BACKGROUND: Artificial Neural Networks (ANN) are extensively used to model 'omics' data. Different modeling methodologies and combinations of adjustable parameters influence model performance and complicate model optimization. METHODOLOGY: We evaluated optimization of four ANN modeling parameters (learning rate annealing, stopping criteria, data split method, network architecture) using retention index (RI) data for 390 compounds. Models were assessed by independent validation (I-Val) using newly measured RI values for 1492 compounds. CONCLUSION: The best model demonstrated an I-Val standard error of 55 RI units and was built using a Ward's clustering data split and a minimally nonlinear network architecture. Use of validation statistics for stopping and final model selection resulted in better independent validation performance than the use of test set statistics.
BACKGROUND: Artificial Neural Networks (ANN) are extensively used to model 'omics' data. Different modeling methodologies and combinations of adjustable parameters influence model performance and complicate model optimization. METHODOLOGY: We evaluated optimization of four ANN modeling parameters (learning rate annealing, stopping criteria, data split method, network architecture) using retention index (RI) data for 390 compounds. Models were assessed by independent validation (I-Val) using newly measured RI values for 1492 compounds. CONCLUSION: The best model demonstrated an I-Val standard error of 55 RI units and was built using a Ward's clustering data split and a minimally nonlinear network architecture. Use of validation statistics for stopping and final model selection resulted in better independent validation performance than the use of test set statistics.
Authors: Joanne T Brindle; Henrik Antti; Elaine Holmes; George Tranter; Jeremy K Nicholson; Hugh W L Bethell; Sarah Clarke; Peter M Schofield; Elaine McKilligin; David E Mosedale; David J Grainger Journal: Nat Med Date: 2002-11-25 Impact factor: 53.440
Authors: Daniel R Albaugh; L Mark Hall; Dennis W Hill; Tzipporah M Kertesz; Marc Parham; Lowell H Hall; David F Grant Journal: J Chem Inf Model Date: 2009-04 Impact factor: 4.956
Authors: L Mark Hall; Lowell H Hall; Tzipporah M Kertesz; Dennis W Hill; Thomas R Sharp; Edward Z Oblak; Ying W Dong; David S Wishart; Ming-Hui Chen; David F Grant Journal: J Chem Inf Model Date: 2012-04-27 Impact factor: 4.956
Authors: Lochana C Menikarachchi; Shannon Cawley; Dennis W Hill; L Mark Hall; Lowell Hall; Steven Lai; Janine Wilder; David F Grant Journal: Anal Chem Date: 2012-10-23 Impact factor: 6.986
Authors: María Eugenia Monge; James N Dodds; Erin S Baker; Arthur S Edison; Facundo M Fernández Journal: Annu Rev Anal Chem (Palo Alto Calif) Date: 2019-03-18 Impact factor: 10.745