Update paths

README.md

@@ -2,7 +2,7 @@
 datasets:
 - genbio-ai/rna-downstream-tasks
 base_model:
-- genbio-ai/rnafm-1.6b
+- genbio-ai/AIDO.RNA-1.6B
 ---
 10-fold cross-validation fully fine-tuned checkpoints for mRNA expression level prediction (pc3).
 
@@ -12,7 +12,7 @@ base_model:
 from huggingface_hub import snapshot_download
 from pathlib import Path
 
-model_name = "genbio-ai/rnafm-1.6b-mrna-expression-level-pc3-ckpt"
+model_name = "genbio-ai/AIDO.RNA-1.6B-mrna-expression-level-pc3"
 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)

config.yaml

@@ -36,8 +36,8 @@ trainer:
   logger:
     class_path: lightning.pytorch.loggers.WandbLogger
     init_args:
-      name: te_muscle_rnafm_1.6B_fold0
-      save_dir: modelgenerator/logs
+      name: te_muscle_AIDO.RNA-1.6B_fold0
+      save_dir: logs
       version: null
       offline: false
       dir: null
@@ -75,7 +75,7 @@ trainer:
       log_weight_decay: false
   - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
-      dirpath: modelgenerator/logs/rna_tasks/te_muscle_rnafm_1.6B_fold0
+      dirpath: logs/rna_tasks/te_muscle_AIDO.RNA-1.6B_fold0
       filename: best_val:{epoch}-{val_spearman:.3f}
       monitor: val_spearman
       verbose: false
@@ -134,12 +134,12 @@ trainer:
   plugins: null
   sync_batchnorm: false
   reload_dataloaders_every_n_epochs: 0
-  default_root_dir: modelgenerator/logs
+  default_root_dir: logs
 model:
   class_path: modelgenerator.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: modelgenerator.backbones.rnafm
+      class_path: modelgenerator.backbones.aido_rna_1b600m
       init_args:
         from_scratch: false
         max_length: 1024