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CNN for relation extraction among problem, treatment and test in clinical text.

Python 100.00%

relation_extraction_in_clinical_text's Introduction

relation_extraction_in_clinical_text

This code is for the paper entitled "Relation extraction from clinical texts using domain invariant convolutional neural network" which have been published in BioNLP at ACL-2016, Berlin, Germany

Dependencies: Python 2.7, Tensorflow, Numpy, nltk, sklearn, geniatagger

Dataset used in this work was partially availble here. For reproducing the results download complete datset from i2b2 challange that required standard Data Use Agreement and process it in the given format.

PS: The code used here is the modified version of code shared by Denny Britz for sentence classification in his blog wildML http://www.wildml.com/2015/12/implementing-a-cnn-for-text-classification-in-tensorflow/

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jhnlp ngoduyvu desh2608 shashank31mar horizon94 kaushalthecoder lyfree132 chongwf ffaisal93 yimingli90 jorgeih amabdelhameed

relation_extraction_in_clinical_text's Issues

Files Missing

Hello,

I was trying to run your code but I didn't now which file to run I suppose cnn_train.py and after fixing some errors it wasn't generating any output. Moreover, there are some files missing like helper file. I'm I missing something?

Thanks,

Question:dataset?

The patient will follow-up with Cardiology in one months time for further management of her coronary artery disease and further evaluation of her remaining RCA lesions .
further evaluation|19|20|test
her remaining rca lesions|22|25|problem
TeCP

I want to know what does each part of this data set represent? Thank you very much.

Why doesn't the model converge?

where is the wefile?

main.py mentioned 'wefile = '/home/sunilnew/python_prog/relation_extraction/word2vec/scripts/50dim_drug_disease_cbow_w9_hs.txt' ', but I cannot find this file.
Looking forward to your help.
(Ps. Please forgive my poor English~)

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