Cannot able to Interpret Output of npz model File about med2vec HOT 6 CLOSED

Hi Shashwat,

W_output and b_output are used in Med2Vec training phase only.
They are used to predict the neighboring visits.
The weights (embeddings) you might be interested are W_emb since they are used to encode medical codes such as diagnosis codes or medication codes.

Best,
Ed

from med2vec.

Thanks, Ed!
But Just to get a more clear picture-

W_emb - These are embedding used for encoding medical codes,So these encoding is based on Med2Vec Architecture.
W_outputs - These are predicted neighbouring visits

Please Correct me if I am getting it wrong
What about W_hidden and b_hidden?

Best ,
Shashwat

from med2vec.

W_output is not the predicted neighboring visits.
It is "used" to predict neighboring visits. It is W_s of Eq.2 in the paper, which is used right before the softmax layer.
W_hidden is used to derive the visit embeddings. It is W_v in Fig.2 of the paper.
(A visit is a set of medical codes)
And, of course, W_emb is W_c in Fig.2 of the paper.
Hope this clarifies.

Best,
Ed

from med2vec.

Ok Ed! I got the point
Sorry for raising so many issues
So how can I get the final output of Med2Vec.
Actually I want to use the learned visit level and code level representation from Med2Vec.
My problem statement is to use these learned visit as well as code representation in RNN for predicting Type II diabetes
Here are some questions-
1.So Is there any way to use these learned visit level and code level representations and how can I derive it without using any mathematical formula?
2. Is there any way to use these learned visit level and code level representations to build the model?

Thank You!

from med2vec.

1. The current implementation does not let you generate visit embeddings and code embeddings after you've trained the parameters (and I don't plan to update the code, since Theano is no longer maintained) So you will need to follow the equations in the paper to generate the embeddings yourself.
   They are pretty straightforward actually. For visit embedding, all you need to do is format your data as described in README, then just follow lines 65, 66, 67. For code embedding, the i-th row of W_emb is the code embedding for the i-th code.

2. That's up to you. Whether you want to use the visit embeddings as input to the RNN, or you want to sum the code embeddings yourself and feed it to the RNN, you can try many different approaches.

from med2vec.

Thanks Ed!

from med2vec.