用多模态信息提升医疗编码的分词精度,让大模型更懂临床逻辑。
Multimodal Medical Code Tokenizer
- 融合文本描述与代码关系图谱,统一编码表征空间。
- 在多个数据集上使预测性能提升4.1%至11.3%,药物推荐增益最大。
- 适合医疗大模型、临床决策系统等需要精准编码理解的场景。
基于电子健康记录(EHR)训练的基础模型需将医疗编码转化为离散词汇序列。现有分词器将编码视为孤立文本,忽略其文本描述、本体层级位置及与其他编码的关系(如疾病共现、药物-治疗关联)。医疗词汇库含超过60万条编码,对临床推理至关重要。本文提出MedTok,一种多模态医疗编码分词器,利用编码的文本描述与关系上下文。它通过语言模型编码器处理文本,用图神经网络编码关系结构,并将双模态信息量化到统一的词元空间,保留模态特异性与跨模态信息。我们将MedTok集成至五个EHR模型,在院内与院外数据集上评估其在结局预测、诊断分类、药物推荐与风险分层等任务上的表现。替换原有分词器后,所有模型的AUPRC均提升:在MIMIC-III上提高4.10%,MIMIC-IV上提升4.78%,EHRShot上提升11.32%,药物推荐任务收益最显著。此外,我们验证了MedTok在医学问答系统中的应用潜力。结果表明,MedTok可作为医疗编码的统一分词器,显著提升医疗基础模型的分词质量。
原文摘要 · Abstract (English)
Foundation models trained on patient electronic health records (EHRs) require tokenizing medical data into sequences of discrete vocabulary items. Existing tokenizers treat medical codes from EHRs as isolated textual tokens. However, each medical code is defined by its textual description, its position in ontological hierarchies, and its relationships to other codes, such as disease co-occurrences and drug-treatment associations. Medical vocabularies contain more than 600,000 codes with critical information for clinical reasoning. We introduce MedTok, a multimodal medical code tokenizer that uses the text descriptions and relational context of codes. MedTok processes text using a language model encoder and encodes the relational structure with a graph encoder. It then quantizes both modalities into a unified token space, preserving modality-specific and cross-modality information. We integrate MedTok into five EHR models and evaluate it on operational and clinical tasks across in-patient and out-patient datasets, including outcome prediction, diagnosis classification, drug recommendation, and risk stratification. Swapping standard EHR tokenizers with MedTok improves AUPRC across all EHR models, by 4.10% on MIMIC-III, 4.78% on MIMIC-IV, and 11.32% on EHRShot, with the largest gains in drug recommendation. Beyond EHR modeling, we demonstrate using MedTok tokenizer with medical QA systems. Our results demonstrate the potential of MedTok as a unified tokenizer for medical codes, improving tokenization for medical foundation models.
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