Token Classification (ValueError: NumPy boolean array indexing assignment)

I was reading and working through “Token Classification with W-NUT Emerging Entities” tutorial on Fine-tuning with custom datasets — transformers 4.5.0.dev0 documentation using a different data.

To replicate the data structure of the tutorial, I used the code below to insert a blank space between sentences/tags

# insert blank row in python dataframe when value in column changes
mask = DF['sentence_id'].ne(DF['sentence_id'].shift(-1))
DF1 = pd.DataFrame('',index=mask.index[mask] + .5, columns=DF.columns)

DF2 = pd.concat([DF, DF1]).sort_index().reset_index(drop=True).iloc[:-1]

I then wrote the data to a file

DF2.to_csv(r'/content/drive/MyDrive/Colab Notebooks/model/dataset.txt', 

          header=None, index=None, sep='\t', mode='a', encoding="utf-8")

I read the data back using the code provided in the tutorial

def read_wnut(file_path):
    file_path = Path(file_path, encoding='utf8')

    raw_text = file_path.read_text().strip()
    raw_docs = re.split(r'\n\t?\n', raw_text)
    token_docs = []
    tag_docs = []
    for doc in raw_docs:
        tokens = []
        tags = []
        for line in doc.split('\n'):
            token, tag = line.split('\t')

    return token_docs, tag_docs

texts_df, tags_df = read_wnut(colab_file_path)

Next, I split up the data into training, validation, and test sets.

I then created encoding for the tags and the tokens as seen below

tag2id = {tag: id for id, tag in enumerate(unique_tags)}
id2tag = {id: tag for tag, id in tag2id.items()}

# import the transformers module
from transformers import BertTokenizerFast

# import the small bert tokenizer
model_name = "google/bert_uncased_L-4_H-512_A-8"
tokenizer = BertTokenizerFast.from_pretrained(model_name)

train_encodings = tokenizer(train_texts, is_split_into_words=True, return_offsets_mapping=True, padding=True, truncation=True)
val_encodings = tokenizer(val_texts, is_split_into_words=True, return_offsets_mapping=True, padding=True, truncation=True)
test_encodings = tokenizer(test_texts, is_split_into_words=True, return_offsets_mapping=True, padding=True, truncation=True)

It’s when I run the offset function that I get an error message

import numpy as np

def encode_tags(tags, encodings):
    labels = [[tag2id[tag] for tag in doc] for doc in tags]
    encoded_labels = []
    for doc_labels, doc_offset in zip(labels, encodings.offset_mapping):
        # create an empty array of -100
        doc_enc_labels = np.ones(len(doc_offset),dtype=int) * -100
        arr_offset = np.array(doc_offset)

        # set labels whose first offset position is 0 and the second is not 0
        doc_enc_labels[(arr_offset[:,0] == 0) & (arr_offset[:,1] != 0)] = doc_labels

    return encoded_labels

# return the encoded labels
train_labels = encode_tags(train_tags, train_encodings)
val_labels = encode_tags(val_tags, val_encodings)
test_labels = encode_tags(test_tags, test_encodings)

The error message is below:

ValueError                                Traceback (most recent call last)
<ipython-input-18-7290e6aeda9c> in <module>()
     18 # return the encoded labels
---> 19 train_labels = encode_tags(train_tags, train_encodings)
     20 val_labels = encode_tags(val_tags, val_encodings)
     21 test_labels = encode_tags(test_tags, test_encodings)

<ipython-input-18-7290e6aeda9c> in encode_tags(tags, encodings)
     12         # set labels whose first offset position is 0 and the second is not 0
---> 13         doc_enc_labels[(arr_offset[:,0] == 0) & (arr_offset[:,1] != 0)] = doc_labels
     14         encoded_labels.append(doc_enc_labels.tolist())

ValueError: NumPy boolean array indexing assignment cannot assign 236 input values to the 120 output values where the mask is true

I am not sure where my error is, as I have tried to replicate what is in the tutorial.


I have the same problem, maybe because of the training data problem, you can try to UTF-8 encoding to UTF-8-SIG

raw_text = file_path.read_text(encoding='UTF-8-sig').strip()

Because UTF-8 may cause an extra \ufeff character in the encoded data

I get this same error, and changing from utf-8 to utf-8-sig didn’t solve it…

Also having this problem…

Not sure if this is related to the problem, but I do not believe that this code is correct.

A Path does not have an encoding - it is just a path, not the contents of that path. However, when trying to read the file from that Path, you can provide the encoding. So the correct code should be:

def read_wnut(file_path):
    file_path = Path(file_path)

    raw_text = file_path.read_text(encoding='utf8').strip()

In case it helps anyone, the cause of this problem in my case was zero-width space characters and other non-standard UTF8 characters.

You can detect them as follows

for char in text:
    if ord(char) > 255:
        *possibly problematic char*

Some of them you might want to normalise, others you might want to keep. I’m not sure exactly which ones break the encoding, but it was certainly more than one specific char in my case.

I have tried this and found some problematic characters and after removing sentences having such characters, I’m still facing the same NumPy boolean issue.