Common Pile v0.1 Filtered Data
Collection
An LLM pre-training dataset produced by filtering and deduplicating the raw text collected in the Common Pile v0.1 • 31 items • Updated • 23
added string | created string | id string | metadata dict | source string | text string |
|---|---|---|---|---|---|
2024-06-05T03:55:45.923570 | 2003-8-18 | PMC176545 | {
"authors": [
{
"first": "Zbynek",
"last": "Bozdech"
},
{
"first": "Manuel",
"last": "Llinás"
},
{
"first": "Brian Lee",
"last": "Pulliam"
},
{
"first": "Edith D",
"last": "Wong"
},
{
"first": "Jingchun",
"last": "Zhu"
... | PubMed Central | Human malaria is caused by four species of the parasitic protozoan genus *Plasmodium*. Of these four species, Plasmodium falciparum is responsible for the vast majority of the 300--500 million episodes of malaria worldwide and accounts for 0.7--2.7 million annual deaths. In many endemic countries, malaria is responsibl... |
2024-06-05T03:55:45.929301 | 2003-8-18 | PMC176546 | {
"authors": [
{
"first": "Prithiviraj",
"last": "Fernando"
},
{
"first": "T. N. C",
"last": "Vidya"
},
{
"first": "John",
"last": "Payne"
},
{
"first": "Michael",
"last": "Stuewe"
},
{
"first": "Geoffrey",
"last": "Daviso... | PubMed Central | Elephants have a very limited distribution in Borneo, being restricted to approximately 5% of the island in the extreme northeast ([Figure 1](#pbio-0000006-g001){ref-type="fig"}). There are no historical records of elephants outside of this range. Fossil evidence for the prehistoric presence of elephants on Borneo is l... |
2024-06-05T03:55:45.932000 | 2003-8-18 | PMC176547 | {
"authors": [],
"journal": "PLoS Biol. 2003 Oct 18; 1(1):e7",
"license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/",
"provenance": "licensed_pubmed-0000.json.gz:3",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC176547/"
} | PubMed Central | A new study settles a long-standing dispute about the genesis of an endangered species. With scant fossil evidence supporting a prehistoric presence, scientists could not say for sure where Borneo\'s elephants came from. Did they descend from ancient prototypes of the Pleistocene era or from modern relatives introduced... |
2024-06-05T03:55:45.932467 | 2003-8-18 | PMC176548 | {
"authors": [],
"journal": "PLoS Biol. 2003 Oct 18; 1(1):e11",
"license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/",
"provenance": "licensed_pubmed-0000.json.gz:4",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC176548/"
} | PubMed Central | Every year, malaria kills as many as 2.5 million people. Of these deaths, 90% occur in sub-Saharan Africa, and most are children. While four species of the single-celled organism Plasmodium cause malaria, Plasmodium falciparum is the deadliest. Harbored in mosquito saliva, the parasite infects its human host as the mos... |
2024-06-05T03:55:45.933052 | 2003-9-15 | PMC193604 | {
"authors": [
{
"first": "Ying",
"last": "Peng"
},
{
"first": "Dan",
"last": "Stoleru"
},
{
"first": "Joel D",
"last": "Levine"
},
{
"first": "Jeffrey C",
"last": "Hall"
},
{
"first": "Michael",
"last": "Rosbash"
}
... | PubMed Central | Circadian rhythms of diverse organisms are based on similar intracellular molecular feedback loops ([@pbio-0000013-Dunlap1]; [@pbio-0000013-Allada2]; [@pbio-0000013-Panda1]). Based on this view, it is believed that one or a small number of clock cells are sufficient for self-sustained rhythms ([@pbio-0000013-Dunlap1]).... |
2024-06-05T03:55:45.935792 | 2003-9-15 | PMC193605 | {
"authors": [
{
"first": "Emmanuelle",
"last": "Lerat"
},
{
"first": "Vincent",
"last": "Daubin"
},
{
"first": "Nancy A",
"last": "Moran"
}
],
"journal": "PLoS Biol. 2003 Oct 15; 1(1):e19",
"license": "Creative Commons - Attribution - https://creative... | PubMed Central | The availability of complete sequences of genomes for clusters of related organisms presents the first opportunity to reconstruct events of genomic evolution. By comparing related genomes and inferring ancestral ones, we can identify events, such as specific chromosomal rearrangements, gene acquisitions, duplications, ... |
2024-06-05T03:55:45.939512 | 2003-9-15 | PMC193606 | {
"authors": [],
"journal": "PLoS Biol. 2003 Oct 15; 1(1):e23",
"license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/",
"provenance": "licensed_pubmed-0000.json.gz:7",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC193606/"
} | PubMed Central | How do people subjected to the endless dark days of winter in the far northern latitudes maintain normal daily rhythms? Though many might feel like hibernating, a highly regulated internal system keeps such impractical yearnings in check. From fruit flies to humans, nearly every living organism depends on an internal c... |
2024-06-05T03:55:45.940002 | 2003-9-15 | PMC193607 | {
"authors": [],
"journal": "PLoS Biol. 2003 Oct 15; 1(1):e31",
"license": "Creative Commons - Attribution - https://creativecommons.org/licenses/by/4.0/",
"provenance": "licensed_pubmed-0000.json.gz:8",
"url": "https://www.ncbi.nlm.nih.gov/pmc/articles/PMC193607/"
} | PubMed Central | Bacteria are an indiscriminate lot. While most organisms tend to pass their genes on to the next generation of their species, bacteria often exchange genetic material with totally unrelated species. That is why skeptics doubted that bacteria researchers could ever hope to map a reliable history of cell lineages in bact... |
2024-06-05T03:55:45.940651 | 2003-9-11 | PMC212319 | {"authors":[{"first":"Hai-Sheng","last":"Li"},{"first":"Kuntala","last":"Shome"},{"first":"Raúl","l(...TRUNCATED) | PubMed Central | "Small GTPases of the ADP-ribosylation factor (ARF) family play a major role in membrane trafficking(...TRUNCATED) |
2024-06-05T03:55:45.943420 | 2003-10-13 | PMC212687 | {"authors":[{"first":"Alfred Ian","last":"Lee"},{"first":"Sebastian D","last":"Fugmann"},{"first":"L(...TRUNCATED) | PubMed Central | "During B- and T-lymphocyte development, the immunoglobulin (Ig) and T-cell receptor (TCR) genes are(...TRUNCATED) |
End of preview. Expand in Data Studio
PubMed
Description
PubMed Central is an open-access archive of biomedical and life sciences research papers maintained by the U.S. National Institutes of Health’s National Library of Medicine.
We collected papers from PubMed whose metadata indicated that the publishing journal had designated a CC BY, CC BY-SA, or CC0 license.
PubMed stores the text content of each article as a single nXML file, which we convert to markdown using pandoc.
Per-document license information is available in the license entry of the metadata field of each example.
Code for collecting, processing, and preparing this dataset is available in the common-pile GitHub repo.
Dataset Statistics
| Documents | UTF-8 GB |
|---|---|
| 3,829,689 | 147.1 |
License Issues
While we aim to produce datasets with completely accurate licensing information, license laundering and inaccurate metadata can cause us to erroneously assign the incorrect license to some documents (for further discussion of this limitation, please see our paper). If you believe you have found an instance of incorrect licensing in this dataset, please start a discussion on this repository.
Other Versions
This is the "filtered" version of the PubMed dataset. If you are looking for the raw version, you can find it here.
Citation
If you use this dataset, please cite:
@article{kandpal2025common,
title={{The Common Pile v0.1: An 8TB Dataset of Public Domain and Openly Licensed Text}},
author={Nikhil Kandpal and Brian Lester and Colin Raffel and Sebastian Majstorovic and Stella Biderman and Baber Abbasi and Luca Soldaini and Enrico Shippole and A. Feder Cooper and Aviya Skowron and Shayne Longpre and Lintang Sutawika and Alon Albalak and Zhenlin Xu and Guilherme Penedo and Loubna Ben and Elie Bakouch and John David and Honglu Fan and Dashiell Stander and Guangyu Song and Aaron Gokaslan and John Kirchenbauer and Tom Goldstein and Brian R and Bhavya Kailkhura and Tyler Murray},
journal={arXiv preprint},
year={2025}
}
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