/scikit-learn

# Wikipedia principal eigenvector

A classical way to assert the relative importance of vertices in a graph is to compute the principal eigenvector of the adjacency matrix so as to assign to each vertex the values of the components of the first eigenvector as a centrality score:

https://en.wikipedia.org/wiki/Eigenvector_centrality

On the graph of webpages and links those values are called the PageRank scores by Google.

The goal of this example is to analyze the graph of links inside wikipedia articles to rank articles by relative importance according to this eigenvector centrality.

The traditional way to compute the principal eigenvector is to use the power iteration method:

https://en.wikipedia.org/wiki/Power_iteration

Here the computation is achieved thanks to Martinsson’s Randomized SVD algorithm implemented in scikit-learn.

The graph data is fetched from the DBpedia dumps. DBpedia is an extraction of the latent structured data of the Wikipedia content.

```# Author: Olivier Grisel <[email protected]>

from __future__ import print_function

from bz2 import BZ2File
import os
from datetime import datetime
from pprint import pprint
from time import time

import numpy as np

from scipy import sparse

from sklearn.decomposition import randomized_svd
from sklearn.utils import Memory
from sklearn.externals.six.moves.urllib.request import urlopen
from sklearn.externals.six import iteritems

print(__doc__)

# #############################################################################
redirects_filename = redirects_url.rsplit("/", 1)[1]

resources = [
(redirects_url, redirects_filename),
]

for url, filename in resources:
if not os.path.exists(filename):
opener = urlopen(url)
print()

# #############################################################################

memory = Memory(cachedir=".")

def index(redirects, index_map, k):
"""Find the index of an article name after redirect resolution"""
k = redirects.get(k, k)
return index_map.setdefault(k, len(index_map))

DBPEDIA_RESOURCE_PREFIX_LEN = len("http://dbpedia.org/resource/")
SHORTNAME_SLICE = slice(DBPEDIA_RESOURCE_PREFIX_LEN + 1, -1)

def short_name(nt_uri):
"""Remove the < and > URI markers and the common URI prefix"""
return nt_uri[SHORTNAME_SLICE]

def get_redirects(redirects_filename):
"""Parse the redirections and build a transitively closed map out of it"""
redirects = {}
print("Parsing the NT redirect file")
for l, line in enumerate(BZ2File(redirects_filename)):
split = line.split()
if len(split) != 4:
print("ignoring malformed line: " + line)
continue
redirects[short_name(split[0])] = short_name(split[2])
if l % 1000000 == 0:
print("[%s] line: %08d" % (datetime.now().isoformat(), l))

# compute the transitive closure
print("Computing the transitive closure of the redirect relation")
for l, source in enumerate(redirects.keys()):
transitive_target = None
target = redirects[source]
seen = set([source])
while True:
transitive_target = target
target = redirects.get(target)
if target is None or target in seen:
break
redirects[source] = transitive_target
if l % 1000000 == 0:
print("[%s] line: %08d" % (datetime.now().isoformat(), l))

return redirects

# disabling joblib as the pickling of large dicts seems much too slow
#@memory.cache
"""Extract the adjacency graph as a scipy sparse matrix

Redirects are resolved first.

Returns X, the scipy sparse adjacency matrix, redirects as python
dict from article names to article names and index_map a python dict
from article names to python int (article indexes).
"""

print("Computing the redirect map")
redirects = get_redirects(redirects_filename)

print("Computing the integer index map")
index_map = dict()
split = line.split()
if len(split) != 4:
print("ignoring malformed line: " + line)
continue
i = index(redirects, index_map, short_name(split[0]))
j = index(redirects, index_map, short_name(split[2]))
if l % 1000000 == 0:
print("[%s] line: %08d" % (datetime.now().isoformat(), l))

if limit is not None and l >= limit - 1:
break

X = sparse.lil_matrix((len(index_map), len(index_map)), dtype=np.float32)
X[i, j] = 1.0
print("Converting to CSR representation")
X = X.tocsr()
print("CSR conversion done")
return X, redirects, index_map

# stop after 5M links to make it possible to work in RAM
names = dict((i, name) for name, i in iteritems(index_map))

print("Computing the principal singular vectors using randomized_svd")
t0 = time()
U, s, V = randomized_svd(X, 5, n_iter=3)
print("done in %0.3fs" % (time() - t0))

# print the names of the wikipedia related strongest components of the
# principal singular vector which should be similar to the highest eigenvector
pprint([names[i] for i in np.abs(U.T[0]).argsort()[-10:]])
pprint([names[i] for i in np.abs(V[0]).argsort()[-10:]])

def centrality_scores(X, alpha=0.85, max_iter=100, tol=1e-10):
"""Power iteration computation of the principal eigenvector

This method is also known as Google PageRank and the implementation
is based on the one from the NetworkX project (BSD licensed too)

Aric Hagberg <[email protected]>
Dan Schult <[email protected]>
Pieter Swart <[email protected]>
"""
n = X.shape[0]
X = X.copy()
incoming_counts = np.asarray(X.sum(axis=1)).ravel()

print("Normalizing the graph")
for i in incoming_counts.nonzero()[0]:
X.data[X.indptr[i]:X.indptr[i + 1]] *= 1.0 / incoming_counts[i]
dangle = np.asarray(np.where(np.isclose(X.sum(axis=1), 0),
1.0 / n, 0)).ravel()

scores = np.full(n, 1. / n, dtype=np.float32)  # initial guess
for i in range(max_iter):
print("power iteration #%d" % i)
prev_scores = scores
scores = (alpha * (scores * X + np.dot(dangle, prev_scores))
+ (1 - alpha) * prev_scores.sum() / n)
# check convergence: normalized l_inf norm
scores_max = np.abs(scores).max()
if scores_max == 0.0:
scores_max = 1.0
err = np.abs(scores - prev_scores).max() / scores_max
print("error: %0.6f" % err)
if err < n * tol:
return scores

return scores

print("Computing principal eigenvector score using a power iteration method")
t0 = time()
scores = centrality_scores(X, max_iter=100, tol=1e-10)
print("done in %0.3fs" % (time() - t0))
pprint([names[i] for i in np.abs(scores).argsort()[-10:]])
```

Total running time of the script: ( 0 minutes 0.000 seconds)

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