BiomedBERT Small Embeddings

This is a BiomedBERT Small model fined-tuned using sentence-transformers. It maps sentences & paragraphs to a 384 dimensional dense vector space and can be used for tasks like clustering or semantic search.

The training dataset was generated using a random sample of PubMed title-abstract pairs along with similar title pairs. The training workflow was a two step distillation process as follows.

• Distill embeddings from the larger pubmedbert-base-embeddings model using this model distillation script from Sentence Transformers.
• Build a distilled dataset of teacher scores using the biomedbert-base-reranker cross-encoder for a separate random sample of title-abstract pairs.
• Further fine-tune the model on the distilled dataset using KLDivLoss.

Usage (txtai)

This model can be used to build embeddings databases with txtai for semantic search and/or as a knowledge source for retrieval augmented generation (RAG).

import txtai

embeddings = txtai.Embeddings(path="neuml/biomedbert-small-embeddings", content=True)
embeddings.index(documents())

# Run a query
embeddings.search("query to run")

Usage (Sentence-Transformers)

Alternatively, the model can be loaded with sentence-transformers.

from sentence_transformers import SentenceTransformer
sentences = ["This is an example sentence", "Each sentence is converted"]

model = SentenceTransformer("neuml/biomedbert-small-embeddings")
embeddings = model.encode(sentences)
print(embeddings)

Usage (Hugging Face Transformers)

The model can also be used directly with Transformers.

from transformers import AutoTokenizer, AutoModel
import torch

# Mean Pooling - Take attention mask into account for correct averaging
def meanpooling(output, mask):
    embeddings = output[0] # First element of model_output contains all token embeddings
    mask = mask.unsqueeze(-1).expand(embeddings.size()).float()
    return torch.sum(embeddings * mask, 1) / torch.clamp(mask.sum(1), min=1e-9)

# Sentences we want sentence embeddings for
sentences = ['This is an example sentence', 'Each sentence is converted']

# Load model from HuggingFace Hub
tokenizer = AutoTokenizer.from_pretrained("neuml/biomedbert-small-embeddings")
model = AutoModel.from_pretrained("neuml/biomedbert-small-embeddings")

# Tokenize sentences
inputs = tokenizer(sentences, padding=True, truncation=True, return_tensors='pt')

# Compute token embeddings
with torch.no_grad():
    output = model(**inputs)

# Perform pooling. In this case, mean pooling.
embeddings = meanpooling(output, inputs['attention_mask'])

print("Sentence embeddings:")
print(embeddings)

Evaluation Results

Performance of this model compared to the top base models on the MTEB leaderboard is shown below. A popular smaller model was also evaluated along with the most downloaded PubMed similarity model on the Hugging Face Hub.

The following datasets were used to evaluate model performance.

• PubMed QA
  • Subset: pqa_labeled, Split: train, Pair: (question, long_answer)
• PubMed Subset
  • Split: test, Pair: (title, text)
• PubMed Summary
  • Subset: pubmed, Split: validation, Pair: (article, abstract)

Evaluation results are shown below. The Pearson correlation coefficient is used as the evaluation metric.

This model is a solid performer at a small size. It even beats the original PubMedBERT Embeddings model across the board at only 20% of the parameters. It also does much better than all-MiniLM-L6-v2, a commonly used small model which is roughly the same size.

This is a great model that can be used in CPU-only setups without trading off much on the accuracy front.

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False, 'architecture': 'BertModel'})
  (1): Pooling({'word_embedding_dimension': 384, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False, 'pooling_mode_weightedmean_tokens': False, 'pooling_mode_lasttoken': False, 'include_prompt': True})
)

More Information

Read more about the model in this article.