Deep Neural Networks for Real-Time Spectroscopic Analysis

Lead Research Organisation: Newcastle University
Department Name: Sch of Natural & Environmental Sciences

Abstract

Scientific breakthroughs are often strongly associated with technological developments, which enable the measurement of matter to an increased level of detail. A modern revolution is underway in X-ray spectroscopy (XS), driven by the transformative effect of next-generation, high-brilliance light sources e.g. Diamond Light Source and the European X-ray Free Electron Laser and the emergence of laboratory-based X-ray spectrometers. Alongside instrumental and methodological developments, the advances enabled in X-ray absorption (XAS) and (non-)resonant emission (XES and RXES/RIXS) spectroscopies are having far-reaching effects across the natural sciences. However, these new kinds of experiments, and their ever-higher resolution and data acquisition rates, have brought acutely into focus a new challenge: How do we efficiently and accurately analyse these data to ensure that valuable quantitative information encoded in each spectrum can be extracted?

The high information content of an XS, demands detailed theoretical treatments to link the spectroscopic observables to the underlying geometric, electronic and spin structure. However, this is a far from trivial task. A prime example is found in the XS of disordered systems, e.g. in operando catalysts, in which the spectrum represents an average signal recorded from many inequivalent absorption sites. The disorder of the system must be modelled for a quantitative analysis, but to treat theoretically every possible chemically inequivalent absorption site (or even to sample a meaningful number of such sites) is computationally challenging, resource-intensive, and time-consuming. It is presently out of reach for the majority of XS end-users and, for the most complex systems, even expert theoreticians. To add to this, it is not always apparent to end-users: a) how to apply the most appropriate theoretical treatments, or b) where more insight might be attainable from the data by their application. Consequently, the status quo is to rely heavily on empirical rules, e.g. the scaling of absorption edge position with oxidation state, or to collect reference spectra and use linear combinations of these to fit the absorption profile. As long as this status quo is unchallenged, the many XS experiments remain useful for little more than fingerprinting, and a wealth of valuable quantitative information is left unexploited, ultimately limiting our understanding.

The objective of this fellowship proposal is to develop and subsequently equip researchers with easy-to-use, computationally inexpensive, and accessible tools for the fast and automated analysis and prediction of XS. We will optimize and deploy deep neural networks (DNNs) capable of providing instantaneous predictions of XS for arbitrary absorption sites, introducing a step change in ease and accuracy of the XS data analysis workflow. Using DNNs, it is possible to reduce the time taken to predict XS data from hours/days to seconds, democratise data analysis, open the door to the development of new high-throughput XS experiments, and allow end users to plan and utilise better their beamtime allocations by facilitating on-the-fly 'real-time' analysis/diagnostics for XS data.

Publications

10 25 50
 
Description UK High-End Computing Consortium for X-ray Spectroscopy (HPC-CONEXS)
Amount £371,871 (GBP)
Funding ID EP/X035514/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 01/2023 
End 12/2026
 
Title A Deep Neural Network for Valence-to-Core X-ray Emission Spectroscopy 
Description This data is used to extend our XANESNET deep neural network (DNN) to predict the lineshape of first-row transition metal K-edge valence-to-core X-ray emission (VtC-XES) spectra. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Data set for machine learning for X-ray emission. 
URL https://data.ncl.ac.uk/articles/dataset/A_Deep_Neural_Network_for_Valence-to-Core_X-ray_Emission_Spe...
 
Title Accurate, Affordable, and Generalisable Machine Learning Simulations of Transition Metal X-ray Absorption Spectra using the XANESNET Deep Neural Network 
Description Data Supporting the Publication of the same title. 
Type Of Material Database/Collection of data 
Year Produced 2022 
Provided To Others? Yes  
Impact Training sets for machine learning for X-ray absorption spectroscopy. 
URL https://data.ncl.ac.uk/articles/dataset/Accurate_Affordable_and_Generalisable_Machine_Learning_Simul...
 
Title An On-the-Fly Deep Neural Network for Simulating Time-Resolved Spectroscopy: Predicting the Ultrafast Ring Opening Dynamics of 1,2-Dithiane 
Description Revolutionary developments in ultrafast light source technology are enabling experimental spectro-scopists to probe the structural dynamics of molecules and materials on the femtosecond timescale. The capacity to investigate ultrafast processes afforded by these resources accordingly inspires the-oreticians to carry out high-level simulations which facilitate the interpretation of the underlying dynamics from ultrafast experiments. In this Article, we implement a Deep Neural Network (DNN) to convert excited-state molecular dynamics simulations into time-resolved spectroscopic signals. Our DNN is trained on-the-fly from first-principles theoretical data obtained from a set of time-evolving molecular dynamics. The train-test process iterates for each time-step of the dynamics data until the network can predict spectra with sufficient accuracy to replace the computationally intensive quan-tum chemistry calculations required to produce them, at which point it simulates the time-resolved spectra for longer timescales. The potential of this approach is demonstrated by probing dynamics of the the ring opening of 1,2-dithiane using sulphur K-edge X-ray absorption spectroscopy. The benefits of this strategy will be more markedly apparent for simulations of larger systems which will exhibit a more notable computational burden, making this approach applicable to the study of a diverse range of complex chemical dynamics. 
Type Of Material Database/Collection of data 
Year Produced 2023 
Provided To Others? Yes  
Impact Training sets for machine learning for on-the-Fly Deep Neural Network for Simulating Time-Resolved Spectroscopy: Predicting the Ultrafast Ring Opening Dynamics of 1,2-Dithiane 
URL https://data.ncl.ac.uk/articles/dataset/An_On-the-Fly_Deep_Neural_Network_for_Simulating_Time-Resolv...
 
Description J. Olof Johansson 
Organisation University of Edinburgh
Country United Kingdom 
Sector Academic/University 
PI Contribution Experimental data, using X-ray ray free electron lasers, to study time-resolved X-ray absorption and emission on Mn small molecular magnets.
Collaborator Contribution Performing the experiments and providing the data.
Impact In progress.
Start Year 2023
 
Description Phillippe Wernet 
Organisation Lund University
Country Sweden 
Sector Academic/University 
PI Contribution A collaboration on the analysis of time-resolved x-ray data has been emerged, with the focus of applying our machine learning to time-resolved data.
Collaborator Contribution Provided data.
Impact In progress
Start Year 2023
 
Title XANESET 
Description We have developed and deployed a deep neural network-XANESNET-for predicting the lineshape of first-row transition metal K-edge x-ray absorption near-edge structure (XANES) spectra. XANESNET predicts the spectral intensities using only information about the local coordination geometry of the transition metal complexes encoded in a feature vector of weighted atom-centered symmetry functions. 
Type Of Technology Software 
Year Produced 2022 
Open Source License? Yes  
Impact We think that the theoretical simulation of X-ray spectroscopy (XS) should be fast, affordable, and accessible to all researchers. The popularity of XS is on a steep upward trajectory globally, driven by advances at, and widening access to, high-brilliance light sources such as synchrotrons and X-ray free-electron lasers (XFELs). However, the high resolution of modern X-ray spectra, coupled with ever-increasing data acquisition rates, brings into focus the challenge of accurately and cost-effectively analyzing these data. Decoding the dense information content of modern X-ray spectra demands detailed theoretical calculations that are capable of capturing satisfactorily the complexity of the underlying physics but that are - at the same time - fast, affordable, and accessible enough to appeal to researchers. This is a tall order - but we're using deep neural networks to make this a reality. 
URL https://gitlab.com/team-xnet/xanesnet
 
Title webCONEXS 
Description We have released a web portal where researchers that are not experts in simulations can perform some very simple XANES simulations. Through the web portal, three codes can be run: FDMNES, ORCA and Quantum Expresso. There are instructions of how to access the web-CONEXS and how to run the different codes available at Diamond light source when users are granted beam time. To run web-CONEXS, you need to have a federal ID and password, and also have had a proposal accepted in one of the spectroscopy beamlines at some point in the past. 
Type Of Technology Webtool/Application 
Year Produced 2023 
Open Source License? Yes  
Impact Too early to tell.