remove target classes fp as now its stored in new checkpoints

Author: aditya0by0

chebifier/ensemble/base_ensemble.py

@@ -271,7 +271,6 @@ def predict_smiles_list(
             "resgated_0ps1g189": {
                 "type": "resgated",
                 "ckpt_path": "data/0ps1g189/epoch=122.ckpt",
-                "target_labels_path": "data/chebi_v241/ChEBI50/processed/classes.txt",
                 "molecular_properties": [
                     "chebai_graph.preprocessing.properties.AtomType",
                     "chebai_graph.preprocessing.properties.NumAtomBonds",
@@ -289,7 +288,6 @@ def predict_smiles_list(
             "electra_14ko0zcf": {
                 "type": "electra",
                 "ckpt_path": "data/14ko0zcf/epoch=193.ckpt",
-                "target_labels_path": "data/chebi_v241/ChEBI50/processed/classes.txt",
                 # "classwise_weights_path": "../python-chebai/metrics_electra_14ko0zcf_80-10-10.json",
             },
         }

chebifier/hugging_face.py

@@ -25,7 +25,7 @@ def download_model_files(
         model_config (Dict[str, str | Dict[str, str]]): A dictionary containing:
             - 'repo_id' (str): The Hugging Face repository ID (e.g., 'username/modelname').
             - 'subfolder' (str): The subfolder within the repo where the files are located.
-            - 'files' (Dict[str, str]): A mapping from file type (e.g., 'ckpt_path', 'target_labels_path') to
+            - 'files' (Dict[str, str]): A mapping from file type (e.g., 'ckpt_path') to
               actual file names (e.g., 'electra.ckpt', 'classes.txt').
 
     Returns:

chebifier/model_registry.yml

@@ -4,47 +4,41 @@ electra_chebi50-3star_v244:
     repo_id: chebai/electra_chebi50-3star_v244
     files:
       ckpt_path: electra_chebi50-3star_v244_x2mngani_epoch=180.ckpt
-      target_labels_path: classes.txt
       classwise_weights_path: electra_chebi50-3star_v244_x2mngani_epoch=180_trust_3star.json
 gat_chebi50_v244:
   type: gat
   hugging_face:
     repo_id: chebai/gat_chebi50_v244
     files:
       ckpt_path: gat_chebi50_v244_0nfi19qt_epoch=198.ckpt
-      target_labels_path: classes.txt
       classwise_weights_path: gat_chebi50_v244_0nfi19qt_epoch=198_trust_3star.json
 gat-aug_chebi50_v244:
   type: gat
   hugging_face:
     repo_id: chebai/gat-aug_chebi50_v244
     files:
       ckpt_path: gat-aug_chebi50_v244_8fky8tru_epoch=192.ckpt
-      target_labels_path: classes.txt
       classwise_weights_path: gat-aug_chebi50_v244_8fky8tru_epoch=192_trust_3star.json
 resgated-aug_chebi50-3star_v244:
   type: resgated
   hugging_face:
     repo_id: chebai/resgated-aug_chebi50-3star_v244
     files:
       ckpt_path: resgated-aug_chebi50-3star_v244_w0rhmajx_epoch=190.ckpt
-      target_labels_path: classes.txt
       classwise_weights_path: resgated-aug_chebi50-3star_v244_w0rhmajx_epoch=190_trust_3star.json
 electra_chebi50_v241:
     type: electra
     hugging_face:
       repo_id: chebai/electra_chebi50_v241
       files:
         ckpt_path: 14ko0zcf_epoch=193.ckpt
-        target_labels_path: classes.txt
         classwise_weights_path: metrics_electra_14ko0zcf_80-10-10_short.json
 resgated_chebi50_v241:
     type: resgated
     hugging_face:
       repo_id: chebai/resgated_gcn_chebi50_v241
       files:
         ckpt_path: 0ps1g189_epoch=122.ckpt
-        target_labels_path: classes.txt
         classwise_weights_path: metrics_0ps1g189_80-10-10_short.json
 c3p_with_weights:
   type: c3p

configs/example_config.yml

@@ -5,7 +5,6 @@ chemlog_peptides:
 my_resgated:
   type: resgated
   ckpt_path: my_resgated.ckpt # checkpoint trained with chebai
-  target_labels_path: ../python-chebai/data/chebi_v244/ChEBI50/processed/classes.txt # from the chebai dataset
   molecular_properties: # list of properties used during training
       - chebai_graph.preprocessing.properties.AtomType
       - chebai_graph.preprocessing.properties.NumAtomBonds
@@ -22,5 +21,4 @@ my_resgated:
 my_electra:
   type: electra
   ckpt_path: my_electra.ckpt
-  target_labels_path: ../python-chebai/data/chebi_v244/ChEBI50/processed/classes.txt
   #classwise_weights_path: my_electra_metrics.json # can be calculated with chebai.results.generate_class_properties