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README.md

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+---
+language: rna
+tags:
+  - Biology
+  - RNA
+license:
+  - cc-by-4.0
+source_datasets:
+  - multimolecule/bprna
+  - multimolecule/rfam
+task_categories:
+  - text-generation
+  - fill-mask
+task_ids:
+  - language-modeling
+  - masked-language-modeling
+pretty_name: IPknot++
+library_name: multimolecule
+---
+
+# IPknot++
+
+IPknot++ is a benchmark dataset released with the IPknot++ RNA secondary structure prediction paper.
+It is intended as an external evaluation set rather than a training split.
+A common use is to train or tune RNA secondary structure prediction models on SPOT-RNA-style splits such as [bpRNA-spot](../bprna_spot), then evaluate generalization on IPknot++.
+
+The original release does not define train, validation, and test partitions.
+The converted dataset follows the paper's benchmark blocks as four splits:
+
+- `bprna_1m`: single-sequence structures from bpRNA-1m.
+- `rfam_14_5`: single-sequence structures from Rfam 14.5.
+- `rfam_14_5_ref`: Rfam 14.5 reference alignments for common-structure prediction.
+- `rfam_14_5_mafft`: Rfam 14.5 MAFFT alignments for common-structure prediction.
+
+For alignment entries, `sequence` and `secondary_structure` are taken from the corresponding single-sequence BPSEQ file, and the full alignment is stored in `aligned_ids` and `aligned_sequences`.
+
+## Schema
+
+| Column | Description |
+| --- | --- |
+| `id` | Identifier of the benchmark entry. |
+| `sequence` | Ungapped RNA sequence for the benchmark target. |
+| `secondary_structure` | Target secondary structure in dot-bracket notation. |
+| `aligned_ids` | Sequence IDs in the alignment. Single-sequence entries contain only their own ID. |
+| `aligned_sequences` | Aligned sequences, preserving gap characters. Single-sequence entries contain only the ungapped sequence. |
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the IPknot++ benchmark dataset by Kengo Sato and Yuki Kato.
+
+**The team releasing IPknot++ did not write this dataset card for this dataset so this dataset card has been written by the MultiMolecule team.**
+
+## Dataset Description
+
+- **Homepage**: https://www.sato-lab.org/en/publication/sato-2022-qk/
+- **datasets**: https://huggingface.co/datasets/multimolecule/ipknot-plus-plus
+- **Original URL**: https://zenodo.org/records/4923158
+
+## License
+
+The original IPknot++ benchmark dataset is licensed under the [Creative Commons Attribution 4.0 International](https://creativecommons.org/licenses/by/4.0/) license.
+
+```spdx
+SPDX-License-Identifier: CC-BY-4.0
+```
+
+## Citation
+
+```bibtex
+@article{sato2022prediction,
+  author    = {Sato, Kengo and Kato, Yuki},
+  journal   = {Briefings in Bioinformatics},
+  month     = jan,
+  number    = 1,
+  title     = {Prediction of {RNA} secondary structure including pseudoknots for long sequences},
+  volume    = 23,
+  year      = 2022
+}
+```
+
+```bibtex
+@dataset{sato2021ipknot,
+  author    = {Sato, Kengo and Kato, Yuki},
+  title     = {{IPknot++} benchmark dataset},
+  publisher = {Zenodo},
+  doi       = {10.5281/zenodo.4923158},
+  year      = 2021
+}
+```
+
+> [!NOTE]
+> The artifacts distributed in this repository are part of the MultiMolecule project.
+> If you use MultiMolecule in your research, you must cite the MultiMolecule project as follows:
+
+```bibtex
+@software{chen_2024_12638419,
+  author    = {Chen, Zhiyuan and Zhu, Sophia Y.},
+  title     = {MultiMolecule},
+  doi       = {10.5281/zenodo.12638419},
+  publisher = {Zenodo},
+  url       = {https://doi.org/10.5281/zenodo.12638419},
+  year      = 2024,
+  month     = may,
+  day       = 4
+}
+```

bprna_1m.parquet

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rfam_14_5.parquet

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rfam_14_5_mafft.parquet

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rfam_14_5_ref.parquet

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