Recent years have seen particular interest in using electronic medical
records (EMRs) for secondary purposes to enhance the quality and safety of
healthcare delivery. EMRs tend to contain large amounts of valuable clinical
notes. Learning of embedding is a method for converting notes into a format
that makes them comparable. Transformer-based representation models have
recently made a great leap forward. These models are pre-trained on large
online datasets to understand natural language texts effectively. The quality
of a learning embedding is influenced by how clinical notes are used as input
to representation models. A clinical note has several sections with different
levels of information value. It is also common for healthcare providers to use
different expressions for the same concept. Existing methods use clinical notes
directly or with an initial preprocessing as input to representation models.
However, to learn a good embedding, we identified the most essential clinical
notes section. We then mapped the extracted concepts from selected sections to
the standard names in the Unified Medical Language System (UMLS). We used the
standard phrases corresponding to the unique concepts as input for clinical
models. We performed experiments to measure the usefulness of the learned
embedding vectors in the task of hospital mortality prediction on a subset of
the publicly available Medical Information Mart for Intensive Care (MIMIC-III)
dataset. According to the experiments, clinical transformer-based
representation models produced better results with getting input generated by
standard names of extracted unique concepts compared to other input formats.
The best-performing models were BioBERT, PubMedBERT, and UmlsBERT,
respectively.

本研究基于 Transformers 预训练的语言表示学习方法，将特定医学记录中的信息提取，映射到标准词汇中，并在医院死亡预测任务中测试不同输入格式的性能，结果表明使用提取的唯一概念和标准名称作为输入可以获得更好的性能。