TREC-PM (Precision Medicine)

NOTE Maintenance of this project has moved to the JULIE Lab.

A repository containing support code and resources initially developed at the Institute for Medical Informatics, Statistics and Documentation at the Medical University of Graz (Austria) for participation at the 2017 TREC Precision Medicine Track. For further information on this track and the final results please check the official TREC-PM 2017 overview paper. Team name: imi_mug

It was then further improved for participation at the 2018 TREC Precision Medicine Track. Improvements include: support for subtemplates and the possibility to use disjunctive queries (dis_max) allowing e.g. synonyms and hypernyms to have different weights.

If you use data or code in your work, please cite our TREC 2017 proceedings paper:

TREC 2017 Precision Medicine - Medical University of Graz. Pablo López-García, Michel Oleynik, Zdenko Kasáč and Stefan Schulz. Text REtrieval Conference, Gaithersburg, MD. 2017. Available at https://trec.nist.gov/pubs/trec26/papers/imi_mug-PM.pdf.

The complete TREC 2017 proceedings are available here.

Also of interest:

• Our TREC 2017 presentation slides
• Our TREC 2017 Poster

Code Dependencies

• JDK 8+
• maven
• make (for trec_eval tool)
• gcc (for trec_eval tool)
• perl (for sample_eval tool)
• Elasticsearch 5.4.0+