Visualization of very large high-dimensional data sets as minimum spanning trees

Probst, Daniel; Reymond, Jean-Louis (2020). Visualization of very large high-dimensional data sets as minimum spanning trees. Journal of cheminformatics, 12(1) Springer 10.1186/s13321-020-0416-x

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The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.

Item Type:

Journal Article (Original Article)

Division/Institute:

08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

UniBE Contributor:

Probst, Daniel, Reymond, Jean-Louis

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry

ISSN:

1758-2946

Publisher:

Springer

Language:

English

Submitter:

Sandra Tanja Zbinden Di Biase

Date Deposited:

19 Jan 2021 08:37

Last Modified:

05 Dec 2022 15:42

Publisher DOI:

10.1186/s13321-020-0416-x

BORIS DOI:

10.48350/148840

URI:

https://boris.unibe.ch/id/eprint/148840

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