PubMedBERT ColBERT

This is a PyLate model finetuned from microsoft/BiomedNLP-BiomedBERT-base-uncased-abstract-fulltext. It maps sentences & paragraphs to sequences of 128-dimensional dense vectors and can be used for semantic textual similarity using the MaxSim operator.

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).

Note: txtai 9.0+ is required for late interaction model support

import txtai

embeddings = txtai.Embeddings(
  path="neuml/pubmedbert-base-colbert",
  content=True
)
embeddings.index(documents())

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

Late interaction models excel as reranker pipelines.

from txtai.pipeline import Reranker, Similarity

similarity = Similarity(path="neuml/pubmedbert-base-colbert", lateencode=True)
ranker = Reranker(embeddings, similarity)
ranker("query to run")

Usage (PyLate)

Alternatively, the model can be loaded with PyLate.

from pylate import rank, models

queries = [
    "query A",
    "query B",
]

documents = [
    ["document A", "document B"],
    ["document 1", "document C", "document B"],
]

documents_ids = [
    [1, 2],
    [1, 3, 2],
]

model = models.ColBERT(
    model_name_or_path=pylate_model_id,
)

queries_embeddings = model.encode(
    queries,
    is_query=True,
)

documents_embeddings = model.encode(
    documents,
    is_query=False,
)

reranked_documents = rank.rerank(
    documents_ids=documents_ids,
    queries_embeddings=queries_embeddings,
    documents_embeddings=documents_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.

Model	PubMed QA	PubMed Subset	PubMed Summary	Average
all-MiniLM-L6-v2	90.40	95.92	94.07	93.46
bge-base-en-v1.5	91.02	95.82	94.49	93.78
gte-base	92.97	96.90	96.24	95.37
pubmedbert-base-colbert	93.94	97.21	95.27	95.47
pubmedbert-base-colbert (MUVERA)	88.77	93.51	95.18	92.49
pubmedbert-base-embeddings	93.27	97.00	96.58	95.62
S-PubMedBert-MS-MARCO	90.86	93.68	93.54	92.69

While this isn't the highest scoring model, note how it is the best model for the first two datasets, which are retrieval datasets. ColBERT models can be better at picking up on query nuances given that vectors are not mean pooled together.

The model also performs well enough for MUVERA encoding. The goal with MUVERA is "good enough" recall that picks up on the signal and is then paired with a reranker pipeline.

Full Model Architecture

ColBERT(
  (0): Transformer({'max_seq_length': 512, 'do_lower_case': False}) with Transformer model: BertModel 
  (1): Dense({'in_features': 768, 'out_features': 128, 'bias': False, 'activation_function': 'torch.nn.modules.linear.Identity'})
)