title: Practical outcomes of applying ensemble machine learning classifiers to High-Throughput Screening (HTS) data analysis and screening.
abstract: Over the years numerous papers have presented the effectiveness of various machine learning methods in analyzing drug discovery biological screening data. The predictive performance of models developed using these methods has traditionally been evaluated by assessing performance of the developed models against a portion of the data randomly selected for holdout. It has been our experience that such assessments, while widely practiced, result in an optimistic assessment. This paper describes the development of a series of ensemble-based decision tree models, shares our experience at various stages in the model development process, and presents the impact of such models when they are applied to vendor offerings and the forecasted compounds are acquired and screened in the relevant assays. We have seen that well developed models can significantly increase the hit-rates observed in HTS campaigns.
authors.affiliation: Simmons Consulting, 52 Windybush Way, Titusville, New Jersey 08560, DuPont Stine Haskell Research Laboratories, 1090 Elkton Road, Newark, Delaware 19711, USA. KirkASimmons@gmail.com
authors.forename: Kirk
authors.initials: K
authors.lastname: Simmons
authors.forename: John
authors.initials: J
authors.lastname: Kinney
authors.forename: Aaron
authors.initials: A
authors.lastname: Owens
authors.forename: Daniel A
authors.initials: DA
authors.lastname: Kleier
authors.forename: Karen
authors.initials: K
authors.lastname: Bloch
authors.forename: Dave
authors.initials: D
authors.lastname: Argentar
authors.forename: Alicia
authors.initials: A
authors.lastname: Walsh
authors.forename: Ganesh
authors.initials: G
authors.lastname: Vaidyanathan
mesh_terms: D001185:Artificial Intelligence; D003627:Data Interpretation, Statistical; D003663:Decision Trees; D055808:Drug Discovery / Q000706:statistics & numerical data; D004353:Drug Evaluation, Preclinical / Q000706:statistics & numerical data*; D048088:Informatics; D015394:Molecular Structure; D016571:Neural Networks, Computer