Upload folder using huggingface_hub

README.md

@@ -0,0 +1,117 @@
+---
+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-External
+library_name: multimolecule
+---
+
+# EternaBench-External
+
+![EternaBench-External](https://eternagame.org/sites/default/files/thumb_eternabench_paper.png)
+
+EternaBench-External consists of 31 independent RNA datasets from various biological sources, including viral genomes, mRNAs, and synthetic RNAs.
+These sequences were probed using techniques such as SHAPE-CE, SHAPE-MaP, and DMS-MaP-seq to understand RNA secondary structures under different experimental and biological conditions.
+This dataset serves as a benchmark for evaluating RNA structure prediction models, with a particular focus on generalization to natural RNA molecules.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the [EternaBench-External](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al.
+
+**The team releasing EternaBench-External 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_external
+- **Point of Contact**: [Rhiju Das](https://biochemistry.stanford.edu/people/rhiju-das/)
+
+This dataset includes RNA sequences from various biological origins, including viral genomes and mRNAs, and covers a wide range of probing methods like SHAPE-CE and icSHAPE.
+Each dataset entry provides sequence information, reactivity profiles, and RNA secondary structure data.
+This dataset can be used to examine how RNA structures vary under different conditions and to validate structural predictions for diverse RNA types.
+
+## Example Entry
+
+| name                                                        | sequence                | reactivity                       | seqpos               | class      | dataset        |
+| ----------------------------------------------------------- | ----------------------- | -------------------------------- | -------------------- | ---------- | -------------- |
+| Dadonaite,2019 Influenza genome SHAPE(1M7) SSII-Mn(2+) Mut. | TTTACCCACAGCTGTGAATT... | [0.639309,0.813297,0.622869,...] | [7425,7426,7427,...] | viral_gRNA | Dadonaite,2019 |
+
+## Column Description
+
+- **name**:
+  The name of the dataset entry, typically including the experimental setup and biological source.
+
+- **sequence**:
+    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:
+
+    - **A**: Adenine
+    - **C**: Cytosine
+    - **G**: Guanine
+    - **U**: Uracil
+
+- **reactivity**:
+    A list of normalized reactivity values for each nucleotide, representing the likelihood that a nucleotide is unpaired.
+    High reactivity indicates high flexibility (unpaired regions), and low reactivity corresponds to paired or structured regions.
+
+- **seqpos**:
+  A list of sequence positions corresponding to each nucleotide in the **sequence**.
+
+- **class**:
+  The type of RNA sequence, can be one of the following:
+
+    - SARS-CoV-2_gRNA
+    - mRNA
+    - rRNA
+    - small RNAs
+    - viral_gRNA
+
+- **dataset**:
+    The source or reference for the dataset entry, indicating its origin.
+
+## Variations
+
+This dataset is available in four variants:
+
+- [eternabench-external.1200](https://huggingface.co/datasets/multimolecule/eternabench-external.1200): EternaBench-External dataset with maximum sequence length of 1200 nucleotides.
+- [eternabench-external.900](https://huggingface.co/datasets/multimolecule/eternabench-external.900): EternaBench-External dataset with maximum sequence length of 900 nucleotides.
+- [eternabench-external.600](https://huggingface.co/datasets/multimolecule/eternabench-external.600): EternaBench-External dataset with maximum sequence length of 600 nucleotides.
+- [eternabench-external.300](https://huggingface.co/datasets/multimolecule/eternabench-external.300): EternaBench-External dataset with maximum sequence length of 300 nucleotides.
+
+## Related Datasets
+
+- [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
+}
+```

test.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:f76fcfe5e7893988134cbd71251a77c137fe42abf8c9265d55b64e7f3738198c
+size 7528444