Multi-Level Representation Learning for Chinese Medical Entity Recognition: Model Development and Validation

Automatic quantitative stroke severity assessment based on Chinese clinical named entity recognition with domain-adaptive pre-trained large language model

BACKGROUND

Stroke is a prevalent disease with a significant global impact. Effective assessment of stroke severity is vital for an accurate diagnosis, appropriate treatment, and optimal clinical outcomes. The National Institutes of Health Stroke Scale (NIHSS) is a widely used scale for quantitatively assessing stroke severity. However, the current manual scoring of NIHSS is labor-intensive, time-consuming, and sometimes unreliable. Applying artificial intelligence (AI) techniques to automate the quantitative assessment of stroke on vast amounts of electronic health records (EHRs) has attracted much interest.

OBJECTIVE

This study aims to develop an automatic, quantitative stroke severity assessment framework through automating the entire NIHSS scoring process on Chinese clinical EHRs.

METHODS

Our approach consists of two major parts: Chinese clinical named entity recognition (CNER) with a domain-adaptive pre-trained large language model (LLM) and automated NIHSS scoring. To build a high-performing CNER model, we first construct a stroke-specific, densely annotated dataset "Chinese Stroke Clinical Records" (CSCR) from EHRs provided by our partner hospital, based on a stroke ontology that defines semantically related entities for stroke assessment. We then pre-train a Chinese clinical LLM coined "CliRoberta" through domain-adaptive transfer learning and construct a deep learning-based CNER model that can accurately extract entities directly from Chinese EHRs. Finally, an automated, end-to-end NIHSS scoring pipeline is proposed by mapping the extracted entities to relevant NIHSS items and values, to quantitatively assess the stroke severity.

RESULTS

Results obtained on a benchmark dataset CCKS2019 and our newly created CSCR dataset demonstrate the superior performance of our domain-adaptive pre-trained LLM and the CNER model, compared with the existing benchmark LLMs and CNER models. The high F1 score of 0.990 ensures the reliability of our model in accurately extracting the entities for the subsequent automatic NIHSS scoring. Subsequently, our automated, end-to-end NIHSS scoring approach achieved excellent inter-rater agreement (0.823) and intraclass consistency (0.986) with the ground truth and significantly reduced the processing time from minutes to a few seconds.

CONCLUSION

Our proposed automatic and quantitative framework for assessing stroke severity demonstrates exceptional performance and reliability through directly scoring the NIHSS from diagnostic notes in Chinese clinical EHRs. Moreover, this study also contributes a new clinical dataset, a pre-trained clinical LLM, and an effective deep learning-based CNER model. The deployment of these advanced algorithms can improve the accuracy and efficiency of clinical assessment, and help improve the quality, affordability and productivity of healthcare services.

An Entity Extraction Pipeline for Medical Text Records Using Large Language Models: Analytical Study

BACKGROUND

The study of disease progression relies on clinical data, including text data, and extracting valuable features from text data has been a research hot spot. With the rise of large language models (LLMs), semantic-based extraction pipelines are gaining acceptance in clinical research. However, the security and feature hallucination issues of LLMs require further attention.

OBJECTIVE

This study aimed to introduce a novel modular LLM pipeline, which could semantically extract features from textual patient admission records.

METHODS

The pipeline was designed to process a systematic succession of concept extraction, aggregation, question generation, corpus extraction, and question-and-answer scale extraction, which was tested via 2 low-parameter LLMs: Qwen-14B-Chat (QWEN) and Baichuan2-13B-Chat (BAICHUAN). A data set of 25,709 pregnancy cases from the People's Hospital of Guangxi Zhuang Autonomous Region, China, was used for evaluation with the help of a local expert's annotation. The pipeline was evaluated with the metrics of accuracy and precision, null ratio, and time consumption. Additionally, we evaluated its performance via a quantified version of Qwen-14B-Chat on a consumer-grade GPU.

RESULTS

The pipeline demonstrates a high level of precision in feature extraction, as evidenced by the accuracy and precision results of Qwen-14B-Chat (95.52% and 92.93%, respectively) and Baichuan2-13B-Chat (95.86% and 90.08%, respectively). Furthermore, the pipeline exhibited low null ratios and variable time consumption. The INT4-quantified version of QWEN delivered an enhanced performance with 97.28% accuracy and a 0% null ratio.

CONCLUSIONS

The pipeline exhibited consistent performance across different LLMs and efficiently extracted clinical features from textual data. It also showed reliable performance on consumer-grade hardware. This approach offers a viable and effective solution for mining clinical research data from textual records.

Disease prediction based on multi-type data fusion from Chinese electronic health record

Disease prediction by using a variety of healthcare data to assist doctors in disease diagnosis is becoming a more and more important research topic recently. This paper proposes a disease prediction model that fuses multiple types of encoded representations of Chinese electronic health records (EHRs). The model framework utilizes a multi-head self-attention mechanism, which combines textual and numerical features to enhance text representations. The BiLSTM-CRF and TextCNN models are used, respectively, to extract entities and then obtain the embedding representations of them. The representations of text and entities in it are combined together for formulating representations of EHRs. The experimental results on EHRs data collected from a Three Grade Class B Hospital General in Gansu Province, China, show that our model achieved an F1 score of 91.92%, which outperforms the previous baseline methods.

Health Natural Language Processing: Methodology Development and Applications

With the rapid growth of information technology, the necessity for processing substantial amounts of health data using advanced information technologies is increasing. A large amount of valuable data exists in natural text such as diagnosis text, discharge summaries, online health discussions, and eligibility criteria of clinical trials. Health natural language processing, as an interdisciplinary field of natural language processing and health care, plays a substantial role in a wide scope of both methodology development and applications. This editorial shares the most recent methodology innovations of health natural language processing and applications in the medical domain published in this JMIR Medical Informatics special theme issue entitled "Health Natural Language Processing: Methodology Development and Applications".

Year 2020 (with COVID): Observation of Scientific Literature on Clinical Natural Language Processing

Objectives: To analyze the content of publications within the medical NLP domain in 2020.

Methods: Automatic and manual preselection of publications to be reviewed, and selection of the best NLP papers of the year. Analysis of the important issues.

Results: Three best papers have been selected in 2020. We also propose an analysis of the content of the NLP publications in 2020, all topics included.

Conclusion: The two main issues addressed in 2020 are related to the investigation of COVID-related questions and to the further adaptation and use of transformer models. Besides, the trends from the past years continue, such as diversification of languages processed and use of information from social networks