Datasets:
pmid int64 21 2.74M | embedding list | text_sha256 stringlengths 64 64 | pub_year int16 1.98k 1.99k | pub_month int8 | raw_token_count int32 18 1.14k | used_token_count int32 18 512 | was_truncated bool 2
classes |
|---|---|---|---|---|---|---|---|
21 | [
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0... | fbb8aee1cd9f88b10e871b57cd847014b1ab5ed8af59c336dfe4e14df68bd149 | 1,975 | null | 135 | 135 | false |
22 | [
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23 | [
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24 | [
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0... | 5757090f3b9cf6bd5887b4cc2565cf2315cd25ed5b771088e5ad13228bba116c | 1,975 | null | 171 | 171 | false |
25 | [
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0.026... | e4204c7ad849377c5384df2c25df79bb350c4f7c18e14a5b5c07e8c4d53934a6 | 1,975 | null | 388 | 388 | false |
26 | [
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0.011594714596867561,
0.... | 10acd6e09f902b4129fa723f6e4154c15540a8425361bc5bb516b35124cded8a | 1,975 | null | 396 | 396 | false |
30 | [
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... | 65870d8470c42c03909f61a0c26117833527286e9c0e26a9bea3015f5e92bc62 | 1,975 | null | 90 | 90 | false |
31 | [
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0.0008943627472035587,
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... | 17e794b95c65cfa8ff2a13ad432b27cd1ee35925de5d611b14e494bbe48e90c6 | 1,975 | null | 66 | 66 | false |
32 | [
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0.020369531586766243,
0.06928080320358276,
0.022565050050616264,
-0.017... | 464213cc967cae2431760c2a4df4b19c0b0faa2aac0c9d63263ffa42a6eb2eac | 1,975 | null | 100 | 100 | false |
33 | [
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0.022433707490563393,
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0.041697435081005096,
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0.010302436538040638,
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-0... | e3a269232b4bf0bc6f7476f6d2fc6b41d5648df209ad240b114fff8ebb62c655 | 1,975 | null | 179 | 179 | false |
35 | [
0.008557886816561222,
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0.024817870929837227,
0.014487279579043388,
0.026407193392515182,
0.00984156969934702,
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0.03594312444329262,
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0.02836328186094761,
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... | 7ca4c26a356cfd3747e74b9e45a816955954a5a6e5ddc8af8a5b84165bb216df | 1,975 | null | 99 | 99 | false |
36 | [
0.010201135650277138,
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0.019424917176365852,
0.01685936190187931,
0.025044703856110573,
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0.05473184213042259,
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0.001244599581696093,
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0.004947856068611145,
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-... | f3bc96cc129be1bc40af1d3f13a81674160c8aeaca35bd2424d45f738bf743c5 | 1,975 | null | 285 | 285 | false |
End of preview. Expand in Data Studio
PubMed Embedding Vectors
This dataset contains embedding vectors generated from local PubMed title and abstract text. It is designed for biomedical retrieval and nearest-neighbor research.
The public files intentionally do not include PubMed titles, abstracts, or full text. Rows contain PMIDs, embeddings, hashes, and lightweight metadata so researchers can join against their own authorized PubMed mirror or the official NCBI/PubMed services.
Configs
| Config | Model | Dim | Rows | Qdrant collection |
|---|---|---|---|---|
| neuml_pubmedbert_base_embeddings | NeuML/pubmedbert-base-embeddings |
768 | 28,460,827 | pubmed_emb_neuml_pubmedbert_base_embeddings_ddbc790c |
| qwen3_embedding_0_6b | Qwen/Qwen3-Embedding-0.6B |
1024 | 28,460,827 | pubmed_emb_qwen_qwen3_embedding_0_6b_cdca07b0 |
Columns
pmid: PubMed identifier.embedding: fixed-size embedding vector for the selected config.text_sha256: SHA-256 of the local title+abstract text used for embedding, when available.pub_year,pub_month: publication date metadata, when available.raw_token_count,used_token_count,was_truncated: embedding input token metadata, when available.
Usage
from datasets import load_dataset
repo_id = "aaekay/pubmed-embedding"
ds = load_dataset(repo_id, "qwen3_embedding_0_6b", split="train", streaming=True)
row = next(iter(ds))
print(row["pmid"], len(row["embedding"]))
Use the PMID to retrieve citation details from PubMed:
pmid = row["pmid"]
url = f"https://pubmed.ncbi.nlm.nih.gov/{pmid}/"
Source And Redistribution Notes
- Source records come from a local PubMed baseline/update mirror.
- NLM notes that PubMed abstracts may be protected by third-party copyright, so this dataset excludes article titles, abstracts, and full text.
- The generated embedding dataset is released as
cc-by-4.0; upstream PubMed records and embedding models remain subject to their own terms.
Relevant upstream documentation:
- PubMed download page: https://pubmed.ncbi.nlm.nih.gov/download/
- NLM copyright information: https://www.nlm.nih.gov/databases/download.html
- Hugging Face large repository guidance: https://huggingface.co/docs/hub/storage-limits
Manifest
Export metadata, shard checksums, and source collection details are stored in
metadata/manifest.json. The public schema is stored in metadata/schema.json.
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