ner_transformers.ipynb

Kernel: Python 3

Named Entity Recognition using Transformers

Author: Varun Singh
Date created: 2021/06/23
Last modified: 2024/04/05
Description: NER using the Transformers and data from CoNLL 2003 shared task.

Introduction

Named Entity Recognition (NER) is the process of identifying named entities in text. Example of named entities are: "Person", "Location", "Organization", "Dates" etc. NER is essentially a token classification task where every token is classified into one or more predetermined categories.

In this exercise, we will train a simple Transformer based model to perform NER. We will be using the data from CoNLL 2003 shared task. For more information about the dataset, please visit the dataset website. However, since obtaining this data requires an additional step of getting a free license, we will be using HuggingFace's datasets library which contains a processed version of this dataset.

Install the open source datasets library from HuggingFace

We also download the script used to evaluate NER models.

!pip3 install datasets
!wget https://raw.githubusercontent.com/sighsmile/conlleval/master/conlleval.py

import os

os.environ["KERAS_BACKEND"] = "tensorflow"

import keras
from keras import ops
import numpy as np
import tensorflow as tf
from keras import layers
from datasets import load_dataset
from collections import Counter
from conlleval import evaluate

We will be using the transformer implementation from this fantastic example.

Let's start by defining a TransformerBlock layer:

class TransformerBlock(layers.Layer):
    def __init__(self, embed_dim, num_heads, ff_dim, rate=0.1):
        super().__init__()
        self.att = keras.layers.MultiHeadAttention(
            num_heads=num_heads, key_dim=embed_dim
        )
        self.ffn = keras.Sequential(
            [
                keras.layers.Dense(ff_dim, activation="relu"),
                keras.layers.Dense(embed_dim),
            ]
        )
        self.layernorm1 = keras.layers.LayerNormalization(epsilon=1e-6)
        self.layernorm2 = keras.layers.LayerNormalization(epsilon=1e-6)
        self.dropout1 = keras.layers.Dropout(rate)
        self.dropout2 = keras.layers.Dropout(rate)

    def call(self, inputs, training=False):
        attn_output = self.att(inputs, inputs)
        attn_output = self.dropout1(attn_output, training=training)
        out1 = self.layernorm1(inputs + attn_output)
        ffn_output = self.ffn(out1)
        ffn_output = self.dropout2(ffn_output, training=training)
        return self.layernorm2(out1 + ffn_output)

Next, let's define a TokenAndPositionEmbedding layer:

class TokenAndPositionEmbedding(layers.Layer):
    def __init__(self, maxlen, vocab_size, embed_dim):
        super().__init__()
        self.token_emb = keras.layers.Embedding(
            input_dim=vocab_size, output_dim=embed_dim
        )
        self.pos_emb = keras.layers.Embedding(input_dim=maxlen, output_dim=embed_dim)

    def call(self, inputs):
        maxlen = ops.shape(inputs)[-1]
        positions = ops.arange(start=0, stop=maxlen, step=1)
        position_embeddings = self.pos_emb(positions)
        token_embeddings = self.token_emb(inputs)
        return token_embeddings + position_embeddings

Build the NER model class as a keras.Model subclass

class NERModel(keras.Model):
    def __init__(
        self, num_tags, vocab_size, maxlen=128, embed_dim=32, num_heads=2, ff_dim=32
    ):
        super().__init__()
        self.embedding_layer = TokenAndPositionEmbedding(maxlen, vocab_size, embed_dim)
        self.transformer_block = TransformerBlock(embed_dim, num_heads, ff_dim)
        self.dropout1 = layers.Dropout(0.1)
        self.ff = layers.Dense(ff_dim, activation="relu")
        self.dropout2 = layers.Dropout(0.1)
        self.ff_final = layers.Dense(num_tags, activation="softmax")

    def call(self, inputs, training=False):
        x = self.embedding_layer(inputs)
        x = self.transformer_block(x)
        x = self.dropout1(x, training=training)
        x = self.ff(x)
        x = self.dropout2(x, training=training)
        x = self.ff_final(x)
        return x

Load the CoNLL 2003 dataset from the datasets library and process it

conll_data = load_dataset("conll2003")

We will export this data to a tab-separated file format which will be easy to read as a tf.data.Dataset object.

def export_to_file(export_file_path, data):
    with open(export_file_path, "w") as f:
        for record in data:
            ner_tags = record["ner_tags"]
            tokens = record["tokens"]
            if len(tokens) > 0:
                f.write(
                    str(len(tokens))
                    + "\t"
                    + "\t".join(tokens)
                    + "\t"
                    + "\t".join(map(str, ner_tags))
                    + "\n"
                )


os.mkdir("data")
export_to_file("./data/conll_train.txt", conll_data["train"])
export_to_file("./data/conll_val.txt", conll_data["validation"])

Make the NER label lookup table

NER labels are usually provided in IOB, IOB2 or IOBES formats. Checkout this link for more information: Wikipedia

Note that we start our label numbering from 1 since 0 will be reserved for padding. We have a total of 10 labels: 9 from the NER dataset and one for padding.

def make_tag_lookup_table():
    iob_labels = ["B", "I"]
    ner_labels = ["PER", "ORG", "LOC", "MISC"]
    all_labels = [(label1, label2) for label2 in ner_labels for label1 in iob_labels]
    all_labels = ["-".join([a, b]) for a, b in all_labels]
    all_labels = ["[PAD]", "O"] + all_labels
    return dict(zip(range(0, len(all_labels) + 1), all_labels))


mapping = make_tag_lookup_table()
print(mapping)

Get a list of all tokens in the training dataset. This will be used to create the vocabulary.

all_tokens = sum(conll_data["train"]["tokens"], [])
all_tokens_array = np.array(list(map(str.lower, all_tokens)))

counter = Counter(all_tokens_array)
print(len(counter))

num_tags = len(mapping)
vocab_size = 20000

# We only take (vocab_size - 2) most commons words from the training data since
# the `StringLookup` class uses 2 additional tokens - one denoting an unknown
# token and another one denoting a masking token
vocabulary = [token for token, count in counter.most_common(vocab_size - 2)]

# The StringLook class will convert tokens to token IDs
lookup_layer = keras.layers.StringLookup(vocabulary=vocabulary)

Create 2 new Dataset objects from the training and validation data

train_data = tf.data.TextLineDataset("./data/conll_train.txt")
val_data = tf.data.TextLineDataset("./data/conll_val.txt")

Print out one line to make sure it looks good. The first record in the line is the number of tokens. After that we will have all the tokens followed by all the ner tags.

print(list(train_data.take(1).as_numpy_iterator()))

We will be using the following map function to transform the data in the dataset:

def map_record_to_training_data(record):
    record = tf.strings.split(record, sep="\t")
    length = tf.strings.to_number(record[0], out_type=tf.int32)
    tokens = record[1 : length + 1]
    tags = record[length + 1 :]
    tags = tf.strings.to_number(tags, out_type=tf.int64)
    tags += 1
    return tokens, tags


def lowercase_and_convert_to_ids(tokens):
    tokens = tf.strings.lower(tokens)
    return lookup_layer(tokens)


# We use `padded_batch` here because each record in the dataset has a
# different length.
batch_size = 32
train_dataset = (
    train_data.map(map_record_to_training_data)
    .map(lambda x, y: (lowercase_and_convert_to_ids(x), y))
    .padded_batch(batch_size)
)
val_dataset = (
    val_data.map(map_record_to_training_data)
    .map(lambda x, y: (lowercase_and_convert_to_ids(x), y))
    .padded_batch(batch_size)
)

ner_model = NERModel(num_tags, vocab_size, embed_dim=32, num_heads=4, ff_dim=64)

We will be using a custom loss function that will ignore the loss from padded tokens.

class CustomNonPaddingTokenLoss(keras.losses.Loss):
    def __init__(self, name="custom_ner_loss"):
        super().__init__(name=name)

    def call(self, y_true, y_pred):
        loss_fn = keras.losses.SparseCategoricalCrossentropy(
            from_logits=False, reduction=None
        )
        loss = loss_fn(y_true, y_pred)
        mask = ops.cast((y_true > 0), dtype="float32")
        loss = loss * mask
        return ops.sum(loss) / ops.sum(mask)


loss = CustomNonPaddingTokenLoss()

Compile and fit the model

tf.config.run_functions_eagerly(True)
ner_model.compile(optimizer="adam", loss=loss)
ner_model.fit(train_dataset, epochs=10)


def tokenize_and_convert_to_ids(text):
    tokens = text.split()
    return lowercase_and_convert_to_ids(tokens)


# Sample inference using the trained model
sample_input = tokenize_and_convert_to_ids(
    "eu rejects german call to boycott british lamb"
)
sample_input = ops.reshape(sample_input, shape=[1, -1])
print(sample_input)

output = ner_model.predict(sample_input)
prediction = np.argmax(output, axis=-1)[0]
prediction = [mapping[i] for i in prediction]

# eu -> B-ORG, german -> B-MISC, british -> B-MISC
print(prediction)

Metrics calculation

Here is a function to calculate the metrics. The function calculates F1 score for the overall NER dataset as well as individual scores for each NER tag.

def calculate_metrics(dataset):
    all_true_tag_ids, all_predicted_tag_ids = [], []

    for x, y in dataset:
        output = ner_model.predict(x, verbose=0)
        predictions = ops.argmax(output, axis=-1)
        predictions = ops.reshape(predictions, [-1])

        true_tag_ids = ops.reshape(y, [-1])

        mask = (true_tag_ids > 0) & (predictions > 0)
        true_tag_ids = true_tag_ids[mask]
        predicted_tag_ids = predictions[mask]

        all_true_tag_ids.append(true_tag_ids)
        all_predicted_tag_ids.append(predicted_tag_ids)

    all_true_tag_ids = np.concatenate(all_true_tag_ids)
    all_predicted_tag_ids = np.concatenate(all_predicted_tag_ids)

    predicted_tags = [mapping[tag] for tag in all_predicted_tag_ids]
    real_tags = [mapping[tag] for tag in all_true_tag_ids]

    evaluate(real_tags, predicted_tags)


calculate_metrics(val_dataset)

Conclusions

In this exercise, we created a simple transformer based named entity recognition model. We trained it on the CoNLL 2003 shared task data and got an overall F1 score of around 70%. State of the art NER models fine-tuned on pretrained models such as BERT or ELECTRA can easily get much higher F1 score -between 90-95% on this dataset owing to the inherent knowledge of words as part of the pretraining process and the usage of subword tokenization.

You can use the trained model hosted on Hugging Face Hub and try the demo on Hugging Face Spaces."""