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DOE OSTI2026

Determination of proton PDF uncertainties with Markov chain Monte Carlo

We present an analysis of parton distribution functions (PDFs) of the proton using Markov chain Monte Carlo (MCMC) methods. The MCMC approach naturally implements Bayes’ theorem and, thus, provides a means to directly sample the underlying probability distribution—in this case, the probability distribution of the PDF parameters. This allows for a straightforward propagation of the resulting uncertainties into any PDF-dependent observable, preserving their simple probabilistic interpretation. In our analysis we include a broad set of deep inelastic scattering data from HERA, BCDMS and NMC experiments along with the Drell-Yan, 𝑊 and 𝑍 boson data from LHC and Tevatron experiments, which combined with theoretical calculations at next-to-next-to-leading order in QCD allow for realistic determination of PDFs. The main focus of this analysis is to explore alternative methods for PDF uncertainty estimation that are more firmly grounded in statistical principles. We show that the flexibility of the Bayes framework, allowing one, e.g., to account for non-Gaussianity or inconsistencies of datasets, is crucial to extract realistic uncertainties when such assumptions are not fulfilled. We also demonstrate that MCMC allows one to determine the Δ⁢𝜒 2 value corresponding to a given confidence level in the sample, which can, in turn, be used as a statistically well-founded tolerance criterion used in the Hessian method, thus addressing one of its main long-standing drawbacks.

Risse, Peter Clemens [Universität Münster (Germany↗

DOE OSTI2021

Detecting operons in bacterial genomes via visual representation learning

Contiguous genes in prokaryotes are often arranged into operons. Detecting operons plays a critical role in inferring gene functionality and regulatory networks. Human experts annotate operons by visually inspecting gene neighborhoods across pileups of related genomes. These visual representations capture the inter-genic distance, strand direction, gene size, functional relatedness, and gene neighborhood conservation, which are the most prominent operon features mentioned in the literature. By studying these features, an expert can then decide whether a genomic region is part of an operon. We propose a deep learning based method named Operon Hunter that uses visual representations of genomic fragments to make operon predictions. Using transfer learning and data augmentation techniques facilitates leveraging the powerful neural networks trained on image datasets by re-training them on a more limited dataset of extensively validated operons. Our method outperforms the previously reported state-of-the-art tools, especially when it comes to predicting full operons and their boundaries accurately. Furthermore, our approach makes it possible to visually identify the features influencing the network’s decisions to be subsequently cross-checked by human experts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Advancing Understanding of Deep Convective Anvil Clouds

In this project we use ground-based DOE ARM observations, satellite observations, and Weather Research and Forecasting (WRF) model simulations to arrive at a more complete understanding (or, new theory) of how atmospheric heating profiles in thunderstorm cores drives how quickly air rises in the storms. The rate at which air motion increases or decreases with altitude directly relates to how much cloud mass is ejected laterally into the adjacent atmosphere, which then influences the development and maintenance of “stratiform raining cloud anvils”. Our work has led to new equations connecting the heating in these thunderstorms to these stratiform clouds, with the connection modulated by the stability structure of the atmosphere (i.e., if more stable, then a more rapid change in thunderstorm heating with altitude results in more stratiform cloud, independent of whether over land or ocean, or how organized the thunderstorms are). Improving knowledge of stratiform clouds is important, since they contribute to substantial accumulated rainfall (important to agriculture and local hydrology) as well as radiation, given their large areal extents and lifetime. The radiation impacts likely impact simulated cloud feedback in all Earth System models (ESMs).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Thermodynamically Optimized Machine-Learned Reaction Coordinates for Hydrophobic Ligand Dissociation

Ligand unbinding is mediated by its free energy change, which has intertwined contributions from both energy and entropy. It is important, but not easy, to quantify their individual contributions to the free energy profile. We model hydrophobic ligand unbinding for two systems, a methane particle and a C 60 fullerene, both unbinding from hydrophobic pockets in all-atom water. Using a modified deep learning framework, we learn a thermodynamically optimized reaction coordinate to describe the hydrophobic ligand dissociation for both systems. Interpretation of these reaction coordinates reveals the roles of entropic and enthalpic forces as the ligand and pocket sizes change. In both cases, we observe that the free-energy barrier to unbinding is dominated by entropy considerations. Furthermore, the process of methane unbinding is driven by methane solvation, while fullerene unbinding is driven first by pocket wetting and then fullerene wetting. For both solutes, the direct importance of the distance from the binding pocket to the learned reaction coordinate is present, but low. Furthermore, our framework and subsequent feature important analysis thus give useful thermodynamic insight into hydrophobic ligand dissociation problems that are otherwise difficult to glean.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Computationally Efficient Multiscale Neural Networks Applied to Fluid Flow in Complex 3D Porous Media

Abstract The permeability of complex porous materials is of interest to many engineering disciplines. This quantity can be obtained via direct flow simulation, which provides the most accurate results, but is very computationally expensive. In particular, the simulation convergence time scales poorly as the simulation domains become less porous or more heterogeneous. Semi-analytical models that rely on averaged structural properties (i.e., porosity and tortuosity) have been proposed, but these features only partly summarize the domain, resulting in limited applicability. On the other hand, data-driven machine learning approaches have shown great promise for building more general models by virtue of accounting for the spatial arrangement of the domains’ solid boundaries. However, prior approaches building on the convolutional neural network (ConvNet) literature concerning 2D image recognition problems do not scale well to the large 3D domains required to obtain a representative elementary volume (REV). As such, most prior work focused on homogeneous samples, where a small REV entails that the global nature of fluid flow could be mostly neglected, and accordingly, the memory bottleneck of addressing 3D domains with ConvNets was side-stepped. Therefore, important geometries such as fractures and vuggy domains could not be modeled properly. In this work, we address this limitation with a general multiscale deep learning model that is able to learn from porous media simulation data. By using a coupled set of neural networks that view the domain on different scales, we enable the evaluation of large ( $$>512^3$$ > 512 3 ) images in approximately one second on a single graphics processing unit. This model architecture opens up the possibility of modeling domain sizes that would not be feasible using traditional direct simulation tools on a desktop computer. We validate our method with a laminar fluid flow case using vuggy samples and fractures. As a result of viewing the entire domain at once, our model is able to perform accurate prediction on domains exhibiting a large degree of heterogeneity. We expect the methodology to be applicable to many other transport problems where complex geometries play a central role.

36 MATERIALS SCIENCE↗

DOE OSTI2024

Optimizing Deep Geothermal Drilling for Energy Sustainability in the Appalachian Basin

This study investigates the geological and geomechanical characteristics of the MIP 1S geothermal well in the Appalachian Basin to optimize drilling and address the wellbore stability issues encountered. Data from well logs, sidewall core analysis, and injection tests were used to derive elastic and rock strength properties, as well as stress and pore pressure profiles. A robust 1D-geomechanical model was developed and validated, correlating strongly with wellbore instability observations. This revealed significant wellbore breakout, widening the diameter from 12 ¼ inches to over 16 inches. Advanced technologies like Cerebro Force™ In-Bit Sensing were used to monitor drilling performance with high accuracy. This technology tracks critical metrics such as bit acceleration, vibration in the x, y, and z directions, Gyro RPM, stick-slip indicators, and bending on the bit. Cerebro Force™ readings identified hole drag caused by poor hole conditions, including friction between the drill string and wellbore walls and the presence of cuttings or debris. This led to higher torque and weight on bit (WOB) readings at the surface compared to downhole measurements, affecting drilling efficiency and wellbore stability. Optimal drilling parameters for future deep geothermal wells were determined based on these findings.

Environmental Sciences & Ecology↗

DOE OSTI2024

Neural Networks to Find the Optimal Forcing for Offsetting the Anthropogenic Climate Change Effects

Abstract Of great relevance to climate engineering is the systematic relationship between the radiative forcing to the climate system and the response of the system, a relationship often represented by the linear response function (LRF) of the system. However, estimating the LRF often becomes an ill-posed inverse problem due to high-dimensionality and nonunique relationships between the forcing and response. Recent advances in machine learning make it possible to address the ill-posed inverse problem through regularization and sparse system fitting. Here, we develop a convolutional neural network (CNN) for regularized inversion. The CNN is trained using the surface temperature responses from a set of Green’s function perturbation experiments as imagery input data together with data sample densification. The resulting CNN model can infer the forcing pattern responsible for the temperature response from out-of-sample forcing scenarios. This promising proof of concept suggests a possible strategy for estimating the optimal forcing to negate certain undesirable effects of climate change. The limited success of this effort underscores the challenges of solving an inverse problem for a climate system with inherent nonlinearity. Significance Statement Predicting the climate response for a given climate forcing is a direct problem, while inferring the forcing for a given desired climate response is often an inverse, ill-posed, problem, posing a new challenge to the climate community. This study makes the first attempt to infer the radiative forcing for a given target pattern of global surface temperature response using a deep learning approach. The resulting deeply trained convolutional neural network inversion model shows promise in capturing the forcing pattern corresponding to a given surface temperature response, with a significant implication on the design of an optimal solar radiation management strategy for curbing global warming. This study also highlights the technical challenges that future research should prioritize in seeking feasible solutions to the inverse climate problem.

Ren, Huiying↗

DOE OSTI2024

Materials Characterization, Prediction and Control Project: Summary Report on Data Analytics Framework

This report summarizes the activities performed under the data analytics Vertex in the Materials Characterization, Prediction and Control Project funded under laboratory directed research and development at Pacific Northwest National Laboratory. The data analytics Vertex developed models for associating global or local process parameters, microstructural features, and performance properties of friction-stir-processed 316L stainless steel plates. Statistical, machine learning, and deep learning models, as well as generative artificial intelligence approaches, were used to develop the associations between the process-structure-property data streams. These associations formed the basis for predicting global properties of parts manufactured under different process envelopes, providing a basis for predicting performance using data driven as well as physics-informed and physics-constrained approaches. Additionally, the associations were used to predict local process parameters and microstructural features of the product, predictive relationships that have the potential to form the basis of a control framework that could eventually modulate a friction-stir process to maintain product quality.

316L stainless steel↗

DOE OSTI2025

Joint Modeling of Quasar Variability and Accretion Disk Reprocessing Using Latent Stochastic Differential Equations

Quasars are bright active galactic nuclei powered by the accretion of matter around supermassive black holes at the center of galaxies. Their stochastic brightness variability depends on the physical properties of the accretion disk and black hole. The upcoming Rubin Observatory Legacy Survey of Space and Time (LSST) is expected to observe tens of millions of quasars, so there is a need for efficient techniques like machine learning that can handle the large volume of data. Quasar variability is believed to be driven by an X-ray corona, which is reprocessed by the accretion disk and emitted as UV/optical variability. We are the first to introduce an auto-differentiable simulation of the accretion disk and reprocessing. We use the simulation as a direct component of our neural network to jointly model the driving variability and reprocessing, trained with supervised learning on simulated LSST-like 10 yr quasar light curves. We encode the light curves using a transformer encoder, and the driving variability is reconstructed using latent stochastic differential equations, a physically motivated generative deep learning method that can model continuous-time stochastic dynamics. By embedding the physical processes of the driving signal and reprocessing into our network, we achieve a model that is more robust and interpretable. We demonstrate that our model outperforms a Gaussian process regression baseline and can infer accretion disk parameters and time delays between wave bands, even for out-of-distribution driving signals. Our approach provides a powerful framework that can be adapted to solve other inverse problems in multivariate time series.

Fagin, Joshua [City Univ. of New York (CUNY), NY (↗

DOE OSTI2020

End-to-End Physics Event Classification with CMS Open Data: Applying Image-Based Deep Learning to Detector Data for the Direct Classification of Collision Events at the LHC

This paper describes the construction of novel end-to-end image-based classifiers that directly leverage low-level simulated detector data to discriminate signal and background processes in pp collision events at the Large Hadron Collider at CERN. To better understand what end-to-end classifiers are capable of learning from the data and to address a number of associated challenges, we distinguish the decay of the standard model Higgs boson into two photons from its leading background sources using high-fidelity simulated CMS Open Data. We demonstrate the ability of end-to-end classifiers to learn from the angular distribution of the photons recorded as electromagnetic showers, their intrinsic shapes, and the energy of their constituent hits, even when the underlying particles are not fully resolved, delivering a clear advantage in such cases over purely kinematics-based classifiers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Neutron Tagging From Neutrino Interactions in DUNE-ND 2x2 Prototype

The Deep Underground Neutrino Experiment (DUNE) is a long-baseline neutrino oscillation experiment that aims to measure whether CP is violated in the leptonic sector (if violated, how much) and unambiguously determine the neutrino mass ordering. DUNE consists of near and far detectors that rely on liquid argon time projection chamber (LArTPC) technology to observe neutrino interactions. The near detector (ND) will be placed in Fermilab, near the neutrino source, while the far detector (FD) will be deployed in Sanford Lab, 1.5 km deep underground, which is 1300 km away from the source. LArTPCs provide excellent particle identification and calorimetry; however, detecting neutrons is challenging, as they do not leave direct ionization signals in LArTPCs. Neutrons can carry away up to 25% of the neutrino energy, introducing a significant uncertainty in DUNE measurements. The DUNE near detector (ND) features a novel modular LArTPC with pixelated charge readout, which enhances event recons truction. The modular design enables precise correlation between ionization signals and light signals in a high-rate environment, improving the identification of delayed energy depositions from neutrons in neutrino interactions. We introduce a neutron tagging technique using the 2x2 Demonstrator, a small-scale prototype of the DUNE ND LArTPC. The analysis utilizes Monte Carlo simulations and deep-learning techniques to identify neutron-induced energy depositions and reconstruct low-energy activity.

Kufatty, Georgette [Florida State U.]↗

DOE OSTI2022

High-Throughput Microfluidics Platform for Intracellular Delivery and Sampling of Biomolecules from Live Cells

Nondestructive cell membrane permeabilization systems enable the intracellular delivery of exogenous biomolecules for cell engineering tasks as well as the temporal sampling of cytosolic contents from live cells for the analysis of dynamic processes. Here, in this paper, we report a microwell array format live-cell analysis device (LCAD) that can perform localized-electroporation induced membrane permeabilization, for cellular delivery or sampling, and directly interfaces with surface-based biosensors for analyzing the extracted contents. We demonstrate the capabilities of the LCAD via an automated high-throughput workflow for multimodal analysis of live-cell dynamics, consisting of quantitative measurements of enzyme activity using self-assembled monolayers for MALDI mass spectrometry (SAMDI) and deep-learning enhanced imaging and analysis. By combining a fabrication protocol that enables robust assembly and operation of multilayer devices with embedded gold electrodes and an automated imaging workflow, we successfully deliver functional molecules (plasmid and siRNA) into live cells at multiple time-points and track their effect on gene expression and cell morphology temporally. Furthermore, we report sampling performance enhancements, achieving saturation levels of protein tyrosine phosphatase activity measured from as few as 60 cells, and demonstrate control over the amount of sampled contents by optimization of electroporation parameters using a lumped model. Lastly, we investigate the implications of cell morphology on electroporation-induced sampling of fluorescent molecules using a deep-learning enhanced image analysis workflow.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Parametrizing the detector response with neural networks

In high energy physics, characterizing the response of a detector to radiation is one of the most important and fundamental experimental tasks. In many cases, this task is accomplished by parameterizing summary statistics of the full detector response probability density. The parameterized detector response can then be used for calibration as well as for directly improving physics analysis sensitivity. This paper reports on how to parameterize summary statistics of the detector response using neural networks. Specifically, neural networks are powerful tools for incorporating multidimensional data and the loss function used during training determines which summary statistic is learned. One common summary statistic that has not been combined with deep learning (as far as the authors are aware) is the mode. A neural network-based approach to mode learning is proposed and empirically demonstrated in the context of high energy jet calibrations. Altogether, the neural network-based toolkit for detector response parameterization can enhance the utility of data collected at high energy physics experiments and beyond.

47 OTHER INSTRUMENTATION↗

DOE OSTI2021

PRISM3D: a 3-D reference seismic model for Iberia and adjacent areas

SUMMARY We present PRISM3D, a 3-D reference seismic model of P- and S-wave velocities for Iberia and adjacent areas. PRISM3D results from the combination of the most up-to-date earth models available for the region. It extends horizontally from 15°W to 5°E in longitude, 34°N to 46°N in latitude and vertically from 3.5 km above to 200 km below sea level, and is modelled on a regular grid with 10 and 0.5 km of grid node spacing in the horizontal and vertical directions, respectively. It was designed using models inferred from local and teleseismic body-wave tomography, earthquake and ambient noise surface wave tomography, receiver function analysis and active source experiments. It includes two interfaces, namely the topography/bathymetry and the Mohorovičić (Moho) discontinuity. The Moho was modelled from previously published receiver function analysis and deep seismic sounding results. To that end we used a probabilistic surface reconstruction algorithm that allowed to extract the mean of the Moho depth surface along with its associated standard deviation, which provides a depth uncertainty estimate. The Moho depth model is in good agreement with previously published models, although it presents slightly sharper gardients in orogenic areas such as the Pyrenees or the Betic-Rif system. Crustal and mantle P- and S-wave wave speed grids were built separately on each side of the Moho depth surface by weighted average of existing models, thus allowing to realistically render the speed gradients across that interface. The associated weighted standard deviation was also calculated, which provides an uncertainty estimation on the average wave speed values at any point of the grid. At shallow depths (<10 km), low P and S wave speeds and high VP/VS are observed in offshore basins, while the Iberian Massif, which covers a large part of western Iberia, appears characterized by a rather flat Moho, higher than average VP and VS and low VP/VS. Conversely, the Betic-Rif system seems to be associated with low VP and VS, combined with high VP/VS in comparison to the rest of the study area. The most prominent feature of the mantle is the well known high wave speed anomaly related to the Alboran slab imaged in various mantle tomography studies. The consistency of PRISM3D with previous work is verified by comparing it with two recent studies, with which it shows a good general agreement.The impact of the new 3-D model is illustrated through a simple synthetic experiment, which shows that the lateral variations of the wave speed can produce traveltime differences ranging from –1.5 and 1.5 s for P waves and from –2.5 and 2.5 s for S waves at local to regional distances. Such values are far larger than phase picking uncertainties and would likely affect earthquake hypocentral parameter estimations. The new 3-D model thus provides a basis for regional studies including earthquake source studies, Earth structure investigations and geodynamic modelling of Iberia and its surroundings.

Arroucau, P.↗

DOE OSTI2023

Data-Driven Affinely Adjustable Robust Volt/VAr Control

Recent years have seen the increasing proliferation of distributed energy resources with intermittent power outputs, posing new challenges to the voltage management in distribution networks. To this end, this paper proposes a data-driven affinely adjustable robust Volt/VAr control (AARVVC) scheme, which modulates the smart inverter’s reactive power in an affine function of its active power, based on the voltage sensitivities with respect to real/reactive power injections. To achieve a fast and accurate estimation of voltage sensitivities, we propose a data-driven method based on deep neural network (DNN), together with a rule-based bus-selection process using the bidirectional search method. Our method only uses the operating statuses of selected buses as inputs to DNN, thus significantly improving the training efficiency and reducing information redundancy. Finally, a distributed consensus-based solution, based on the alternating direction method of multipliers (ADMM), for the AARVVC is applied to decide the inverter’s reactive power adjustment rule with respect to its active power. Only limited information exchange is required between each local agent and the central agent to obtain the slope of the reactive power adjustment rule, and there is no need for the central agent to solve any (sub)optimization problems. Finally, numerical results on the modified IEEE-123 bus system validate the effectiveness and superiority of the proposed data-driven AARVVC method.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2026

Learning thermodynamic master equations for open quantum systems

The characterization of Hamiltonians and other components of open quantum dynamical systems plays a crucial role in quantum computing and other applications. Scientific machine learning techniques have been applied to this problem in a variety of ways, including by modeling with deep neural networks. However, the majority of mathematical models describing open quantum systems are linear, and the natural nonlinearities in learnable models have not been incorporated using physical principles. We present a data-driven model for open quantum systems that includes learnable, thermodynamically consistent terms. The trained model is interpretable, as it directly estimates the system Hamiltonian and linear components of coupling to the environment. We validate the model on synthetic two and three-level data, as well as experimental two-level data collected from a quantum device at Lawrence Livermore National Laboratory.

Mathematics and Computing↗

DOE OSTI2024

Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3–20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.

42 ENGINEERING↗

DOE OSTI2024

Measurement of Nuclear Dependence in Inclusive Antineutrino Scattering

One of the fundamental questions in physics is the matter-antimatter asymmetry of the Universe, explored through charge-parity violation searches in neutrino oscillation experiments. Next-generation oscillation experiments like DUNE need to constrain the systematic uncertainties arising from our understanding of (anti)neutrino-nucleus scattering to within a few percent to achieve their physics goals. MINERvA, a dedicated (anti)neutrino-nucleus scattering experiment, plays a crucial role in constraining these uncertainties. This thesis presents MINERvA's first high-statistics direct measurement of nuclear dependence in charged-current inclusive antineutrino scattering on carbon, hydrocarbon, iron, and lead as a function of antimuon transverse momentum, $p_{\text{T}}$, and Bjorken~$x$. The analysis utilises interactions with a mean antineutrino energy of approximately~6~GeV, with reconstructed antimuons having a scattering angle of less than 17$^\circ$ relative to the antin eutrino beam and an antimuon energy of 2--20 GeV. The measured per-nucleon differential cross-sections are reported with a precision of 7--9\%, while the cross-section ratios of carbon, iron, and lead to hydrocarbon have uncertainties of 5\% or less. The cross-sections for iron and lead indicate strong suppression at low $p_{\text{T}}$ and Bjorken~$x$, and an enhancement at high $p_{\text{T}}$. These effects are observed to be more pronounced with the increasing size of the target nucleus and are not reproduced by the underlying simulation prediction. Comparisons to alternative models used in current (anti)neutrino interaction generators show some improvements in modelling over the base prediction model, yet they are still unable to fully reproduce the observed nuclear dependence in this analysis. Importantly, the analysis provides a direct test of nuclear effects in inclusive antineutrino scattering, with major contributions from resonant pion production, deep inelastic scattering, and the transition region between these channels, which will be significant in DUNE. This measurement also represents one of the largest antineutrino datasets in this energy regime analysed to date.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗