lemuria-wchen / DxFormer

Code for our Bioinformatics 2022 paper: "DxFormer: A Decoupled Automatic Diagnostic System Based on Decoder-Encoder Transformer with Dense Symptom Representations"

DxFormer

Code for our Bioinformatics 2022 paper: DxFormer: A Decoupled Automatic Diagnostic System Based on Decoder-Encoder Transformer with Dense Symptom Representations.

Download data

Download the datasets, then decompress them and put them in the corrsponding documents in data/{dxy|mz4|mz10}/raw. For example, download mz4 dataset and put the dataset to the data/mz4/raw.

The dataset can be downloaded as following links:

• Dxy dataset
• MZ-4 dataset
• MZ-10 dataset

Preprocess

python preprocess.py

Accuracy Bound

The default dataset is MZ-10, please modify the code to change dataset by just replace mz10 to dxy or mz4.

python bound.py

Pre-training

python pretrain.py

Training & Inference

python train.py

Citation

If you use or extend this work, please cite this paper where it is introcuded.

@article{10.1093/bioinformatics/btac744,
    author = {Chen, Wei and Zhong, Cheng and Peng, Jiajie and Wei, Zhongyu},
    title = "{DxFormer: a decoupled automatic diagnostic system based on decoder–encoder transformer with dense symptom representations}",
    journal = {Bioinformatics},
    year = {2022},
    month = {11},
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btac744},
    url = {https://doi.org/10.1093/bioinformatics/btac744},
    note = {btac744},
    eprint = {https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btac744/47804760/btac744.pdf},
}