Generalized Zero-Shot Text Classification for ICD Coding

Implementation for IJCAI 2020 paper: Generalized Zero-Shot Text Classification for ICD Coding

Dependencies

• Python 3
• torch==1.4.0
• numpy==1.18.2
• nltk==3.4.4
• scikit-learn==0.21.2
• matplotlib==3.1.1
• gensim==3.7.3
• tqdm==4.43.0
• pandas==0.24.2

Dataset and preprocessing

Please modify ICD_DATA_DIR in constant.py, which will be the main directory for saving processed data, models etc. To get started, download resources.tar.gz and extract it to ICD_DATA_DIR/resources. The resources directory contains all the necessary vocabulary, embeddings, data splits files which will be used for preprocessing and training.

The preprocessing script is expecting raw MIMIC-III database saved in /path/to/MIMIC-III/. In particular, there should be two csv files: /path/to/MIMIC-III/NOTEEVENTS.csv and /path/to/MIMIC-III/DIAGNOSES_ICD.csv

For preprocessing the raw MIMIC-III datasets, run: python3 preprocess.py --mimic_dir=/path/to/MIMIC-III/, which will extract and tokenizing patient notes accordingly and save to ICD_DATA_DIR/processed directory.

Step 0 (optional): Training base feature extractor model

The GAN model is based on a pre-trained feature extractor. To train the feature extractor model, run python3 train_base.py. The default hyper-parameters is set in get_base_config function in config.py. In particular, we use LDAM loss function by setting --class_margin C=2.0 and GRNN for encoding ICD hierarcy by setting --graph_encoder=gate.

We also provide our trained base model. Please download models.tar.gz and extract it to ICD_DATA_DIR/models. To evaluate the base model, run python3 train_base.py --evaluate.

Step 1: Training GAN model

To train the GAN model, run python3 train_gan.py. The default hyper-parameters is set in get_gan_config function in config.py.

• To include keywords prediction task when training GAN, add the arguments --top_k=20 --reg_ratio=0.01, which will include a linear layer on top of generated GAN features for predicting the top_k=20 ICD code related keywords in the patient notes. reg_ratio is the coefficient for keywords prediction loss. This task can be turned off by setting --reg_ratio=0.0.
• To include zero-shot ICD codes when training GAN, add the arguments --add_zero.

Step 2: Fine-tuning ICD code classifiers

The final step is to fine-tune the classifiers in pre-trained model using GAN generated features for few-shot and zero-shot codes. For fine-tuning, run python3 finetune.py. The default hyper-parameters is set in get_finetune_config function in config.py. Please set the arguments related to base model the same as in Step 0 and arguments related to GAN model the same as in Step 1.