mogam-ai/CDS-BART-SARS-CoV-2-vaccine-degradation

📊 SARS-CoV2-vaccine dataset

This dataset includes thousands of mRNA sequences related to SARS-CoV-2, along with measured degradation rates. It was created to systematically study the relationship between mRNA sequence, structure, stability and protein expression efficiency. The original dataset is from CodonBERT.

⁉️ Dataset Contents

• Sequence: The mRNA sequence of the mRNA degradation
• Degradation: the average degradation at 50°C with magnesium ions values at each nucleotide position

🎯 Purpose

This dataset serves as a benchmark for fine-tuning models on a regression task, predicting degradation behavior from its sequence. We used this dataset to fine-tune CDS-BART, a BART-based foundation model trained on massive mRNA sequences. Demonstrating its ability to perform downstream tasks related to mRNA regulation which are fine-tuned for various mRNA-related downstream task. CDS-BART available at GitHub

🔧Usage

from datasets import load_dataset

dataset = load_dataset('mogam-ai/CDS-BART-SARS-CoV-2-vaccine-degradation')

📚 Dataset Reference

• Leppek, Kathrin, et al. "Combinatorial optimization of mRNA structure, stability, and translation for RNA-based therapeutics." Nature communications 13.1 (2022): 1536.
• Li, Sizhen, et al. "CodonBERT large language model for mRNA vaccines." Genome research 34.7 (2024): 1027-1035.