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This repository holds a polished subset of the main MOLIERE repository. Here is a single tool with a easy to use python interface for running the Moliere Query Pipeline.
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README.md

MOLIERE QUERY RUNNER

This repo stores a polished subset of the main MOLIERE code, and provides a simple python interface to query the MOLIERE knowledge network for new hypotheses.

System Requirements

  • gcc (something recent enough to support c++11)
  • mpich (mpich 1, NOT 2, needs to provide mpicxx)
  • python 3
  • preferred: some sort of parallel file system

To run on Palmetto simply use module load gcc mpich python.

Install Process

The install process is pretty informal. The following steps are how I would setup Moliere on a linux system.

export MOLIERE_HOME=<some install directory>
mkdir -p $MOLIERE_HOME
cd $MOLIERE_HOME
git clone https://github.com/JSybrandt/Moliere_Query_Runner .
make

Next, you just need to get the data file into $MOLIERE_HOME/data. The latest data we have avalible can be found in the following link:

Get Data Here (Google Drive Link)

Running

Okay, now you have everything you need, assuming you ran make, setup the $MOLIERE_HOME environment variable, and downloaded the provided data in to $MOLIERE_HOME/data. To run our system, you will be executing runQuery.py. Note, feel free to move this file anywhere you would like, as long as $MOLIERE_HOME is set, you're good to go.

If you run runQuery.py -h you can see the options for the system. But, the general usage is going to be runQuery.py -n $TOPIC_COUNT -m $TERM_A $TERM_B. Note that -n sets the number of topics (defaults to 100) and -m moves the resulting topic model and evaluation files from the local cache (default to /tmp) to the working directory.

Citation

The work shown here is primarily based off this paper so if you use our tool in research, please include the following citation:

@inproceedings{Sybrandt:2017:MAB:3097983.3098057,
 author = {Sybrandt, Justin and Shtutman, Michael and Safro, Ilya},
 title = {MOLIERE: Automatic Biomedical Hypothesis Generation System},
 booktitle = {Proceedings of the 23rd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
 series = {KDD '17},
 year = {2017},
 isbn = {978-1-4503-4887-4},
 location = {Halifax, NS, Canada},
 pages = {1633--1642},
 numpages = {10},
 url = {http://doi.acm.org/10.1145/3097983.3098057},
 doi = {10.1145/3097983.3098057},
 acmid = {3098057},
 publisher = {ACM},
 address = {New York, NY, USA},
 keywords = {hypothesis generation, mining scientific publications, topic modeling, undiscovered public knowledge},
}
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