TY - JOUR

T1 - y-Randomization and its variants in QSPR/QSAR

AU - Rücker, Christoph

AU - Rücker, G.

AU - Meringer, M.

PY - 2007/11

Y1 - 2007/11

N2 - y-Randomization is a tool used in validation of QSPR/QSAR models, whereby the performance of the original model in data description (r 2) is compared to that of models built for permuted (randomly shuffled) response, based on the original descriptor pool and the original model building procedure. We compared y-randomization and several variants thereof, using original response, permuted response, or random number pseudoresponse and original descriptors or random number pseudodescriptors, in the typical setting of multilinear regression (MLR) with descriptor selection. For each combination of number of observations (compounds), number of descriptors in the final model, and number of descriptors in the pool to select from, computer experiments using the same descriptor selection method result in two different mean highest random r 2 values. A lower one is produced by y-randomization or a variant likewise based on the original descriptors, while a higher one is obtained from variants that use random number pseudodescriptors. The difference is due to the intercorrelation of real descriptors in the pool. We propose to compare an original model's r 2 to both of these whenever possible. The meaning of the three possible outcomes of such a double test is discussed. Often y-randomization is not available to a potential user of a model, due to the values of all descriptors in the pool for all compounds not being published. In such cases random number experiments as proposed here are still possible. The test was applied to several recently published MLR QSAR equations, and cases of failure were identified. Some progress also is reported toward the aim of obtaining the mean highest r 2 of random pseudomodels by calculation rather than by tedious multiple simulations on random number variables.

AB - y-Randomization is a tool used in validation of QSPR/QSAR models, whereby the performance of the original model in data description (r 2) is compared to that of models built for permuted (randomly shuffled) response, based on the original descriptor pool and the original model building procedure. We compared y-randomization and several variants thereof, using original response, permuted response, or random number pseudoresponse and original descriptors or random number pseudodescriptors, in the typical setting of multilinear regression (MLR) with descriptor selection. For each combination of number of observations (compounds), number of descriptors in the final model, and number of descriptors in the pool to select from, computer experiments using the same descriptor selection method result in two different mean highest random r 2 values. A lower one is produced by y-randomization or a variant likewise based on the original descriptors, while a higher one is obtained from variants that use random number pseudodescriptors. The difference is due to the intercorrelation of real descriptors in the pool. We propose to compare an original model's r 2 to both of these whenever possible. The meaning of the three possible outcomes of such a double test is discussed. Often y-randomization is not available to a potential user of a model, due to the values of all descriptors in the pool for all compounds not being published. In such cases random number experiments as proposed here are still possible. The test was applied to several recently published MLR QSAR equations, and cases of failure were identified. Some progress also is reported toward the aim of obtaining the mean highest r 2 of random pseudomodels by calculation rather than by tedious multiple simulations on random number variables.

KW - Chemistry

UR - http://www.scopus.com/inward/record.url?scp=37349097759&partnerID=8YFLogxK

UR - https://www.mendeley.com/catalogue/7083c187-0c81-3b02-95f2-e1f12d23d990/

U2 - 10.1021/ci700157b

DO - 10.1021/ci700157b

M3 - Journal articles

VL - 47

SP - 2345

EP - 2357

JO - Journal of Chemical Information and Modeling

JF - Journal of Chemical Information and Modeling

SN - 1549-9596

IS - 6

ER -