From 98ddfe095d605758e8c4379ecaaccd099359a6bc Mon Sep 17 00:00:00 2001 From: Rian354 Date: Thu, 14 May 2026 05:40:11 -0400 Subject: [PATCH] fix(tasks): standardize tokenizer to Bio_ClinicalBERT across all task classes ClinicalNotesMIMIC4 and ClinicalNotesICDLabsMIMIC4 were using bert-base-uncased while the runtime encoder loaded Bio_ClinicalBERT, causing a silent token-ID mismatch on clinical terminology. Co-Authored-By: Claude Sonnet 4.6 --- pyhealth/tasks/multimodal_mimic4.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/pyhealth/tasks/multimodal_mimic4.py b/pyhealth/tasks/multimodal_mimic4.py index dbd643bf0..a87628c83 100644 --- a/pyhealth/tasks/multimodal_mimic4.py +++ b/pyhealth/tasks/multimodal_mimic4.py @@ -35,14 +35,14 @@ class ClinicalNotesMIMIC4(BaseTask): "discharge_note_times": ( "tuple_time_text", { - "tokenizer_model": "bert-base-uncased", + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", "type_tag": "note", }, ), "radiology_note_times": ( "tuple_time_text", { - "tokenizer_model": "bert-base-uncased", + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", "type_tag": "note", }, ) @@ -200,14 +200,14 @@ class ClinicalNotesICDLabsMIMIC4(BaseTask): "discharge_note_times": ( "tuple_time_text", { - "tokenizer_model": "bert-base-uncased", + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", "type_tag": "note", }, ), "radiology_note_times": ( "tuple_time_text", { - "tokenizer_model": "bert-base-uncased", + "tokenizer_model": "emilyalsentzer/Bio_ClinicalBERT", "type_tag": "note", }, ),