Flaws in evaluation schemes for pair-input computational predictions

Yungki Park and Edward M. Marcotte
Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712

README

README.txt
uniprot_yeast.seq
uniprot_human.seq

1. Yeast data set with negative examples sampled in a random manner (Park, Bioinformatics 2011 27:3024)

(File format: Positive/Negative Uniprot_ID Uniprot_ID)

yeast_random.tar.gz

Resuls for the seven methods for this data set

yeast_random_M1_results.tar.gz
yeast_random_M2_results.tar.gz
yeast_random_M3_results.tar.gz
yeast_random_M4_results.tar.gz
yeast_random_M5_results.tar.gz
yeast_random_M6_results.tar.gz
yeast_random_M7_results.tar.gz

2. Yeast data set with negative examples sampled in a balanced manner (Park, Bioinformatics 2011 27:3024)

yeast_balanced.tar.gz

Resuls for the six methods for this data set

yeast_balanced_M1_results.tar.gz
yeast_balanced_M2_results.tar.gz
yeast_balanced_M3_results.tar.gz
yeast_balanced_M4_results.tar.gz
yeast_balanced_M5_results.tar.gz
yeast_balanced_M7_results.tar.gz

3. Human data set with negative examples sampled in a random manner

human_random.tar.gz

Resuls for the seven methods for this data set

human_random_M1_results.tar.gz
human_random_M2_results.tar.gz
human_random_M3_results.tar.gz
human_random_M4_results.tar.gz
human_random_M5_results.tar.gz
human_random_M6_results.tar.gz
human_random_M7_results.tar.gz

4. Human data set with negative examples sampled in a balanced manner

human_balanced.tar.gz

Resuls for the six methods for this data set

human_balanced_M1_results.tar.gz
human_balanced_M2_results.tar.gz
human_balanced_M3_results.tar.gz
human_balanced_M4_results.tar.gz
human_balanced_M5_results.tar.gz
human_balanced_M7_results.tar.gz

Y. Park, yungki at mail utexas edu
Feb 2011