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DOE OSTI2023

Evolving efforts to maintain and improve XPS analysis quality in an era of increasingly diverse uses and users

Based on literature analysis, X-ray photoelectron spectroscopy (XPS) use continues to increase exponentially. This increased use is accompanied by anecdotal reports and systematic analyses indicating a growing presence of significantly flawed data analyses. Recognition of this problem within the surface analysis community has increased with an understanding that both inexperienced users and increased use of XPS outside the surface analysis community contribute to the problem. The XPS community has initiated several efforts to help address the problem, which is not unique to XPS. This paper describes some of the specific problems identified and some of the community efforts intended to address them. Here, we describe activities focused on three specific issues: (i) requests for detailed guides and protocols and bite-sized versions of information for non-experts, (ii) incomplete data and analysis reporting, and (iii) the high rate of peak fitting problems. A 2019 survey identified the need for guides, protocols, and standards to assist XPS users. One set of such guides has been published, and another is being assembled. Providing incremental bites of useful information is the goal of a series of papers on specific challenges to surface analysis with example solutions has been initiated as Notes and Insights papers in Surface and Interface Analysis. Examination of XPS-containing papers finds that information to establish the credibility and reproducibility of XPS results is often very incomplete. Unfortunately, ISO and ASTM standards require an amount of parameter reporting that seems excessive and unrealistic for many research publications. Initial approaches to develop and distribute a graded approach to parameter reporting are briefly described. Multiple efforts are underway to address the high rate of problems associated with photoelectron peak fitting. These include guides to peak fitting, guides to peak identification and fitting for specific elements, and the development of a peak fitting social network. The fitting social network is designed to facilitate interactions between new and experienced XPS users; analysts trying to fit XPS data (for publication or other reasons) can ask questions and establish dynamic conversations. Encouraging and enabling high-quality XPS analysis and reporting requires several different types of effort from all members of the surface and interface analysis community.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Advancing Fusion with Machine Learning Research Needs Workshop Report

Abstract Machine learning and artificial intelligence (ML/AI) methods have been used successfully in recent years to solve problems in many areas, including image recognition, unsupervised and supervised classification, game-playing, system identification and prediction, and autonomous vehicle control. Data-driven machine learning methods have also been applied to fusion energy research for over 2 decades, including significant advances in the areas of disruption prediction, surrogate model generation, and experimental planning. The advent of powerful and dedicated computers specialized for large-scale parallel computation, as well as advances in statistical inference algorithms, have greatly enhanced the capabilities of these computational approaches to extract scientific knowledge and bridge gaps between theoretical models and practical implementations. Large-scale commercial success of various ML/AI applications in recent years, including robotics, industrial processes, online image recognition, financial system prediction, and autonomous vehicles, have further demonstrated the potential for data-driven methods to produce dramatic transformations in many fields. These advances, along with the urgency of need to bridge key gaps in knowledge for design and operation of reactors such as ITER, have driven planned expansion of efforts in ML/AI within the US government and around the world. The Department of Energy (DOE) Office of Science programs in Fusion Energy Sciences (FES) and Advanced Scientific Computing Research (ASCR) have organized several activities to identify best strategies and approaches for applying ML/AI methods to fusion energy research. This paper describes the results of a joint FES/ASCR DOE-sponsored Research Needs Workshop on Advancing Fusion with Machine Learning, held April 30–May 2, 2019, in Gaithersburg, MD (full report available at https://science.osti.gov/-/media/fes/pdf/workshop-reports/FES_ASCR_Machine_Learning_Report.pdf ). The workshop drew on broad representation from both FES and ASCR scientific communities, and identified seven Priority Research Opportunities (PRO’s) with high potential for advancing fusion energy. In addition to the PRO topics themselves, the workshop identified research guidelines to maximize the effectiveness of ML/AI methods in fusion energy science, which include focusing on uncertainty quantification, methods for quantifying regions of validity of models and algorithms, and applying highly integrated teams of ML/AI mathematicians, computer scientists, and fusion energy scientists with domain expertise in the relevant areas.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2020

ATLAS data quality operations and performance for 2015–2018 data-taking

The ATLAS detector at the Large Hadron Collider reads out particle collision data from over 100 million electronic channels at a rate of approximately $100$ kHz, with a recording rate for physics events of approximately 1 kHz. Before being certified for physics analysis at computer centres worldwide, the data must be scrutinised to ensure they are clean from any hardware or software related issues that may compromise their integrity. Prompt identification of these issues permits fast action to investigate, correct and potentially prevent future such problems that could render the data unusable. This is achieved through the monitoring of detector-level quantities and reconstructed collision event characteristics at key stages of the data processing chain. This paper presents the monitoring and assessment procedures in place at ATLAS during 2015-2018 data-taking. Through the continuous improvement of operational procedures, ATLAS achieved a high data quality efficiency, with 95.6% of the recorded proton-proton collision data collected at $\sqrt{s}=13$ TeV certified for physics analysis.

43 PARTICLE ACCELERATORS↗

DOE OSTI2020

Protein Conformational States—A First Principles Bayesian Method

Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naïve Bayes classifier from the machine learning community for use on atom-to-atom pairwise contacts. The result is an unsupervised learning algorithm that samples a ‘distribution’ over potential classification schemes. We apply the classifier to a series of test structures and one real protein, showing that it identifies the conformational transition with >95% accuracy in most cases. A nontrivial feature of our adaptation is a new connection to information entropy that allows us to vary the level of structural detail without spoiling the categorization. This is confirmed by comparing results as the number of atoms and time-samples are varied over 1.5 orders of magnitude. Further, the method’s derivation from Bayesian analysis on the set of inter-atomic contacts makes it easy to understand and extend to more complex cases.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Questionnaire for Radioisotope Identification and Estimation from Gamma Spectra using PyRIID v2

Accurate targeting of radioisotope classifiers and estimators requires an understanding of the target problem space. In order to facilitate clear communication on expected model behavior and performance between practitioners and stakeholders on their problems, this questionnaire was created. Stakeholder responses form the basis of a trained model as well as the start of usage requirements for the model as it is integrated with analysis processes or detection systems. This questionnaire may also be useful to machine learning practitioners and gamma spectroscopists developing new algorithms as a starting point for characterizing their problem space, especially if they are using PyRIID.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

tapir: A tool for topologies, amplitudes, partial fraction decomposition and input for reductions

The demand for precision predictions in the field of high energy physics has dramatically increased over recent years. Experiments conducted at the LHC, as well as precision measurements at the intensity frontier such as Belle II require equally precise theoretical predictions to make full use of the acquired data. To match the experimental precision, second-, third- and, for certain quantities, even higher-order calculations in perturbative quantum field theory are required. To facilitate such calculations, computer software automating as many steps as possible is required. Yet, each calculation poses different challenges and thus, a high level of configurability is required. In this context we present tapir: a tool for identification, manipulation and minimization of Feynman integral families. It is designed to integrate in toolchains based on the computer algebra system FORM, the use of which is common practice in the field. tapir can be used to reduce the complexity of multi-loop problems with cut-filters, topology mapping, partial fraction decomposition and alike. Program Title:tapir CPC Library link to program files:https://doi.org/10.17632/ptc9t46xyn.1 Developer's repository link:https://gitlab.com/tapir-devs/tapir Licensing provisions: GPLv3 Programming language:python 3, C++ Nature of problem: Multi-loop computations require the automatization of a large number of different tasks related to Feynman integral topologies. Among them are the identification and minimization of integral topologies, partial fraction decomposition of topologies in the case of linearly dependent propagators as well as mapping scalar products of loop momenta to scalar functions. Solution method: The minimization of topologies is performed by comparison of their respective Nickel indices [1], even further minimization utilizes Pak's algorithm [2]. To efficiently map scalar products of loop momenta to scalar functions FORM [3] code is generated. Additional comments including restrictions and unusual features: Minimization based on Pak's algorithm slows down for many lines and scales. A coarser minimization using the Nickel indices, however, is still possible. [1]B. Nickel, D. Meiron, G.A.J. Baker, Compilation of 2-pt and 4-pt graphs for continuous spin model, Report, University of Guelph, 1977.[2]A. Pak, J. Phys. Conf. Ser. 368 (2012) 012049, https://doi.org/10.1088/1742-6596/368/1/012049, arXiv:1111.0868.[3]B. Ruijl, T. Ueda, J. Vermaseren, FORM version 4.2, arXiv:1707.06453, 7 2017.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2021

Commissioning the DIRC Detector and Searching for Axion-like Particles at GlueX

This thesis centers around problems in the study of the strong nuclear force. The GlueX DIRC, a Cherenkov radiation-based detector, was proposed to upgrade the particle identification capability of the GlueX experiment, which aims to perform quantitative tests of Quantum Chromodynamics in the nonperturbative regime by searching for and studying hybrid mesons. This thesis describes the construction, commissioning, reconstruction, and calibration of the GlueX DIRC detector. Originally proposed to solve the strong CP problem, axions and axion-like particles are hypothetical pseudoscalar particles found in many proposed extensions to the Standard Model of particle physics. This thesis presents a search for photoproduction of axion-like particles using data in photon-proton interactions collected by the GlueX experiment at Jefferson Laboratory in the $\gamma\gamma$ and $\pi^+\pi^-\pi^0$ final states of the axion-like particles. In addition, the Monte Carlo modeling of the strong interaction at low energies leads to challenges known as the event generator tuning problem. This thesis presents a novel approach to the Monte Carlo event generator tuning problem using Bayesian optimization.

Yang, Yunjie↗

DOE OSTI2023

EI_MS_ML

The unambiguous identification of compounds from their electron ionization mass (EI-MS) spectra remains a significant unsolved problem in the field of metabolomics and analytical chemistry as a whole. Typically EI-MS spectra are compared using various mathematical operations that convert the spectral similarity or differences into a distance-like metric that roughly approximates the similarity of any two spectra. A commonly used metric for this is the cosine similarity metric which has values close to one for very similar spectra and a value of zero for very dissimilar spectra; however, no metric is perfect. Due to the prevalence of structurally-similar compounds such as isomers and the prevalence of certain fragmentation patterns across structurally-dissimilar compounds, the unambiguous assignment of EI-MS spectra compounds remains difficult. Frequently, querying an observed EI-MS spectrum against a large database such as the NIST17 library yields multiple possible assignments requiring the end user to distinguish between multiple high scoring hits, or multiple low scoring hits while keeping in mind that the correct hit may not be in the database at all. Although techniques such as orthogonal information from techniques such as chromatography can greatly aid in unambiguous assignment, this also requires more complicated experimental designs and access to more complicated analytical instrumentation. Substructures can be trivially detected and represented as strings using a previously published technique called node coloring from a known chemical structure. However, for experimentally-derived EI-MS spectra this information must be derived from the spectra itself (i.e., because we do not know what compound it represents). To achieve this, the software uses techniques from the field of machine learning and a large training dataset of EI-MS spectra corresponding to known structures annotated with substructure strings, to build models that can predict the presence of a given chemical substructure from an EI-MS spectrum directly.If these predictions are of high-quality (i.e., are unlikely to be false positives), the presence of one or more predicted substructures can be used to constrain the number of possible hits for a query spectrum. Mathematically, this restriction could be expressed in many forms, but the most straight-forward implementation is to weight the cosine similarity of a query spectrum and a plausible database match with a Tanimoto-like coefficient based on the ratio of the number of substructures predicted to the number of substructures present in the potential database hit. Determining which combination of models best reduces assignment ambiguity will be achieved using a combination of manual curation and optimization techniques such as genetic algorithms. This software will perform all the steps necessary to construct said models from a training dataset and evaluate them using a holdout dataset. Various statistical analyses can be performed to determine if this approach does decrease assignment ambiguity. For example, if this approach works, on average, the rank-order of the correct assignment for the holdout set of EI-MS spectra should decrease and the weighted cosine similarities for most of the possible matches in the database should be better than the unweighted cosine similarities. Furthermore, this same pipeline can be used on real experimental data to generate less ambiguous assignments.

Mitchell, Joshua↗

DOE OSTI2022

Artificial Intelligence for Accelerating Nuclear Applications, Science, and Technology

Artificial intelligence (AI) and machine learning (ML) methods have had significant impacts in science and technology in recent years. These methods for generating models from datasets or logic-based algorithms that emulate aspects of human performance can similarly accelerate the fields of nuclear applications, science, and technology toward the IAEA goals of contributing to peace, health, and prosperity. In order to accomplish advances with AI in general and ML in particular across these fields, IAEA can play a significant role by establishing, hosting and curating centralised resources, including databases, adhering to FAIR (findable, accessible, interoperable and reusable) principles and Open Science best practices, providing stewardship of data sharing, supporting training efforts and development of relevant workforces, as well as enabling connections among the scientific, technology, mathematics, AI and ethics communities. Many areas can benefit from the use of AI in the realm of nuclear applications. In human health, these areas include clinical research, epidemiology, nutrition, medical imaging, radiotherapy and education of health professionals. AI-based tools are also being used to facilitate different clinical tasks in imaging, computer-assisted diagnosis in mammography and lung cancer screening programmes, and dose prediction in nuclear medicine procedures. ML methods in particular may also increase the efficiency and accuracy of the analysis of computerised tomography and dual-energy absorptiometry scans for body composition and bone analysis. The application of AI methods to nuclear and related technologies in food and agriculture can lead to significant advances and improved efficiency in the optimisation of agricultural production, food product development, management of supply chains, food safety and food authenticity control. In the water and environmental sector, AI can help inform policies to mitigate the world’s water problems. The application of AI techniques to hydrology and environmental sciences is expected to improve patterns identification and enable model predictions under a changing climate.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2021

Jet tagging in the Lund plane with graph networks

The identification of boosted heavy particles such as top quarks or vector bosons is one of the key problems arising in experimental studies at the Large Hadron Collider. In this article, we introduce LundNet, a novel jet tagging method which relies on graph neural networks and an efficient description of the radiation patterns within a jet to optimally disentangle signatures of boosted objects from background events. We apply this framework to a number of different benchmarks, showing significantly improved performance for top tagging compared to existing state-of-the-art algorithms. We study the robustness of the LundNet taggers to non-perturbative and detector effects, and show how kinematic cuts in the Lund plane can mitigate overfitting of the neural network to model-dependent contributions. Finally, we consider the computational complexity of this method and its scaling as a function of kinematic Lund plane cuts, showing an order of magnitude improvement in speed over previous graph-based taggers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2023

Advanced Monitoring and Control in the ANL METL Facility Using an Engineering Digital Twin

The potential benefits of using an engineering digital twin to achieve greater autonomy for monitoring and control functions in advanced reactors was investigated for the Mechanisms Engineering Test Loop (METL) liquid sodium facility at Argonne National Laboratory. The METL sodium purification system served as a representative system as it requires significant human in-the-loop interaction to accomplish its design function. The objective was to demonstrate how real-time operation could be automated while preserving oversight of the operator for ensuring that the system design functions are met. A digital twin model of the purification system was developed for both the cold trap purification loop and plugging meter diagnostic loop using information from the METL piping and instrumentation diagram (P&ID). Automated monitoring and diagnosis of component degradation in the METL facility was demonstrated in tests using the PRO-AID health monitoring software with the digital twin model incorporated in the library of components. Component failures were introduced and were successfully diagnosed in real time. These tests serve to demonstrate an advanced monitoring capability able to differentiate sensor degradation from component degradation, to generate a rank ordering of probabilities of different failure mechanisms that serves to circumvent the false alarm problem with current anomaly detection methods, and how facility monitoring can be transformed from anomaly detection to identification of a specific fault. Automated control of the purification system was demonstrated through simulations that exercised a model predictive controller designed using the digital twin model. Results of these simulations compared favorably with experimental data showing very good reference tracking response with negligible overshoot. In conclusion, these pilot tests and simulations successfully demonstrated the use of a digital twin for improved automation of monitoring and control. It was shown how the digital twin enables switching between control modes from cold trap operation where impurities are removed to plugging meter operation where impurity concentrations are measured.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2022

Latent Space Dynamics Identification

LaSDI is a data-driven physical simulation software that forms a latent space for a given high-fidelity model and discovers a set of ordinary differential equations for the latent space dynamics. It allows a fast and accurate solution process, which is useful for multi-query decision making applications, such as design optimization and uncertainty quantification. The performance of the LaSDI framework is demonstrated on four different problems, i.e., 1D and 2D Burgers equations, nonlinear heat conduction, and radial advection problems. Both linear and nonlinear compression techniques, such as neural network and proper orthogonal decomposition, are used to form a latent space. A concept of local dynamics identification procedure is introduced to enable a parametric model, which enhances the accuracy level over a given parameter space.

Fries, William↗

DOE OSTI2024

Red-QAOA: Efficient Variational Optimization through Circuit Reduction

The Quantum Approximate Optimization Algorithm (QAOA) provides a quantum solution for combinatorial optimization problems. However, the optimal parameter searching process of QAOA is greatly affected by noise, leading to non-optimal solutions. This paper introduces a novel approach to optimize QAOA by exploiting the energy landscape concentration of similar instances via graph reduction, thus addressing the effect of noise. We formalize the notion of similar instances in QAOA and develop a Simulated Annealing-based graph reduction algorithm, called Red-QAOA, to identify the most similar subgraph for efficient parameter optimization. Red-QAOA outperforms state-of-the-art Graph Neural Network (GNN) based graph pooling techniques in performance and demonstrates effectiveness on a diverse set of real-world optimization problems encompassing 3200 graphs. Red-QAOA reduced the node counts and edge counts by 28% and 37%, respectively, while maintaining a low mean square error of 2%. These enable the identification of an optimal parameter set that is closer to the ideal true optimal solution in the presence of noise. By substantially streamlining the search for QAOA parameters, our approach sets the stage for the practical application of quantum algorithms in solving complex optimization problems.

Wang, Meng↗

DOE OSTI2020

Source identification by non-negative matrix factorization combined with semi-supervised clustering

Machine-learning methods and apparatus are provided to solve blind source separation problems with an unknown number of sources and having a signal propagation model with features such as wave-like propagation, medium-dependent velocity, attenuation, diffusion, and/or advection, between sources and sensors. In exemplary embodiments, multiple trials of non-negative matrix factorization are performed for a fixed number of sources, with selection criteria applied to determine successful trials. A semi-supervised clustering procedure is applied to trial results, and the clustering results are evaluated for robustness using measures for reconstruction quality and cluster separation. The number of sources is determined by comparing these measures for different trial numbers of sources. Source locations and parameters of the signal propagation model can also be determined. Disclosed methods are applicable to a wide range of spatial problems including chemical dispersal, pressure transients, and electromagnetic signals, and also to non-spatial problems such as cancer mutation.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2023

Source identification by non-negative matrix factorization combined with semi-supervised clustering

Alexandrov, Boian S.↗

DOE OSTI2020

Novel strategies for modal-based structural material identification

Here, we present modal-based methods for model calibration in structural dynamics, and address several key challenges in the solution of gradient-based optimization problems with eigenvalues and eigenvectors, including the solution of singular Helmholtz problems encountered in sensitivity calculations, non-differentiable objective functions caused by mode swapping during optimization, and cases with repeated eigenvalues. Unlike previous literature that relied on direct solution of the eigenvector adjoint equations, we present a parallel iterative domain decomposition strategy (Adjoint Computation via Modal Superposition with Truncation Augmentation) for the solution of the singular Helmholtz problems. For problems with repeated eigenvalues we present a novel Mode Separation via Projection algorithm, and in order to address mode swapping between inverse iterations we present a novel Injective mode ordering metric. We present the implementation of these methods in a massively parallel finite element framework with the ability to use measured modal data to extract unknown structural model parameters from large complex problems. A series of increasingly complex numerical examples are presented that demonstrate the implementation and performance of the methods in a massively parallel finite element framework [7], [5], using gradient-based optimization techniques in the Rapid Optimization Library (ROL) [21].

36 MATERIALS SCIENCE↗

DOE OSTI2020

Structural characterization and computational analysis of PDZ domains in Monosiga brevicollis

Abstract Identification of the molecular networks that facilitated the evolution of multicellular animals from their unicellular ancestors is a fundamental problem in evolutionary cellular biology. Choanoflagellates are recognized as the closest extant nonmetazoan ancestors to animals. These unicellular eukaryotes can adopt a multicellular‐like “rosette” state. Therefore, they are compelling models for the study of early multicellularity. Comparative studies revealed that a number of putative human orthologs are present in choanoflagellate genomes, suggesting that a subset of these genes were necessary for the emergence of multicellularity. However, previous work is largely based on sequence alignments alone, which does not confirm structural nor functional similarity. Here, we focus on the PDZ domain, a peptide‐binding domain which plays critical roles in myriad cellular signaling networks and which underwent a gene family expansion in metazoan lineages. Using a customized sequence similarity search algorithm, we identified 178 PDZ domains in the Monosiga brevicollis proteome. This includes 11 previously unidentified sequences, which we analyzed using Rosetta and homology modeling. To assess conservation of protein structure, we solved high‐resolution crystal structures of representative M. brevicollis PDZ domains that are homologous to human Dlg1 PDZ2, Dlg1 PDZ3, GIPC, and SHANK1 PDZ domains. To assess functional conservation, we calculated binding affinities for mbGIPC, mbSHANK1, mbSNX27, and mbDLG‐3 PDZ domains from M. brevicollis . Overall, we find that peptide selectivity is generally conserved between these two disparate organisms, with one possible exception, mbDLG‐3. Overall, our results provide novel insight into signaling pathways in a choanoflagellate model of primitive multicellularity.

Gao, Melody↗

DOE OSTI2021

Predicting temperature-dependent ultimate strengths of body-centered-cubic (BCC) high-entropy alloys

This paper presents a bilinear log model, for predicting temperature-dependent ultimate strength of high-entropy alloys (HEAs) based on 21 HEA compositions. We consider the break temperature, T break , introduced in the model, an important parameter for design of materials with attractive high-temperature properties, one warranting inclusion in alloy specifications. For reliable operation, the operating temperature of alloys may need to stay below T break . We introduce a technique of global optimization, one enabling concurrent optimization of model parameters over low-temperature and high-temperature regimes. Furthermore, we suggest a general framework for joint optimization of alloy properties, capable of accounting for physics-based dependencies, and show how a special case can be formulated to address the identification of HEAs offering attractive ultimate strength. We advocate for the selection of an optimization technique suitable for the problem at hand and the data available, and for properly accounting for the underlying sources of variations.

36 MATERIALS SCIENCE↗