migrate checkpoit based on config.yaml

fold0/config.yaml

@@ -1,4 +1,3 @@
-# lightning.pytorch==2.4.0
 seed_everything: 42
 trainer:
   accelerator: auto
@@ -73,7 +72,7 @@ trainer:
       logging_interval: step
       log_momentum: false
       log_weight_decay: false
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint # save ckpt at the end of each epoch, and save the best val_mcc ckpt
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: null
       filename: epoch_{epoch}-val_mcc:{val_spearman:.3f}
@@ -144,7 +143,7 @@ model:
   class_path: genbio_finetune.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: genbio_finetune.models.proteinfm_ct
+      class_path: genbio_finetune.models.proteinfm_v1
       init_args:
         from_scratch: false
         use_peft: true
@@ -192,7 +191,7 @@ data:
     train_split_files:
     - singles_substitutions/VRPI_BPT7_Tsuboyama_2023_2WNM.tsv
     normalize: true
-    train_split_name: 'train'
+    train_split_name: train
     test_split_files: null
     valid_split_files: null
     random_seed: 42

fold0/model.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:9e480816f48fe3e5174308e59c615794656a6989d19b5a9b1ec8e35127bab38a
-size 147655320
+oid sha256:a6b2efc91fd635c59bd03cd00dad2198eed181ab1aeda508a68084d7179ce3d0
+size 147638872

fold1/config.yaml

@@ -1,4 +1,3 @@
-# lightning.pytorch==2.4.0
 seed_everything: 42
 trainer:
   accelerator: auto
@@ -73,7 +72,7 @@ trainer:
       logging_interval: step
       log_momentum: false
       log_weight_decay: false
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint # save ckpt at the end of each epoch, and save the best val_mcc ckpt
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: null
       filename: epoch_{epoch}-val_mcc:{val_spearman:.3f}
@@ -144,7 +143,7 @@ model:
   class_path: genbio_finetune.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: genbio_finetune.models.proteinfm_ct
+      class_path: genbio_finetune.models.proteinfm_v1
       init_args:
         from_scratch: false
         use_peft: true
@@ -192,7 +191,7 @@ data:
     train_split_files:
     - singles_substitutions/VRPI_BPT7_Tsuboyama_2023_2WNM.tsv
     normalize: true
-    train_split_name: 'train'
+    train_split_name: train
     test_split_files: null
     valid_split_files: null
     random_seed: 42

fold1/model.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:3f881173949cc7b1686f6b5b729ae07c940ae9ab280a07e85cfb601c254df5d5
-size 147655320
+oid sha256:2e9bb11c2261745dfd18b1b4d078bb9b517e04d33cccdc16da635af1d953cdc2
+size 147638872

fold2/config.yaml

@@ -1,4 +1,3 @@
-# lightning.pytorch==2.4.0
 seed_everything: 42
 trainer:
   accelerator: auto
@@ -73,7 +72,7 @@ trainer:
       logging_interval: step
       log_momentum: false
       log_weight_decay: false
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint # save ckpt at the end of each epoch, and save the best val_mcc ckpt
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: null
       filename: epoch_{epoch}-val_mcc:{val_spearman:.3f}
@@ -144,7 +143,7 @@ model:
   class_path: genbio_finetune.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: genbio_finetune.models.proteinfm_ct
+      class_path: genbio_finetune.models.proteinfm_v1
       init_args:
         from_scratch: false
         use_peft: true
@@ -192,7 +191,7 @@ data:
     train_split_files:
     - singles_substitutions/VRPI_BPT7_Tsuboyama_2023_2WNM.tsv
     normalize: true
-    train_split_name: 'train'
+    train_split_name: train
     test_split_files: null
     valid_split_files: null
     random_seed: 42

fold2/model.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:bc47c1d7bf189d204fd6a9e24ab0016a45d5a045722169adbaec8681c486da24
-size 147655192
+oid sha256:90183c1aa4bc6d7e71c768eabcd49c0951795baf692ced616c39e7b164a154d6
+size 147638680

fold3/config.yaml

@@ -1,4 +1,3 @@
-# lightning.pytorch==2.4.0
 seed_everything: 42
 trainer:
   accelerator: auto
@@ -73,7 +72,7 @@ trainer:
       logging_interval: step
       log_momentum: false
       log_weight_decay: false
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint # save ckpt at the end of each epoch, and save the best val_mcc ckpt
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: null
       filename: epoch_{epoch}-val_mcc:{val_spearman:.3f}
@@ -144,7 +143,7 @@ model:
   class_path: genbio_finetune.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: genbio_finetune.models.proteinfm_ct
+      class_path: genbio_finetune.models.proteinfm_v1
       init_args:
         from_scratch: false
         use_peft: true
@@ -192,7 +191,7 @@ data:
     train_split_files:
     - singles_substitutions/VRPI_BPT7_Tsuboyama_2023_2WNM.tsv
     normalize: true
-    train_split_name: 'train'
+    train_split_name: train
     test_split_files: null
     valid_split_files: null
     random_seed: 42

fold3/model.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a0be8be168dfcc252e5aa95d07bfca7714030e470e3fa12c49c61b024a5cbcdd
-size 147655192
+oid sha256:741820684f971e859a6560635674c82f4a2c0a1dbd05638acb892b7bc2c1c6fc
+size 147638680

fold4/config.yaml

@@ -1,4 +1,3 @@
-# lightning.pytorch==2.4.0
 seed_everything: 42
 trainer:
   accelerator: auto
@@ -73,7 +72,7 @@ trainer:
       logging_interval: step
       log_momentum: false
       log_weight_decay: false
-  - class_path: lightning.pytorch.callbacks.ModelCheckpoint # save ckpt at the end of each epoch, and save the best val_mcc ckpt
+  - class_path: lightning.pytorch.callbacks.ModelCheckpoint
     init_args:
       dirpath: null
       filename: epoch_{epoch}-val_mcc:{val_spearman:.3f}
@@ -144,7 +143,7 @@ model:
   class_path: genbio_finetune.tasks.SequenceRegression
   init_args:
     backbone:
-      class_path: genbio_finetune.models.proteinfm_ct
+      class_path: genbio_finetune.models.proteinfm_v1
       init_args:
         from_scratch: false
         use_peft: true
@@ -192,7 +191,7 @@ data:
     train_split_files:
     - singles_substitutions/VRPI_BPT7_Tsuboyama_2023_2WNM.tsv
     normalize: true
-    train_split_name: 'train'
+    train_split_name: train
     test_split_files: null
     valid_split_files: null
     random_seed: 42

fold4/model.ckpt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:90550f106f85dee4f40e58dc0f6909aa4bcc3cdf70db0170f4b1eed1775ae879
-size 147655192
+oid sha256:8c62b5b63af9a960a25ec29b50c87c5c29f8eac638cccd341d46e2f93b1944d4
+size 147638680