Chemoinformatics Strasbourg Summer School 2018
University of Strasbourg, 25 June - 29 June 2018
The tutorial aims at presenting the Generative Topographic Mapping (GTM) algorithm [Bishop et al, Neural Computation 10, No. 1, 215–234 (1998)].
The GTM is an unsupervised method to map high dimensional data to a two-dimensional representation. In the process, the GTM builds a probabilistic model of the data that can be exploited for data characterization, comparison or classification and regression model building. The GTM approach will be used to analyze a dataset of flavors and to explore structure-flavor relationships. It will be the occasion to get some deeper insight into the method with a particular focus on the effects of the GTM parameterization on the obtained map.
The tutorial is based on three pieces of software :
The software are supplied on the USB key and can be downloaded for the OS of your choice :
Updated versions can be requested by contacting F. Bonachera
The licence of the software is distributed freely and a licence file, called « licence.dat » is distributed with the software for the OS of your choice (Windows, Mac or Linux).
The licence file must be installed in a proper location to be found.
C :\Users\username\AppData\local\ISIDAGTM2018\licence.dat
The file and the directory should have read and write permissions.
/Users/username/.config/ISIDAGTM2018/licence.dat
/home/username/.config/ISIDAGTM2018/licence.dat
The tutorial uses a dataset of organoleptic compounds mined (in February 2018) from the FlavorDB database [Nucleic Acids Research, 2018, Vol. 46, Database issue].
The data are distributed on the USB key and can be downloaded here : http://infochim.u-strasbg.fr/CS3_2018/Tuto1/Data/FDB.zip
The protocol of the tutorial session is available in the following document : http://infochim.u-strasbg.fr/CS3_2018/Tuto1/Tutorial_GTM+DH_20_06_2018.pdf