'formaldehyde', u'vaccine ingredients'): u'is questionable',
 (u'vaccine safety', u'vaccination issue'): u'if you question',
 (u'thimerosal-free',
  u'Bush Administration'): u'granted pharmaceutical companies the ability to claim',
 (u'military records', u'measles decline'): u'show before measles vaccine',
 (u'Western medicine', u'Americans'): u'most have no clue',
 (u'Vaccine Injury Compensation Fund',
  u'U.S. citizens'): u'have to try and get a piece of the',
 (u'National Vaccine Injury Compensation Program',
  u'patients'): u'are uninformed about',
 (u'mercury', u'mandatory vaccines'): u'poison children with',
 (u'children', u'health'): u'are moving in the opposite direction of',
 (u'Pandemrix', u'GlaxoSmithKline'): u'is produced by',
 (u'government partnership with Big Pharma', u'profit-making'): u'based on',
 (u'children', u'victims'): u'include 60',
 (u'Gardasil', u'fever'): u'causes',
 (u'airports', u'toxic and ineffective flu shots'): u'are sold in',
 (u'member of the lunatic fringe',
  u'anti-vaccination'): u'will automatically be labeled a',
 (u'childhood diseases',
  u'vaccine proponents'): u'always claim widespread use of vaccines has solely reduced incidence of',
 (u'defective vaccines',
  u'mainstream media'): u'reports case after case where children are damaged by',
 (u'CDC', u'autism'): u'obscure an existing link between vaccines and',
 (u'vaccine industry', u'generation of children'): u'is destroying',
 (u'exemptions', u'vaccine industry'): u'fight against',
 (u'revenues', u'mainstream media'): u'fear losing advertising',
 (u'deliberate release of pathogens',
  u'people'): u'more than 500 million have died as a result of',
 (u'fetal bovine serum',
  u'toxic chemical ingredients'): u'in vaccines including',
 (u'vaccine injuries', u'real'): u'are',
 (u'thimerosal', u'neurological disorders'): u'has correlation with',
 (u'behavior changes',
  u'parents of vaccine-injured children'): u'often report',
 (u'settlement',
  u'Vaccine Injury Compensation Fund'): u'reported frustration is common trying to receive',
 (u'vaccine-autism link', u'unconcscionable'): u'dismissal is',
 (u'elopement', u'children with autism'): u'49 percent',
 (u'vaccine additives', u'antibiotics'): u'include',
 (u'unvaccinated children',
  u'allergies'): u'tests would show to be better off in terms of',
 (u'Flinstones', u'Chocks'): u'followed shortly after',
 (u'children', u'financial compensation'): u'to receive $90 million in',
 (u'vaccine choices',
  u'medical trade associations'): u'are being threatened by lobbyists representing',
 (u'doctors',
  u'people'): u'no longer possible to rely on the judgment of trusted',
 (u'Pandemrix', u'unprecedented drive'): u'given in',
 (u'autism cases', u'neurological damage'): u'include',
 (u'omitting deaths',
  u'pharmaceutical companies'): u'numerous times accused of',
 (u"California's vaccine violence", u'SB 277'): u'is',
 (u'delusions', u'vaccine-injured children'): u'are',
 (u'parents',
  u'real risks'): u'want to warn others that vaccinating comes with',
 (u"GlaxoSmithKine's Energix B", u'thimerosal-free'): u'licensed as',
 (u'children',
  u'neonatal infection'): u'240,000 die each year in low income countries from',
 (u'vaccines',
  u'vaccine industry'): u'seems to view the 308 million people living in the U.S. as little more than pin cushions for their profitable',
 (u'flu shots', u'flu-related doctor visits'): u'have no impact on',
 (u'time-consuming', u'National Vaccine Injury Compensation Program'): u'is',
 (u'diabetes deaths', u'deaths'): u'1.26 million each year from',
 (u'UK government',
  u'pandemic H1N1 swine flu vaccine'): u'agreed to pay $90 million to families of children permanently brain-damaged by',
 (u'herd mentality', u'pack of lemmings'): u'is like',
 (u'financial compensation',
  u'UK government'): u'agreed to pay $90 million in',
 (u'preservative', u'autism'): u'in vaccine causes',
 (u'Secretary of U.S. Department of Health and Human Services',
  u'The Advisory Committee on Immunization Practices'): u'selected by',
 (u'drug companies', u'toxic and ineffective flu shots'): u'sell',
 (u'Nichole Rolfe', u'silenced'): u'when she questioned rationale was',
 (u'initiatives that helped the poor',
  u'Robert F. Kennedy Jr.'): u'continued to support until his death in November 1963',
 (u'push vaccines on sick children',
  u'Baker College nursing school instructors'): u'instructed Nichole Rolfe and classmates to',
 (u'conversation about vaccination',
  u'medical trade associations'): u'we cannot allow them to dominate',
 (u'vaccine industry', u'state level'): u'begging for',
 (u'state', u'parents'): u'government to incarcerate in prison',
 (u'questionable ethical practices',
  u'pharmaceutical companies'): u'long associated with',
 (u'violation of basic human rights', u'mandatory vaccines'): u'is blatant',
 (u'chewable multivitamin', u'Chocks'): u'was first',
 (u'neurotoxin', u'flu shots'): u'remains in 60 percent of',
 (u'Rep. Bill Posey', u'whistleblower'): u'worked with',
 (u'cancer', u'Americans'): u'exposed to SV40 could have developed',
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 (u'vaccine insert sheets',
  u'pregnant women'): u'openly admit most of have never been tested for safety in',
 (u'mainstream media', u'facts'): u'refuses to report',
 (u'trace amounts of thimerosal', u'vaccine industry'): u'in many cases use',
 (u'childhood vaccines',
  u'severe autism issues'): u"our sons don't have due to our insistence in ensuring no thimerosal from",
 (u'vaccine safety', u'autism'): u'questionable in relation to',
 (u'professional liars', u'mainstream media'): u'has',
 (u'vaccine choices', u'legal right'): u'to make in America voluntary',
 (u'science', u'vaccines spread disease'): u'shows',
 (u'CDC',
  u'number of measles cases'): u'uses rather than rate of measles cases',
 (u'toxic', u'folic acid'): u'accumulates and becomes',
 (u'vaccines', u'debate'): u'are hot topic for',
 (u'issue', u'Hollywood celebrities'): u'has been another',
 (u'Octoxinol-9', u'flu shots'): u'contain questionable ingredients such as',
 (u'holocaust', u'vaccination'): u'is',
 (u'scientific fraud',
  u'Rep. Bill Posey'): u'statement contained astonishing description of brazen CDC',
 (u'lemming society', u'shut up'): u'is where public is told to',
 (u'residual components of MRC-5 cells',
  u'shingles vaccine ingredients'): u'include',
 (u'vaccination coverage', u'elderly'): u'increased since 1980 among',
 (u'job',
  u'larger campaign'): u'in future may end up dictating whether you will be allowed',
 (u'doctors', u'vaccines are safe'): u'repeated',
 (u'digestive tract',
  u'injecting any substance'): u'bypasses the protections of the',
 (u'lab results',
  u'mumps vaccine'): u'fabricated to claim 95% efficacy rate for',
 (u'adverse effects',
  u'convulsions'): u'experienced after flu shot vaccines include',
 (u'pandemic H1N1 swine flu vaccine',
  u'Guillain-Barre syndrome'): u'federal oversight committee found possible link to',
 (u'herd mentality', u'questions'): u'expects people to ask no honest',
 (u'big Ag', u'toxic chemical ingredients'): u'regulated by',
 (u'children', u'vaccination'): u'number has dramatically increased for',
 (u'flu shot while pregnant',
  u'thimerosal'): u'I never took because I knew flu shots had high levels of',
 (u'endangered children', u'immunocompromised children'): u'are those who are',
 (u'Big Pharma', u'you'): u'refuses to protect',
 (u'vaccination decisions',
  u'informed consent'): u'people want to exercise when it comes to making voluntary',
 (u'immunization', u'vaccination'): u'doctors fraudulently call',
 (u'vaccine ingredients',
  u'brain damage'): u'cause negative reactions that result in',
 (u'public', u'chronic disease'): u'wonders why they have many other',
 (u'mainstream media', u'conflict of interest'): u'exhibits extreme',
 (u'questions', u'line up'): u'expected of people without asking any honest',
 (u'scientists',
  u'troubling data'): u"top government group plotting how to protect industry's bottom line by getting rid of",
 (u'trace amounts of thimerosal', u'spectrum'): u'therefore',
 (u'public health', u'vaccines'): u'are not great for',
 (u'vaccine safety',
  u'pharmaceutical companies'): u'trusted voices in defense are closely tied to paid shills for',
 (u'Dr. Paul Offit', u'vaccine efficacy'): u'is a proponent for',
 (u'seizures', u'vaccine-related adverse outcomes'): u'include',
 (u'healthy gut flora', u'antibiotics'): u'destroy',
 (u'Dr. Paul Offit',
  u"Merck's RotaTeq vaccine"): u'is a listed inventor on cluster of patents that protect',
 (u'doctors', u'delusional'): u'who inject children with vaccines are',
 (u'distractions', u'Disneyland measles outbreak'): u'include',
 (u'improved healthcare', u'vaccines'): u'played big role after',
 (u'IRF1',
  u'smallpox vaccination'): u'genetic polymorphism in gene was associated with adverse events after',
 (u'additive', u'thimerosal'): u'is',
 (u'immunity', u'measles vaccine'): u'does not confer',
 (u'efficacy', u'mumps vaccine'): u'was fabricated for',
 (u'rules of due process and law',
  u'vaccine court'): u'is granted extraordinary powers to operate utterly outside the',
 (u'children', u'narcolepsy'): u'caused by swine flu vaccine in hundreds of',
 (u'disclosure', u'mandatory vaccines'): u'needs to be mandated prior to',
 (u'VAERS hepatitis B reports', u'serious reactions'): u'show 9,673',
 (u'whistleblower', u'CDC study'): u'provided documents related to 2004',
 (u'aluminum',
  u'rational doctor'): u'cannot believe it is somehow safe injecting infants and children with',
 (u'Pandemrix',
  u'European countries'): u'was used to inoculate up to 30 million people in 47 other',
 (u'obedient', u'mainstream media'): u'is',
 (u'childhood vaccines',
  u'vaccine ingredients'): u'many are manufactured with disturbing',
 (u'pharmaceutical companies', u'alternative media'): u'is not sponsored by',
 (u'vaccines',
  u'ethylmercury'): u'review disclosed hitherto-unrecognized levels in',
 (u'nurse', u'Nichole Rolfe'): u'is more qualified to be a',
 (u'clinical trials',
  u'vaccine safety'): u'there are none showing simultaneous',
 (u'children',
  u'International Business Times'): u'reports more than 800 across Europe made ill by swine flu vaccine',
 (u'False Claims Act', u'Merck'): u'filed',
 (u'vaccine injuries', u'people'): u'affect thousands every year',
 (u'pregnant women', u'amniocentesis'): u'were given thimerosal if was done',
 (u'Gardasil injuries',
  u'alternative media'): u'information inside the U.S. comes mainly from',
 (u'vaccine ingredients',
  u'shingles vaccine ingredients'): u'virtually the same as other',
 (u'Dr. Paul Offit', u'mandatory vaccines'): u'promotes',
 (u'vaccines', u'population'): u'no vaccine is completely safe in the entire',
 (u'vaccine effects', u'fetal development'): u'are unknown on',
 (u'measles mortality',
  u'cod-liver oil'): u'ended up lowering rate significantly',
 (u'CDC', u'measles decline'): u'shows',
 (u'sanctions', u'doctors'): u'by',
 (u'shingles', u'shingles risk'): u'very slim if already had',
 (u'ineffective flu vaccine', u'disabled children'): u'being forced on',
 (u'medical trade associations', u'drug companies'): u'funded by',
 (u'truth', u'SV40'): u'took 50 years to come out about',
 (u'deadly diseases', u'vaccines'): u'have eradicated many once',
 (u'human beings', u'people'): u'should be treated like',
 (u'genetic correlation', u'vaccine damage'): u'there is with',
 (u'vaccines', u'Americans'): u'fly under the radar of most',
 (u'FDA', u'additives'): u'regulated by',
 (u'vaccine choices',
  u'drug companies'): u"want taken out of people's hands the right to make informed",
 (u'MTHFR C677T defect',
  u'Italian descent'): u'approximately 30% have inherited both',
 (u'pain and suffering', u'millions of dollars'): u'awarded under name of',
 (u'FETCH.news', u'alternative media'): u'now favored on',
 (u'flu shots',
  u'pharmaceutical companies'): u'selling vaccines have proved safety and efficacy of',
 (u'children with autism', u'peer bullying'): u'experience',
 (u'vaccines', u'CDC'): u'recommends by age 6 48 doses of 14',
 (u'trace amounts of thimerosal',
  u'number of vaccines'): u'how many have caused an issue due to increased',
 (u'lawsuit', u'circuit court'): u'filed in',
 (u'nursing school at Baker College',
  u'Nichole Rolfe'): u'says she was wrongfully dismissed from',
 (u'children',
  u'toxic chemical ingredients'): u'could become brain damaged by',
 (u'settlement',
  u'government'): u'did not want to admit guilt likely a part of the huge',
 (u'United States', u'vaccination rate'): u'has some of the highest',
 (u'pharmaceutical companies',
  u'vaccine-injured children'): u'were damaged in the first place by',
 (u'recombinant human albumin',
  u'genetically engineered human protein'): u'also known as',
 (u'children',
  u'vaccine dangers'): u'parents would never take the chance to subject their',
 (u'thimerosal',
  u'The Vaccine and Autism Congressional Hearing'): u'testimony given from respected research doctor at Baylor College of Medicine at',
 (u'petitioner-friendly',
  u'National Vaccine Injury Compensation Program'): u'was created to be',
 (u'lobbying', u'drug companies'): u'manipulate through',
 (u'National Vaccine Injury Compensation Program',
  u'claims'): u'allows for a fair and much more simple process of filing',
 (u'vaccines', u'problem'): u'could be major part of',
 (u'scientists',
  u'thimerosal'): u'top government secretly gathered to discuss use of in childhood vaccines',
 (u'vaccines', u'immune system'): u'more and more is atypical manipulation of',
 (u'vaccines',
  u'scientifically irresponsible assertion'): u'receiving up to 10,000 vaccines at once and 100,000 in a lifetime is',
 (u'risks', u'hepatitis B vaccine'): u'little to no protection to real',
 (u'vaccine insert sheets',
  u'side effects'): u'disclose long list of frightening and bizarre',
 (u'vaccines', u'widespread health problems'): u'more and more not solving',
 (u'scientific fraud', u'investigations'): u'none into',
 (u'doctors', u'financial influence'): u'may have',
 (u'vaccine reactions',
  u'Vaccine Adverse Event Reporting System'): u'developed by government to report',
 (u'healthier children',
  u'vaccination'): u'dramatically increasing the number during the past 30 years may not have led to',
 (u'American Academy of Pediatrics',
  u'vaccine industry'): u'gives millions to',
 (u'swelling of the brain',
  u'adverse effects'): u'experienced after flu shot vaccines include',
 (u'special education services',
  u'hepatitis B vaccine'): u'was associated with the receipt of',
 (u'pharma-controlled U.S. media',
  u'vaccine-damaged children'): u'claims none in the United States',
 ...}

In [11]:

    

for e in a:
    if edgelabels.has_key(e):
        print e,edgelabels[e]
    else:
        rev_e = e[::-1]
        print rev_e, edgelabels[rev_e]


    

    




(u"alzheimer's", u'autism') brain cells same patterns with
(u'Vaccine Injury Compensation Program', u'autism') found in two kids after being vaccinated awarded by
(u'toxic chemical ingredients', u'autism') may be significant contributing factor to
(u'studies', u'autism') but where are of all the others in relation to
(u'vaccine safety', u'autism') questionable in relation to
(u'vaccination', u'autism') caused
(u'MMR', u'African American males') were at increased risk for autism who received before age 36 months
(u'CDC', u'link') obscure an existing
(u'autism', u'vaccine-injured children') often revealed to have
(u'vaccines', u'autism') debate rages on
(u'newborn boys', u'hepatitis B vaccine') more than tripled their risk of developing autism spectrum disorder in
(u'public', u'autism') wonders why they have
(u'preservative', u'autism') in vaccine causes
(u'autism', u'measles') some parents feel more dangerous than
(u'thimerosal', u'autism') was directly caused by
(u'glutathione', u'autism') significantly lower in patients diagnosed with
(u'military records', u'measles decline') show before measles vaccine
(u'CDC', u'autism') obscure an existing link between vaccines and
(u'children', u'autism') every year tens of thousands more diagnosed with
(u'hepatitis B vaccine', u'autism') giving to newborn baby boys more than triples their risk of developing
(u'mainstream media', u'CDC whistleblower') total nationwide blackout on news about
(u'encephalopathy', u'autism') caused by vaccines produces a permanent injury and creates symptoms of
(u'Ryan Mojabi', u'autism') parents testified that vaccinations and MMR caused 
(u'MMR', u'autism') only one studied in association with

In [ ]:

    

# this takes forever
# average connectivity k of a graph G is the average of local node connectivity over all pairs of nodes of G

#nx.average_node_connectivity(Gc)


    

In [12]:

    

# NEW SUMMARY

print "List of connected components =", [len(c) for c in sorted(nx.connected_components(ugraph), key=len, reverse=True)]
print "Size of greatest component =", len(Gc)
print "# of cutsets =", len(cutsets)
print "Min node cut =", nx.minimum_node_cut(Gc)
print "Min edge cut =", nx.minimum_edge_cut(Gc)


    

    




List of connected components = [1140, 7, 4, 4, 4, 3, 3, 3, 3, 3, 3, 3, 3, 3, 3, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2]
Size of greatest component = 1140
# of cutsets = 226
Min node cut =





    




---------------------------------------------------------------------------
KeyboardInterrupt                         Traceback (most recent call last)
<ipython-input-12-688701a61e6c> in <module>()
      4 print "Size of greatest component =", len(Gc)
      5 print "# of cutsets =", len(cutsets)
----> 6 print "Min node cut =", nx.minimum_node_cut(Gc)
      7 print "Min edge cut =", nx.minimum_edge_cut(Gc)

/Users/gloriakang/anaconda2/lib/python2.7/site-packages/networkx/algorithms/connectivity/cuts.pyc in minimum_node_cut(G, s, t, flow_func)
    428     # Compute st node cuts between v and all its non-neighbors nodes in G.
    429     for w in set(G) - set(neighbors(v)) - set([v]):
--> 430         this_cut = minimum_st_node_cut(G, v, w, **kwargs)
    431         if len(min_cut) >= len(this_cut):
    432             min_cut = this_cut

/Users/gloriakang/anaconda2/lib/python2.7/site-packages/networkx/algorithms/connectivity/cuts.pyc in minimum_st_node_cut(G, s, t, flow_func, auxiliary, residual)
    292     # original graph.
    293     edge_cut = minimum_st_edge_cut(H, '%sB' % mapping[s], '%sA' % mapping[t],
--> 294                                    **kwargs)
    295     # Each node in the original graph maps to two nodes of the auxiliary graph
    296     node_cut = set(H.node[node]['id'] for edge in edge_cut for node in edge)

/Users/gloriakang/anaconda2/lib/python2.7/site-packages/networkx/algorithms/connectivity/cuts.pyc in minimum_st_edge_cut(G, s, t, flow_func, auxiliary, residual)
    148     kwargs = dict(capacity='capacity', flow_func=flow_func, residual=residual)
    149 
--> 150     cut_value, partition = nx.minimum_cut(H, s, t, **kwargs)
    151     reachable, non_reachable = partition
    152     # Any edge in the original graph linking the two sets in the

/Users/gloriakang/anaconda2/lib/python2.7/site-packages/networkx/algorithms/flow/maxflow.pyc in minimum_cut(G, s, t, capacity, flow_func, **kwargs)
    450     cutset = [(u, v, d) for u, v, d in R.edges(data=True)
    451               if d['flow'] == d['capacity']]
--> 452     R.remove_edges_from(cutset)
    453 
    454     # Then, reachable and non reachable nodes from source in the

/Users/gloriakang/anaconda2/lib/python2.7/site-packages/networkx/classes/digraph.pyc in remove_edges_from(self, ebunch)
    722         for e in ebunch:
    723             (u,v)=e[:2]  # ignore edge data
--> 724             if u in self.succ and v in self.succ[u]:
    725                 del self.succ[u][v]
    726                 del self.pred[v][u]

KeyboardInterrupt: 

In [ ]:

    

# OLD summary DON'T DELETE YET

print "List of connected components =", [len(c) for c in sorted(nx.connected_components(ugraph), key=len, reverse=True)]
print "Size of greatest component =", len(Gc)
print "# of cutsets =", len(cutsets)
print "Min node cut =", nx.minimum_node_cut(Gc)
print "Min edge cut =", nx.minimum_edge_cut(Gc)


    

In [ ]: