license: cc-by-4.0
pretty_name: miRBench (curated)
size_categories:
- 1M<n<10M
tags:
- genomics
- benchmark
- rna
- binary-classification
miRBench, curated
miRBench, as published in quality-curated genomic benchmarks - one format, fixed row order, a permanent ID on every row. 3 datasets, 6 files, 2,849,872 rows, one gzipped CSV per split, all Homo sapiens.
Getting the data
Two packages are the way in: genomic-benchmarks-data for people, 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.
pip install genomic-benchmarks-data
from genomic_benchmarks_data import load_dataset
df = load_dataset("miRBench", "AGO2_CLASH_Hejret2023", "train")
A number measured on these files belongs on the 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 - the project: the QC tool, the curated corpus and the leaderboard.
- github.com/genomic-benchmarks - all three as source, and issues.
Datasets
| dataset | task | train | test | test_leftout |
|---|---|---|---|---|
AGO2_CLASH_Hejret2023 |
Binary classification | 8140 | 1018 | - |
AGO2_eCLIP_Klimentova2022 |
Binary classification | - | 954 | - |
AGO2_eCLIP_Manakov2022 |
Binary classification | 2495535 | 324171 | 20054 |
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/10.1093/bioinformatics/btaf233
- Covers every dataset here: CC BY 4.0 (https://creativecommons.org/licenses/by/4.0/)
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/10.1093/bioinformatics/btaf233) 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.