Model Overview Orthrus is a mature RNA foundation model for RNA property prediction. Orthrus is pre trained using contrastive learning on 45M+ mature RNA transcripts to capture functional and evolutionary relationships across all Mammailian organisms. Orthrus is built on a Mamba encoder backbone, enabling the embedding of arbitrarily long RNA sequence data. We offer two sizes of Orthrus: base is trained using ~1M parameters, and large is trained using ~10M parameters. Three versions of Orthrus are available for use via HuggingFace (See collection): Orthrus base 4 track : Encodes the mRNA sequence with a simplified one hot approach. Orthrus large 4 track : Larger version of the above. Orthrus large 6 track : Adds biological context by including splice site indicators and coding sequence markers, which is crucial for accurate mRNA property prediction such as RNA half life, ribosome load, and exon junction detection. This HF repo contains the orthrus large 6 track model. Additional project files and the github repository can be found at: https://huggingface.co/antichronology/orthrus https://github.com/bowang lab/Orthrus Using Orthrus (6 track) To generate embeddings using Orthrus for…
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