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At least 505 records · Page 28

Deep neural network improves the estimation of polygenic risk scores for breast cancer

Polygenic risk scores (PRS) estimate the genetic risk of an individual for a complex disease based on many genetic variants across the whole genome. Here, we compared a series of computational models for estimation of breast cancer PRS. A deep neural network (DNN) was found to outperform alternative machine learning techniques and established statistical algorithms, including BLUP, BayesA, and LDpred. In the test cohort with 50% prevalence, the Area Under the receiver operating characteristic Curve (AUC) were 67.4% for DNN, 64.2% for BLUP, 64.5% for BayesA, and 62.4% for LDpred. BLUP, BayesA, and LPpred all generated PRS that followed a normal distribution in the case population. However, the PRS generated by DNN in the case population followed a bimodal distribution composed of two normal distributions with distinctly different means. This suggests that DNN was able to separate the case population into a high-genetic-risk case subpopulation with an average PRS significantly higher than the control population and a normal-genetic-risk case subpopulation with an average PRS similar to the control population. This allowed DNN to achieve 18.8% recall at 90% precision in the test cohort with 50% prevalence, which can be extrapolated to 65.4% recall at 20% precision in a general population with 12% prevalence. Interpretation of the DNN model identified salient variants that were assigned insignificant p values by association studies, but were important for DNN prediction. These variants may be associated with the phenotype through nonlinear relationships.

59 BASIC BIOLOGICAL SCIENCES↗

Train Like a (Var)Pro: Efficient Training of Neural Networks with Variable Projection

Deep neural networks (DNNs) have achieved state-of-the-art performance across a variety of traditional machine learning tasks, e.g., speech recognition, image classification, and segmentation. The ability of DNNs to efficiently approximate high-dimensional functions has also motivated their use in scientific applications, e.g., to solve partial differential equations and to generate surrogate models. In this paper, we consider the supervised training of DNNs, which arises in many of the above applications. We focus on the central problem of optimizing the weights of the given DNN such that it accurately approximates the relation between observed input and target data. Devising effective solvers for this optimization problem is notoriously challenging due to the large number of weights, nonconvexity, data sparsity, and nontrivial choice of hyperparameters. To solve the optimization problem more efficiently, we propose the use of variable projection (VarPro), a method originally designed for separable nonlinear least-squares problems. Our main contribution is the Gauss--Newton VarPro method (GNvpro) that extends the reach of the VarPro idea to nonquadratic objective functions, most notably cross-entropy loss functions arising in classification. These extensions make GNvpro applicable to all training problems that involve a DNN whose last layer is an affine mapping, which is common in many state-of-the-art architectures. In our four numerical experiments from surrogate modeling, segmentation, and classification, GNvpro solves the optimization problem more efficiently than commonly used stochastic gradient descent (SGD) schemes. Finally, GNvpro finds solutions that generalize well, and in all but one example better than well-tuned SGD methods, to unseen data points.

97 MATHEMATICS AND COMPUTING↗

Learning model combining convolutional deep neural network with a self-attention mechanism for AC optimal power flow

Alternating current optimal power flow (OPF) analysis is critical for efficient and reliable operation of power systems. For large systems or repetitive computations, the traditional methods such as the direct and gradient methods, or non-traditional methods, such as the genetic algorithm and simulating annealing, are time-consuming and unsuitable for real-time computing. The work in this paper proposes a novel framework to obtain the optimal solution of power flow in real-time using a combination of convolutional neural networks and a self-attention mechanism. All parameters of the power networks are rearranged in an image-like shape of a multi-channel image where each channel is a two-dimensional matrix. The proposed approach is adaptive with every input size of power systems as well as frequent variations of network topologies without intervention to the framework core. The encompassment of all power system contexts in which all parameters of internal elements, generation costs, and topology information are included, contributes to the higher accuracy of inference compared to other current machine-learning-based OPF-solving methods. Besides, the proposed framework established on ubiquitous platforms is effortlessly integrated into current infrastructures of power systems, and the great efficiency along with the computation speed may serve as a critical point for practical implications, such as enabling faster decision-making during real-time operations, predicting system contingencies, and remedial actions based on an offline pre-trained model. Furthermore, this supervised learning process is applied to the dataset of four case studies of meshed power systems: the IEEE 5-bus system (IEEE-5), the IEEE 30-bus system (IEEE-30), the IEEE 39-bus system (IEEE-39), and the IEEE 57-bus system (IEEE-57) to prove the efficacy of the proposed method.

42 ENGINEERING↗

Extracting low energy signals from raw LArTPC waveforms using deep learning techniques — A proof of concept

Here, we investigate the feasibility of using deep learning techniques, in the form of a one-dimensional convolutional neural network (1D-CNN), for the extraction of signals from the raw waveforms produced by the individual channels of liquid argon time projection chamber (LArTPC) detectors. A minimal generic LArTPC detector model is developed to generate realistic noise and signal waveforms used to train and test the 1D-CNN, and evaluate its performance on low-level signals. We demonstrate that our approach overcomes the inherent shortcomings of traditional cut-based methods by extending sensitivity to signals with ADC values below their imposed thresholds. This approach exhibits great promise in enhancing the capabilities of future generation neutrino experiments like DUNE to carry out their low-energy neutrino physics programs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Electron scattering and neutrino physics

Abstract A thorough understanding of neutrino–nucleus scattering physics is crucial for the successful execution of the entire US neutrino physics program. Neutrino–nucleus interaction constitutes one of the biggest systematic uncertainties in neutrino experiments—both at intermediate energies affecting long-baseline deep underground neutrino experiment, as well as at low energies affecting coherent scattering neutrino program—and could well be the difference between achieving or missing discovery level precision. To this end, electron–nucleus scattering experiments provide vital information to test, assess and validate different nuclear models and event generators intended to test, assess and validate different nuclear models and event generators intended to be used in neutrino experiments. Similarly, for the low-energy neutrino program revolving around the coherent elastic neutrino–nucleus scattering (CEvNS) physics at stopped pion sources, such as at ORNL, the main source of uncertainty in the evaluation of the CEvNS cross section is driven by the underlying nuclear structure, embedded in the weak form factor, of the target nucleus. To this end, parity-violating electron scattering (PVES) experiments, utilizing polarized electron beams, provide vital model-independent information in determining weak form factors. This information is vital in achieving a percent level precision needed to disentangle new physics signals from the standard model expected CEvNS rate. In this white paper, we highlight connections between electron- and neutrino–nucleus scattering physics at energies ranging from 10 s of MeV to a few GeV, review the status of ongoing and planned electron scattering experiments, identify gaps, and lay out a path forward that benefits the neutrino community. We also highlight the systemic challenges with respect to the divide between the nuclear and high-energy physics communities and funding that presents additional hurdles in mobilizing these connections to the benefit of neutrino programs.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Field Emission Mitigation in CEBAF SRF Cavities Using Deep Learning

The Continuous Electron Beam Accelerator Facility (CEBAF) operates hundreds of superconducting radio frequency (SRF) cavities in its two main linear accelerators. Field emission can occur when the cavities are set to high operating RF gradients and is an ongoing operational challenge. This is especially true in newer, higher gradient SRF cavities. Field emission results in damage to accelerator hardware, generates high levels of neutron and gamma radiation, and has deleterious effects on CEBAF operations. So, field emission reduction is imperative for the reliable, high gradient operation of CEBAF that is required by experimenters. Here we explore the use of deep learning architectures via multilayer perceptron to simultaneously model radiation measurements at multiple detectors in response to arbitrary gradient distributions. These models are trained on collected data and could be used to minimize the radiation production through gradient redistribution. This work builds on previous efforts in developing machine learning (ML) models, and is able to produce similar model performance as our previous ML model without requiring knowledge of the field emission onset for each cavity.

Ahammed, K.↗

EPiC-GAN: Equivariant point cloud generation for particle jets

With the vast data-collecting capabilities of current and future high-energy collider experiments, there is an increasing demand for computationally efficient simulations. Generative machine learning models enable fast event generation, yet so far these approaches are largely constrained to fixed data structures and rigid detector geometries. In this paper, we introduce EPiC-GAN - equivariant point cloud generative adversarial network - which can produce point clouds of variable multiplicity. This flexible framework is based on deep sets and is well suited for simulating sprays of particles called jets. The generator and discriminator utilize multiple EPiC layers with an interpretable global latent vector. Crucially, the EPiC layers do not rely on pairwise information sharing between particles, which leads to a significant speed-up over graph- and transformer-based approaches with more complex relation diagrams. We demonstrate that EPiC-GAN scales well to large particle multiplicities and achieves high generation fidelity on benchmark jet generation tasks.

Buhmann, Erik↗

Field Emission Mitigation in CEBAF SRF Cavities Using Deep Learning

The Continuous Electron Beam Accelerator Facility (CEBAF) operates hundreds of superconducting radio frequency (SRF) cavities in its two main linear accelerators. Field emission can occur when the cavities are set to high operating RF gradients and is an ongoing operational challenge. This is especially true in newer, higher gradient SRF cavities. Field emission results in damage to accelerator hardware, generates high levels of neutron and gamma radiation, and has deleterious effects on CEBAF operations. So, field emission reduction is imperative for the reliable, high gradient operation of CEBAF that is required by experimenters. Here we explore the use of deep learning architectures via multilayer perceptron to simultaneously model radiation measurements at multiple detectors in response to arbitrary gradient distributions. These models are trained on collected data and could be used to minimize the radiation production through gradient redistribution. This work builds on previous efforts in developing machine learning (ML) models, and is able to produce similar model performance as our previous ML model without requiring knowledge of the field emission onset for each cavity.

Ahammed, K.↗

Hector-FACTS Technical Report & User Guide: Integrating Hector into the Framework for Assessing Changes To Sea-level

The Framework for Assessing Changes To Sea-level (FACTS) platform was developed by (Kopp et al., 2023) as an open-source modular tool capable of generating probabilistic projections for global mean sea-level change and future relative and extreme sea-level change at New York City (Kopp et al., 2023). FACTS is the first open-source modular tool designed to explore deep uncertainty in SLR while also synthesizing across different modeling groups and integrating the various components of SLR used in key climate reports.

54 ENVIRONMENTAL SCIENCES↗

Applications of Nickelate perovskites for neuromorphic computing from electronic structure and Machine Learning

While the limit of Moore's law is presently being reached with current microelectronic technologies, we need to develop new paradigms that overcome this limitation. In that respect, neuromorphic computing is a concept that emulates the neural behavior and response of the human brain, and it has been recognized as a promising alternative approach. In this research project, we will perform multi-fidelity scale bridging to explore the potential use of materials with metal to insulator transition for neuromorphic applications. In particular, rare earth nickelates are promising for such purposes, as the transition in these materials is quite sensitive to a broad set of different external stimuli. Our multi-fidelity approach will bridge the high-fidelity electronic structure calculations with classical potentials. We will bridge dynamical mean field theory with a classical atomistic representation via a deep learning force field. The neural network is trained with energies, charges, and forces obtained by accurate electronic structure theories based on Dynamical Mean Field Theory. The configurational space is generated from known crystal phases, ab initio molecular dynamics with exchange-correlation functionals corrected with the Hubbard model, disordered phases with different concentrations of oxygen vacancies, and nonsymmetrical positions and induced strain by grain interfaces or contact with a substrate. Strategies to train the model with a reduced number of training examples are obtained from active learning methods, and new structures for improving the learning process are generated by using machine learning autoencoders. This classical potential will be validated through a diversity of electronic structure methods and represents an important step to combine the flexibility and accuracy of first-principles with the speed of classical potentials. The generated multi-fidelity surrogate model will be used to understand the role of strain, oxygen vacancies, proton doping, the variation of the crystal phase, substrate effects, vibrational effects as the octahedral rotation, grain boundaries and defect effects on the response of a Metal to Insulator Transition (MIT) in correlated materials. Long time and large-scale simulations will help understand the role of different stimuli to control the hysteresis of the MIT, as it has been experimentally suggested. Selected configurations will be analyzed with higher-level theories to provide an accurate electronic description and to study how the orbitals and charges are rearranged under different conditions.

36 MATERIALS SCIENCE↗

The Deep Underground Neutrino Experiment (DUNE) Program

The Deep Underground Neutrino Experiment (DUNE) is a next-generation long-baseline neutrino oscillation experiment aimed at determining the neutrino mass hierarchy and the CP-violating phase. The DUNE physics program also includes the detection of astrophysical neutrinos and the search for signatures beyond the Standard Model, such as nucleon decays. DUNE consists of a near detector complex located at Fermilab and four 17 kton Liquid Argon Time Projection Chamber (LArTPC) far detector modules to be built 1.5 km underground at SURF, approximately 1300 km away. The detectors are exposed to a wideband neutrino beam generated by a 1.2 MW proton beam with a planned upgrade to $>$ 2 MW. Two 770 ton LArTPCs (ProtoDUNEs) have been operated at CERN for over 2 years as a testbed for DUNE far detectors and have been optimized to take new cosmic and test-beam data in 2024-2025. The DUNE and ProtoDUNE experiments and physics goals, as well as recent progress and results, are presented.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Simulation-based inference for parameter estimation of complex watershed simulators

High-resolution, spatially distributed process-based (PB) simulators are widely employed in the study of complex catchment processes and their responses to a changing climate. However, calibrating these PB simulators using observed data remains a significant challenge due to several persistent issues, including the following: (1) intractability stemming from the computational demands and complex responses of simulators, which renders infeasible calculation of the conditional probability of parameters and data, and (2) uncertainty stemming from the choice of simplified representations of complex natural hydrologic processes. Here, we demonstrate how simulation-based inference (SBI) can help address both of these challenges with respect to parameter estimation. SBI uses a learned mapping between the parameter space and observed data to estimate parameters for the generation of calibrated simulations. To demonstrate the potential of SBI in hydrologic modeling, we conduct a set of synthetic experiments to infer two common physical parameters – Manning's coefficient and hydraulic conductivity – using a representation of a snowmelt-dominated catchment in Colorado, USA. We introduce novel deep-learning (DL) components to the SBI approach, including an “emulator” as a surrogate for the PB simulator to rapidly explore parameter responses. We also employ a density-based neural network to represent the joint probability of parameters and data without strong assumptions about its functional form. While addressing intractability, we also show that, if the simulator does not represent the system under study well enough, SBI can yield unreliable parameter estimates. Approaches to adopting the SBI framework for cases in which multiple simulator(s) may be adequate are introduced using a performance-weighting approach. The synthetic experiments presented here test the performance of SBI, using the relationship between the surrogate and PB simulators as a proxy for the real case.

54 ENVIRONMENTAL SCIENCES↗

Extracting low energy signals from raw LArTPC waveforms using deep learning techniques -- A proof of concept

We investigate the feasibility of using deep learning techniques, in the form of a one-dimensional convolutional neural network (1D-CNN), for the extraction of signals from the raw waveforms produced by the individual channels of liquid argon time projection chamber (LArTPC) detectors. A minimal generic LArTPC detector model is developed to generate realistic noise and signal waveforms used to train and test the 1D-CNN, and evaluate its performance on low-level signals. We demonstrate that our approach overcomes the inherent shortcomings of traditional cut-based methods by extending sensitivity to signals with ADC values below their imposed thresholds. This approach exhibits great promise in enhancing the capabilities of future generation neutrino experiments like DUNE to carry out their low-energy neutrino physics programs.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Data-based filtered dissipation rate modelling for multi-modal turbulent combustion: evaluating a priori model generalizability

Manifold-based models offer a computationally efficient alternative to directly transporting the thermochemical state in computational simulations of turbulent reacting flows, projecting the high-dimensional thermochemical state-space onto a low-dimensional manifold. Recent efforts have yielded a manifold-based model applicable to multi-modal combustion, enabling reconstruction of the thermochemical state from solutions to two-dimensional manifold equations in mixture fraction and generalized progress variable that are parameterised by three scalar dissipation rates. In coarse-grained simulations such as Large Eddy Simulation (LES), closure of the multi-modal manifold equations and subfilter variances/covariance requires closure of three filtered scalar dissipation rates. Here, the present work adopts a data-based approach, providing closure for the three filtered scalar dissipation rates via deep neural networks (DNNs). High-fidelity datasets corresponding to an autoigniting n-dodecane jet flame and a bluff body swirl-stabilized confined lifted spray flame of two aviation fuels (Jet-A and C1) with different ignition propensities are leveraged to generate training data that spans a diverse range of thermodynamic conditions and combustion modes, including low- and high-temperature ignition regimes in addition to premixed and nonpremixed behaviour. A final DNN model is trained to enforce inherent physical constraints by learning nonlinear functional transformations of the three filtered scalar dissipation rates. The generalizability of this constrained DNN model is demonstrated a priori via conditional statistics evaluated on the lifted spray flame with C1–a configuration that had not been included in the training data. Excellent DNN agreement with conditional DNS statistics is observed, and integrated gradients are computed to identify the most sensitive input variables. The similarity of the marginal PDFs of the most informative input variables and outputs across configurations are quantified via the Wasserstein metric, demonstrating that data-based models may successfully generalize to unseen parametric conditions so long as the most informative input variables share similar distributions across training and testing datasets.

Data-based modelling↗

Quasi-Classical Trajectory Calculation of Rate Constants Using an Ab Initio Trained Machine Learning Model (aML-MD) with Multifidelity Data

Machine learning (ML) provides a great opportunity for the construction of models with improved accuracy in classical molecular dynamics (MD). However, the accuracy of a ML trained model is limited by the quality and quantity of the training data. Generating large sets of accurate ab initio training data can require significant computational resources. Furthermore, inconsistent or incompatible data with different accuracies obtained using different methods may lead to biased or unreliable ML models that do not accurately represent the underlying physics. Recently, transfer learning showed its potential for avoiding these problems as well as for improving the accuracy, efficiency, and generalization of ML models using multifidelity data. In this work, ab initio trained ML-based MD (aML-MD) models are developed through transfer learning using DFT and multireference data from multiple sources with varying accuracy within the Deep Potential MD framework. Further, the accuracy of the force field is demonstrated by calculating rate constants for the H + HO 2 → H 2 + 3 O 2 reaction using quasi-classical trajectories. We show that the aML-MD model with transfer learning can accurately predict the rate constants while reducing the computational cost by more than five times compared to the use of more expensive quantum chemistry training data sets. Hence, the aML-MD model with transfer learning shows great potential in using multifidelity data to reduce the computational cost involved in generating the training set for these potentials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Demand-side solutions in the US building sector could achieve deep emissions reductions and avoid over $100 billion in power sector costs

Buildings are energy-intensive and a primary source of US end-use sector carbon emissions. Although building emissions today are 25% below their 2005 peak, far deeper reductions are needed to reach the US 2050 net-zero emissions goal. However, plausible decarbonization pathways that consider both buildings and their interactions with the power grid remain poorly understood. Here, we couple detailed modeling of building energy use and the grid to quantify building decarbonization potential and associated grid impacts. We find up to a 91% reduction in building CO 2 emissions from 2005 levels by 2050 using a portfolio of building efficiency, demand flexibility, and electrification measures alongside rapid grid decarbonization. Building efficiency and flexibility could generate up to $107 billion in annual power system cost savings by 2050, offsetting over a third of the incremental cost of full grid decarbonization. Our results underscore multiple benefits of demand-side solutions for deep decarbonization of US buildings.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Heterogeneous energetic material damage simulator (HEDS): A deep learning approach to simulate damage–sensitivity linkages

Damage in the microstructures of energetic materials (EMs), such as propellants and plastic bonded explosives (PBXs), can significantly alter their response to external loads. Both sensitization and desensitization can occur, causing concerns with safety and performance in the field; predictive models that connect damage and the sensitivity of EMs can enable design and provide confidence in their robustness and reliability. However, modeling of damage evolution is challenging for real microstructures of EMs; samples of damaged EMs are difficult to obtain, thereby hindering experiments and direct numerical simulations to determine the sensitivity of EMs at various stages of damage. Here, we develop an approach to generate synthetic, i.e., in silico produced, damaged microstructures for use in simulations to connect damage levels to sensitivity. The development of the present workflow to generate and impose varying levels of damage in microstructures, known as HEDS (Heterogeneous Energetic Material Damage Simulator), begins with a small set of images of damaged PBXs and combines a collection of deep neural network techniques to generate microstructures with varying levels of damage. By making the synthetic microstructures conform closely to those observed in available real, imaged microstructures, we develop an ensemble of damaged microstructures that can be used for in silico shock experiments. HEDS develops these microstructure ensembles as level set fields, which are directly employed in a sharp interface Eulerian hydrocode where shock simulations are performed to quantify the energy release rate from hotspot fields generated in the microstructure. These capabilities can be useful for the analysis and assessment of changes in the sensitivity of EMs and to design formulations that are less susceptible to damage-induced changes in sensitivity and performance.

Fang, Irene (ORCID:0009000844557122)↗

Automatic Detection of Defects in High-Reliability Components

Disastrous consequences can result from defects in manufactured parts—particularly the high consequence parts developed at Sandia. Identifying flaws in as-built parts can be done with nondestructive means, such as X-ray Computed Tomography (CT). However, due to artifacts and complex imagery, the task of analyzing the CT images falls to humans. Human analysis is inherently unreproducible, unscalable, and can easily miss subtle flaws. We hypothesized that deep learning methods could improve defect identification, increase the number of parts that can effectively be analyzed, and do it in a reproducible manner. We pursued two methods: 1) generating a defect-free version of a scan and looking for differences (PandaNet), and 2) using pre-trained models to develop a statistical model of normality (Feature-based Anomaly Detection System: FADS). Both PandaNet and FADS provide good results, are scalable, and can identify anomalies in imagery. In particular, FADS enables zero-shot (training-free) identification of defects for minimal computational cost and expert time. It significantly outperforms prior approaches in computational cost while achieving comparable results. FADS’ core concept has also shown utility beyond anomaly detection by providing feature extraction for downstream tasks.

47 OTHER INSTRUMENTATION↗