Update paths

README.md

@@ -2,7 +2,7 @@
 datasets:
 - Bo1015/peptide_HLA_MHC_affinity
 base_model:
-- genbio-ai/proteinMoE-16b
+- genbio-ai/AIDO.Protein-16B
 ---
 LoRA fine-tuned checkpoint for peptide_HLA_MHC_affinity prediction.
 
@@ -12,7 +12,7 @@ LoRA fine-tuned checkpoint for peptide_HLA_MHC_affinity prediction.
 from huggingface_hub import snapshot_download
 from pathlib import Path
 
-model_name = "genbio-ai/proteinfm-16b-peptide_HLA_MHC_affinity-ckpt"
+model_name = "genbio-ai/AIDO.Protein-16B-peptide_HLA_MHC_affinity"
 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

@@ -36,14 +36,14 @@ trainer:
   logger:
     class_path: lightning.pytorch.loggers.WandbLogger
     init_args:
-      name: peptide_HLA_MHC_affinity_proteinmoe_16B_1113
-      save_dir: /lustre/scratch/shared-folders/bio_project/shuxian/modelgenerator/logs
+      name: peptide_HLA_MHC_affinity_AIDO.Protein-16B_1113
+      save_dir: logs
       version: null
       offline: false
       dir: null
       id: null
       anonymous: null
-      project: xtrimo_benchmark_gbft_reproduction
+      project: xtrimo_benchmark_mgen_reproduction
       log_model: false
       experiment: null
       prefix: ''
@@ -75,7 +75,7 @@ trainer:
       log_weight_decay: false
   - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
-      dirpath: /lustre/scratch/shared-folders/bio_project/shuxian/modelgenerator/logs/xtrimo_benchmark_gbft_reproduction/peptide_HLA_MHC_affinity_proteinmoe_16B_1113
+      dirpath: logs/xtrimo_benchmark_mgen_reproduction/peptide_HLA_MHC_affinity_AIDO.Protein-16B_1113
       filename: best_val:{epoch}-{val_auroc:.3f}
       monitor: val_auroc
       verbose: false
@@ -134,12 +134,12 @@ trainer:
   plugins: null
   sync_batchnorm: false
   reload_dataloaders_every_n_epochs: 0
-  default_root_dir: /lustre/scratch/shared-folders/bio_project/shuxian/modelgenerator/logs
+  default_root_dir: logs
 model:
   class_path: modelgenerator.tasks.SequenceClassification
   init_args:
     backbone:
-      class_path: modelgenerator.backbones.proteinfm
+      class_path: modelgenerator.backbones.aido_protein_16b
       init_args:
         from_scratch: false
         max_length: 64
@@ -201,7 +201,7 @@ model:
 data:
   class_path: modelgenerator.data.PeptideHlaMhcAffinity
   init_args:
-    path: biomap-research/peptide_hla_mhc_affinity
+    path: proteinglm/peptide_HLA_MHC_affinity
     class_filter: null
     config_name: null
     train_split_name: train