mogam-ai/CDS-BART-mRNA-stability

📊 mRNA Stability dataset

This dataset contains thousands of mRNA stability profiles obtained from various species, including humans, mice, frogs, and fish. It provides essential information on the stability of mRNA molecules, contributing to our understanding of post-transcriptional regulation. The original dataset is from CodonBERT.

⁉️ Dataset Contents

• Sequence: The mRNA sequence of the mRNA stability
• Stability: Half life, the time it takes for half of the mRNA molecules in a population to be degraded within a cell.

🎯 Purpose

This dataset serves as a benchmark for fine-tuning models on a regression task, predicting riboswitch 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-mRNA-stability')

📚 Dataset Reference

Diez, Michay, et al. "iCodon customizes gene expression based on the codon composition." Scientific Reports 12.1 (2022): 12126. Li, Sizhen, et al. "CodonBERT large language model for mRNA vaccines." Genome research 34.7 (2024): 1027-1035.