Creating an inverted index from text documents

Question

I am working on an information retrieval project, where I have to process a ~1.5 GB text data and create a Dictionary (words, document frequency) and posting list (document id, term frequency). According to the professor, it should take around 10-15 minutes. But my code is running for more than 8 hours now! I tried a smaller dataset (~35 MB) and it took 5 hours to process.

I am a newbie in python and I think it is taking so long because i have created many python dictionaries and lists in my code. I tried to use generator, but I am not sure how to work around with it.

file = open(filename, 'rt')
text = file.read()
file.close()

p = r'<P ID=\d+>.*?</P>' 
tag = RegexpTokenizer(p)
passage = tag.tokenize(text)
doc_re = re.compile(r"<P ID=(\d+)>")

def process_data(docu):
    tokens = RegexpTokenizer(r'\w+')    
    lower_tokens = [word.lower() for word in tokens.tokenize(docu)] #convert to lower case  
    table = str.maketrans('','', string.punctuation)
    stripped = [w.translate(table) for w in lower_tokens] #remove punctuation   
    alpha = [word for word in stripped if word.isalpha()] #remove tokens that are not alphabetic    
    stopwordlist = stopwords.words('english')
    stopped = [w for w in alpha if not w in stopwordlist] #remove stopwords

    return stopped

data = {} #dictionary: key = Doc ID, value: word/term
for doc in passage:
    group_docID = doc_re.match(doc)
    docID = group_docID.group(1)
    tokens = process_data(doc)
    data[docID] = list(set(tokens))

vocab = [item for i in data.values() for item in i] #all words in the dataset
total_vocab = list(set(vocab)) #unique word/vocbulary for the whole dataset
total_vocab.sort()
print('Document Size = ', len(data)) #no. of documents
print('Collection Size = ', len(vocab)) #no. of words
print('Vocabulary Size= ', len(total_vocab)) #no. of unique words


inv_index = {} #dictionary: key =word/term, value: [docid, termfrequency]
for x in total_vocab:
    for y, z in data.items():
        if x in z:
            wordfreq = z.count(x)
            inv_index.setdefault(x, []).append((int(y), wordfreq)) 

flattend = [item for tag in inv_index.values() for item in tag] #[(docid, tf)]
posting = [item  for tag in flattend for item in tag ] #[docid, tf]

#document frequency for each vocabulary/words
doc_freq=[]
for k,v in inv_index.items():
    freq1=len([item for item in v if item])
    doc_freq.append((freq1))

#offset value of each vocabulary/words
offset = []
offset1=0
for i in range(len(doc_freq)):
    if i>0:
        offset1 =offset1 + (doc_freq[i-1]*2)
    offset.append((offset1))

#create dcitionary of words, document frequency and offset
dictionary = {}
for i in range(len(total_vocab)):
    dictionary[total_vocab[i]]=(doc_freq[i],offset[i])

#dictionary of word, inverse document frequency
idf = {}
for i in range(len(dictionary)):
    a = np.log2(len(data)/doc_freq[i])
    idf[total_vocab[i]] = a

with open('dictionary.json', 'w') as f:
    json.dump(dictionary,f)

with open('idf.json', 'w') as f:
    json.dump(idf, f)

binary_file = open('binary_file.txt', 'wb')

for i in range(0, len(posting)):
    binary_int = (posting[i]).to_bytes(4, byteorder = 'big')
    #print(binary_int)
    binary_file.write(binary_int)

binary_file.close()

Could someone please help me to rewrite this code so that it becomes more computationally and time efficient?

There are around 57982 documents like that. Input File:

<P ID=2630932>
Background
Adrenal cortex oncocytic carcinoma (AOC) represents an exceptional 
pathological entity, since only 22 cases have been documented in the 
literature so far.
Case presentation
Our case concerns a 54-year-old man with past medical history of right 
adrenal excision with partial hepatectomy, due to an adrenocortical 
carcinoma. The patient was admitted in our hospital to undergo surgical 
resection of a left lung mass newly detected on chest Computed Tomography 
scan. The histological and immunohistochemical study revealed a metastatic 
AOC. Although the patient was given mitotane orally in adjuvant basis, he 
experienced relapse with multiple metastases in the thorax twice.....
<\P>

I am trying to tokenize each document by word and store document frequency of each word in a dictionary. Trying to save it in json file. Dictionary

word document_frequency offset
medical 2500 3414
research 320 4200

Also, generating a index where each word has a posting list of document ID and term frequency

medical (2630932, 20), (2795320, 2), (26350421, 31).... 
research (2783546, 243), (28517364, 310)....

and then save this postings in a binary file:

2630932 20 2795320 2 2635041 31....

with an offset value for each word. SO that when i load the posting list from disk, i could use seek function to get the posting for each corresponding word.

Answer 1

One way to probably speed this up a bit is to use generator expressions. Currently your process_data function has many list comprehensions after another. Each of them results in a list in memory, but you only care about the end result. In addition, you call set on it directly afterwards, so include that in the function itself. I also extracted some constants from the function, no need to always redefine them, and made the stopwords a set so in is \$\mathcal{O}(1)\$ instead of \$\mathcal{O}(n)\$.

STOPWORDS = set(stopwords.words('english'))
TOKENIZER = RegexpTokenizer(r'\w+')
TABLE = str.maketrans('', '', string.punctuation)

def process_data(docu):
    # convert to lower case  
    lower_tokens = (word.lower() for word in tokens.TOKENIZER(docu))
    #remove punctuation
    stripped = (w.translate(TABLE) for w in lower_tokens)
    #remove tokens that are not alphabetic    
    alpha = (word for word in stripped if word.isalpha())
    # remove stopwords
    stopped = (w for w in alpha if w not in STOPWORDS)
    return set(stopped)

I would also keep data[docID] a set, because you later check for in there as well.

Similarly, you can directly build a set using a set comprehension, instead of creating a list, and then putting it into a set. This way you can turn

vocab = [item for i in data.values() for item in i] #all words in the dataset
total_vocab = list(set(vocab)) #unique word/vocbulary for the whole dataset
total_vocab.sort()

into

total_vocab = sorted({item for i in data.values() for item in i})

Incidentally, wordfreq = z.count(x) should always give you 1, because you made sure before that z only has unique words.

Instead of inv_index being a normal dictionary and having to use inv_index.setdefault(x, []).append((int(y), wordfreq)), just make it a collections.defaultdict(list), so you can just do inv_index.append((int(y), wordfreq)).