Calculating the "fingerprints" of molecules with artificial intelligence

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.

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"."

 

Annotation:

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.

 

arö


You might also be interested in

  • 14 parameters in one go: New instrument for optoelectronics
    Science Highlight
    21.02.2024
    14 parameters in one go: New instrument for optoelectronics
    An HZB physicist has developed a new method for the comprehensive characterisation of semiconductors in a single measurement. The "Constant Light-Induced Magneto-Transport (CLIMAT)" is based on the Hall effect and allows to record 14 different parameters of transport properties of negative and positive charge carriers. The method was tested now on twelve different semiconductor materials and will save valuable time in assessing new materials for optoelectronic applications such as solar cells.
  • Sodium-ion batteries: How doping works
    Science Highlight
    20.02.2024
    Sodium-ion batteries: How doping works
    Sodium-ion batteries still have a number of weaknesses that could be remedied by optimising the battery materials. One possibility is to dope the cathode material with foreign elements. A team from HZB and Humboldt-Universität zu Berlin has now investigated the effects of doping with Scandium and Magnesium. The scientists collected data at the X-ray sources BESSY II, PETRA III, and SOLARIS to get a complete picture and uncovered two competing mechanisms that determine the stability of the cathodes.
  • BESSY II: Molecular orbitals determine stability
    Science Highlight
    07.02.2024
    BESSY II: Molecular orbitals determine stability
    Carboxylic acid dianions (fumarate, maleate and succinate) play a role in coordination chemistry and to some extent also in the biochemistry of body cells. An HZB team at BESSY II has now analysed their electronic structures using RIXS in combination with DFT simulations. The results provide information not only on electronic structures but also on the relative stability of these molecules which can influence an industry's choice of carboxylate dianions, optimizing both the stability and geometry of coordination polymers.