Update README.md

README.md

@@ -2,8 +2,8 @@
 datasets:
 - genbio-ai/transcript_isoform_expression_prediction
 base_model:
-- EleutherAI/enformer-official-rough
 - genbio-ai/AIDO.RNA-1.6B-CDS
+- EleutherAI/enformer-official-rough
 - facebook/esm2_t30_150M_UR50D
 metrics:
 - spearmanr
@@ -13,6 +13,10 @@ tags:
 ---
 # Tri-modal model for RNA isoform expression prediction
 
+## RNA isoform expression prediction
+* Input: dna_seq, rna_seq, protein_seq
+* Output: expression level in 30 tissues
+
 
 ## Model architecture 
 
@@ -20,13 +24,34 @@ tags:
 <img src="https://cdn-uploads.huggingface.co/production/uploads/63008d4bc1e149ceaff724a3/wKWIDdLu418MpXyihbCj9.png" alt="description" style="width:100%; height:auto;">
 </p>
 
-Task:
-* Input: dna_seq, rna_seq, protein_seq
-* Output: expression level in 30 tissues
+* Backbones: 
+  * DNA: Enformer (fully finetuning)
+  * RNA: AIDO.RNA-1.6B-CDS (lora finetuning)
+  * Protein: ESM2-150M (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-ESM2-150M-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)
+```
 
-Backbones: 
-* DNA: Enformer (fully finetuning)
-* RNA: AIDO.RNA-1.6B-CDS (lora finetuning)
-* Protein: ESM2-150M (lora finetuning)
+**Evaluation script**
+```bash
+CONFIG_FILE=...     # put the config file path here
+CKPT_PATH=...       # put the model checkpoint path here
 
-Multimodal Fusion: concat fusion
+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
+```