17. June 2022

Calculating the "fingerprints" of molecules with artificial intelligence

HZB team uses self-learning graphical neural networks to correctly interpret experimentally obtained measurement data

The graphical neural network GNN receives small molecules as input with the task of determining their spectral responses. By matching them with the known spectra, the GNN programme learns to calculate spectra reliably. © K. Singh, A. Bande/HZB

With conventional methods, it is extremely time-consuming to calculate the spectral fingerprint of larger molecules. But this is a prerequisite for correctly interpreting experimentally obtained data. Now, a team at HZB has achieved very good results in significantly less time using self-learning graphical neural networks.

“Macromolecules but also quantum dots, which often consist of thousands of atoms, can hardly be calculated in advance using conventional methods such as DFT,” says PD Dr. Annika Bande at HZB. With her team she has now investigated how the computing time can be shortened by using methods from artificial intelligence.

The idea: a computer programme from the group of "graphical neural networks" or GNN receives small molecules as input with the task of determining their spectral responses. In the next step, the GNN programme compares the calculated spectra with the known target spectra (DFT or experimental) and corrects the calculation path accordingly. Round after round, the result becomes better. The GNN programme thus learns on its own how to calculate spectra reliably with the help of known spectra.

“We have trained five newer GNNs and found that enormous improvements can be achieved with one of them, the SchNet model: The accuracy increases by 20% and this is done in a fraction of the computation time,” says first author Kanishka Singh. Singh participates in the HEIBRiDS graduate school and is supervised by two experts from different backgrounds: computer science expert Prof. Ulf Leser from Humboldt University Berlin and theoretical chemist Annika Bande.

“Recently developed GNN frameworks could do even better,” she says. “And the demand is very high. We therefore want to strengthen this line of research and are planning to create a new postdoctoral position for it from summer onwards as part of the Helmholtz project eXplainable Artificial Intelligence for X-ray Absorption Spectroscopy.”


Graph Neural Networks for Learning Molecular Excitation Spectra
Kanishka Singh, Jannes Münchmeyer, Leon Weber, Ulf Leser and Annika Bande
Journal of Chemical Theory and Computation (2022). DOI: 10.1021/acs.jctc.2c00255


The work was carried out within the framework of the HEIBRiDS graduate school and is being supported by the Helmholtz project “eXplainable Artificial Intelligence for X-ray Absorption Spectroscopy” (XAI-4-XAS). The core of the project is to extend GNN, as used at HZB, to very large molecules in combination with the probabilistic analysis of molecular motifs developed at HEREON. It is used to capture only the relevant part of the configuration phase space of the molecules, which is necessary for the accurate prediction of X-ray spectra. The results of the ML predictions allow a rigorous interpretation of XAS experiments, so that characteristic parts of the spectrum of an extended material can be assigned 1:1 to its specific structural subgroups.


Helmholtz-Zentrum Berlin für Materialien und Energie
Young Investigator Group Theory of Electron Dynamics and Spectroscopy
Dr. Annika Bande
Phone: +49 30 8062-42026

Press Officer:
Dr. Antonia Rötger
Phone: +49 30 8062-43733


Press release HZB, 13 June 2022