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--- |
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datasets: |
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- genbio-ai/transcript_isoform_expression_prediction |
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metrics: |
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- spearmanr |
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- r_squared |
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base_model: |
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- genbio-ai/AIDO.RNA-1.6B-CDS |
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- EleutherAI/enformer-official-rough |
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tags: |
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- biology |
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--- |
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# Bi-modal model for RNA isoform expression prediction |
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## RNA isoform expression prediction |
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* Input: dna_seq, rna_seq |
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* Output: expression level in 30 tissues |
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## Model architecture |
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* Backbones: |
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* DNA: Enformer (fully finetuning) |
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* RNA: AIDO.RNA-1.6B-CDS (lora finetuning) |
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* Fusion method: concat fusion |
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## Usage |
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**Download model** |
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```python |
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from huggingface_hub import snapshot_download |
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from pathlib import Path |
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model_name = "genbio-ai/AIDO.MM-Enformer-RNA-1.6B-CDS-ConcatFusion-rna-isoform-expression-ckpt" |
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genbio_models_path = Path.home().joinpath('genbio_models', model_name) |
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genbio_models_path.mkdir(parents=True, exist_ok=True) |
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snapshot_download(repo_id=model_name, local_dir=genbio_models_path) |
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``` |
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**Evaluation script** |
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Once you download the model, you can use the model in [ModelGenertor](https://github.com/genbio-ai/ModelGenerator) using the following script: |
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```bash |
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CONFIG_FILE=... # put the config file path here |
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CKPT_PATH=... # put the model checkpoint path here |
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mgen test --config $CONFIG_FILE \ |
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--data.batch_size 16 \ |
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--trainer.logger null \ |
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--model.strict_loading False \ |
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--model.reset_optimizer_states True \ |
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--ckpt_path $CKPT_PATH |
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``` |
