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At least 127 records · Page 7

Identifying microbial drivers in biological phenotypes with a Bayesian network regression model

Abstract In Bayesian Network Regression models, networks are considered the predictors of continuous responses. These models have been successfully used in brain research to identify regions in the brain that are associated with specific human traits, yet their potential to elucidate microbial drivers in biological phenotypes for microbiome research remains unknown. In particular, microbial networks are challenging due to their high dimension and high sparsity compared to brain networks. Furthermore, unlike in brain connectome research, in microbiome research, it is usually expected that the presence of microbes has an effect on the response (main effects), not just the interactions. Here, we develop the first thorough investigation of whether Bayesian Network Regression models are suitable for microbial datasets on a variety of synthetic and real data under diverse biological scenarios. We test whether the Bayesian Network Regression model that accounts only for interaction effects (edges in the network) is able to identify key drivers (microbes) in phenotypic variability. We show that this model is indeed able to identify influential nodes and edges in the microbial networks that drive changes in the phenotype for most biological settings, but we also identify scenarios where this method performs poorly which allows us to provide practical advice for domain scientists aiming to apply these tools to their datasets. BNR models provide a framework for microbiome researchers to identify connections between microbes and measured phenotypes. We allow the use of this statistical model by providing an easy‐to‐use implementation which is publicly available Julia package at https://github.com/solislemuslab/BayesianNetworkRegression.jl .

59 BASIC BIOLOGICAL SCIENCES↗

Digital Twin for Hydropower System Object Modeling: Alder Dam (FY2023)

Hydropower is the world's largest source of renewable electricity, and hydropower plants are distributed all over the world. Typical major components of a hydropower plant are the governor, excitation, generator, thrust bearing, hydraulic turbine, transformer, the main lead, metering and control, tailwater depression, and dissolved oxygen. For each component, various measures are taken. The measurements are acquired by various heterogeneous systems, including standalone sensors, programmable logic controllers (PLC), Supervisory control and data acquisition (SCADA), Internet of Things (IoT), and data acquisition and integration platforms such as OSI/PI. The measured data are often archived within the plant by a data management platform, and many institutions have cloud-based archive systems, such as Hydropower Research Institution (HRI), U.S. Army Corps of Engineers (USACE), and Columbia River Data Access in Real Time (DART). Object Modeling is a general framework for designing information systems. It focuses on objects, the actions they perform, and the messages they send to one another to cause those actions to be taken. The major differences among object modeling, network modeling, data modeling, and process modeling are that in the first we focus on the actions in response to information, objects which form the system, the actions they perform, and how they pass information to one another, while in the second we concentrate on where, when and how much information is moved, while in the third we focus on what information is moved and where it is moved, while in the last we focus on how it is moved and when it is moved. Object modeling was developed basically as a method to develop object-oriented systems and to support object-oriented programming. It describes the static structure of the system. The object Modeling Technique is easy to draw and use. That is why we choose object modeling to connect physical hydropower plants to Digital Twin. It recognizes the objects and the relationship between them. It identifies the attributes and functions of each class. Dynamic Modeling: It explains how objects respond to events. Functional Modeling indicates the processes executed in an object and how data changes when it moves to objects. It has been used in many applications like telecommunication, transportation, etc.

13 HYDRO ENERGY↗

Neural Network Water Model Based on the MB-Pol Many-Body Potential

The MB-pol many-body potential accurately predicts many properties of water, including cluster, liquid phase, and vapor–liquid equilibrium properties, but its high computational cost can make applying it in large-scale simulations quite challenging. Here, in order to address this limitation, we developed a “deep potential” neural network (DPMD) model based on the MB-pol potential for water. We find that a DPMD model trained on mostly liquid configurations yields a good description of the bulk liquid phase but severely underpredicts vapor–liquid coexistence densities. By contrast, adding cluster configurations to the neural network training set leads to a good agreement for the vapor coexistence densities. Liquid phase densities under supercooled conditions are also represented well, even though they were not included in the training set. These results confirm that neural network models can combine accuracy and transferability if sufficient attention is given to the construction of a representative training set for the target system.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Phase Identification in Real Distribution Networks with High PV Penetration Using Advanced Metering Infrastructure Data

Many distribution network monitoring and control applications - including state estimation, volt/VAR optimization, and network reconfiguration - rely on accurate network models; however, the network models maintained by utilities can become outdated because of restoration activities, network reconfiguration, and missing data. With the widespread deployment of advanced metering infrastructure (AMI), abundant measurement data from low-voltage secondary networks are available. The AMI measurement data can be used for phase identification to improve the network models. Although the existing phase identification techniques work well in passive distribution feeders that do not have photovoltaic (PV) generation, they can fail to accurately identify the phases in the presence of PV. This paper proposes a robust phase identification algorithm based on supervised machine learning that accurately identifies the AMI meter phase connectivity in the presence of significant PV generation. The proposed algorithm does not require network topology information or feeder head measurement data. The algorithm is validated using the AMI measurement data collected in the field and the field-validated phase connectivity database on two real distribution feeders from San Diego Gas & Electric Company that have significant PV generation.

advanced metering infrastructure↗

Phase Identification in Real Distribution Networks with High PV Penetration Using Advanced Metering Infrastructure Data: Preprint

Many distribution network monitoring and control applications - including state estimation, volt/VAR optimization, and network reconfiguration - rely on accurate network models; however, the network models maintained by utilities can become outdated because of restoration activities, network reconfiguration, and missing data. With the widespread deployment of advanced metering infrastructure (AMI), abundant measurement data from low-voltage secondary networks are available. The AMI measurement data can be used for phase identification to improve the network models. Although the existing phase identification techniques work well in passive distribution feeders that do not have photovoltaic (PV) generation, they can fail to accurately identify the phases in the presence of PV. This paper proposes a robust phase identification algorithm based on supervised machine learning that accurately identifies the AMI meter phase connectivity in the presence of significant PV generation. The proposed algorithm does not require network topology information or feeder head measurement data. The algorithm is validated using the AMI measurement data collected in the field and the field-validated phase connectivity database on two real distribution feeders from San Diego Gas & Electric Company that have significant PV generation.

advanced metering infrastructure↗

Phase Identification in Real Distribution Networks with High PV Penetration Using Advanced Metering Infrastructure Data

Many distribution network monitoring and control applications - including state estimation, Volt/VAr optimization, and network reconfiguration - rely on accurate network models; however, the network models maintained by utilities can become outdated because of restoration activities, network reconfiguration, and missing data. With the widespread deployment of advanced metering infrastructure (AMI), abundant measurement data from low-voltage secondary networks are available. The AMI measurement data can be used for phase identification to improve the network models. Although the existing phase identification techniques work well in passive distribution feeders that do not have photovoltaic (PV) generation, they can fail to accurately identify the phases in the presence of PV. This paper proposes a robust phase identification algorithm based on supervised machine learning that accurately identifies the AMI meter phase connectivity in the presence of significant PV generation. The proposed algorithm does not require network topology information or feeder-head measurement data. The algorithm is validated using the AMI measurement data collected in the field and the field-validated phase connectivity database on two real distribution feeders from San Diego Gas & Electric Company that have significant PV generation.

advanced metering infrastructure (AMI)↗

Implementing a neural network interatomic model with performance portability for emerging exascale architectures

The two main thrusts of computational science are increasingly accurate predictions and faster calculations; to this end, the zeitgeist in molecular dynamics (MD) simulations is pursuing machine learned and data driven interatomic models, e.g. neural network potentials, and novel hardware architectures, e.g. GPUs. Current implementations of neural network potentials are orders of magnitude slower than traditional interatomic models and while looming exascale computing offers the ability to run large, accurate simulations with these models, achieving portable performance for MD with new and varied exascale hardware requires rethinking traditional algorithms, using novel data structures, and library solutions. We re-implement a neural network interatomic model in CabanaMD, an MD proxy application, built on libraries developed for performance portability. Our implementation shows significantly improved thread scaling in this complex kernel as compared to a current LAMMPS implementation, across both strong and weak scaling. Our single-source solution enables simulations up to 20 million atoms on a single CPU node and 4 million atoms with improved performance on a single GPU. Furthermore, we also explore parallelism and data layout choices (using flexible data structures called AoSoAs) and their effect on performance, seeing up to ~50% and ~5% improvements in performance on a GPU by choosing the right level of parallelism and data layout respectively.

97 MATHEMATICS AND COMPUTING↗

Models and Methods for Sparse (Hyper)Network Science in Business, Industry, and Government

The authors are hosting an AMS sponsored Mathematics Research Community (MRC) focusing on two themes that have garnered intense attention in network models of complex relational data: (1) how to faithfully model multi-way relations in hypergraphs, rather than only pairwise interactions in graphs; and (2) challenges posed by modelling networks with extreme sparsity. Here we introduce and explore these two themes and their challenges. In this work, we hope to generate interest from researchers in pure and applied mathematics and computer science.

97 MATHEMATICS AND COMPUTING↗

Validation of Power Distribution Models using Load Flow Analysis in an ADMS Environment

Electric utilities are facing the need for better monitoring, analysis, and control of their distribution systems. An accurate mathematical model is a key to both the development of cutting-edge, scalable model-based algorithms and the assessment of emerging technologies such as distributed energy resources (DER) for grid planning and operation. However, the constantly evolving nature of power distribution systems poses challenges to maintaining accurate models. In this paper, we propose a novel load flow based approach to validate power distribution models. Networked equipment models described according to the Common Information Model (CIM) standard and a measurement model are used to formulate the distribution load flow problem. First, a system admittance matrix (Ybus) is derived from device-level CIM parameters. Next, the operational parameters (dynamic Ybus and nodal injections) are extracted from the measurement model using sensor configuration and equipment state. An iterative power flow method is then used to compute nodal voltages and branch flows that are compared against the measurement data to find any inconsistencies in the networked equipment model. This approach is implemented within GridAPPS-D, an open-source standards-based platform for advanced distribution management system (ADMS) application development, and demonstrated on the IEEE 13-bus, 123-bus, and 8500-node test feeders.

Common information model, model validation, power ↗

Interface diagnostics platform for thin-film solid-state batteries

Understanding the impedances of battery materials and their interfaces remains a major challenge, usually addressed by electrochemical impedance spectroscopy (EIS) where frequency-dependent complex impedance of full battery cells is measured and then modeled by a network of connected electrical elements. As conventionally applied, this approach produces ambiguity in that (1) multiple different network configurations may fit the data convincingly and (2) the method offers no direct association of the electrical elements with physical features of the battery. Here we present a new methodology that resolves both sources of ambiguity, enabled by expanding the experimental scope to directly inform the configuration of elements and their parameters in the network model. We demonstrate this methodology using thin film fabrication of solid state battery devices patterned by shadow masked sputter deposition, so that diagnostic devices corresponding to individual interface and material components can be fabricated simultaneously with full cell batteries. EIS models for the diagnostic devices can then be connected to form full cell networks whose topology matches the well-known physical configuration of the battery. When connected in this way, the full network model – made from connecting the diagnostic device EIS models – fits the full cell EIS data. For the case of a thin film solid state battery composed of amorphous silicon anode, lithium phosphorus oxynitride (LiPON) solid electrolyte, and lithium vanadium oxide (Li x V 2 O 5 ) cathode, we show that the approach allows us to identify ionic impedance/conductivity of the cathode/electrolyte as a limiting impedance and the anode/electrolyte interface cycling instability as a primary degradation factor.

25 ENERGY STORAGE↗

Interpretable Models for Workflow Differentiation in High-Performance Scientific Networks

Scientific workflows in high-performance networks spawn hundreds of interdependent flows that must be managed collectively—yet existing network classifiers treat each flow in isolation, leading to fragmented QoS decisions and missed interflow patterns. We present a novel traffic classification solution that operates at the workflow level, distinguishing entire filetransfer operations from streaming analytics by capturing how concurrent flows interact and burst together. We introduce a workflow identification window (WIW) that ingests raw packet headers from parallel flows into unified tensors, preserving the spatial-temporal patterns that differentiate scientific workflows. This approach achieves 98.7% accuracy using CNN, LSTM, and hybrid architectures, while maintaining 84% accuracy on production traffic collected a week later—demonstrating robustness to temporal drift. By integrating SHAP and GradCAM explainability, we reveal that early-packet timing patterns and cross-flow correlations drive classification decisions, providing operators with interpretable insights. Our system enables coherent workflow-level QoS enforcement and dynamic bandwidth allocation in scientific networks, eliminating manual per-flow configuration while maintaining classification latency at millisecond level.

Giannakou, Anna [LBL, Berkeley]↗

A generalized distillation network synthesis model

In this report we propose a generalized superstructure-based distillation network synthesis model with improved modeling capabilities resulting in an extended solution space. The model can assign multiple mixtures to be separated (e.g., reactor network effluents) to different columns of the network while considering the interactions among different separation steps. In terms of outlets, products with general specifications, including pure components and multi-component mixtures, as well as streams without strict specifications (e.g., reactor recycle streams) can be readily handled. Furthermore, stream bypass is considered to avoid unnecessary separations, and thermal coupling is considered to yield novel solutions. The proposed model enables seamless integration with reactor network synthesis models thereby leading to solutions that are superior to the ones obtained by conventional sequential approaches.

42 ENGINEERING↗

Neural network surrogate models for equations of state

Equation of state (EOS) data provide necessary information for accurate multiphysics modeling, which is necessary for fields such as inertial confinement fusion. Here, we suggest a neural network surrogate model of energy and entropy and use thermodynamic relationships to derive other necessary thermodynamic EOS quantities. We incorporate phase information into the model by training a phase classifier and using phase-specific regression models, which improves the modal prediction accuracy. Our model predicts energy values to 1% relative error and entropy to 3.5% relative error in a log-transformed space. Although sound speed predictions require further improvement, the derived pressure values are accurate within 10% relative error. Our results suggest that neural network models can effectively model EOS for inertial confinement fusion simulation applications.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

A framework for strategic discovery of credible neural network surrogate models under uncertainty

The widespread integration of deep neural networks in developing data-driven surrogate models for high-fidelity simulations of complex physical systems highlights the critical necessity for robust uncertainty quantification techniques and credibility assessment methodologies, ensuring the reliable deployment of surrogate models in consequential decision-making. Here, this study presents the Occam Plausibility Algorithm for surrogate models (OPAL-surrogate), providing a systematic framework to uncover predictive neural network-based surrogate models within the large space of potential models, including various neural network classes and choices of architecture and hyperparameters. The framework is grounded in hierarchical Bayesian inferences and employs model validation tests to evaluate the credibility and prediction reliability of the surrogate models under uncertainty. Leveraging these principles, OPAL-surrogate introduces a systematic and efficient strategy for balancing the trade-off between model complexity, accuracy, and prediction uncertainty. The effectiveness of OPAL-surrogate is demonstrated through two modeling problems, including the deformation of porous materials for building insulation and turbulent combustion flow for ablation of solid fuels within hybrid rocket motors.

42 ENGINEERING↗

Machine Learning Models for Network Traffic Classification in Programmable Logic

Network traffic classification via machine learning on network packet payloads has emerged as an active area of research for network security due to the high accuracy machine learning models have achieved in classifying payloads. For effective deployment as part of network security, these machine learning models must not only classify malicious packet payloads accurately, they must also identify anomalous payloads and perform inference at speeds generally faster than 10,000 packets per second to be effective. This work explores the in- ference speeds and accuracy of several neural network models implemented in programmable logic on various field programmable gate arrays (FPGA) including the Xilinx VC1902 and Xilinx Zynq Ultrascale+. This work also presents the design and performance of both an autoencoder and variational autoencoder programmed on the FPGA for identifying anomalous packet payloads. The performance benefits of the FPGA implementation for this type of packet payload inspection driven by machine learning are compared against graphics processing unit (GPU) inference implementations run on two state-of-the-art datacenter GPU devices, the NVIDIA V100 and A100. The model accuracy difference between the FPGA and GPU implementations was found to be 4% or less while the Xilinx VC1902 outperformed both the NVIDIA V100 and A100 for inference speeds on all the models explored except the variational autoencoder.

97 MATHEMATICS AND COMPUTING↗

Recurrent convolutional neural networks for modeling nonadiabatic dynamics of quantum-classical systems

Recurrent neural networks (RNNs) have recently been extensively applied to model the time evolution in fluid dynamics, weather predictions, and even chaotic systems due to their ability to capture temporal dependencies and sequential patterns in data. Here we present an RNN model based on convolutional neural networks for modeling the nonlinear nonadiabatic dynamics of hybrid quantum-classical systems. The dynamical evolution of the hybrid systems is governed by equations of motion for classical degrees of freedom and von Neumann equation for electrons. The Physics-Aware Recurrent Convolution (PARC) neural network structure incorporates a differentiator-integrator architecture that inductively models the spatiotemporal dynamics of generic physical systems. Here, we apply our RNN approach to learn the space-time evolution of a one-dimensional semiclassical Holstein model after an interaction quench. For shallow quenches (small changes in electron-lattice coupling), the deterministic dynamics can be accurately captured using a single-CNN-based recurrent network. In contrast, deep quenches induce chaotic evolution, making long-term trajectory prediction significantly more challenging. Nonetheless, we demonstrate that the PARC-CNN architecture can effectively learn the statistical climate of the Holstein model under deep-quench conditions.

Holstein model↗

Risk-Averse Bi-Level Stochastic Network Interdiction Model for Cyber-Security Risk Management

Security of cyber networks is crucial; recent severe cyber-attacks have had a devastating effect on many large organizations. The attack graph, which maps the potential attack paths of a cyber network, is a popular tool for analyzing cyber system vulnerability. In this study, we propose a bi-level stochastic network interdiction model on an attack graph to enable a risk-averse, resource constrained cyber network defender to optimally deploy security countermeasures that protect against attackers with an uncertain budget. This risk- averse conditional-value-at-risk (CVaR) model minimizes a weighted sum of the expected maximum loss over all scenarios and the expected maximum loss from the most damaging attack scenarios. We develop a customized constraint and column generation algorithm to solve our model as well as several acceleration techniques to improve the computational efficiency. Numerical experiments demonstrate that the acceleration techniques enable the solution of relatively large problems within a reasonable amount of time: applying all the acceleration techniques also reduces the average computation time of the basic algorithm by 71% for 100-node graphs. Using metrics called mean-risk value of stochastic solution and value of risk-aversion, computational results suggest that our stochastic risk-averse model significantly outperforms deterministic and risk-neutral models when 1) the distribution of attacker budget is heavy-right-tailed and 2) the defender is highly risk-averse.

Bhuiyan, Tanveer H.↗