This is the official cleaned repo we used to train, evaluate and interpret for VetTag paper.

Please feel free to contact [email protected] if you have any problem using these scripts.

Please create a json file in /path/to/hypes/ with the following format.

psvg.json
{
  "data_dir": "/path/to/data/psvg/",
  "encoder_path": "/path/to/data/encoder.json",
  "prefix": "psvg_oneline",
  "label_size": 0
}

• data_dir and prefix: save data in /path/to/data/psvg/psvg_oneline_train.tsv, /path/to/data/psvg/psvg_oneline_valid.tsv and /path/to/data/psvg/psvg_oneline_test.tsv for training, validation and test. The file should only contain one line for the whole text.

• encoder_path: save vocabulary in /path/to/data/encoder.json. It is a json file with format {'hello': 0, 'world': 1, ...}.

• label_size: for unsupervised learning, label size should equal to 0.

Then use the following command to train and save the model in /path/to/exp/psvg/.

python trainer.py --outputdir /path/to/exp/psvg/ --train_emb --corpus psvg --hypes /path/to/hypes/psvg.json --batch_size 5 --bptt_size 600 --model_type transformer

Please create a json file in /path/to/hypes/ with the following format.

csu.json
{
  "data_dir": "/path/to/data/csu/",
  "encoder_path": "/path/to/data/encoder.json",
  "prefix": "csu",
  "label_size": 4577
}

• data_dir and prefix: save data in /path/to/data/csu/csu_train.tsv, /path/to/data/csu/csu_valid.tsv and /path/to/data/csu/csu_test.tsv for training, validation and test. The file contains lines of annotated clinical notes with format text <tab> label_1 <space> label_2 <space> ... <space> label_k for each line.

• encoder_path: save vocabulary in /path/to/data/encoder.json (the same file for unsupervised learning). It is a json file with format {'hello': 0, 'world': 1, ...}.

• label_size: for supervised learning, we use 4577 finegrained SNOMED diagnosis codes.

Then use the following command to train and save the model in /path/to/exp/csu/.

python trainer.py --outputdir /path/to/exp/csu/ --corpus csu --hypes /path/to/hypes/csu.json --batch_size 5 --model_type transformer --cut_down_len 600 --train_emb --hierachical --inputdir /path/to/exp/psvg/pretrained_model.pickle

Please create a json file in /path/to/hypes/ with the following format.

pp.json
{
  "data_dir": "/path/to/data/pp/",
  "encoder_path": "/path/to/data/encoder.json",
  "prefix": "pp",
  "label_size": 4577
}

• data_dir and prefix: save data in /path/to/data/csu/pp_test.tsv for test. The file contains lines of annotated clinical notes with format text <tab> label_1 <space> label_2 <space> ... <space> label_k for each line.

• encoder_path: save vocabulary in /path/to/data/encoder.json (the same file for unsupervised learning). It is a json file with format {'hello': 0, 'world': 1, ...}.

• label_size: for supervised learning, we use 4577 finegrained SNOMED diagnosis codes (the same for supervised learning).

Then use the following command to evaluate the model.

python trainer.py --outputdir /path/to/exp/pp/ --corpus pp --hypes /path/to/hypes/pp.json --batch_size 5 --model_type transformer --cut_down_len 600 --hierachical --inputdir /path/to/exp/psvg/pretrained_model.pickle

Refer to jupyter/snomed_stat.ipynb, jupyter/species_stat.ipynb, jupyter/length_label_distribution.ipynb and jupyter/analysis.ipynb

Two files are required: parents.json and labels.json (in data dir).

• labels.json: the format is [SNOMED_ID_1, SNOMED_ID_2, …, SNOMED_ID_4577], which is all 4577 SNOMED labels we use.
• parents.json: the format is {SNOMED_ID_i: parent_of_SNOMED_ID_i}, which is all SNOMED labels and their parents in the shortest path from the root node (introduced in the method section).

Refer to jupyter/interpret.ipynb and jupyter/salient_words.ipynb