sajaddarabi / med2vec-pytorch

Pytorch implementation of Med2Vec.

Med2Vec in Pytorch

This is a re-implementation of Med2Vec [1] in Pytorch. It simply embeds clinical concepts into a distributed representation using skip-gram model with an aditional code loss.

To run the code first obtain the ADMISSION.CSV and DIAGNOSES_ICD.CSV from MIMIC-III database here.

Compile the data by running bash gen_data.sh make sure you set the correct paths to the files.

The directories are structured as follows:

• ./base: base trainer, data loader.
• ./configs: json files for experiments. This where you pass in arguments to the model/trainer and what have you.
• ./trainer: contains training logic, and anything that must be done to train the model.
• ./model: directory containing the med2vec model.

To train the model run the following:

python train_med2vec.py -c ./configs/config.json

note: make sure the directories are set appropiatly in ./configs/config.json.

[1] Choi, Edward, et al. "Multi-layer representation learning for medical concepts." Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining. ACM, 2016.

med2vec-pytorch's Issues

med2vec model class

In the med2vec.py, there is a self.embedding in the __init__, and there is an embedding as method. In the forward method, which one is being used?

class Med2Vec(BaseModel):
    def __init__(self, icd9_size, demographics_size=0, embedding_size=2000, hidden_size=100,):
       ...
        self.embedding = nn.Embedding(self.vocabulary_size, self.embedding_size)
...


    def embedding(self, x):
        return F.linear(x, self.embedding_w, self.embedding_b)

cannot find data_loader.utils.vocab

Hello

I am trying to run your code with mimiic data but got the following error

Traceback (most recent call last):
  File "gen_data.py", line 13, in <module>
    from data_loader.utils.vocab import Vocab
ModuleNotFoundError: No module named 'data_loader.utils'

I checked the code and could not find any implementation about Vocab.

What's more, the following lines in base_trainer.py seems also problematic

from utils.util import ensure_dir
from utils.visualization import WriterTensorboardX

I could not find the module/directory utils in the repository