title: Nonlinear dimensionality reduction for visualizing toxicity data: distance-based versus topology-based approaches.
abstract: Over the years, a number of dimensionality reduction techniques have been proposed and used in chemoinformatics to perform nonlinear mappings. In this study, four representatives of nonlinear dimensionality reduction methods related to two different families were analyzed: distance-based approaches (Isomap and Diffusion Maps) and topology-based approaches (Generative Topographic Mapping (GTM) and Laplacian Eigenmaps). The considered methods were applied for the visualization of three toxicity datasets by using four sets of descriptors. Two methods, GTM and Diffusion Maps, were identified as the best approaches, which thus made it impossible to prioritize a single family of the considered dimensionality reduction methods. The intrinsic dimensionality assessment of data was performed by using the Maximum Likelihood Estimation. It was observed that descriptor sets with a higher intrinsic dimensionality contributed maps of lower quality. A new statistical coefficient, which combines two previously known ones, was proposed to automatically rank the maps. Instead of relying on one of the best methods, we propose to automatically generate maps with different parameter values for different descriptor sets. By following this procedure, the maps with the highest values of the introduced statistical coefficient can be automatically selected and used as a starting point for visual inspection by the user.
authors.affiliation: Laboratory of New Physical-Chemical Problems, Frumkin Institute of Physical, Chemistry & Electrochemistry, Russian Academy of Sciences, Leninsky pr-t 31, 119071 Moscow (Russia); Department of Molecular Physics, Moscow Institute of Physics & Technology, Institutsky per. 9, 141700, Dolgoprudny (Russia). nkireeva@gmail.com.
authors.forename: Natalia V
authors.initials: NV
authors.lastname: Kireeva
authors.forename: Svetlana I
authors.initials: SI
authors.lastname: Ovchinnikova
authors.forename: Igor V
authors.initials: IV
authors.lastname: Tetko
authors.forename: Abdullah M
authors.initials: AM
authors.lastname: Asiri
authors.forename: Konstantin V
authors.initials: KV
authors.lastname: Balakin
authors.forename: Aslan Yu
authors.initials: AY
authors.lastname: Tsivadze
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D016208:Databases, Factual; D004058:Diffusion; D051638:Ether-A-Go-Go Potassium Channels / Q000037:antagonists & inhibitors; D006801:Humans; D015233:Models, Statistical; D017711:Nonlinear Dynamics; D010084:Oxidation-Reduction; D010743:Phospholipids / Q000378:metabolism; D013223:Statistics as Topic / Q000379:methods*; D023382:Toxicity Tests, Acute
chemical_list: D051638:Ether-A-Go-Go Potassium Channels; D010743:Phospholipids
keywords: chemography; chemoinformatics; dimensionality reduction; drug design; topographic mapping