User Warning: Your stop_words may be inconsistent with your preprocessing

Question

I am following this document clustering tutorial. As an input I give a txt file which can be downloaded here. It's a combined file of 3 other txt files divided with a use of \n. After creating a tf-idf matrix I received this warning:

,,UserWarning: Your stop_words may be inconsistent with your preprocessing. 
Tokenizing the stop words generated tokens ['abov', 'afterward', 'alon', 'alreadi', 'alway', 'ani', 'anoth', 'anyon', 'anyth', 'anywher', 'becam', 'becaus', 'becom', 'befor', 'besid', 'cri', 'describ', 'dure', 'els', 'elsewher', 'empti', 'everi', 'everyon', 'everyth', 'everywher', 'fifti', 'forti', 'henc', 'hereaft', 'herebi', 'howev', 'hundr', 'inde', 'mani', 'meanwhil', 'moreov', 'nobodi', 'noon', 'noth', 'nowher', 'onc', 'onli', 'otherwis', 'ourselv', 'perhap', 'pleas', 'sever', 'sinc', 'sincer', 'sixti', 'someon', 'someth', 'sometim', 'somewher', 'themselv', 'thenc', 'thereaft', 'therebi', 'therefor', 'togeth', 'twelv', 'twenti', 'veri', 'whatev', 'whenc', 'whenev', 'wherea', 'whereaft', 'wherebi', 'wherev', 'whi', 'yourselv'] not in stop_words.
  'stop_words.' % sorted(inconsistent))". 

I guess it has something to do with the order of lemmatization and stop words removal, but as this is my first project in txt processing, I am a bit lost and I don't know how to fix this...

import pandas as pd
import nltk
from nltk.corpus import stopwords
import re
import os
import codecs
from sklearn import feature_extraction
import mpld3
from nltk.stem.snowball import SnowballStemmer
from sklearn.feature_extraction.text import TfidfVectorizer


stopwords = stopwords.words('english')
stemmer = SnowballStemmer("english")

def tokenize_and_stem(text):
    # first tokenize by sentence, then by word to ensure that punctuation is caught as it's own token
    tokens = [word for sent in nltk.sent_tokenize(text) for word in nltk.word_tokenize(sent)]
    filtered_tokens = []
    # filter out any tokens not containing letters (e.g., numeric tokens, raw punctuation)
    for token in tokens:
        if re.search('[a-zA-Z]', token):
            filtered_tokens.append(token)
    stems = [stemmer.stem(t) for t in filtered_tokens]
    return stems


def tokenize_only(text):
    # first tokenize by sentence, then by word to ensure that punctuation is caught as it's own token
    tokens = [word.lower() for sent in nltk.sent_tokenize(text) for word in nltk.word_tokenize(sent)]
    filtered_tokens = []
    # filter out any tokens not containing letters (e.g., numeric tokens, raw punctuation)
    for token in tokens:
        if re.search('[a-zA-Z]', token):
            filtered_tokens.append(token)
    return filtered_tokens


totalvocab_stemmed = []
totalvocab_tokenized = []
with open('shortResultList.txt', encoding="utf8") as synopses:
    for i in synopses:
        allwords_stemmed = tokenize_and_stem(i)  # for each item in 'synopses', tokenize/stem
        totalvocab_stemmed.extend(allwords_stemmed)  # extend the 'totalvocab_stemmed' list
        allwords_tokenized = tokenize_only(i)
        totalvocab_tokenized.extend(allwords_tokenized)

vocab_frame = pd.DataFrame({'words': totalvocab_tokenized}, index = totalvocab_stemmed)
print ('there are ' + str(vocab_frame.shape[0]) + ' items in vocab_frame')
print (vocab_frame.head())

#define vectorizer parameters
tfidf_vectorizer = TfidfVectorizer(max_df=0.8, max_features=200000,
                                 min_df=0.2, stop_words='english',
                                 use_idf=True, tokenizer=tokenize_and_stem, ngram_range=(1,3))

with open('shortResultList.txt', encoding="utf8") as synopses:
    tfidf_matrix = tfidf_vectorizer.fit_transform(synopses) #fit the vectorizer to synopses

print(tfidf_matrix.shape)

Answer 1

The warning is trying to tell you that if your text contains "always" it will be normalised to "alway" before matching against your stop list which includes "always" but not "alway". So it won't be removed from your bag of words.

The solution is to make sure that you preprocess your stop list to make sure that it is normalised like your tokens will be, and pass the list of normalised words as stop_words to the vectoriser.

Answer 2

I had the same problem and for me the following worked:

1. include stopwords into tokenize function and then
2. remove stopwords parameter from tfidfVectorizer

Like so:

1.

stopwords = stopwords.words('english')
stemmer = SnowballStemmer("english")

def tokenize_and_stem(text):
    tokens = [word for sent in nltk.sent_tokenize(text) for word in nltk.word_tokenize(sent)]
    filtered_tokens = []
    for token in tokens:
        if re.search('[a-zA-Z]', token):
            filtered_tokens.append(token)

    #exclude stopwords from stemmed words
    stems = [stemmer.stem(t) for t in filtered_tokens if t not in stopwords]

    return stems

2. Delete stopwords parameter from vectorizer:

tfidf_vectorizer = TfidfVectorizer(
    max_df=0.8, max_features=200000, min_df=0.2,
    use_idf=True, tokenizer=tokenize_and_stem, ngram_range=(1,3)
)

Answer 3

I faced this problem because of PT-BR language.

TL;DR: Remove the accents of your language.

# Special thanks for the user Humberto Diogenes from Python List (answer from Aug 11, 2008)
# Link: http://python.6.x6.nabble.com/O-jeito-mais-rapido-de-remover-acentos-de-uma-string-td2041508.html

# I found the issue by chance (I swear, haha) but this guy gave the tip before me
# Link: https://github.com/scikit-learn/scikit-learn/issues/12897#issuecomment-518644215

import spacy
nlp = spacy.load('pt_core_news_sm')

# Define default stopwords list
stoplist = spacy.lang.pt.stop_words.STOP_WORDS

def replace_ptbr_char_by_word(word):
  """ Will remove the encode token by token"""
    word = str(word)
    word = normalize('NFKD', word).encode('ASCII','ignore').decode('ASCII')
    return word

def remove_pt_br_char_by_text(text):
  """ Will remove the encode using the entire text"""
    text = str(text)
    text = " ".join(replace_ptbr_char_by_word(word) for word in text.split() if word not in stoplist)
    return text

df['text'] = df['text'].apply(remove_pt_br_char_by_text)

I put the solution and references in this gist.