MaartenGr / MaartenGr/BERTopic

ValueError: Distance matrix cannot contain negative values

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Description

First off, massive congrats and a huge thank you for the library - I can't even express in words how good it is ;)

I'm working on a fairly large (~388k) multilingual dataset and am encountering a strange error when calculating the hierarchical topics relate to the distance matrix.

Here is my code:

`texts = data['text'].astype(str).to_list()
ids = data.index.to_list()

sentence_model = SentenceTransformer("paraphrase-multilingual-MiniLM-L12-v2", cache_folder=cache_folder)
embeddings = sentence_model.encode(texts, show_progress_bar=True)
np.save(f'{results_path}/embeddings', embeddings)

umap_model = UMAP(
n_neighbors=100,
n_components=5,
min_dist=0.01,
metric="cosine",
low_memory=True,
n_jobs=5,
random_state=42,
)

sws = list(get_stopwords(language='multi'))
vectorizer_model = CountVectorizer(stop_words=sws, ngram_range=(1,2), min_df=10)

bertopic_args = {
"language":'multilingual',
"embedding_model": sentence_model,
"vectorizer_model": vectorizer_model,
"umap_model": umap_model,
"verbose":True,
"low_memory":True,
"calculate_probabilities":False,
}
bertopic_model = BERTopic(**bertopic_args)
topic, probs = bertopic_model.fit_transform(texts, embeddings)
test_tuned = bertopic_model.get_topic_info()

data['topic'] = topic
hierarchical_topics = bertopic_model.hierarchical_topics(texts)
`

Here the error I get:

ValueError                                Traceback (most recent call last)
File <timed exec>:2

File....../lib/python3.11/site-packages/bertopic/_bertopic.py:939, in BERTopic.hierarchical_topics(self, docs, linkage_function, distance_function)
    937 embeddings = self.c_tf_idf_[self._outliers:]
    938 X = distance_function(embeddings)
--> 939 X = validate_distance_matrix(X, embeddings.shape[0])
    941 # Use the 1-D condensed distance matrix as an input instead of the raw distance matrix
    942 Z = linkage_function(X)

File ..../lib/python3.11/site-packages/bertopic/_utils.py:141, in validate_distance_matrix(X, n_samples)
    139 # Make sure its entries are non-negative
    140 if np.any(X < 0):
--> 141     raise ValueError("Distance matrix cannot contain negative values.")
    143 return X

ValueError: Distance matrix cannot contain negative values.

This code works fine for all the other datasets I've used it on.

Am I doing something wrong, or is there some issue?

Contributor guide

Open the contributing guide

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by reproducing the report with the supplied BERTopic, UMAP, CountVectorizer, and embedding setup. Trace BERTopic.hierarchical_topics in bertopic/_bertopic.py into validate_distance_matrix in bertopic/_utils.py and inspect the distance matrix produced for this dataset. Done means the cause of the negative values is identified and hierarchical_topics handles the reported case without raising this error.

Written by the indexing model from the issue text.

Assessment

Tech stack
numpy, python, scikit-learn
Domain
data, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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