| --- |
| 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. |
|
|
