| --- |
| dataset_info: |
| features: |
| - name: Taxa |
| list: string |
| - name: Relative Abundances |
| list: float64 |
| - name: Run Accession |
| dtype: string |
| - name: Data Type |
| dtype: large_string |
| - name: Sequencing Method |
| dtype: large_string |
| - name: Pipeline Version |
| dtype: large_string |
| - name: Study Accession |
| dtype: large_string |
| splits: |
| - name: pretrain |
| num_bytes: 5027475729 |
| num_examples: 485377 |
| - name: benchmark |
| num_bytes: 557448072 |
| num_examples: 53931 |
| download_size: 5552785595 |
| dataset_size: 5584923801 |
| configs: |
| - config_name: default |
| data_files: |
| - split: pretrain |
| path: data/pretrain-* |
| - split: benchmark |
| path: data/benchmark-* |
| license: apache-2.0 |
| --- |
| |
| # Atlas |
|
|
| ## Dataset summary |
| See [our preprint](https://www.biorxiv.org/content/10.64898/2026.05.02.722381v1) for details |
|
|
| Join [our slack community](https://join.slack.com/t/outpostbio-waypoint/shared_invite/zt-3w6ivgtba-WJOCkdxiISxQpwVq9ZZxTA) for support and discussion about microbiome foundation models. |
|
|
| Each row is one sample. **Taxa** and **Relative Abundances** are aligned lists (same length per row): semicolon-separated rank strings for taxa, and matching relative abundances. Additional columns record data type, sequencing method, pipeline version, and study accession. |
|
|
| Data come from processed abundance matrices, filtered, then randomly split into **pretrain** (90%) and **benchmark** (10%) with `seed=42`. |
|
|
| ## Splits |
|
|
| | Split | Description | Num Examples | |
| |-------|-------------|-------------| |
| | `pretrain` | Pretraining subset. | 485377 | |
| | `benchmark` | Held-out benchmark subset. | 53931 | |
|
|
| ## Data fields |
|
|
| | Column | Type | Description | |
| |--------|------|-------------| |
| | Taxa | list of string | Taxon labels. | |
| | Relative Abundances | list of float | Relative abundances in the same order as Taxa. | |
| | Sample | string | Sample identifier, if present. | |
| | Data Type, Sequencing Method, Pipeline Version, Study Accession | string | Provenance metadata; exact set of columns matches the published Parquet schema. | |
|
|
| ## Filtering |
|
|
| Filtering used: |
| - `min_relative_abundance`: 0.0001 |
| - `min_num_taxa`: 10 |
|
|
| ## Usage |
| This repository is **gated**. To use it you'll need to: |
|
|
| 1. **Request access** — click the "Request access" button at the top of this repo's page on Hugging Face. Requests are auto-approved. |
| 2. **Authenticate** — log in to Hugging Face from your environment so the download tooling can use your token: |
|
|
| ```bash |
| huggingface-cli login |
| ``` |
|
|
| Or set the token directly: |
|
|
| ```bash |
| export HF_TOKEN=hf_xxxxxxxxxxxxxxxxxxxx |
| ``` |
|
|
| You can create a token at https://huggingface.co/settings/tokens. |
|
|
| Once both steps are done, you can load the model/dataset normally: |
|
|
| ```python |
| from datasets import load_dataset |
| |
| ds = load_dataset("outpost-bio/Atlas") |
| row = ds["pretrain"][0] |
| taxa = row["Taxa"] |
| abund = row["Relative Abundances"] |
| ``` |
|
|
| ## License |
| apache-2.0 |
|
|
| ## References to public data used |
| Lorna Richardson, Ben Allen, Germana Baldi, Martin Beracochea, |
| Maxwell L Bileschi, Tony Burdett, Josephine Burgin, Juan Caballero- |
| Pérez, Guy Cochrane, Lucy J Colwell, Tom Curtis, Alejandra Escobar- |
| Zepeda, Tatiana A Gurbich, Varsha Kale, Anton Korobeynikov, Shriya |
| Raj, Alexander B Rogers, Ekaterina Sakharova, Santiago Sanchez, Dar- |
| ren J Wilkinson, and Robert D Finn. Mgnify: the microbiome sequence |
| data analysis resource in 2023. Nucleic Acids Research, 51(D1):D753– |
| D759, 12 2022. ISSN 0305-1048. doi: 10.1093/nar/gkac1080. URL |
| https://doi.org/10.1093/nar/gkac1080 |
|
|
|
|
|
|
| ## Citation |
| Learning the Language of the Microbiome with Transformers\ |
| Neythen J Treloar, Saif Ur-Rehman, Jenny Yang\ |
| bioRxiv 2026.05.02.722381; doi: https://doi.org/10.64898/2026.05.02.722381 |
|
|
|
|
