PubMedBERT Embeddings

This is a PubMedBERT-base model fined-tuned using sentence-transformers. It maps sentences & paragraphs to a 768 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.

PubMedBERT Embeddings produces higher quality embeddings than generalized models for medical literature. Further fine-tuning for a medical subdomain will result in even better performance.

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/pubmedbert-base-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/pubmedbert-base-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/pubmedbert-base-embeddings")
model = AutoModel.from_pretrained("neuml/pubmedbert-base-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.

Training

The model was trained with the parameters:

DataLoader:

torch.utils.data.dataloader.DataLoader of length 20191 with parameters:

{'batch_size': 24, 'sampler': 'torch.utils.data.sampler.RandomSampler', 'batch_sampler': 'torch.utils.data.sampler.BatchSampler'}

Loss:

sentence_transformers.losses.MultipleNegativesRankingLoss.MultipleNegativesRankingLoss with parameters:

{'scale': 20.0, 'similarity_fct': 'cos_sim'}

Parameters of the fit() method:

{
    "epochs": 1,
    "evaluation_steps": 500,
    "evaluator": "sentence_transformers.evaluation.EmbeddingSimilarityEvaluator.EmbeddingSimilarityEvaluator",
    "max_grad_norm": 1,
    "optimizer_class": "<class 'torch.optim.adamw.AdamW'>",
    "optimizer_params": {
        "lr": 2e-05
    },
    "scheduler": "WarmupLinear",
    "steps_per_epoch": null,
    "warmup_steps": 10000,
    "weight_decay": 0.01
}

Full Model Architecture

SentenceTransformer(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Pooling({'word_embedding_dimension': 768, 'pooling_mode_cls_token': False, 'pooling_mode_mean_tokens': True, 'pooling_mode_max_tokens': False, 'pooling_mode_mean_sqrt_len_tokens': False})
)

More Information

Read more about PubMedBERT Embeddings in this article and this paper.