Update README.md

README.md

@@ -1,15 +1,53 @@
 ---
 datasets:
 - genbio-ai/transcript_isoform_expression_prediction
+metrics:
+- spearmanr
+- r_squared
+base_model:
+- genbio-ai/AIDO.RNA-1.6B-CDS
+- EleutherAI/enformer-official-rough
+tags:
+- biology
 ---
 # Bi-modal model for RNA isoform expression prediction
 
-Task:
+## RNA isoform expression prediction
 * Input: dna_seq, rna_seq
 * Output: expression level in 30 tissues
 
-Backbones: 
-* DNA: Enformer (fully finetuning)
-* RNA: AIDO.RNA-1.6B-CDS (lora finetuning)
 
-Multimodal Fusion: concat fusion
+## Model architecture 
+* Backbones: 
+  * DNA: Enformer (fully finetuning)
+  * RNA: AIDO.RNA-1.6B-CDS (lora finetuning)
+* Fusion method: concat fusion
+
+
+## Usage
+
+**Download model**
+```python
+from huggingface_hub import snapshot_download
+from pathlib import Path
+
+model_name = "genbio-ai/AIDO.MM-Enformer-RNA-1.6B-CDS-ConcatFusion-rna-isoform-expression-ckpt"
+genbio_models_path = Path.home().joinpath('genbio_models', model_name)
+genbio_models_path.mkdir(parents=True, exist_ok=True)
+snapshot_download(repo_id=model_name, local_dir=genbio_models_path)
+```
+
+**Evaluation script**
+
+Once you download the model, you can use the model in [ModelGenertor](https://github.com/genbio-ai/ModelGenerator) using the following script:
+```bash
+CONFIG_FILE=...     # put the config file path here
+CKPT_PATH=...       # put the model checkpoint path here
+
+mgen test --config $CONFIG_FILE \
+    --data.batch_size 16 \
+    --trainer.logger null \
+    --model.strict_loading False \
+    --model.reset_optimizer_states True \
+    --ckpt_path $CKPT_PATH
+```