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DOE OSTI2024

Evaluating the Use of Foundational Chemical Language Models in Multimodal Graph Fusion

Rapid and accurate prediction of the physicochemical properties of molecules given their structures remains a key challenge in cheminformatics. Machine learning approaches offer high-throughput options, but the optimality of inductive biases and data representations are up for debate. For example, BERT-based masked language models (MLMs) can be trained in a self-supervised way on hundreds of millions to billions of readily available SMILES strings. Another option is graph neural networks (GNNs), which can operate directly on molecular structures. Yet, generating accurate molecular geometry is computationally expensive, leading to a relative scarcity in data compared to SMILES strings. It is attractive to combine these two paradigms by pre-training an LM on a large corpus of SMILES strings and embedding these representation into a geometric graph neural network. Despite the promise of such an approach, and contrary to previous studies, we find mixed results with the combination of the LMs and GNNs on several molecule datasets. In particular, we found evidence for improvement on the FreeSolv and QM7 benchmarks, but degraded performance on the ESOL, LIPO and QM9 datasets compared to a GNN baseline.

Francel, Collin [University of Alabama]↗

DOE OSTI2016

SOL: An end-to-end solution for real-world remote monitoring systems

This paper introduces SOL, which is both an efficient data representation for sensor measurements and network statistics, and a complete low-power wireless sensor management system that builds around it. A SOL system consists of multiple low-power wireless mesh networks in which motes connected to sensors and actuators send data to a single server. It offers multi-tier data replication and the associated data recovery. SOL is used in 3 pilot deployments for micro-climate monitoring, building automation and agriculture applications. In conjunction with Metronome Systems' NeoMote and Manager devices, SOL is a turn-key ready-to-deploy end-to-end system.

47 OTHER INSTRUMENTATION↗

DOE OSTI2016

SchemaOnRead: A Package for Schema-on-Read in R

Schema-on-read is an agile approach to data storage and retrieval that defers investments in data organization until production queries need to be run by working with data directly in native form. Schema-on-read functions have been implemented in a wide range of analytical systems, most notably Hadoop. SchemaOnRead is a CRAN package that uses R’s flexible data representations to provide transparent and convenient support for the schema-on-read paradigm in R. The schema-on- read tools within the package include a single function call that recursively reads folders with text, comma separated value, raster image, R data, HDF5, NetCDF, spreadsheet, Weka, Epi Info, Pajek network, R network, HTML, SPSS, Systat, and Stata files. The provided tools can be used as-is or easily adapted to implement customized schema-on-read tool chains in R. This paper’s contribution is that it introduces and describes SchemaOnRead, the first R package specifically focused on providing explicit schema-on-read support in R.

Data Science↗

DOE OSTI2016

SchemaOnRead: A Package for Schema-on-Read in R

Data Science↗

DOE OSTI2023

Toward extracting $$\gamma $$ from $$B\rightarrow DK$$ without binning

Abstract $$B^\pm \rightarrow DK^\pm $$ B ± → D K ± transitions are known to provide theoretically clean information about the CKM angle $$\gamma $$ γ , with the most precise available methods exploiting the cascade decay of the neutral D into CP self-conjugate states. Such analyses currently require binning in the D decay Dalitz plot, while a recently proposed method replaces this binning with the truncation of a Fourier series expansion. In this paper, we present a proof of principle of a novel alternative to these two methods, in which no approximations at the level of the data representation are required. In particular, our new strategy makes no assumptions about the amplitude and strong phase variation over the Dalitz plot. This comes at the cost of a degree of ambiguity in the choice of test statistic quantifying the compatibility of the data with a given value of $$\gamma $$ γ , with improved choices of test statistic yielding higher sensitivity. While our current proof-of-principle implementation does not demonstrate optimal sensitivity to $$\gamma $$ γ , its conceptually novel approach opens the door to new strategies for $$\gamma $$ γ extraction. More studies are required to see if these can be competitive with the existing methods.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2018

Human attitude analysis based on fuzzy soft differential equations with Bonferroni mean

In this paper, we model a system of fuzzy soft differential equations to analyze the behavior over the time of an individual depending on their companion’s actions under any particular situation against some decision. The Bonferroni mean (BM) is a very useful tool for group decision-making problems when arguments are interrelated to each other as Bonferroni mean can capture the interrelationship of the individual arguments. Using this ability of BM, we define Bonferroni fuzzy soft matrix (BFSM) and weighted Bonferroni fuzzy soft matrix (WBFSM) for data representation. WBFSM is a decision matrix and provide the optimum fuzzy soft constant (OFSC) which is the key element of fuzzy soft differential equation. By utilizing the OFSC, we develop a system of fuzzy soft differential equations to study a dynamical process with nonlinear uncertain and vague data. Second, we present a novel efficient technique for analyzing the future attitude of people due to their present decisions. To illustrate the practicality and feasibility of proposed technique an illustrative example is also discussed with the help of phase portrait and line graphs.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2026

GPU-Accelerated Analytic Simulation of Sparse Ionization Signal Formation in Pixelated Projection Detector

This paper presents a GPU-accelerated simulation package, TRED, for next-generation neutrino detectors with pixelated charge readout, leveraging community-driven software ecosystems to ensure adaptability and extensibility. We introduce two generic contributions: (i) an effective-charge representation based on Gaussian quadrature rules, in which the linear- interpolation factors for the field response inside each voxel are absorbed into the effective charge, and (ii) a sparse, block- binned tensor representation that enables efficient FFT-based computation of induced signals on readout electrodes for sparsely activated detector volumes. The former captures structure inside a voxel without dense sampling, while the latter achieves low memory usage and scalable runtime, as demonstrated in bench- mark studies. The underlying data representation is applicable to large-scale detectors and to other computational problems involving sparse activity.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2016

Treatments for Neutron Resonance Elastic Scattering Using the Multipole Formalism in Monte Carlo Codes

The elastic scattering cross sections of resonant nuclides can vary drastically within small energy intervals. In reactor physics simulations, accurate treatment of neutron resonance elastic scattering is vital, as the phenomenon can have a strong effect on scattering kinematics which, in turn, affect macroscopic values, such as the fuel temperature reactivity coefficient. To reduce memory requirements and facilitate coupling with heat transfer, a new representation for cross sections was recently adopted in OpenMC based on the multipole formalism. However, this new approach invalidates the previous implementations of correct resonance treatments, including the Doppler Broadening Rejection Correction (DBRC) method. This work thus developed a modified DBRC algorithm, called DBRC-MP, compatible with the new data representation. This new method is also verified against the previous DBRC method. While slightly more computationally costly than the traditional DBRC approach using ACE format cross sections, the use of the multipole representation in treating resonance scattering enables the reduction of memory requirements by a hundred-fold and facilitates the representation of temperature dependent cross sections. (authors)

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2019

Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography

We have developed a deep learning algorithm for chemical shift prediction for atoms in molecular crystals that utilizes an atom-centered Gaussian density model for the 3D data representation of a molecule. We define multiple channels that describe different spatial resolutions for each atom type that utilizes cropping, pooling, and concatenation to create a multiresolution 3D-DenseNet architecture (MR-3D-DenseNet). Because the training and testing time scale linearly with the number of samples, the MR-3D-DenseNet can exploit data augmentation that takes into account the property of rotational invariance of the chemical shifts, thereby also increasing the size of the training data set by an order of magnitude without additional cost. We obtain very good agreement for 13 C, 15 N, and 17 O chemical shifts when compared to ab initio quantum chemistry methods, with the highest accuracy found for 1 H chemical shifts that is comparable to the error between the ab initio results and experimental measurements. Principal component analysis (PCA) is used to both understand these greatly improved predictions for 1 H , as well as indicating that chemical shift prediction for 13 C, 15 N, and 17 O, which have far fewer training environments than the 1 H atom type, will improve once more unique training samples are made available to exploit the deep network architecture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

A scalable framework for efficient coupling of thermal and microstructural simulations in additive manufacturing

Predicting microstructure evolution in metal additive manufacturing (AM) is important for process optimization, but spatiotemporal scale disparities between thermal transport and microstructure evolution create significant challenges for efficient data transfer between simulation codes. To address this, we present Stork, a scalable framework for coupling thermal and microstructural simulations. Stork uses a sparse data representation to identify and store active solidification sub-volumes, enabling highly parallel quad-linear interpolation from coarse thermal grids to fine microstructure grids without large intermediate storage. We demonstrate the framework by coupling the semi-analytic heat transfer code 3DThesis with the time-parallel cellular automata code Toucan. This approach achieves over two orders of magnitude reduction in data generation time and file size compared to prior workflows. Numerical studies show that quad-linear interpolation preserves grain morphology and crystallographic texture in laser powder bed fusion (LPBF) simulations for coarsening ratios up to 16. Overall, Stork provides a scalable pathway for high-throughput, component-scale AM simulations on modern high-performance computing systems.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Improving deep learning model performance under parametric constraints for materials informatics applications

Abstract Modern machine learning (ML) and deep learning (DL) techniques using high-dimensional data representations have helped accelerate the materials discovery process by efficiently detecting hidden patterns in existing datasets and linking input representations to output properties for a better understanding of the scientific phenomenon. While a deep neural network comprised of fully connected layers has been widely used for materials property prediction, simply creating a deeper model with a large number of layers often faces with vanishing gradient problem, causing a degradation in the performance, thereby limiting usage. In this paper, we study and propose architectural principles to address the question of improving the performance of model training and inference under fixed parametric constraints. Here, we present a general deep-learning framework based on branched residual learning (BRNet) with fully connected layers that can work with any numerical vector-based representation as input to build accurate models to predict materials properties. We perform model training for materials properties using numerical vectors representing different composition-based attributes of the respective materials and compare the performance of the proposed models against traditional ML and existing DL architectures. We find that the proposed models are significantly more accurate than the ML/DL models for all data sizes by using different composition-based attributes as input. Further, branched learning requires fewer parameters and results in faster model training due to better convergence during the training phase than existing neural networks, thereby efficiently building accurate models for predicting materials properties.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Evaluation of the Near-Surface Variables in the HRRR Weather Model Using Observations from the ARM SGP Site

Abstract The performance of version 4 of the NOAA High-Resolution Rapid Refresh (HRRR) numerical weather prediction model for near-surface variables, including wind, humidity, temperature, surface latent and sensible fluxes, and longwave and shortwave radiative fluxes, is examined over the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) region. The study evaluated the model’s bias and bias-corrected mean absolute error relative to the observations on different time scales. Forecasts of near-surface geophysical variables at five SGP sites (HRRR at 3-km scale) were found to agree well with observations, but some consistent observation–forecast differences also occurred. Sensible and latent heat fluxes are the most challenging variables to be reproduced. The diurnal cycle is the main temporal scale affecting observation–forecast differences of the near-surface variables, and almost all of the variables showed different biases throughout the diurnal cycle. Results show that the overestimation of downward shortwave and the underestimation of downward longwave radiative flux are the two major biases found in this study. The timing and magnitude of downward longwave flux, wind speed, and sensible and latent heat fluxes are also different with contributions from model representations, data assimilation limitations, and differences in scales between HRRR and SGP sites. The positive bias in downward shortwave and negative bias in longwave radiation suggests that the model is underestimating cloud fraction in the study domain. The study concludes by showing a brief comparison with version 3 of the HRRR and shows that version 4 has better performance in almost all near-surface variables. Significance Statement A correct representation of the near-surface variables is important for numerical weather prediction models. This study investigates the capability of the latest NOAA High-Resolution Rapid Refresh (HRRRv4) model in simulating the near-surface variables by comparing against the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) in situ observations. Among others, we find that the surface heat fluxes, such as sensible and latent heat fluxes, are the most difficult variables to be reproduced. This study also shows that the diurnal cycle has the dominant impact on the model’s performance, which means the majority of the outputted near-surface variables have the strong diurnal cycle in their bias errors.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Nonlinear encoding in diffractive information processing using linear optical materials

Nonlinear encoding of optical information can be achieved using various forms of data representation. Here, we analyze the performances of different nonlinear information encoding strategies that can be employed in diffractive optical processors based on linear materials and shed light on their utility and performance gaps compared to the state-of-the-art digital deep neural networks. For a comprehensive evaluation, we used different datasets to compare the statistical inference performance of simpler-to-implement nonlinear encoding strategies that involve, e.g., phase encoding, against data repetition-based nonlinear encoding strategies. We show that data repetition within a diffractive volume (e.g., through an optical cavity or cascaded introduction of the input data) causes the loss of the universal linear transformation capability of a diffractive optical processor. Therefore, data repetition-based diffractive blocks cannot provide optical analogs to fully connected or convolutional layers commonly employed in digital neural networks. However, they can still be effectively trained for specific inference tasks and achieve enhanced accuracy, benefiting from the nonlinear encoding of the input information. Our results also reveal that phase encoding of input information without data repetition provides a simpler nonlinear encoding strategy with comparable statistical inference accuracy to data repetition-based diffractive processors. Our analyses and conclusions would be of broad interest to explore the push-pull relationship between linear material-based diffractive optical systems and nonlinear encoding strategies in visual information processors.

42 ENGINEERING↗

DOE OSTI2017

Anomaly Detection in Moving-Camera Video Sequences Using Principal Subspace Analysis

This study presents a family of algorithms based on sparse decompositions that detect anomalies in video sequences obtained from slow moving cameras. These algorithms start by computing the union of subspaces that best represents all the frames from a reference (anomaly free) video as a low-rank projection plus a sparse residue. Then, they perform a low-rank representation of a target (possibly anomalous) video by taking advantage of both the union of subspaces and the sparse residue computed from the reference video. Such algorithms provide good detection results while at the same time obviating the need for previous video synchronization. However, this is obtained at the cost of a large computational complexity, which hinders their applicability. Another contribution of this paper approaches this problem by using intrinsic properties of the obtained data representation in order to restrict the search space to the most relevant subspaces, providing computational complexity gains of up to two orders of magnitude. The developed algorithms are shown to cope well with videos acquired in challenging scenarios, as verified by the analysis of 59 videos from the VDAO database that comprises videos with abandoned objects in a cluttered industrial scenario.

47 OTHER INSTRUMENTATION↗

DOE OSTI2017

Energy Efficient Stochastic-Based Deep Spiking Neural Networks for Sparse Datasets

With large deep neural networks (DNNs) neces- sary to solve complex and data-intensive problems, energy efficiency is a key bottleneck for effectively deploying DL in the real world. Deep spiking NNs have gained much research at- tention recently due to the interest in building biological neural networks and the availability of neuromorphic platforms, which can be orders of magnitude more energy efficient compared to CPUs and GPUs. Although spiking NNs have proven to be an efficient technique for solving many machine learning and computer vision problems, to the best of our knowledge, this is the first attempt to adapt spiking NNs to sparse datasets. In this paper, we study the behaviour of spiking NNs in handling NLP datasets and the sparsity in their data representation. Then, we propose a novel framework for spiking NN using the concept of stochastic computing. Specifically, instead of generating spike trains with firing rates proportional to the intensity of each value in the feature set separately, the whole feature set is treated as a distribution function and a stochastic spiking train that follow this distribution is generated. This framework reduces the connectivity between NN layers from O(N) to O(logN). Also, it encodes input data differently and make suitable to handle sparse datasets. Finally, the framework achieves high energy efficiency since it uses Integrate and Fire neurons same as conventional spiking NNs. The results show that our proposed stochastic-based SNN achieves nearly the same accuracy as the original DNN on MNIST dataset, and it has better performance than state- of-the-art SNN. Besides that stochastic-based SNN is energy efficient, where the fully connected DNN, the conventional SNN, and the data normalized SNN consume 38.24, 1.83, and 1.85 -times more energy than the stochastic-based SNN, respectively. For sparse datasets, including IMDb and In-House clinical datasets, stochastic-based SNN achieves performance comparable to that of the conventional DNN. However, the conventional spiking NN has a significant decline in classification accuracy.

Alawad, Mohammed↗

DOE OSTI2021

Methods for neutron diffraction studies on hydride superconductors and other metal hydrides

High-pressure neutron diffraction is an extremely useful technique in the quest for making and understanding novel hydride superconductors. Neutron diffraction can be used to directly determine elemental stoichiometries and atomic positions of many light elements such as hydrogen or deuterium, even in the presence of heavy elements such as rare-earth metals. In this work, we report on the current status and ongoing developments on high-pressure neutron diffraction for hydride superconductors and other metal hydrides with a special focus on current advancements at the Spallation Neutrons and Pressure (SNAP) beamline of the Spallation Neutron Source at Oak Ridge National Laboratory. For broader context, an overview of high-pressure neutron diffractometers and pressure cells is included together with insight into critical sample considerations. There, attention is given to the requirements for powdered hydride samples and the need for deuterium rather than hydrogen. Additionally, the advantages of angular access and data representation as possible at SNAP are described. We demonstrate the current capability for high-pressure neutron diffraction on two different samples created via hydrogen gas loading, specifically pure deuterium and nickel-deuteride. The deuterium example highlights the usefulness of adding sample materials that facilitate the formation of a good powder while the nickel-deuteride example demonstrates that atomic deuterium positions and stoichiometry can be directly determined. Both examples highlight the importance of large scattering apertures. These enable investigation of the data resolved by scattering angle that is needed to identify parasitic peaks and background features. Finally, future directions beyond current high-pressure neutron powder diffraction are also discussed.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2022

Replication Data for: Latent Representation Learning for Structural Characterization of Catalysts

The data underlying this published work have been made publicly available in this repository as part of the IMASC Data Management Plan. This work was supported as part of the Integrated Mesoscale Architectures for Sustainable Catalysis (IMASC), an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Basic Energy Sciences under Award # DE-SC0012573.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Transportation and Systems Analysis Collaborations in Support of a Federal Consolidated Interim Storage Facility

The U.S. Department of Energy’s Integrated Waste Management (IWM) program under the Office of Nuclear Energy is planning for the future transportation, storage, and eventual disposal of spent nuclear fuel (SNF) and high-level radioactive waste (HLW) from nuclear power plant sites across the United States. To better enable informed decision-making regarding the back end of the nuclear fuel cycle, the IWM program has been sponsoring the development and application of system analysis tools capable of analyzing various options for managing SNF and HLW. With these tools, integrated waste management system (IWMS) architecture analyses are being conducted to support the future deployment of a comprehensive nuclear waste management system that considers all major back-end aspects of the nuclear fuel cycle (i.e., transportation, storage, and disposal). System analyses and assessments typically use these modeling and simulation tools to investigate implications of changes in various assumptions and parameters such as acceptance rates, receipt logic, facility capacities and capabilities, use of standardized canisters, start and stop dates of facilities, etc. The Next Generation System Analysis Model (NGSAM) is an agent-based simulation toolkit that is used for a system-level simulation and analysis focused on SNF management in the United States. An analyst using NGSAM has the ability to define several factors like the number of storage facilities, capacity at each facility, transportation schedules, shipment rates, and other conditions. NGSAM’s primary purpose is to provide a system analyst with capabilities to model the IWMS and gain insights into SNF and HLW management alternatives including the impact of system choices, associated cost estimates, and development of integrated yet flexible approaches. IWM is also developing the Stakeholder Tool for Assessing Radioactive Transportation (START). START is a web-based geospatial tool developed to provide visualization and initial evaluation of transportation options associated with future SNF and HLW shipment planning and operations. This includes characterizing safety, economic, and environmental conditions on and in proximity to shipment origins as well as along prospective transportation routes. Information from the START tool can be presented/shared as maps, graphics, geospatial files, and tabular form to enable easy data representation and export functionality. The system analysis, NGSAM, and START teams had been working closely for several years before formalizing this collaboration. START provides the SNF routing information for use in NGSAM. System analysts use the NGSAM tool to generate results (schedule, costs, infrastructure acquisitions, shipment rates, etc.). Subject-matter experts and system analysts work together to inform how NGSAM should model the waste management system. Specifically, this paper discusses the collaborations between the system analysis, NGSAM, and START teams and their accomplishments over the past year. Some examples of these efforts include calibrating and adding data to the START output files to meet NGSAM needs, gaining a better understanding of START data used in NGSAM, as well as how updates in START data could result in an improved NGSAM analysis. Detailed examples of various tasks that have been performed by the team will be discussed in the full paper. Continued efforts in this direction are expected in the coming years.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗