---
license:
- cc-by-4.0
- other
pretty_name: mRNABench (curated)
size_categories:
- 1M<n<10M
tags:
- genomics
- benchmark
- rna
- regression
---

# mRNABench, curated

`mRNABench`, as published in quality-curated genomic benchmarks - one format, fixed row order, a permanent ID on every row. 11 datasets, 33 files, 1,413,237 rows, one gzipped CSV per split.

## Getting the data

Two packages are the way in: [`genomic-benchmarks-data`](https://pypi.org/project/genomic-benchmarks-data/) for people, [`genomic-benchmarks-data4agents`](https://pypi.org/project/genomic-benchmarks-data4agents/) for agents, the same functions either way. They resolve the URL, check the checksum, and carry each dataset's QC results, which this repository does not.

```bash
pip install genomic-benchmarks-data
```

```python
from genomic_benchmarks_data import load_dataset

df = load_dataset("mRNABench", "mrl-sample-designed", "train")
```

A number measured on these files belongs on the [leaderboard](https://genomic-benchmarks.github.io/genomic-benchmarks-leaderboard/), which is what makes two of them comparable, and which prints what QC found about a dataset above every table.

- [genomic-benchmarks.github.io](https://genomic-benchmarks.github.io/) - the project: the QC tool, the curated corpus and the leaderboard.
- [github.com/genomic-benchmarks](https://github.com/genomic-benchmarks) - all three as source, and issues.

## Datasets

| dataset | task | species | train | val | test |
|---|---|---|---|---|---|
| `mrl-sample-designed` | Regression | Homo sapiens |   70011 |   15003 |   15003 |
| `mrl-sample-egfp-m1pseudo` | Regression | Homo sapiens |  222927 |   47770 |   47771 |
| `mrl-sample-egfp-pseudo` | Regression | Homo sapiens |  222927 |   47770 |   47771 |
| `mrl-sample-egfp-unmod` | Regression | Homo sapiens |  222927 |   47770 |   47771 |
| `mrl-sample-mcherry` | Regression | Homo sapiens |  134257 |   28770 |   28770 |
| `mrl-sample-varying` | Regression | Homo sapiens |   74571 |   15979 |   15980 |
| `mrl-sugimoto` | Regression | Homo sapiens |    8186 |    1753 |    1754 |
| `rnahl-human` | Regression | Homo sapiens |    9057 |    1942 |    1940 |
| `rnahl-mouse` | Regression | Mus musculus |    9606 |    2058 |    2059 |
| `translation-efficiency-human` | Regression | Homo sapiens |    7196 |    1543 |    1542 |
| `translation-efficiency-mouse` | Regression | Mus musculus |    7597 |    1628 |    1628 |

Files are `v1/<dataset>/<dataset>_<split>.csv.gz`, where `v1` is the version of the data. A dataset whose sequences change appears under a new prefix rather than being rewritten here.

## Licence and provenance

- Collection DOI: https://doi.org/10.1101/2025.07.05.662870

| dataset | licence |
|---|---|
| `mrl-sample-designed` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sample-egfp-m1pseudo` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sample-egfp-pseudo` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sample-egfp-unmod` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sample-mcherry` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sample-varying` | [No restrictions (GEO deposition)](https://www.ncbi.nlm.nih.gov/home/about/policies/) |
| `mrl-sugimoto` | [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) |
| `rnahl-human` | [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) |
| `rnahl-mouse` | [CC BY 4.0](https://creativecommons.org/licenses/by/4.0/) |
| `translation-efficiency-human` | [No restrictions (author statement)](https://doi.org/10.1038/s41587-025-02712-x) |
| `translation-efficiency-mouse` | [No restrictions (author statement)](https://doi.org/10.1038/s41587-025-02712-x) |

## Every row has an identity

Each file carries two columns the upstream release does not:

- `id` - `<collection>:<dataset>:<version>:<split>:<row index>`, the index zero-padded to 7 digits.
- `row_index` - the row's 0-based position in this file.

Row order is fixed within a major version, so an `id` names the same sequence for as long as that version exists - which is what makes a reported number traceable to what it was computed on. The corpus metadata carries the SHA-256 of every split file, so a copy can be checked against the audited one.

## Citation

Cite the collection's own publication (https://doi.org/10.1101/2025.07.05.662870) for the data, and *Automated quality control for genomic sequence benchmarks reveals pervasive single-feature separability and train-test leakage* for the curation and the audit.