DOI: 10.1002/minf.201100163. Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure‐Activity Modeling and Dataset Comparison

Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure‐Activity Modeling and Dataset Comparison

10.1002/minf.201100163

Crossref journal-article

Wiley

Molecular Informatics (311)

Abstract

AbstractHere, the utility of Generative Topographic Maps (GTM) for data visualization, structure‐activity modeling and database comparison is evaluated, on hand of subsets of the Database of Useful Decoys (DUD). Unlike other popular dimensionality reduction approaches like Principal Component Analysis, Sammon Mapping or Self‐Organizing Maps, the great advantage of GTMs is providing data probability distribution functions (PDF), both in the high‐dimensional space defined by molecular descriptors and in 2D latent space. PDFs for the molecules of different activity classes were successfully used to build classification models in the framework of the Bayesian approach. Because PDFs are represented by a mixture of Gaussian functions, the Bhattacharyya kernel has been proposed as a measure of the overlap of datasets, which leads to an elegant method of global comparison of chemical libraries.

Bibliography

Kireeva, N., Baskin, I. I., Gaspar, H. A., Horvath, D., Marcou, G., & Varnek, A. (2012). Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, StructureâActivity Modeling and Dataset Comparison. Molecular Informatics, 31(3â4), 301â312. Portico.

Authors 6

N. Kireeva (first)
I. I. Baskin (additional)
H. A. Gaspar (additional)
D. Horvath (additional)
G. Marcou (additional)
A. Varnek (additional)

References 39 Referenced 113

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Dates

Type	When
Created	13 years, 4 months ago (April 4, 2012, 11:40 a.m.)
Deposited	1 year, 3 months ago (April 22, 2024, 3:56 p.m.)
Indexed	3 hours, 33 minutes ago (Aug. 21, 2025, 12:42 p.m.)
Issued	13 years, 4 months ago (April 1, 2012)
Published	13 years, 4 months ago (April 1, 2012)
Published Online	13 years, 4 months ago (April 4, 2012)
Published Print	13 years, 4 months ago (April 1, 2012)

Funders 0

None

BibTeX

@article{Kireeva_2012, title={Generative Topographic Mapping (GTM): Universal Tool for Data Visualization, Structure‐Activity Modeling and Dataset Comparison}, volume={31}, ISSN={1868-1751}, url={http://dx.doi.org/10.1002/minf.201100163}, DOI={10.1002/minf.201100163}, number={3–4}, journal={Molecular Informatics}, publisher={Wiley}, author={Kireeva, N. and Baskin, I. I. and Gaspar, H. A. and Horvath, D. and Marcou, G. and Varnek, A.}, year={2012}, month=apr, pages={301–312} }

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