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Semi Structured ICD Coding

Partial code for the NeurIPS 2023 paper: Towards Semi-Structured Automatic ICD Coding via Tree-based Contrastive Learning.

@article{lu2023towards,
  title={Towards Semi-Structured Automatic ICD Coding via Tree-based Contrastive Learning},
  author={Lu, Chang and Reddy, Chandan K and Wang, Ping and Ning, Yue},
  journal={37th Conference on Neural Information Processing Systems (NeurIPS 2023)},
  year={2023}
}

Requirements

# For CUDA user
pip install -r requirements.txt

# For CPU user, change the torch==1.13.1+cu116 in the requirements.txt to torch==1.13.1

Running

Data Preprocessing

  1. Put DIAGNOSES_ICD.csv and NOTEEVENTS.csv to data/mimic3.
  2. Extract json files using hadm_id in the data/mimic3/ids:
python extract_data.py

The mimic3 and mimic3-50 ids are following the ICD-MSMN project. The mimic3-50l ids are following the KEPT project.

  1. Extract section titles:
python df_iapf.py

The top 23 extracted titles will be saved to data/mimic3/titles/titles.txt. All title candidates will be saved to data/mimic3/titles/all_titles.txt.

Note: Some optimization based on the paper:

  • We only selected sentences containing less than 5 words.
  • The final order of the extracted titles may be different from the paper.

Optional: Here, since it is strict to require all clinical notes to have the same titles, we performed a title synonym extraction based on cosine similarity between top titles and all titles using Sentence-Transformer. We provide the synonyms in data/mimic3/titles/title_synonyms.json.

  1. Segment clinical notes into sections:
python segment.py

The sections will be saved to data/mimic3/sections.

Contrastive Pretraining

We provide a dataset class ContrastiveDataset in the dataset.py. It can be used as follows:

dataset = ContrastiveDataset()

texts, similarity, loss_weight = dataset[0]
# texts: a dict containing positive pairs from s_i and neighbor pairs from s_j:
# texts = {
#     'text_1_i': 'xxx',
#     'text_2_i': 'xxx' or '',
#     'text_1_j': 'xxx' or '',
#     'text_2_j': 'xxx' or ''
# }
# Some field can be an empty string if the clinical note does not have the corresponding part.
#
# similarity: float. The similarity between two label trees.
#
# loss_weight: The indicator to control whether this loss should be reflected in the final loss function.
# loss_weight = {
#     'w_1i_2i': 1 if len(texts['text_1_i']) > 0 and len(texts['text_2_i']) > 0 else 0,
#     'w_1i_1j': 1 if len(texts['text_1_i']) > 0 and len(texts['text_1_j']) > 0 else 0,
#     'w_1j_2j': 1 if len(texts['text_1_j']) > 0 and len(texts['text_2_j']) > 0 else 0,
#     'w_2i_2j': 1 if len(texts['text_2_i']) > 0 and len(texts['text_2_j']) > 0 else 0
# }

Masked Section Training

We provide a dataset class MaskedSectionDataset in the dataset.py. It can be used as follows:

dataset = MaskedSectionDataset(task='mimic3', version='train', mask_rate=0.2)
# task can be chosen from ['mimic3', 'mimic3-50', 'mimic3-50l'].
# version can be chosen from ['train', 'dev', 'test'].
# mask_rate: float. It is similar to dropout rate.

text = dataset[0]
# When version == 'train', the text will be masked based on section and re-concatenated. Otherwise, the text will be the same.

Acknowledgement

  • The mimic3 and mimic3-50 ids are following the ICD-MSMN project.
  • The mimic3-50l ids are following the KEPT project.
  • The word_count_dict.json is provided by the ICD-MSMN project.
  • The word2vec models are provided by the LAAT project.
  • The diagnosis_codes.json is provided by the icd_hierarchical_structure project.