Clinical event sequences consist of hundreds of clinical events that
represent records of patient care in time. Developing accurate predictive
models of such sequences is of a great importance for supporting a variety of
models for interpreting/classifying the current patient condition, or
predicting adverse clinical events and outcomes, all aimed to improve patient
care. One important challenge of learning predictive models of clinical
sequences is their patient-specific variability. Based on underlying clinical
conditions, each patient's sequence may consist of different sets of clinical
events (observations, lab results, medications, procedures). Hence, simple
population-wide models learned from event sequences for many different patients
may not accurately predict patient-specific dynamics of event sequences and
their differences. To address the problem, we propose and investigate multiple
new event sequence prediction models and methods that let us better adjust the
prediction for individual patients and their specific conditions. The methods
developed in this work pursue refinement of population-wide models to
subpopulations, self-adaptation, and a meta-level model switching that is able
to adaptively select the model with the best chance to support the immediate
prediction. We analyze and test the performance of these models on clinical
event sequences of patients in MIMIC-III database.

通过对 MIMIC-III 数据库中的患者临床事件序列进行分析和测试，我们提出并研究了多种新的事件序列预测模型和方法，旨在更好地调整个体患者和其特定状况的预测。

电子健康记录的个性化事件预测

Personalized Event Prediction for Electronic Health Records

International Classification of Diseases (ICD) coding plays an important role
in systematically classifying morbidity and mortality data. In this study, we
propose a hierarchical label-wise attention Transformer model (HiLAT) for the
explainable prediction of ICD codes from clinical documents. HiLAT firstly
fine-tunes a pretrained Transformer model to represent the tokens of clinical
documents. We subsequently employ a two-level hierarchical label-wise attention
mechanism that creates label-specific document representations. These
representations are in turn used by a feed-forward neural network to predict
whether a specific ICD code is assigned to the input clinical document of
interest. We evaluate HiLAT using hospital discharge summaries and their
corresponding ICD-9 codes from the MIMIC-III database. To investigate the
performance of different types of Transformer models, we develop
ClinicalplusXLNet, which conducts continual pretraining from XLNet-Base using
all the MIMIC-III clinical notes. The experiment results show that the F1
scores of the HiLAT+ClinicalplusXLNet outperform the previous state-of-the-art
models for the top-50 most frequent ICD-9 codes from MIMIC-III. Visualisations
of attention weights present a potential explainability tool for checking the
face validity of ICD code predictions.

本文提出了一种基于层次化标签关注 Transformer 模型（HiLAT）的方法，用于从医疗文件中解释预测 ICD 代码。研究结果表明 HiLAT 与 ClinicalplusXLNet 相比在 MIMIC-III 中的前五十个 ICD-9 代码的 F1 得分更高，且关注权重的可视化表现出潜在的解释性工具。

用于可解释 ICD 编码的层级标签关注 Transformer 模型

Hierarchical Label-wise Attention Transformer Model for Explainable ICD Coding

Objective: We investigate whether deep learning techniques for natural
language processing (NLP) can be used efficiently for patient phenotyping.
Patient phenotyping is a classification task for determining whether a patient
has a medical condition, and is a crucial part of secondary analysis of
healthcare data. We assess the performance of deep learning algorithms and
compare them with classical NLP approaches.
Materials and Methods: We compare convolutional neural networks (CNNs),
n-gram models, and approaches based on cTAKES that extract pre-defined medical
concepts from clinical notes and use them to predict patient phenotypes. The
performance is tested on 10 different phenotyping tasks using 1,610 discharge
summaries extracted from the MIMIC-III database.
Results: CNNs outperform other phenotyping algorithms in all 10 tasks. The
average F1-score of our model is 76 (PPV of 83, and sensitivity of 71) with our
model having an F1-score up to 37 points higher than alternative approaches. We
additionally assess the interpretability of our model by presenting a method
that extracts the most salient phrases for a particular prediction.
Conclusion: We show that NLP methods based on deep learning improve the
performance of patient phenotyping. Our CNN-based algorithm automatically
learns the phrases associated with each patient phenotype. As such, it reduces
the annotation complexity for clinical domain experts, who are normally
required to develop task-specific annotation rules and identify relevant
phrases. Our method performs well in terms of both performance and
interpretability, which indicates that deep learning is an effective approach
to patient phenotyping based on clinicians' notes.

本文研究了深度学习技术在自然语言处理中是否可以有效用于患者表型特征提取和预测，并与传统 NLP 方法进行比较。结果表明，卷积神经网络是一种性能优良且易解释的深度学习方法，可以有效提高患者表型预测的性能，降低注释复杂度，并自动学习与每个患者表型相关的短语。