| --- |
| dataset_info: |
| - config_name: handuo |
| features: |
| - name: Sample ID |
| dtype: large_string |
| - name: Taxa |
| list: string |
| - name: Relative Abundances |
| list: float64 |
| - name: SIC Name |
| dtype: large_string |
| - name: Control |
| dtype: bool |
| - name: ATC Class |
| dtype: large_string |
| - name: Split |
| dtype: large_string |
| splits: |
| - name: train |
| num_bytes: 6676068 |
| num_examples: 3168 |
| - name: validation |
| num_bytes: 834508 |
| num_examples: 396 |
| - name: test |
| num_bytes: 834508 |
| num_examples: 396 |
| download_size: 8165547 |
| dataset_size: 8345084 |
| - config_name: mastrorilli |
| features: |
| - name: Taxa |
| list: string |
| - name: Relative Abundances |
| list: float64 |
| - name: Sample ID |
| dtype: large_string |
| - name: Degradation Rate |
| dtype: float64 |
| - name: Drug |
| dtype: large_string |
| - name: Split |
| dtype: large_string |
| splits: |
| - name: train |
| num_bytes: 98959509 |
| num_examples: 9282 |
| - name: validation |
| num_bytes: 32879888 |
| num_examples: 3084 |
| - name: test |
| num_bytes: 32549383 |
| num_examples: 3053 |
| download_size: 163722477 |
| dataset_size: 164388780 |
| - config_name: mgnify-biomes |
| features: |
| - name: Taxa |
| list: string |
| - name: Relative Abundances |
| list: float64 |
| - name: Run Accession |
| dtype: large_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 |
| - name: Biome 1 |
| dtype: large_string |
| - name: Biome 2 |
| dtype: large_string |
| - name: Biome 3 |
| dtype: large_string |
| - name: Biome 4 |
| dtype: large_string |
| - name: Biome 5 |
| dtype: large_string |
| - name: Split |
| dtype: large_string |
| - name: __index_level_0__ |
| dtype: int64 |
| splits: |
| - name: train |
| num_bytes: 343694740 |
| num_examples: 33121 |
| - name: validation |
| num_bytes: 42950168 |
| num_examples: 4139 |
| - name: test |
| num_bytes: 42950168 |
| num_examples: 4139 |
| download_size: 423262451 |
| dataset_size: 429595076 |
| - config_name: roswall |
| features: |
| - name: Sample ID |
| dtype: large_string |
| - name: Timepoint |
| dtype: large_string |
| - name: Delivery Mode |
| dtype: large_string |
| - name: Taxa |
| list: string |
| - name: Relative Abundances |
| list: float64 |
| - name: Split |
| dtype: large_string |
| splits: |
| - name: train |
| num_bytes: 8135648 |
| num_examples: 1625 |
| - name: validation |
| num_bytes: 1016330 |
| num_examples: 203 |
| - name: test |
| num_bytes: 1016330 |
| num_examples: 203 |
| download_size: 10078148 |
| dataset_size: 10168308 |
| configs: |
| - config_name: handuo |
| data_files: |
| - split: train |
| path: handuo/train-* |
| - split: validation |
| path: handuo/validation-* |
| - split: test |
| path: handuo/test-* |
| - config_name: mastrorilli |
| data_files: |
| - split: train |
| path: mastrorilli/train-* |
| - split: validation |
| path: mastrorilli/validation-* |
| - split: test |
| path: mastrorilli/test-* |
| - config_name: mgnify-biomes |
| data_files: |
| - split: train |
| path: mgnify-biomes/train-* |
| - split: validation |
| path: mgnify-biomes/validation-* |
| - split: test |
| path: mgnify-biomes/test-* |
| - config_name: roswall |
| data_files: |
| - split: train |
| path: roswall/train-* |
| - split: validation |
| path: roswall/validation-* |
| - split: test |
| path: roswall/test-* |
| license: apache-2.0 |
| --- |
| # Compass |
|
|
| This dataset collects **processed** 16S / shotgun-derived microbiome tables formatted for machine learning. Each **config** is one benchmark task; column sets differ between configs, but within a config the **train**, **validation**, and **test** splits use the same schema. |
|
|
| ## 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. |
|
|
| | Config | Task theme | Typical use | Num examples | |
| |--------|------------|-------------|--------------| |
| | `mgnify-biomes` | MGnify sample → biome hierarchy | Biome prediction from genus-level abundances and study metadata | 41399 | |
| | `roswall` | Infant gut (PRJEB38986) | Timepoint and delivery mode prediction from gut profiles | 2031 | |
| | `handuo` | Species-in-context (drug exposure) | Classification with drug / ATC context and abundances | 3960 | |
| | `mastrorilli` | Drug degradation | Regression: degradation rate from community composition | 15419 | |
|
|
| Each row includes a **`Split`** field (`train`, `validation`, or `test`) consistent with the Hugging Face split you load. |
|
|
| ## 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 |
| |
| REPO_ID = "outpost-bio/Compass" # adjust if your namespace/name differs |
| |
| # One benchmark (DatasetDict: train, validation, test) |
| ds = load_dataset(REPO_ID, "mgnify-biomes") |
| |
| train = ds["train"] |
| val = ds["validation"] |
| test = ds["test"] |
| |
| # Optional: default config (library-defined ordering) |
| ds_default = load_dataset(REPO_ID) |
| ``` |
|
|
|
|
| ## Column reference |
|
|
| **Taxa:** `Taxa` and **`Relative Abundances`** are parallel lists containing taxon identifiers and relative abundances |
|
|
| ### `mgnify-biomes` |
|
|
| - **Context / labels:** `Run Accession`, `Data Type`, `Sequencing Method`, `Pipeline Version`, `Study Accession`, `Biome 1` … `Biome 5` (biome lineage). |
| - **Features:** `Taxa`, `Relative Abundances` |
| - **Split:** `Split` |
|
|
| ### `roswall` |
|
|
| - **Sample / environment:** `Sample ID` (run accession), `Timepoint`, `Delivery Mode` |
| - **Features:** `Taxa`, `Relative Abundances` |
| - **Split:** `Split` |
| - |
| ### `handuo` |
|
|
| - **Metadata:** `SIC Name`, `Control`, `ATC Class` |
| - **Features:** `Taxa`, `Relative Abundances`, `Sample ID` |
| - **Split:** `Split` |
|
|
| ### `mastrorilli` |
|
|
| - **Targets / metadata:** `Degradation Rate`, `Drug`, `Sample ID` |
| - **Features:** `Taxa`, `Relative Abundances` |
| - **Split:** `Split` |
| - Splits follow **sample** boundaries (no overlap of `Sample ID` across splits). |
|
|
| ## 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 |
|
|
| Handuo Shi, Daniel P Newton, Taylor H Nguyen, Sylvie Estrela, Juan |
| Sanchez, Michael Tu, Po-Yi Ho, Qinglin Zeng, Brian DeFelice, Justin |
| Sonnenburg, and Kerwyn Casey Huang. Nutrient competition predicts |
| gut microbiome restructuring under drug perturbations. August 2024. |
|
|
| Eleonora Mastrorilli, Pamela Herd, Federico E. Rey, Andrew L. Good- |
| man, and Michael Zimmermann. Linking interpersonal differences in gut |
| microbiota composition and drug biotransformation activity. bioRxiv, |
| 2026. doi: 10.64898/2026.01.21.700809. URL https://www.biorxiv. |
| org/content/early/2026/01/21/2026.01.21.700809. |
|
|
| Josefine Roswall, Lisa M Olsson, Petia Kovatcheva-Datchary, Staffan |
| Nilsson, Valentina Tremaroli, Marie-Christine Simon, Pia Kiilerich, |
| Rozita Akrami, Manuela Krämer, Mathias Uhlén, Anders Gummesson, |
| Karsten Kristiansen, Jovanna Dahlgren, and Fredrik Bäckhed. Develop- |
| mental trajectory of the healthy human gut microbiota during the first |
| 5 years of life. Cell Host Microbe, 29(5):765–776.e3, May 2021. |
|
|
| ## 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 |
|
|
|
|
