How to calculate TF-IDF similarity matrix of a complete corpus with Gensim

gensim_workflow.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-

'''

This script just show the basic workflow to compute TF-IDF similarity matrix with Gensim 


OUTPUT :

clemsos@miner $ python gensim_workflow.py 


How to use Gensim to compute TF-IDF similarity step by step
----------
Let's start with a raw corpus :<type 'list'>

STEP 1 : Index and vectorize
----------
We create a dictionary, an index of all unique values: <class 'gensim.corpora.dictionary.Dictionary'>
Then convert convert tokenized documents to vectors: <type 'list'>
Save the vectorized corpus as a .mm file

STEP 2 : Transform and compute similarity between corpuses
----------
We load our dictionary : <class 'gensim.corpora.dictionary.Dictionary'>
We load our vector corpus : <class 'gensim.corpora.mmcorpus.MmCorpus'> 
We initialize our TF-IDF transformation tool : <class 'gensim.models.tfidfmodel.TfidfModel'>
We convert our vectors corpus to TF-IDF space : <class 'gensim.interfaces.TransformedCorpus'>

STEP 3 : Create similarity matrix of all files
----------
We compute similarities from the TF-IDF corpus : <class 'gensim.similarities.docsim.MatrixSimilarity'>
We get a similarity matrix for all documents in the corpus <type 'numpy.ndarray'>

Done in 0.011s

'''
from gensim import corpora, models, similarities
from time import time

t0=time()

# keywords have been extracted and stopwords removed.

tweets=[['human', 'interface', 'computer'],
 ['survey', 'user', 'computer', 'system', 'response', 'time'],
 ['eps', 'user', 'interface', 'system'],
 ['system', 'human', 'system', 'eps'],
 ['user', 'response', 'time'],
 ['trees'],
 ['graph', 'trees'],
 ['graph', 'minors', 'trees'],
 ['graph', 'minors', 'survey']] 

print "How to use Gensim to compute TF-IDF similarity step by step"
print '-'*10
print "Let's start with a raw corpus :%s"%type(tweets)
print
# STEP 1 : Compile corpus and dictionary
print "STEP 1 : Index and vectorize"
print '-'*10

# create dictionary (index of each element)
dictionary = corpora.Dictionary(tweets)
dictionary.save('/tmp/tweets.dict') # store the dictionary, for future reference
print "We create a dictionary, an index of all unique values: %s"%type(dictionary)

# compile corpus (vectors number of times each elements appears)
raw_corpus = [dictionary.doc2bow(t) for t in tweets]
print "Then convert convert tokenized documents to vectors: %s"% type(raw_corpus)
corpora.MmCorpus.serialize('/tmp/tweets.mm', raw_corpus) # store to disk
print "Save the vectorized corpus as a .mm file"
print

# STEP 2 : similarity between corpuses
print "STEP 2 : Transform and compute similarity between corpuses"
print '-'*10
dictionary = corpora.Dictionary.load('/tmp/tweets.dict')
print "We load our dictionary : %s"% type(dictionary)

corpus = corpora.MmCorpus('/tmp/tweets.mm')
print "We load our vector corpus : %s "% type(corpus) 

# Transform Text with TF-IDF
tfidf = models.TfidfModel(corpus) # step 1 -- initialize a model
print "We initialize our TF-IDF transformation tool : %s"%type(tfidf)

# corpus tf-idf
corpus_tfidf = tfidf[corpus]
print "We convert our vectors corpus to TF-IDF space : %s"%type(corpus_tfidf)
print

# STEP 3 : Create similarity matrix of all files
print "STEP 3 : Create similarity matrix of all files"
print '-'*10
index = similarities.MatrixSimilarity(tfidf[corpus])
print "We compute similarities from the TF-IDF corpus : %s"%type(index)
index.save('/tmp/deerwester.index')
index = similarities.MatrixSimilarity.load('/tmp/deerwester.index')

sims = index[corpus_tfidf]
print "We get a similarity matrix for all documents in the corpus %s"% type(sims)
print 
print "Done in %.3fs"%(time()-t0)

# print sims
# print list(enumerate(sims))
# sims = sorted(enumerate(sims), key=lambda item: item[1])
# print sims # print sorted (document number, similarity score) 2-tuples

I think you can add new document to corpus index and retrain the model

https://radimrehurek.com/gensim/similarities/docsim.html#how-it-works
add_documents(corpus)

sims = sorted(enumerate(sims), key=lambda item: item[1])
ValueError: The truth value of an array with more than one element is ambiguous. Use a.any() or a.all()

sims = sorted(enumerate(sims[1]), key=lambda item: -item[1])