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DOE OSTI2022

Neural Network Solver for Small Quantum Clusters

Machine learning approaches have recently been applied to the study of various problems in physics. Most of these studies are focused on interpreting the data generated by conventional numerical methods or the data on an existing experimental database. An interesting question is whether it is possible to use a machine learning approach, in particular a neural network, for solving the many-body problem. In this paper, we present a neural network solver for the single impurity Anderson model, the paradigm of an interacting quantum problem in small clusters. We demonstrate that the neural-network-based solver provides quantitative accurate results for the spectral function as compared to the exact diagonalization method. This opens the possibility of utilizing the neural network approach as an impurity solver for other many-body numerical approaches, such as the dynamical mean field theory.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Towards robust surrogate models: Benchmarking machine learning approaches to expediting phase field simulations of brittle fracture

Data-driven approaches have the potential to make modeling complex, nonlinear physical phenomena significantly more computationally tractable. For example, computational modeling of fracture is a core challenge where machine learning techniques have the potential to provide a much needed speedup that would enable progress in areas such as multi-scale modeling and uncertainty quantification. Currently, phase field modeling (PFM) of fracture is one such approach that offers a convenient variational formulation to model crack nucleation, branching and propagation. To date, machine learning techniques have shown promise in approximating PFM simulations. While standard fracture benchmarks represent realistic scenarios frequently observed in practice, they typically do not provide sufficiently challenging tests for data-driven methods. Here, to address this gap, we introduce a challenging dataset based on PFM simulations designed to benchmark and advance ML methods for fracture modeling. This dataset includes three energy decomposition methods, two boundary conditions, and 1000 random initial crack configurations for a total of 6000 simulations. Each sample contains 100 time steps capturing the temporal evolution of the crack field. Alongside this dataset, we also implement and evaluate Physics Informed Neural Networks (PINN), Fourier Neural Operators (FNO), and UNet models as baselines, and explore the impact of ensembling strategies on prediction accuracy. With this combination of our dataset and baseline models drawn from the literature we aim to provide a standardized and challenging benchmark for evaluating machine learning approaches to solid mechanics. Our results highlight both the promise and limitations of popular current models, and demonstrate the utility of this dataset as a testbed for advancing machine learning in fracture mechanics research.

Benchmark dataset↗

DOE OSTI2022

Kingdom-Wide Analysis of Fungal Protein-Coding and tRNA Genes Reveals Conserved Patterns of Adaptive Evolution

Protein-coding genes evolved codon usage bias due to the combined but uneven effects of adaptive and nonadaptive influences. Studies in model fungi agree on codon usage bias as an adaptation for fine-tuning gene expression levels; however, such knowledge is lacking for most other fungi. Our comparative genomics analysis of over 450 species supports codon usage and transfer RNAs (tRNAs) as coadapted for translation speed and this is most likely a realization of convergent evolution. Rather than drift, phylogenetic reconstruction inferred adaptive radiation as the best explanation for the variation of interspecific codon usage bias. Although the phylogenetic signals for individual codon and tRNAs frequencies are lower than expected by genetic drift, we found remarkable conservation of highly expressed genes being codon optimized for translation by the most abundant tRNAs, especially by inosine-modified tRNAs. As an application, we present a sequence-to-expression neural network that uses codons to reliably predict highly expressed transcripts. The kingdom Fungi, with over a million species, includes many key players in various ecosystems and good targets for biotechnology. Collectively, our results have implications for better understanding the evolutionary success of fungi, as well as informing the biosynthetic manipulation of fungal genes.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

A Machine‐Learning‐Assisted Stochastic Cloud Population Model as a Parameterization of Cumulus Convection

Abstract A machine‐learning‐assisted stochastic cloud population model is coupled with the Advanced Research Weather Research and Forecasting (WRF) model to represent fluctuations in the cloud‐base mass flux associated with the life cycles and interactions among cumulus convection cells. In this cloud population model, the size distribution and the associated cloud‐base mass flux of the convective cells are related to their previous state and to the change in the total convective area via a transition function. The convective area tendency in turn is assumed to depend on the cloud‐base mass flux that is resolved by the host WRF model. The transition function is represented by a single hidden‐layer neural network trained by the evolution of convective cell size distributions in a 1‐km grid‐spacing WRF simulation run over the Australian Monsoon region. At every grid point of the host model, the cloud population model predicts the cell size and cloud‐base mass flux distributions from which a random sample of cells is fed to an entraining parcel model that calculates precipitation as well as the associated liquid water potential temperature and total moisture tendencies. These tendencies are averaged over the cells and provided to the host model. Several regional simulations are performed over tropical and midlatitude domains to test this as a potential approach to scale‐aware parameterization. It is shown that such an approach could be a new promising path to simulating realistic precipitation statistics and propagation of precipitation associated with the Madden‐Julian Oscillation while maintaining realistic depictions of the diurnal cycle over both land and ocean.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

Benchmarking materials property prediction methods: the Matbench test set and Automatminer reference algorithm

Abstract We present a benchmark test suite and an automated machine learning procedure for evaluating supervised machine learning (ML) models for predicting properties of inorganic bulk materials. The test suite, Matbench, is a set of 13 ML tasks that range in size from 312 to 132k samples and contain data from 10 density functional theory-derived and experimental sources. Tasks include predicting optical, thermal, electronic, thermodynamic, tensile, and elastic properties given a material’s composition and/or crystal structure. The reference algorithm, Automatminer, is a highly-extensible, fully automated ML pipeline for predicting materials properties from materials primitives (such as composition and crystal structure) without user intervention or hyperparameter tuning. We test Automatminer on the Matbench test suite and compare its predictive power with state-of-the-art crystal graph neural networks and a traditional descriptor-based Random Forest model. We find Automatminer achieves the best performance on 8 of 13 tasks in the benchmark. We also show our test suite is capable of exposing predictive advantages of each algorithm—namely, that crystal graph methods appear to outperform traditional machine learning methods given ~10 4 or greater data points. We encourage evaluating materials ML algorithms on the Matbench benchmark and comparing them against the latest version of Automatminer.

36 MATERIALS SCIENCE↗

DOE OSTI2026

How Silica Surface Chemistry Modulates Interfacial Water: Insights from Machine Learning Molecular Dynamics

Controlling water structure and dynamics at silica interfaces are central to a wide range of technologies, including protective oxide layers for solar water splitting and nanoporous membranes. In this work, we develop a machine learning interatomic potential, trained via active learning, to achieve ab initio accuracy for water confined between hydroxylated silica surfaces over a range of silanol coverages and slit widths. We find that partially hydroxylated surfaces (50 and 75% OH) support stronger water−surface hydrogen bonding and more extended interfacial density profiles than fully hydroxylated (100% OH) surfaces, indicating that increasing OH coverage does not necessarily strengthen interfacial hydrogenbond networks. Translational diffusion decreases approximately linearly with slit width and OH coverage, whereas rotational dynamics respond nonlinearly. In particular, at the smallest slit width of 5 Å, 75% OH coverage produces an enhanced local tetrahedral ordered interfacial network that strongly suppresses reorientation, while 100% coverage yields a crowded, disordered interfacial layer that also hinders rotation. In contrast, the 50% OH coverage is sufficiently sparse that it does not markedly alter water structure or dynamics under confinement. These results show that coupled control of pore size and surface chemistry enables nonlinear tuning of interfacial water structure and transport, providing a design strategy for optimizing porous silica for either enhanced interfacial stability and controlled reactivity or rapid and selective transport.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2023

Refining fast simulation using machine learning

At the CMS experiment, a growing reliance on the fast Monte Carlo application (FastSim) will accompany the high luminosity and detector granularity expected in Phase 2. The FastSim chain is roughly 10 times faster than the application based on the GEANT4 detector simulation and full reconstruction referred to as FullSim. However, this advantage comes at the price of decreased accuracy in some of the final analysis observables. In this contribution, a machine learning-based technique to refine those observables is presented. We employ a regression neural network trained with a sophisticated combination of multiple loss functions to provide post-hoc corrections to samples produced by the FastSim chain. The results show considerably improved agreement with the FullSim output and an improvement in correlations among output observables and external parameters. This technique is a promising replacement for existing correction factors, providing higher accuracy and thus contributing to the wider usage of FastSim.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2020

Predicting lake surface water phosphorus dynamics using process-guided machine learning

Phosphorus (P) loading to lakes is degrading the quality and usability of water globally. Accurate predictions of lake P dynamics are needed to understand whole-ecosystem P budgets, as well as the consequences of changing lake P concentrations for water quality. However, complex biophysical processes within lakes, along with limited observational data, challenge our capacity to reproduce short-term lake dynamics needed for water quality predictions, as well as long-term dynamics needed to understand broad scale controls over lake P. Here we use an emerging paradigm in modeling, process-guided machine learning (PGML), to produce a phosphorus budget for Lake Mendota (Wisconsin, USA) and to accurately predict epilimnetic phosphorus over a time range of days to decades. In our implementation of PGML, which we term a Process-Guided Recurrent Neural Network (PGRNN), we combine a process-based model for lake P with a recurrent neural network, and then constrain the predictions with ecological principles. We test independently the process-based model, the recurrent neural network, and the PGRNN to evaluate the overall approach. The process-based model accounted for most of the observed pattern in lake P; however it missed the long-term trend in lake P and had the worst performance in predicting winter and summer P in surface waters. The root mean square error (RMSE) for the process-based model, the recurrent neural network, and the PGRNN was 33.0 μg P L -1 , 22.7 μg P L -1 , and 20.7 μg P L -1 , respectively. All models performed better during summer, with RMSE values for the three models (same order) equal to 14.3 μg P L -1 , 10.9 μg P L -1 , and 10.7 μg P L -1 . Although the PGRNN had only marginally better RMSE during summer, it had lower bias and reproduced long-term decreases in lake P missed by the other two models. For all seasons and all years, the recurrent neural network had better predictions than process alone, with root mean square error (RMSE) of 23.8 μg P L -1 and 28.0 μg P L -1 , respectively. The output of PGRNN indicated that new processes related to water temperature, thermal stratification, and long term changes in external loads are needed to improve the process model. By using ecological knowledge, as well as the information content of complex data, PGML shows promise as a technique for accurate prediction in messy, real-world ecological dynamics, while providing valuable information that can improve our understanding of process.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2023

Harnessing Neural Networks for Elucidating X-ray Absorption Structure–Spectrum Relationships in Amorphous Carbon

Improved understanding of structural and chemical properties through local experimental probes, such as X-ray absorption near-edge structure (XANES) spectroscopy, is crucial for the understanding and design of functional materials. In recent years, significant advancements have been made in the development of data science approaches for the automated interpretation of XANES structure–spectrum relationships. However, existing studies have primarily focused on crystalline solids and small molecules, while fewer efforts have been devoted to disordered systems. Thus, in this work, we demonstrate the development of neural network models for predicting and interpreting XANES spectra of amorphous carbon (a-C) from local structural descriptors. Comparison between different structural descriptors expectedly shows that the inclusion of both bond length and bond angle information is necessary for an accurate prediction of the spectra. Among the descriptors considered in this work, we find that the local many-body tensor representation yields the highest accuracy and greatest interpretability so that it can be leveraged to understand the importance of structural motifs in determining XANES spectra. Furthermore, we also discuss performance of neural network models for predicting both local structure features, such as bond lengths and bond angles, and global chemical composition, such as the sp:sp 2 :sp 3 ratio.

36 MATERIALS SCIENCE↗

NASA NTRS2020

NeMO-Net – The Neural Multi-Modal Observation & Training Network for Global Coral Reef Assessment

We present NeMO-Net, the Srst open-source deep convolutional neural network (CNN) and interactive learning and training software aimed at assessing the present and past dynamics of coral reef ecosystems through habitat mapping into 10 biological and physical classes. Shallow marine systems, particularly coral reefs, are under significant pressures due to climate change, ocean acidification, and other anthropogenic pressures, leading to rapid, often devastating changes, in these fragile and diverse ecosystems. Historically, remote sensing of shallow marine habitats has been limited to meter-scale imagery due to the optical effects of ocean wave distortion, refraction, and optical attenuation. NeMO-Net combines 3D cm-scale distortion-free imagery captured using NASA FluidCam and Fluid lensing remote sensing technology with low resolution airborne and spaceborne datasets of varying spatial resolutions, spectral spaces, calibrations, and temporal cadence in a supercomputer-based machine learning framework. NeMO-Net augments and improves the benthic habitat classification accuracy of low-resolution datasets across large geographic ad temporal scales using high-resolution training data from FluidCam.NeMO-Net uses fully convolutional networks based upon ResNet and ReSneNet to perform semantic segmentation of remote sensing imagery of shallow marine systems captured by drones, aircraft, and satellites, including WorldView and Sentinel. Deep Laplacian Pyramid Super-Resolution Networks (LapSRN) alongside Domain Adversarial Neural Networks (DANNs) are used to reconstruct high resolution information from low resolution imagery, and to recognize domain-invariant features across datasets from multiple platforms to achieve high classification accuracies, overcoming inter-sensor spatial, spectral and temporal variations.Finally, we share our online active learning and citizen science platform, which allows users to provide interactive training data for NeMO-Net in 2D and 3D, integrated within a deep learning framework. We present results from the PaciSc Islands including Fiji, Guam and Peros Banhos 1 1 2 1 3 1 where 24-class classification accuracy exceeds 91%.

Chirayath, Ved↗

DOE OSTI2022

Machine-learning from Pseudomonas putida KT2440 transcriptomes reveals its transcriptional regulatory network

Bacterial gene expression is orchestrated by numerous transcription factors (TFs). Elucidating how gene expression is regulated is fundamental to understanding bacterial physiology and engineering it for practical use. In this study, a machine-learning approach was applied to uncover the genome-scale transcriptional regulatory network (TRN) in Pseudomonas putida KT2440, an important organism for bioproduction. We performed independent component analysis of a compendium of 321 high-quality gene expression profiles, which were previously published or newly generated in this study. We identified 84 groups of independently modulated genes (iModulons) that explain 75.7% of the total variance in the compendium. With these iModulons, we (i) expand our understanding of the regulatory functions of 39 iModulon associated TFs (e.g., HexR, Zur) by systematic comparison with 1993 previously reported TF-gene interactions; (ii) outline transcriptional changes after the transition from the exponential growth to stationary phases; (iii) capture group of genes required for utilizing diverse carbon sources and increased stationary response with slower growth rates; (iv) unveil multiple evolutionary strategies of transcriptome reallocation to achieve fast growth rates; and (v) define an osmotic stimulon, which includes the Type VI secretion system, as coordination of multiple iModulon activity changes. Taken together, this study provides the first quantitative genome-scale TRN for P. putida KT2440 and a basis for a comprehensive understanding of its complex transcriptome changes in a variety of physiological states.

09 BIOMASS FUELS↗

DOE OSTI2022

2022 AI Testbed Expeditions Report

By exploiting the coherent properties of a light source, coherent diffraction imaging (CDI) is able to obtain the sample image at a nanoscale resolution using the measured diffraction pattern. Bragg Coherent Diffraction Imaging (BCDI) has become valuable for recovering the displacement and strain field of crystals, providing a valuable tool in material science and solid-state physics. X-ray ptychography is another emerging CDI technique that can produce a high-resolution image of the extended sample and has become popular in many research areas (e.g., materials science, biology, electronics, and optics characterization). CDI including BCDI and ptychography has become an established technique in Synchrotron Facilities including the Advanced Photon Source (APS) and will greatly benefit from the 100x coherent flux increase of the upcoming APS Upgrade (APSU). The current image formation process in CDI employs iterative phase retrieval algorithms, which is a time-consuming and computationally expensive process. Especially after APSU, the traditional iterative methods will not be able to match the experimental data acquisition speed. We employ deep learning (DL) approach to replace the iterative approaches, therefore allowing hundreds of times faster recovery of the object. We developed AutoPhaseNN, a DL-based approach which learns to solve the inverse problem without labeled data. Taking 3D BCDI as a representative technique, AutoPhaseNN has been demonstrated to be one hundred times faster than traditional iterative phase retrieval methods while providing comparable image quality. The current network is trained with 64 x 64 x 64 data size, to achieve higher resolution imaging, we will need to scale the network to input and train/infer 3D arrays of size 256 x 256 x 256 (today) and of size 2560x2560x2560 (APSU). However, the scalability of the network is restricted due to the memory-intensive training process. To perform the training for a 256 x 256 x 256 data size, the required memory exceeds the capacity of the current machine. In this project, we explore using Sambanova system to train the network for the direct data inversion for CDI.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Learning and Controlling Silicon Dopant Transitions in Graphene Using Scanning Transmission Electron Microscopy

A machine learning approach is introduced to determine the transition dynamics of silicon atoms on a single layer of carbon atoms, when stimulated by the electron beam of a scanning transmission electron microscope (STEM). This method is data-centric, leveraging data collected on a STEM. The data samples are processed and filtered to produce symbolic representations, which is used to train a neural network to predict transition probabilities. These learned transition dynamics are then leveraged to guide a single silicon atom throughout the lattice to pre-determined target destinations. Empirical analyses are presented that demonstrate the efficacy and generality of the approach.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Building an ab initio solvated DNA model using Euclidean neural networks

Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Selecting Post-Processing Schemes for Accurate Detection of Small Objects in Low-Resolution Wide-Area Aerial Imagery

In low-resolution wide-area aerial imagery, object detection algorithms are categorized as feature extraction and machine learning approaches, where the former often requires a post-processing scheme to reduce false detections and the latter demands multi-stage learning followed by post-processing. In this paper, we present an approach on how to select post-processing schemes for aerial object detection. We evaluated combinations of each of ten vehicle detection algorithms with any of seven post-processing schemes, where the best three schemes for each algorithm were determined using average F-score metric. The performance improvement is quantified using basic information retrieval metrics as well as the classification of events, activities and relationships (CLEAR) metrics. We also implemented a two-stage learning algorithm using a hundred-layer densely connected convolutional neural network for small object detection and evaluated its degree of improvement when combined with the various post-processing schemes. The highest average F-scores after post-processing are 0.902, 0.704 and 0.891 for the Tucson, Phoenix and online VEDAI datasets, respectively. The combined results prove that our enhanced three-stage post-processing scheme achieves a mean average precision (mAP) of 63.9% for feature extraction methods and 82.8% for the machine learning approach.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Physics-informed machine learning

Despite great progress in simulating multiphysics problems using the numerical discretization of partial differential equations (PDEs), one still cannot seamlessly incorporate noisy data into existing algorithms, mesh generation remains complex, and high-dimensional problems governed by parameterized PDEs cannot be tackled. Moreover, solving inverse problems with hidden physics is often prohibitively expensive and requires different formulations and elaborate computer codes. Machine learning has emerged as a promising alternative, but training deep neural networks requires big data, not always available for scientific problems. Instead, such networks can be trained from additional information obtained by enforcing the physical laws (for example, at random points in the continuous space-time domain). Such physics-informed learning integrates (noisy) data and mathematical models, and implements them through neural networks or other kernel-based regression networks. Moreover, it may be possible to design specialized network architectures that automatically satisfy some of the physical invariants for better accuracy, faster training and improved generalization. Furthermore, we review some of the prevailing trends in embedding physics into machine learning, present some of the current capabilities and limitations and discuss diverse applications of physics-informed learning both for forward and inverse problems, including discovering hidden physics and tackling high-dimensional problems.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

HGQ: High Granularity Quantization for Real-time Neural Networks on FPGAs

Neural networks with sub-microsecond inference latency are required by many critical applications. Targeting such applications deployed on FPGAs, we present High Granularity Quantization (HGQ), a quantization-aware training framework that optimizes parameter bit-widths through gradient descent. Unlike conventional methods, HGQ determines the optimal bit-width for each parameter independently, making it suitable for hardware platforms supporting heterogeneous arbitrary precision arithmetic. In our experiments, HGQ shows superior performance compared to existing network compression methods, achieving orders of magnitude reduction in resource consumption and latency while maintaining the accuracy on several benchmark tasks. These improvements enable the deployment of complex models previously infeasible due to resource or latency constraints. HGQ is open-source and is used for developing next-generation trigger systems at the CERN ATLAS and CMS experiments for particle physics, enabling the use of advanced machine learning models for real-time data selection with sub-microsecond latency.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

DOE OSTI2022

Accelerated screening of functional atomic impurities in halide perovskites using high-throughput computations and machine learning

The pressing need for novel materials that can serve rising demands in solar cell and optoelectronic technologies makes the nexus of halide perovskites, high-throughput computations, and machine learning, very promising. Ever increasing amounts of data on the structure, fundamental properties, and device performance of halide perovskites provide opportunities for learning chemical rules and design principles that make these materials attractive, and applying them across wide chemical spaces. In this work, we show that impurity properties of halide perovskites computed using density functional theory (DFT) can be combined with machine learning (ML) to deliver predictive models and quick identification of optoelectronically active impurity atoms. Our computation lead to the largest reported dataset of the formation energies and charge transition levels of Pb-site impurities in methylammonium lead halide (MAPbX 3 ) perovskites. Descriptors are defined to uniquely represent any impurity atom in any MAPbX 3 compound and mapped to the computed impurity properties using regression techniques such as Gaussian process regression, neural networks, and random forests. We use the best optimized predictive models to make predictions for hundreds of impurities across 9 MAPbX 3 compounds and create lists of dominating impurities, that is, impurities that can shift the equilibrium Fermi level in the perovskite as determined by native point defects. Finally, this accelerated screening powered by computations and machine learning can guide the identification of problematic impurities that may cause undesired recombination of charge carriers, as well as impurities that can be deliberately introduced to tune the perovskite conductivity and resulting photovoltaic absorption.

36 MATERIALS SCIENCE↗