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config.json

@@ -61,7 +61,6 @@
       "history"
     ],
     "min_length": 0,
-    "mlp_bias": false,
     "model_type": "llama",
     "no_repeat_ngram_size": 0,
     "num_attention_heads": 12,
@@ -238,5 +237,5 @@
   "model_type": "vision-encoder-decoder",
   "tie_word_embeddings": false,
   "torch_dtype": "float32",
-  "transformers_version": "4.42.3"
+  "transformers_version": "4.40.2"
 }

dataset.py

@@ -5,12 +5,15 @@ import torch
 from torch.utils.data import Dataset
 from torchvision.io import read_image
 
-from tools.utils import mimic_cxr_image_path
-
 # Ordered by oblique, lateral, AP, and then PA views so that PA views are closest in position to the generated tokens (and oblique is furtherest).
 VIEW_ORDER = ['LPO', 'RAO', 'LAO', 'SWIMMERS', 'XTABLE LATERAL', 'LL', 'LATERAL',  'AP AXIAL', 'AP RLD', 'AP LLD', 'AP', 'PA RLD', 'PA LLD', 'PA']
 
 
+def mimic_cxr_image_path(dir, subject_id, study_id, dicom_id, ext='dcm'):
+    return os.path.join(dir, 'p' + str(subject_id)[:2], 'p' + str(subject_id),
+                        's' + str(study_id), str(dicom_id) + '.' + ext)
+
+
 class StudyIDEDStayIDSubset(Dataset):
     """
     Study ID & ED stay ID subset. Examples are indexed by the study identifier.

generation_config.json

@@ -3,5 +3,5 @@
   "bos_token_id": 1,
   "eos_token_id": 2,
   "pad_token_id": 4,
-  "transformers_version": "4.42.3"
+  "transformers_version": "4.40.2"
 }

modelling_cxrmate_ed.py

@@ -25,7 +25,7 @@ from .modelling_uniformer import MultiUniFormerWithProjectionHead
 from .records import EDCXRSubjectRecords
 from .tables import ed_module_tables, mimic_cxr_tables
 
-logger = logging.get_logger(__name__)
+logger = logging.get_logger(__name__)      
 
 
 def create_lookup_table(df, columns, start_idx):
@@ -892,6 +892,7 @@ class MIMICIVEDCXRMultimodalModel(VisionEncoderDecoderModel):
         right = torch.cat((upper_right, lower_right), dim=2)
 
         mixed_causality_4d_attention_mask = torch.cat((left, right), dim=-1)
+        
         return mixed_causality_4d_attention_mask
     
     @staticmethod