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Contains predicate pair sets and validation data as described in Validation and Topic-driven Ranking for Biomedical Hypothesis Generation Systems
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evaluatedResults
evaluatedSubset
wholeSet
README.md

README.md

Validation Set and Results

In this repo are the data and results for our validation effort corresponding with THIS PAPER.

Contents:

  • ./evaluatedResults

    • contains eval files, results from MOLIERE
    • contains scripts to create ROC charts from results
  • ./wholeSet

    • contains three pair.txt files, which are pairs of UMLS terms extracted from SemMedDB.
    • extraction uses cut-year of 2010
    • we sub-sampled this set to perform our validation.
  • ./evaluatedSubset

    • contains three pair.txt files, which are subsets of their ./wholeSet counterparts.
    • these are the predicate pairs we actually used to generated our ROC curves.

You can replicate our results using the code and data provided in THIS REPO.

If you use our validation method or data, please cite us at:

@article {Sybrandt263897,
	author = {Sybrandt, Justin and Safro, Ilya},
	title = {Validation and Topic-driven Ranking for Biomedical Hypothesis Generation Systems},
	year = {2018},
	doi = {10.1101/263897},
	publisher = {Cold Spring Harbor Laboratory},
	URL = {https://www.biorxiv.org/content/early/2018/02/11/263897},
	eprint = {https://www.biorxiv.org/content/early/2018/02/11/263897.full.pdf},
	journal = {bioRxiv}
}
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