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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-CM
+library_name: multimolecule
+---
+
+# EternaBench-CM
+
+![EternaBench-CM](https://eternagame.org/sites/default/files/thumb_eternabench_paper.png)
+
+EternaBench-CM is a synthetic RNA dataset comprising 12,711 RNA constructs that have been chemically mapped using SHAPE and MAP-seq methods.
+These RNA sequences are probed to obtain experimental data on their nucleotide reactivity, which indicates whether specific regions of the RNA are flexible or structured.
+The dataset provides high-resolution, large-scale data that can be used for studying RNA folding and stability.
+
+## Disclaimer
+
+This is an UNOFFICIAL release of the [EternaBench-CM](https://github.com/eternagame/EternaBench) by Hannah K. Wayment-Steele, et al.
+
+**The team releasing EternaBench-CM 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_cm
+- **datasets**: https://huggingface.co/datasets/multimolecule/eternabench-cm
+- **Point of Contact**: [Rhiju Das](https://biochemistry.stanford.edu/people/rhiju-das)
+
+The dataset includes a large set of synthetic RNA sequences with experimental chemical mapping data, which provides a quantitative readout of RNA nucleotide reactivity. These data are ensemble-averaged and serve as a critical benchmark for evaluating secondary structure prediction algorithms in their ability to model RNA folding dynamics.
+
+## Example Entry
+
+| index    | design                 | sequence         | secondary_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
+
+- **id**:
+    A unique identifier for each RNA sequence entry.
+
+- **design**:
+    The name given to each RNA design by contributors, used for easy reference.
+
+- **sequence**:
+    The nucleotide sequence of the RNA molecule, represented using the standard RNA bases:
+
+    - **A**: Adenine
+    - **C**: Cytosine
+    - **G**: Guanine
+    - **U**: Uracil
+
+- **secondary_structure**:
+    The secondary structure of the RNA represented in dot-bracket notation, using up to three types of symbols to indicate base pairing and unpaired regions, as per bpRNA's standard:
+
+    - **Dots (`.`)**: Represent unpaired nucleotides.
+    - **Parentheses (`(` and `)`)**: Represent base pairs in standard stems (page 1).
+    - **Square Brackets (`[` and `]`)**: Represent base pairs in pseudoknots (page 2).
+    - **Curly Braces (`{` and `}`)**: Represent base pairs in additional pseudoknots (page 3).
+
+- **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.
+
+- **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.
+
+- **signal_to_noise**:
+    The signal-to-noise ratio calculated from the reactivity and error values, providing a measure of data quality.
+
+## Related Datasets
+
+- [eternabench-switch](https://huggingface.co/datasets/multimolecule/eternabench-switch)
+- [eternabench-external.1200](https://huggingface.co/datasets/multimolecule/eternabench-external.1200): EternaBench-External dataset with maximum sequence length of 1200 nucleotides.
+
+## Preprocess
+
+The MultiMolecule team preprocess this dataset by the following steps:
+
+1. Remove all sequence whose `signal_to_noise < 1`.
+2. Remove all sequence without proper secondary structure (i.e., the secondary structure in dot-bracket notation do not match).
+3. Padding/truncating all chemical measurements to sequence length.
+
+## 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
+}
+```

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train.parquet

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