README.md

Towards identifying drug side effects from social media using active learning and crowd sourcing

Implementation of an active semi-supervised VAE under representativeness constraints. Accepted in Pacific Symposium for Biocomputing (PSB) 2020.

This project applies a semi-supervised VAEs on pool-based uncertainty active learning. To respect the underlying class distribution different representativeness strategies can be added.

We use this architecture to find self-experiential side-effects in tweets with Amazon Mechanical Turk.

Requirements

Requieres python 3.6+ and tensorflow-1.12+

Project Structure

|
|--data:  db.zip
|         drug_searchterm_map.csv: Contains drugnames and their coresponding searchterms.
|         word_vec_side_effects.txt: Contains side effect synonyms.
|--src
    |--bag_of_words: Contains tweet preprocessing (tweet tagger http://www.cs.cmu.edu/~ark/TweetNLP/#%23parser_down and 
    |        Lucene are requiered) for bag of word representation.
    |
    |--experiments: Contains code to compare VAE with other methods.
	|
	|-active_learning.py: Executes active VAE under representativeness constraints.