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At least 631 records · Page 35

Temporal regulation of cold transcriptional response in switchgrass

Switchgrass low-land ecotypes have significantly higher biomass but lower cold tolerance compared to up-land ecotypes. Understanding the molecular mechanisms underlying cold response, including the ones at transcriptional level, can contribute to improving tolerance of high-yield switchgrass under chilling and freezing environmental conditions. Here, by analyzing an existing switchgrass transcriptome dataset, the temporal cis- regulatory basis of switchgrass transcriptional response to cold is dissected computationally. We found that the number of cold-responsive genes and enriched Gene Ontology terms increased as duration of cold treatment increased from 30 min to 24 hours, suggesting an amplified response/cascading effect in cold-responsive gene expression. To identify genomic sequences likely important for regulating cold response, machine learning models predictive of cold response were established using k -mer sequences enriched in the genic and flanking regions of cold-responsive genes but not non-responsive genes. These k -mers, referred to as putative cis -regulatory elements (pCREs) are likely regulatory sequences of cold response in switchgrass. There are in total 655 pCREs where 54 are important in all cold treatment time points. Consistent with this, eight of 35 known cold-responsive CREs were similar to top-ranked pCREs in the models and only these eight were important for predicting temporal cold response. More importantly, most of the top-ranked pCREs were novel sequences in cold regulation. Our findings suggest additional sequence elements important for cold-responsive regulation previously not known that warrant further studies.

60 APPLIED LIFE SCIENCES↗

A Deep Potential model for liquid–vapor equilibrium and cavitation rates of water

Computational studies of liquid water and its phase transition into vapor have traditionally been performed using classical water models. Here, we utilize the Deep Potential methodology—a machine learning approach—to study this ubiquitous phase transition, starting from the phase diagram in the liquid–vapor coexistence regime. The machine learning model is trained on ab initio energies and forces based on the SCAN density functional, which has been previously shown to reproduce solid phases and other properties of water. Here, we compute the surface tension, saturation pressure, and enthalpy of vaporization for a range of temperatures spanning from 300 to 600 K and evaluate the Deep Potential model performance against experimental results and the semiempirical TIP4P/2005 classical model. Moreover, by employing the seeding technique, we evaluate the free energy barrier and nucleation rate at negative pressures for the isotherm of 296.4 K. Further, we find that the nucleation rates obtained from the Deep Potential model deviate from those computed for the TIP4P/2005 water model due to an underestimation in the surface tension from the Deep Potential model. From analysis of the seeding simulations, we also evaluate the Tolman length for the Deep Potential water model, which is (0.091 ± 0.008) nm at 296.4 K. Finally, we identify that water molecules display a preferential orientation in the liquid–vapor interface, in which H atoms tend to point toward the vapor phase to maximize the enthalpic gain of interfacial molecules. We find that this behavior is more pronounced for planar interfaces than for the curved interfaces in bubbles. This work represents the first application of Deep Potential models to the study of liquid–vapor coexistence and water cavitation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular Simulation of Lithium Carbonate Reactive Vapor–Liquid Equilibria Using a Deep Potential Model

We developed a first-principles machine learning model for the reactive vapor–liquid phase behavior of molten Li 2 CO 3 . The model was trained on ab initio electronic density functional theory data using the Deep Potential (DP) methodology, and its accuracy was evaluated by comparing model predictions of density and viscosity to experimental measurements. Direct coexistence simulations with the DP model over time scales of tens of nanoseconds were used to observe equilibrium dissociation of Li 2 CO 3 into CO 2 residing primarily in the vapor phase and Li 2 O which remains dissolved in the liquid. The simulations covered a range of temperatures, overall system sizes, and vapor-to-liquid volume ratios. Results were analyzed in terms of the observed chemical composition of the liquid and vapor phases, product structure, and CO 2 partial pressures. In addition, we calculated equilibrium constants for the dissociation reaction by assuming ideal-solution behavior for the liquid. As expected on the basis of thermodynamic arguments and prior experiments for this system, the observed partial pressure of CO 2 in the gas phase depends on both the temperature and the ratio of vapor to liquid volumes, while the calculated equilibrium constants only depend on temperature. DP model predictions for the equilibrium constant of the reaction are generally consistent with the available experimental measurements. Furthermore, the present study establishes the validity of the DP methodology for the description of reactive, multiphase equilibria from first principles, with possible applications to many other systems of scientific and technological interest even in the absence of relevant experimental measurements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Particle trajectory representation learning with masked point modeling

Liquid argon time projection chambers (LArTPCs) offer millimeter-scale 3D images of particle trajectories, enabling precision studies of neutrino oscillation, detection of supernova and solar neutrinos, searches for exotic dark matter, and proton decay. Current approaches utilize supervised machine learning models, requiring extensive simulations of particle physics and detector response that can introduce bias. Self-supervised learning (SSL), a machine learning approach that learns useful representations of unlabeled data from the data itself, has significantly advanced how large datasets are utilized for representation learning; however, its potential for applications to sensory data in high precision particle physics experiments remains largely unexplored. We introduce the Point-based liquid argon masked autoencoder (PoLAr-MAE), a self-supervised framework that learns physically meaningful representations directly from unlabeled LArTPC images. PoLAr-MAE achieves remarkable data efficiency for a point-level segmentation task, outperforming fully supervised methods in low data regimes. Linear classifiers on model outputs demonstrate robust performance across multiple downstream tasks. Our results position sensor-level SSL as a practical foundation model strategy for LArTPCs.

Young, Samuel [Stanford Univ., CA (United States)]↗

A tutorial review of machine learning-based model predictive control methods

Abstract This tutorial review provides a comprehensive overview of machine learning (ML)-based model predictive control (MPC) methods, covering both theoretical and practical aspects. It provides a theoretical analysis of closed-loop stability based on the generalization error of ML models and addresses practical challenges such as data scarcity, data quality, the curse of dimensionality, model uncertainty, computational efficiency, and safety from both modeling and control perspectives. The application of these methods is demonstrated using a nonlinear chemical process example, with open-source code available on GitHub. The paper concludes with a discussion on future research directions in ML-based MPC.

Wu, Zhe [Department of Chemical and Biomolecular E↗

Quantification of neural networks uncertainties with applications to SAFARI-1 axial neutron flux profiles

Deep Neural Networks (DNNs) have been widely used as a data-driven modelling tool in nuclear engineering. However, as a Machine Learning model, Artificial Neural Network (ANN) predictions are subjected to uncertainties originating from the noise in training data, incomplete coverage of the domain, and imperfect neural network architectures. In this work, we target at quantifying the prediction/approximation uncertainties of ANNs using Monte Carlo Dropout (MCD), as well as Bayesian Neural Networks (BNNs) which are solved by variational inference. With a demonstration problem in which neural networks are used to predict the assembly axial neutron flux profiles, the results have shown that the three different neural network models (regular DNNs, DNNs solved with MCD and BNNs) can produce results that agree very well among each other and with the measurement data, on cycles that are not used in the training process. Besides the excellent generalization capability, the uncertainty bands produced by MCD and BNN agree very well, and in general, they can fully envelop the noisy measurement data points. (authors)

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

Physics-guided Machine Learning: from Supervised Deep Networks to Unsupervised Lightweight Models [Slides]

Machine learning yields great potentials in improving imaging performance (i.e., accuracy and efficiency). The incorporation of governing equation will improve generalization and alleviate label scarcity. Employ physical properties can reduce model complexity and significantly save training cost without compromising accuracy. Combining SciML imaging and edge computing would allow broader applications in energy, medicine, and other domains.

97 MATHEMATICS AND COMPUTING↗

Applying Machine‐Learning Methods to Laser Acceleration of Protons: Lessons Learned From Synthetic Data

ABSTRACT In this study, we consider three different machine‐learning methods—a three‐hidden‐layer neural network, support vector regression, and Gaussian process regression—and compare how well they can learn from a synthetic data set for proton acceleration in the Target Normal Sheath Acceleration regime. The synthetic data set was generated from a previously published theoretical model by Fuchs et al. 2005 that we modified. Once trained, these machine‐learning methods can assist with efforts to maximize the peak proton energy, or with the more general problem of configuring the laser system to produce a proton energy spectrum with desired characteristics. In our study, we focus on both the accuracy of the machine‐learning methods and the performance on one GPU including memory consumption. Although it is arguably the least sophisticated machine‐learning model we considered, support vector regression performed very well in our tests.

Desai, Ronak↗

Chapter 14: Machine Learning of Combustion LES Models from Reacting Direct Numerical Simulation

In this chapter we demonstrate how supervised deep learning techniques can be used to construct models for the filtered progress variable source term necessary for large eddy simulation (LES). The source data for the model is a direct numerical simulation (DNS) of a reacting flow in a low swirl burner configuration. Filtered quantities taken from the DNS data are used to train a deep neural network (DNN)-based model. An efficient data sampling strategy was devised to ensure that a uniform representation of all the states observed in the filtered DNS data are equally present in the training dataset. A-priori testing of the DNN-based model highlights the representative power of DNN to accurately reproduce the filtered reaction progress variable source term over a range of scales and various flame regimes as seen in an industrial burner.

combustion LES models↗

High-resolution hourly surrogate modeling framework for physics-based large-scale building stock modeling

Surrogate modeling can play a key role in reducing high computational burdens for large-scale physics-based modeling and uncertainty quantification. With the rapid development of large-scale building stock energy modeling, surrogate modeling has also begun to be widely applied in this field; however, most existing surrogate models lack hourly time resolution for regional-scale modeling, which is essential for understanding building demand profiles and grid impacts. Further, there is generally a lack of necessary data and feature engineering frameworks specific to building modeling for efficiently managing large datasets and complex computations. Furthermore, this paper proposes a modeling framework for large-scale (city-/region-scale), high-resolution, high-fidelity surrogate building stock energy models. Our developed framework consists of six modules: (1) building stock energy modeling (ComStock TM and ResStock TM ), (2) data engineering for large simulation data, (3) high performance computing workflow, (4) feature engineering, (5) machine learning model development, and (6) model performance evaluation. Two case studies apply the developed framework in both residential and commercial building stock analysis to demonstrate its computational efficiency and surrogate modeling accuracies. Results show that surrogate models, when efficiently trained using the HPC workflow module, reach a high level of modeling accuracy for two case studies.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Fast and accurate machine learning prediction of phonon scattering rates and lattice thermal conductivity

Abstract Lattice thermal conductivity is important for many applications, but experimental measurements or first principles calculations including three-phonon and four-phonon scattering are expensive or even unaffordable. Machine learning approaches that can achieve similar accuracy have been a long-standing open question. Despite recent progress, machine learning models using structural information as descriptors fall short of experimental or first principles accuracy. This study presents a machine learning approach that predicts phonon scattering rates and thermal conductivity with experimental and first principles accuracy. The success of our approach is enabled by mitigating computational challenges associated with the high skewness of phonon scattering rates and their complex contributions to the total thermal resistance. Transfer learning between different orders of phonon scattering can further improve the model performance. Our surrogates offer up to two orders of magnitude acceleration compared to first principles calculations and would enable large-scale thermal transport informatics.

36 MATERIALS SCIENCE↗

Machine learning-enhanced hybrid modeling approach for better identification of a building thermal network model and improved prediction

The gray-box modeling approach, which uses a semi-physical thermal network model, has been widely used in building prediction applications, such as model predictive control (MPC). However, unmeasured disturbances, such as occupants, lighting, and in/exfiltration loads, make it challenging to apply this approach to practical buildings. In this word, we propose a hybrid modeling approach that integrates the gray-box model with a model for unmeasured disturbance. After reviewing several system identification approaches, we systematically designed the unmeasured disturbance model with a model selection process based on statistical tests to make it robust. We generated data based on the building model calibrated by real operational data and then trained the hybrid model for two different weather conditions. The hybrid model approach demonstrates an RMSE reduction of approximately 0.2–0.9 °C and 0.3–2 °C on 1-day ahead temperature prediction compared to the Conventional approach for mild (Berkeley, CA) and cold (Chicago, IL) climates, respectively. In addition, this approach was applied to experimental data obtained from the laboratory building to be used for the MPC application, showing superior prediction performances.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Initial Implementation Of Machine Learning System for SRF Cavity Fault Classification at CEBAF

The Continuous Electron Beam Accelerator Facility (CEBAF) at Jefferson Laboratory is high power CW electron accelerator. It uses a mixture of two types of SRF modules, older, lower energy C20/C50 modules and newer higher energy C100 modules, arrayed in two anti-parallel linear accelerators. Accurately classifying the type of cavity faults is essential to maintaining and improving accelerator performance. Each C100 cryomodule contains eight 7-cell cavities. When a cavity fault occurs within a cryomodule, all eight cavities generate 17 waveforms each containing 8192 points. This data is exported from EPICS and saved for review. Analysis of these waveforms is time intensive and requires subject matter expertise (SME). SMEs examine the data from each event and label it according to one of several known cavity fault types. Multiple machine learning models have been developed on this labeled dataset with sufficient performance to warrant the creation of a limited machine learning software system for use by accelerator operations staff. This paper discusses the transition from model development to implementation of a prototype system.

Carpenter, A.↗

Machine learning moment closure models for the radiative transfer equation I: Directly learning a gradient based closure

In this paper, we take a data-driven approach and apply machine learning to the moment closure problem for the radiative transfer equation in slab geometry. Instead of learning the unclosed high order moment, we propose to directly learn the gradient of the high order moment using neural networks. This new approach is consistent with the exact closure we derive for the free streaming limit and also provides a natural output normalization. Finally, a variety of benchmark tests, including the variable scattering problem, the Gaussian source problem with both periodic and reflecting boundaries, and the two-material problem, show both good accuracy and generalizability of our machine learning closure model.

Computer science↗

Importance of kernel bandwidth in quantum machine learning

Quantum kernel methods are considered a promising avenue for applying quantum computers to machine learning problems. Identifying hyperparameters controlling the inductive bias of quantum machine learning models is expected to be crucial given the central role hyperparameters play in determining the performance of classical machine learning methods. In this work we introduce the hyperparameter controlling the bandwidth of a quantum kernel and show that it controls the expressivity of the resulting model. We use extensive numerical experiments with multiple quantum kernels and classical data sets to show consistent change in the model behavior from underfitting (bandwidth too large) to overfitting (bandwidth too small), with optimal generalization in between. We draw a connection between the bandwidth of classical and quantum kernels and show analogous behavior in both cases. Furthermore, we show that optimizing the bandwidth can help mitigate the exponential decay of kernel values with qubit count, which is the cause behind recent observations that the performance of quantum kernel methods decreases with qubit count. Here, we reproduce these negative results and show that if the kernel bandwidth is optimized, the performance instead improves with growing qubit count and becomes competitive with the best classical methods.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Observational benchmarks inform representation of soil organic carbon dynamics in land surface models

Abstract. Representing soil organic carbon (SOC) dynamics in Earth system models (ESMs) is a key source of uncertainty in predicting carbon–climate feedbacks. Machine learning models can help identify dominant environmental controllers and establish their functional relationships with SOC stocks. The resulting knowledge can be integrated into ESMs to reduce uncertainty and improve predictions of SOC dynamics over space and time. In this study, we used a large number of SOC field observations (n=54 000), geospatial datasets of environmental factors (n=46), and two machine learning approaches (namely random forest, RF, and generalized additive modeling, GAM) to (1) identify dominant environmental controllers of global and biome-specific SOC stocks, (2) derive functional relationships between environmental controllers and SOC stocks, and (3) compare the identified environmental controllers and predictive relationships with those in models used in Phase 6 of the Coupled Model Intercomparison Project (CMIP6). Our results showed that the diurnal temperature, drought index, cation exchange capacity, and precipitation were important observed environmental predictors of global SOC stocks. While the RF model identified 14 environmental factors that describe climatic, vegetation, and edaphic conditions as important predictors of global SOC stocks (R2=0.61, RMSE = 0.46 kg m−2), current ESMs oversimplify the relationships between environmental factors and SOC, with precipitation, temperature, and net primary productivity explaining > 96 % of the variability in ESM-modeled SOC stocks. Further, our study revealed notable disparities among the functional relationships between environmental factors and SOC stocks simulated by ESMs compared with observed relationships. To improve SOC representations in ESMs, it is imperative to incorporate additional environmental controls, such as the cation exchange capacity, and refine the functional relationships to align more closely with observations.

54 ENVIRONMENTAL SCIENCES↗

Atomate2: modular workflows for materials science

High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science.

97 MATHEMATICS AND COMPUTING↗

Adaptive Generation of Training Data for ML Reduced Model Creation

Machine learning proxy models are often used to speed up or completely replace complex computational models. The greatly reduced and deterministic computational costs enable new use cases such as digital twin control systems and global optimization. The challenge of building these proxy models is generating the training data. A naive uniform sampling of the input space can result in a non-uniform sampling of the output space of a model. This can cause gaps in the training data coverage that can miss finer scale details resulting in poor accuracy. While larger and larger data sets could eventually fill in these gaps, the computational burden of full-scale simulation codes can make this prohibitive. In this paper, we present an adaptive data generation method that utilizes uncertainty estimation to identify regions where training data should be augmented. By targeting data generation to areas of need, representative data sets can be generated efficiently. The effectiveness of this method will be demonstrated on a simple one-dimensional function and a complex multidimensional physics model.

Cianciosa, Mark↗