Debug.

bioscanclip/model/dna_encoder.py

@@ -9,16 +9,22 @@
 from bioscanclip.util.util import PadSequence, KmerTokenizer, load_bert_model
 
 device = "cuda" if torch.cuda.is_available() else "cpu"
-
-
-def load_pre_trained_bioscan_bert(bioscan_bert_checkpoint, k=5):
+def remove_extra_pre_fix(state_dict):
+    new_state_dict = {}
+    for key, value in state_dict.items():
+        if key.startswith("module."):
+            key = key[7:]
+        new_state_dict[key] = value
+    return new_state_dict
+
+def load_pre_trained_bioscan_bert(bioscan_bert_checkpoint, k=5, remove_extra_prefix=False):
     kmer_iter = (["".join(kmer)] for kmer in product("ACGT", repeat=k))
     vocab = build_vocab_from_iterator(kmer_iter, specials=["<MASK>", "<CLS>", "<UNK>"])
     vocab.set_default_index(vocab["<UNK>"])
     vocab_size = len(vocab)
     configuration = BertConfig(vocab_size=vocab_size, output_hidden_states=True)
     bert_model = BertForMaskedLM(configuration)
-    load_bert_model(bert_model, bioscan_bert_checkpoint)
+    load_bert_model(bert_model, bioscan_bert_checkpoint, remove_extra_prefix=remove_extra_prefix)
     return bert_model.to(device)
 
 

bioscanclip/model/simple_clip.py

@@ -263,11 +263,13 @@ def load_clip_model(args, device=None):
             if dna_model == "barcode_bert" or dna_model == "lora_barcode_bert":
                 barcode_BERT_ckpt = args.barcodeBERT_checkpoint
                 k = 5
+                remove_extra_prefix = False
                 if hasattr(args.model_config, "barcodeBERT_ckpt_path"):
                     barcode_BERT_ckpt = args.model_config.barcodeBERT_ckpt_path
                     k=4
+                    remove_extra_prefix = True
                 pre_trained_barcode_bert = load_pre_trained_bioscan_bert(
-                    bioscan_bert_checkpoint=barcode_BERT_ckpt, k=k)
+                    bioscan_bert_checkpoint=barcode_BERT_ckpt, k=k, remove_extra_prefix=remove_extra_prefix)
                 if disable_lora:
                     dna_encoder = LoRA_barcode_bert(model=pre_trained_barcode_bert, r=4,
                                                     num_classes=args.model_config.output_dim, lora_layer=[])

bioscanclip/util/util.py

@@ -115,10 +115,14 @@ def remove_extra_pre_fix(state_dict):
     return new_state_dict
 
 
-def load_bert_model(bert_model, path_to_ckpt):
+def load_bert_model(bert_model, path_to_ckpt, remove_extra_prefix=False):
     state_dict = torch.load(path_to_ckpt, map_location=torch.device("cpu"))
     state_dict = remove_extra_pre_fix(state_dict)
-    bert_model.load_state_dict(state_dict)
+    try:
+        bert_model.load_state_dict(state_dict)
+    except:
+        print(state_dict.keys())
+
 
 
 def print_result(