diff --git a/pyhealth/tasks/multimodal_mimic4.py b/pyhealth/tasks/multimodal_mimic4.py index f4f09744f..de8fbf746 100644 --- a/pyhealth/tasks/multimodal_mimic4.py +++ b/pyhealth/tasks/multimodal_mimic4.py @@ -314,21 +314,21 @@ class ClinicalNotesMIMIC4(BaseMultimodalMIMIC4Task): task_name: str = "ClinicalNotesMIMIC4" input_schema: Dict[str, Union[str, Tuple[str, Dict]]] = { - "discharge_note_times": ( - "tuple_time_text", - { - "tokenizer_model": "bert-base-uncased", - "type_tag": "note", - }, - ), - "radiology_note_times": ( - "tuple_time_text", - { - "tokenizer_model": "bert-base-uncased", - "type_tag": "note", - }, - ), - } + "discharge_note_times": ( + "tuple_time_text", + { + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", + "type_tag": "note", + }, + ), + "radiology_note_times": ( + "tuple_time_text", + { + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", + "type_tag": "note", + }, + ) + } output_schema: Dict[str, str] = {"mortality": "binary"} def __call__(self, patient: Any) -> List[Dict[str, Any]]: @@ -451,23 +451,37 @@ class ClinicalNotesICDLabsMIMIC4(BaseMultimodalMIMIC4Task): task_name: str = "ClinicalNotesICDLabsMIMIC4" input_schema: Dict[str, Union[str, Tuple[str, Dict]]] = { - "discharge_note_times": ( - "tuple_time_text", - { - "tokenizer_model": "bert-base-uncased", - "type_tag": "note", - }, - ), - "radiology_note_times": ( - "tuple_time_text", - { - "tokenizer_model": "bert-base-uncased", - "type_tag": "note", - }, - ), - "icd_codes": ("stagenet", {"padding": PADDING}), - "labs": ("stagenet_tensor", {}), - "labs_mask": ("stagenet_tensor", {}), + "discharge_note_times": ( + "tuple_time_text", + { + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", + "type_tag": "note", + }, + ), + "radiology_note_times": ( + "tuple_time_text", + { + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", + "type_tag": "note", + }, + ), + "icd_codes": ("stagenet", {"padding": PADDING}), + "labs": ("stagenet_tensor", {}), + "labs_mask": ("stagenet_tensor", {}), + } + output_schema: Dict[str, str] = {"mortality": "binary"} + + LAB_CATEGORIES: ClassVar[Dict[str, List[str]]] = { + "Sodium": ["50824", "52455", "50983", "52623"], + "Potassium": ["50822", "52452", "50971", "52610"], + "Chloride": ["50806", "52434", "50902", "52535"], + "Bicarbonate": ["50803", "50804"], + "Glucose": ["50809", "52027", "50931", "52569"], + "Calcium": ["50808", "51624"], + "Magnesium": ["50960"], + "Anion Gap": ["50868", "52500"], + "Osmolality": ["52031", "50964", "51701"], + "Phosphate": ["50970"], } output_schema: Dict[str, str] = {"mortality": "binary"}