For ElMo, FastText and Word2Vec, I'm averaging the word embeddings within a sentence and using HDBSCAN/KMeans clustering to group similar sentences.

A good example of the implementation can be seen in this short article: http://ai.intelligentonlinetools.com/ml/text-clustering-word-embedding-machine-learning/

I would like to do the same thing using BERT (using the BERT python package from hugging face), however I am rather unfamiliar with how to extract the raw word/sentence vectors in order to input them into a clustering algorithm. I know that BERT can output sentence representations - so how would I actually extract the raw vectors from a sentence?

Any information would be helpful.

As Subham Kumar mentioned, one can use this Python 3 library to compute sentence similarity: https://github.com/UKPLab/sentence-transformers

The library has a few code examples to perform clustering:

fast_clustering.py:

"""
This is a more complex example on performing clustering on large scale dataset.

This examples find in a large set of sentences local communities, i.e., groups of sentences that are highly
similar. You can freely configure the threshold what is considered as similar. A high threshold will
only find extremely similar sentences, a lower threshold will find more sentence that are less similar.

A second parameter is 'min_community_size': Only communities with at least a certain number of sentences will be returned.

The method for finding the communities is extremely fast, for clustering 50k sentences it requires only 5 seconds (plus embedding comuptation).

In this example, we download a large set of questions from Quora and then find similar questions in this set.
"""
from sentence_transformers import SentenceTransformer, util
import os
import csv
import time


# Model for computing sentence embeddings. We use one trained for similar questions detection
model = SentenceTransformer('paraphrase-MiniLM-L6-v2')

# We donwload the Quora Duplicate Questions Dataset (https://www.quora.com/q/quoradata/First-Quora-Dataset-Release-Question-Pairs)
# and find similar question in it
url = "http://qim.fs.quoracdn.net/quora_duplicate_questions.tsv"
dataset_path = "quora_duplicate_questions.tsv"
max_corpus_size = 50000 # We limit our corpus to only the first 50k questions


# Check if the dataset exists. If not, download and extract
# Download dataset if needed
if not os.path.exists(dataset_path):
    print("Download dataset")
    util.http_get(url, dataset_path)

# Get all unique sentences from the file
corpus_sentences = set()
with open(dataset_path, encoding='utf8') as fIn:
    reader = csv.DictReader(fIn, delimiter='\t', quoting=csv.QUOTE_MINIMAL)
    for row in reader:
        corpus_sentences.add(row['question1'])
        corpus_sentences.add(row['question2'])
        if len(corpus_sentences) >= max_corpus_size:
            break

corpus_sentences = list(corpus_sentences)
print("Encode the corpus. This might take a while")
corpus_embeddings = model.encode(corpus_sentences, batch_size=64, show_progress_bar=True, convert_to_tensor=True)


print("Start clustering")
start_time = time.time()

#Two parameters to tune:
#min_cluster_size: Only consider cluster that have at least 25 elements
#threshold: Consider sentence pairs with a cosine-similarity larger than threshold as similar
clusters = util.community_detection(corpus_embeddings, min_community_size=25, threshold=0.75)

print("Clustering done after {:.2f} sec".format(time.time() - start_time))

#Print for all clusters the top 3 and bottom 3 elements
for i, cluster in enumerate(clusters):
    print("\nCluster {}, #{} Elements ".format(i+1, len(cluster)))
    for sentence_id in cluster[0:3]:
        print("\t", corpus_sentences[sentence_id])
    print("\t", "...")
    for sentence_id in cluster[-3:]:
        print("\t", corpus_sentences[sentence_id])

kmeans.py:

"""
This is a simple application for sentence embeddings: clustering

Sentences are mapped to sentence embeddings and then k-mean clustering is applied.
"""
from sentence_transformers import SentenceTransformer
from sklearn.cluster import KMeans

embedder = SentenceTransformer('paraphrase-MiniLM-L6-v2')

# Corpus with example sentences
corpus = ['A man is eating food.',
          'A man is eating a piece of bread.',
          'A man is eating pasta.',
          'The girl is carrying a baby.',
          'The baby is carried by the woman',
          'A man is riding a horse.',
          'A man is riding a white horse on an enclosed ground.',
          'A monkey is playing drums.',
          'Someone in a gorilla costume is playing a set of drums.',
          'A cheetah is running behind its prey.',
          'A cheetah chases prey on across a field.'
          ]
corpus_embeddings = embedder.encode(corpus)

# Perform kmean clustering
num_clusters = 5
clustering_model = KMeans(n_clusters=num_clusters)
clustering_model.fit(corpus_embeddings)
cluster_assignment = clustering_model.labels_

clustered_sentences = [[] for i in range(num_clusters)]
for sentence_id, cluster_id in enumerate(cluster_assignment):
    clustered_sentences[cluster_id].append(corpus[sentence_id])

for i, cluster in enumerate(clustered_sentences):
    print("Cluster ", i+1)
    print(cluster)
    print("")

agglomerative.py:

"""
This is a simple application for sentence embeddings: clustering

Sentences are mapped to sentence embeddings and then agglomerative clustering with a threshold is applied.
"""
from sentence_transformers import SentenceTransformer
from sklearn.cluster import AgglomerativeClustering
import numpy as np

embedder = SentenceTransformer('paraphrase-MiniLM-L6-v2')

# Corpus with example sentences
corpus = ['A man is eating food.',
          'A man is eating a piece of bread.',
          'A man is eating pasta.',
          'The girl is carrying a baby.',
          'The baby is carried by the woman',
          'A man is riding a horse.',
          'A man is riding a white horse on an enclosed ground.',
          'A monkey is playing drums.',
          'Someone in a gorilla costume is playing a set of drums.',
          'A cheetah is running behind its prey.',
          'A cheetah chases prey on across a field.'
          ]
corpus_embeddings = embedder.encode(corpus)

# Normalize the embeddings to unit length
corpus_embeddings = corpus_embeddings /  np.linalg.norm(corpus_embeddings, axis=1, keepdims=True)

# Perform kmean clustering
clustering_model = AgglomerativeClustering(n_clusters=None, distance_threshold=1.5) #, affinity='cosine', linkage='average', distance_threshold=0.4)
clustering_model.fit(corpus_embeddings)
cluster_assignment = clustering_model.labels_

clustered_sentences = {}
for sentence_id, cluster_id in enumerate(cluster_assignment):
    if cluster_id not in clustered_sentences:
        clustered_sentences[cluster_id] = []

    clustered_sentences[cluster_id].append(corpus[sentence_id])

for i, cluster in clustered_sentences.items():
    print("Cluster ", i+1)
    print(cluster)
    print("")