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README.md

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+---
+language: rna
+tags:
+  - Biology
+  - RNA
+license:
+  - agpl-3.0
+size_categories:
+  - 1K<n<10K
+task_categories:
+  - text-generation
+  - fill-mask
+task_ids:
+  - language-modeling
+  - masked-language-modeling
+pretty_name: EternaBench
+library_name: multimolecule
+---
+
+# EternaBench
+
+![EternaBench](https://eternagame.org/sites/default/files/thumb_eternabench_paper.png)
+
+EternaBench is a database comprising the diverse high-throughput structural data gathered through the crowdsourced RNA design project Eterna, to evaluate the performance of a wide set of structure algorithms.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the [EternaBench](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al.
+
+**The team releasing EternaBench did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**
+
+## Dataset Description
+
+- **Homepage**: https://multimolecule.danling.org/datasets/eternabench
+- **Point of Contact**: [Rhiju Das](https://biochemistry.stanford.edu/people/rhiju-das/)
+
+## Example Entry
+
+| ID       | design_name            | sequence         | structure        | reactivity                 | errors                      | signal_to_noise |
+| -------- | ---------------------- | ---------------- | ---------------- | -------------------------- | --------------------------- | --------------- |
+| 769337-1 | d+m plots weaker again | GGAAAAAAAAAAA... | ................ | [0.642,1.4853,0.1629, ...] | [0.3181,0.4221,0.1823, ...] | 3.227           |
+
+## Column Description
+
+The EternaBench dataset consists of the following columns, providing crucial insights for understanding RNA stability for vaccine design:
+
+- **ID**:
+  A unique identifier for each RNA sequence entry.
+
+- **design_name**:
+  The name given to each RNA design by contributors, used for easy reference.
+
+- **sequence**:
+  The nucleotide sequence of the RNA, using standard bases.
+
+- **structure**:
+  The predicted secondary structure of the RNA, represented using dot-bracket notation.
+  The structure helps determine the likely secondary interactions within each RNA molecule.
+
+- **reactivity**:
+  A list of floating-point values that provide an estimate of the likelihood of the RNA backbone being cut at each nucleotide position.
+  These values help determine the stability of the RNA structure under various experimental conditions.
+
+- **errors**:
+  Arrays of floating-point numbers indicating the experimental errors corresponding to the measurements in the **reactivity**.
+  These values help quantify the uncertainty in the degradation rates and reactivity measurements.
+
+## Variations
+
+This dataset is available in two subsets:
+
+- [EternaBench-CM](https://huggingface.co/datasets/multimolecule/eternabench-cm)
+- [EternaBench-Switch](https://huggingface.co/datasets/multimolecule/eternabench-switch)
+
+## License
+
+This dataset is licensed under the [AGPL-3.0 License](https://www.gnu.org/licenses/agpl-3.0.html).
+
+```spdx
+SPDX-License-Identifier: AGPL-3.0-or-later
+```
+
+## Citation
+
+```bibtex
+@article{waymentsteele2022rna,
+  author    = {Wayment-Steele, Hannah K and Kladwang, Wipapat and Strom, Alexandra I and Lee, Jeehyung and Treuille, Adrien and Becka, Alex and {Eterna Participants} and Das, Rhiju},
+  journal   = {Nature Methods},
+  month     = oct,
+  number    = 10,
+  pages     = {1234--1242},
+  publisher = {Springer Science and Business Media LLC},
+  title     = {{RNA} secondary structure packages evaluated and improved by high-throughput experiments},
+  volume    = 19,
+  year      = 2022
+}
+```

abc.json

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+{"ID":{"0":"769337-1"},"design_name":{"0":"d+m plots weaker again"},"sequence":{"0":"GGAAAAAAAAAAAAAAAAAAAAACAAAAAGUGCAUCAUACGAUAAAAGGUUGAUAGAGUAUAAAAAAACUGUGUCUUCGGACACAGAAAAGAAACAACAACAACAAC"},"structure":{"0":".............................((((.((((.((((.....)))))).)))))).......(((((((....)))))))....................."},"reactivity":{"0":[0.642,1.4853,0.1629,0.4096,0.1751,0.1281,0.0617,-0.0067,0.1417,0.0456,0.072,0.0655,-0.0305,0.1201,0.2155,0.2864,0.0642,0.5659,0.2943,1.0162,0.6652,1.0094,1.0495,0.5159,0.7695,0.4611,0.5421,0.8893,1.2345,0.7307,0.7062,0.3998,0.475,0.6613,0.2473,0.3627,0.5394,0.8074,0.6891,0.3725,0.8871,1.0228,1.0186,0.6061,0.512,0.8154,1.2662,0.6429,0.1809,0.0591,0.1763,0.4433,0.7039,0.5934,0.7588,0.924,1.0326,0.5312,0.6306,0.9355,0.6093,0.5718,0.9461,0.8072,0.5395,0.5522,0.423,0.3358,0.0289,0.0515,0.0385,0.0316,-0.0068,0.0511,0.1046,0.6316,0.2823,0.4295,0.3637]},"errors":{"0":[0.3181,0.4221,0.1823,0.2391,0.1804,0.1672,0.1462,0.1086,0.1687,0.1342,0.1407,0.1315,0.0712,0.1586,0.1862,0.1989,0.1388,0.2511,0.195,0.3012,0.2521,0.2883,0.2921,0.2161,0.2435,0.2003,0.2071,0.2412,0.2677,0.2132,0.2063,0.1636,0.1699,0.1937,0.1373,0.1521,0.1733,0.201,0.1793,0.1413,0.1948,0.2022,0.1958,0.1546,0.1404,0.1684,0.1963,0.1451,0.0924,0.0719,0.0849,0.1221,0.1425,0.1325,0.1419,0.1508,0.1542,0.1163,0.1256,0.1426,0.1176,0.1114,0.1356,0.123,0.1025,0.102,0.0906,0.0794,0.0403,0.0398,0.0364,0.0452,0.0349,0.0396,0.0545,0.1032,0.0744,0.0841,0.0777]},"signal_to_noise":{"0":3.227}}

test.parquet

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train.parquet

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