GB.RNA-1M-MARS

GB.RNA-1M-MARS is a 1 million parameter RNA foundation model pre-trained on 886 million RNA sequences from the MARS database.

For a more detailed description, refer to the SOTA model in this collection https://huggingface.co/genbio-ai/GB.RNA-1.6B

How to Use

Build any downstream models from this backbone with ModelGenerator

For more information, visit: Model Generator

mgen fit --model SequenceClassification --model.backbone aido_rna_1m_mars --data SequenceClassificationDataModule --data.path <hf_or_local_path_to_your_dataset>
mgen test --model SequenceClassification --model.backbone aido_rna_1m_mars --data SequenceClassificationDataModule --data.path <hf_or_local_path_to_your_dataset>

Or use directly in Python

Embedding

from modelgenerator.tasks import Embed
model = Embed.from_config({"model.backbone": "aido_rna_1m_mars"}).eval()
transformed_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
embedding = model(transformed_batch)
print(embedding.shape)
print(embedding)

Sequence-level Classification

import torch
from modelgenerator.tasks import SequenceClassification
model = SequenceClassification.from_config({"model.backbone": "aido_rna_1m_mars", "model.n_classes": 2}).eval()
transformed_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
logits = model(transformed_batch)
print(logits)
print(torch.argmax(logits, dim=-1))

Token-level Classification

import torch
from modelgenerator.tasks import TokenClassification
model = TokenClassification.from_config({"model.backbone": "aido_rna_1m_mars", "model.n_classes": 3}).eval()
transformed_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
logits = model(transformed_batch)
print(logits)
print(torch.argmax(logits, dim=-1))

Sequence-level Regression

from modelgenerator.tasks import SequenceRegression
model = SequenceRegression.from_config({"model.backbone": "aido_rna_1m_mars"}).eval()
transformed_batch = model.transform({"sequences": ["ACGT", "AGCT"]})
logits = model(transformed_batch)
print(logits)

Get RNA sequence embedding

from genbio_finetune.tasks import Embed
model = Embed.from_config({"model.backbone": "aido_rna_1m_mars"}).eval()
transformed_batch = model.transform({"sequences": ["ACGT", "ACGT"]})
embedding = model(transformed_batch)
print(embedding.shape)
print(embedding)