README.md

How Long Is Enough? Exploring the Optimal Intervals of Long-Range Clinical Note Language Modeling

Overview

Large pre-trained language models (LMs) have been widely adopted in biomedical and clinical domains, introducing many powerful LMs such as bio-lm and BioELECTRA. However, the applicability of these methods to real clinical use cases is hindered, due to the limitation of pre-trained LMs in processing long textual data with thousands of words, which is a common length for a clinical note. In this work, we explore long-range adaptation from such LMs with Longformer, allowing the LMs to capture longer clinical notes context. We conduct experiments on three n2c2 challenges datasets and a longitudinal clinical dataset from Hong Kong Hospital Authority electronic health record (EHR) system to show the effectiveness and generalizability of this concept, achieving 10% F1-score improvement. Based on our experiments, we conclude that capturing a longer clinical note interval is beneficial to the model performance, but there are different cut-off intervals to achieve the optimal performance for different target variables.

Code Provided

Our code repository provides the implementation of four n2c2 classification tasks, i.e., n2c2 2006, n2c2 2008, n2c2 2014, and n2c2 2018. Our code enable the use of BioELECTRA, bio-lm, Longformer-adapted BioELECTRA, and Longformer-adapted bio-lm models.

Setup

To use this repo:

1. Install the dependency through pip install -r requirements.txt
2. Put the local dataset inside data/n2c2_2006_smokers/*, data/n2c2_2008/*, etc
3. Run the finetuning. on your terminal do:
   • bash run_n2c2_2006_smokers.sh to finetune for n2c2_2006_smokers
   • bash run_n2c2_2008.sh to finetune for n2c2_2008
   • bash run_n2c2_2014_risk_factors.sh to finetune for n2c2_2014_risk_factors
   • bash run_n2c2_2018_track1.sh to finetune for n2c2_2018_track1

Supported Tasks

• n2c2_2006_smokers
• n2c2_2008
• n2c2_2014_risk_factors
• n2c2_2018_track1

Citation

@inproceedings{cahyawijaya-etal-2022-long,
    title = "How Long Is Enough? Exploring the Optimal Intervals of Long-Range Clinical Note Language Modeling",
    author = "Cahyawijaya, Samuel  and
      Wilie, Bryan  and
      Lovenia, Holy  and
      Zhong, Huan  and
      Zhong, MingQian  and
      Ip, Yuk-Yu Nancy  and
      Fung, Pascale",
    editor = "Lavelli, Alberto  and
      Holderness, Eben  and
      Jimeno Yepes, Antonio  and
      Minard, Anne-Lyse  and
      Pustejovsky, James  and
      Rinaldi, Fabio",
    booktitle = "Proceedings of the 13th International Workshop on Health Text Mining and Information Analysis (LOUHI)",
    month = dec,
    year = "2022",
    address = "Abu Dhabi, United Arab Emirates (Hybrid)",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.louhi-1.19",
    doi = "10.18653/v1/2022.louhi-1.19",
    pages = "160--172",
    abstract = "Large pre-trained language models (LMs) have been widely adopted in biomedical and clinical domains, introducing many powerful LMs such as bio-lm and BioELECTRA. However, the applicability of these methods to real clinical use cases is hindered, due to the limitation of pre-trained LMs in processing long textual data with thousands of words, which is a common length for a clinical note. In this work, we explore long-range adaptation from such LMs with Longformer, allowing the LMs to capture longer clinical notes context. We conduct experiments on three n2c2 challenges datasets and a longitudinal clinical dataset from Hong Kong Hospital Authority electronic health record (EHR) system to show the effectiveness and generalizability of this concept, achieving {\textasciitilde}10{\%} F1-score improvement. Based on our experiments, we conclude that capturing a longer clinical note interval is beneficial to the model performance, but there are different cut-off intervals to achieve the optimal performance for different target variables.",
}