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README.md
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# RNA Secondary Structure Prediction
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As discussed in our paper [AIDO.RNA](https://doi.org/10.1101/2024.11.28.625345), we finetune the [AIDO.RNA-1.6B](https://huggingface.co/genbio-ai/AIDO.RNA-1.6B) model on the training splits of the following two datasets:
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1. [bpRNA](https://doi.org/10.1093/nar/gky285)
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2. [Archive-II](http://www.rnajournal.org/cgi/doi/10.1261/rna.053694.115)
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1. bpRNA: `${MGEN_DATA_DIR}/modelgenerator/datasets/rna_ss_data/bpRNA`
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2. Archive-II: `${MGEN_DATA_DIR}/modelgenerator/datasets/rna_ss_data/archiveII`
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- Then run a finetuning job on either dataset as following:
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1. To train on bpRNA dataset, run the following command:
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```
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bash rna_secondary_structure_prediction.sh train bpRNA
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#### Outputs:
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- The evaluation scores will be printed on the console.
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---
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# RNA Secondary Structure Prediction
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As with proteins, structure determines RNA function. RNA secondary structure, formed by base pairing, is more stable and accessible than its tertiary form within cells. Accurate prediction of RNA secondary structure is essential for tasks such as higher-order structure prediction and function prediction. As discussed in our paper [AIDO.RNA](https://doi.org/10.1101/2024.11.28.625345), we finetune the [AIDO.RNA-1.6B](https://huggingface.co/genbio-ai/AIDO.RNA-1.6B) model on the training splits of the following two datasets:
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1. [bpRNA](https://doi.org/10.1093/nar/gky285)
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2. [Archive-II](http://www.rnajournal.org/cgi/doi/10.1261/rna.053694.115)
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1. bpRNA: `${MGEN_DATA_DIR}/modelgenerator/datasets/rna_ss_data/bpRNA`
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2. Archive-II: `${MGEN_DATA_DIR}/modelgenerator/datasets/rna_ss_data/archiveII`
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- Then run a finetuning job on either dataset as following (Note that here we are using finetuning scheduler. See [this tutorial](https://github.com/genbio-ai/ModelGenerator/blob/main/docs/docs/tutorials/finetuning_scheduler.md) for details):
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1. To train on bpRNA dataset, run the following command:
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```
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bash rna_secondary_structure_prediction.sh train bpRNA
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#### Outputs:
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- The evaluation scores will be printed on the console.
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