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At least 883 records · Page 49

Cartesian equivariant representations for learning and understanding molecular orbitals

Qualitative and quantitative orbital properties such as bonding/antibonding character, localization, and orbital energies are critical to how chemists understand reactivity, catalysis, and excited-state behavior. Despite this, representations of orbitals in deep learning models have been very underdeveloped relative to representations of molecular geometries and Hamiltonians. Here, we apply state-of-the-art equivariant deep learning architectures to the task of assigning global labels to orbitals, namely energies characterizations, given the molecular coefficients from Hartree–Fock or density functional theory. The architecture we have developed, the Cartesian Equivariant Orbital Network (CEONET), shows how molecular orbital coefficients are readily featurized as equivariant node features common to all graph-based machine-learned potentials. We find that CEONET performs well at predicting difficult quantitative labels such as the orbital energy and orbital entropy. Furthermore, we find that the CEONET representation provides an intuitive latent space for differentiating orbital character for the qualitative assignment of e.g. bonding or antibonding character. In addition to providing a useful representation for further integrating deep learning with electronic structure theory, we expect CEONET to be useful for automatizing and interpreting the results of advanced electronic structure methods such as complete active space self-consistent field theory. In particular, the ability of CEONET to infer multireference character via the orbital entropy paves the way toward the machine-learned selection of active spaces.

chemical reactions↗

Poisson hurdle model-based method for clustering microbiome features

Abstract Motivation High-throughput sequencing technologies have greatly facilitated microbiome research and have generated a large volume of microbiome data with the potential to answer key questions regarding microbiome assembly, structure and function. Cluster analysis aims to group features that behave similarly across treatments, and such grouping helps to highlight the functional relationships among features and may provide biological insights into microbiome networks. However, clustering microbiome data are challenging due to the sparsity and high dimensionality. Results We propose a model-based clustering method based on Poisson hurdle models for sparse microbiome count data. We describe an expectation–maximization algorithm and a modified version using simulated annealing to conduct the cluster analysis. Moreover, we provide algorithms for initialization and choosing the number of clusters. Simulation results demonstrate that our proposed methods provide better clustering results than alternative methods under a variety of settings. We also apply the proposed method to a sorghum rhizosphere microbiome dataset that results in interesting biological findings. Availability and implementation R package is freely available for download at https://cran.r-project.org/package=PHclust. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Quantifying rupture characteristics of microearthquakes in the Parkfield Area using a high-resolution borehole network

It is well known that large earthquakes often exhibit significant rupture complexity such as well separated subevents. With improved recording and data processing techniques, small earthquakes have been found to exhibit rupture complexity as well. Studying these small earthquakes offers the opportunity to better understand the possible causes of rupture complexities. Specifically, if they are random or are related to fault properties. We examine microearthquakes (M < 3) in the Parkfield, California, area that are recorded by a high-resolution borehole network. We quantify earthquake complexity by the deviation of source time functions and source spectra from simple circular (omega-square) source models. We establish thresholds to declare complexity, and find that it can be detected in earthquakes larger than magnitude 2, with the best resolution above M2.5. Comparison between the two approaches reveals good agreement (>90 per cent), implying both methods are characterizing the same source complexity. For the two methods, 60–80 per cent (M 2.6–3) of the resolved events are complex depending on the method. The complex events we observe tend to cluster in areas of previously identified structural complexity; a larger fraction of the earthquakes exhibit complexity in the days following the M w 6 2004 Parkfield earthquake. Ignoring the complexity of these small events can introduce artefacts or add uncertainty to stress drop measurements. Focusing only on simple events however could lead to systematic bias, scaling artefacts and the lack of measurements of stress in structurally complex regions.

58 GEOSCIENCES↗

Image feature extraction and galaxy classification: a novel and efficient approach with automated machine learning

ABSTRACT In this work, we explore the possibility of applying machine learning methods designed for 1D problems to the task of galaxy image classification. The algorithms used for image classification typically rely on multiple costly steps, such as the point spread function deconvolution and the training and application of complex Convolutional Neural Networks of thousands or even millions of parameters. In our approach, we extract features from the galaxy images by analysing the elliptical isophotes in their light distribution and collect the information in a sequence. The sequences obtained with this method present definite features allowing a direct distinction between galaxy types. Then, we train and classify the sequences with machine learning algorithms, designed through the platform Modulos AutoML. As a demonstration of this method, we use the second public release of the Dark Energy Survey (DES DR2). We show that we are able to successfully distinguish between early-type and late-type galaxies, for images with signal-to-noise ratio greater than 300. This yields an accuracy of $86{{\ \rm per\ cent}}$ for the early-type galaxies and $93{{\ \rm per\ cent}}$ for the late-type galaxies, which is on par with most contemporary automated image classification approaches. The data dimensionality reduction of our novel method implies a significant lowering in computational cost of classification. In the perspective of future data sets obtained with e.g. Euclid and the Vera Rubin Observatory, this work represents a path towards using a well-tested and widely used platform from industry in efficiently tackling galaxy classification problems at the peta-byte scale.

79 ASTRONOMY AND ASTROPHYSICS↗

On the parameter combinations that matter and on those that do not: data-driven studies of parameter (non)identifiability

Abstract We present a data-driven approach to characterizing nonidentifiability of a model’s parameters and illustrate it through dynamic as well as steady kinetic models. By employing Diffusion Maps and their extensions, we discover the minimal combinations of parameters required to characterize the output behavior of a chemical system: a set of effective parameters for the model. Furthermore, we introduce and use a Conformal Autoencoder Neural Network technique, as well as a kernel-based Jointly Smooth Function technique, to disentangle the redundant parameter combinations that do not affect the output behavior from the ones that do. We discuss the interpretability of our data-driven effective parameters, and demonstrate the utility of the approach both for behavior prediction and parameter estimation. In the latter task, it becomes important to describe level sets in parameter space that are consistent with a particular output behavior. We validate our approach on a model of multisite phosphorylation, where a reduced set of effective parameters (nonlinear combinations of the physical ones) has previously been established analytically.

Evangelou, Nikolaos↗

Transformer eXplainability and eXploration

The Transformer eXplainability and eXploration library is intended to aid in the explorability and explainability of transformer classification networks, or transformer language models with sequence classification heads. The basic function of this library is to take a trained transformer and test/train dataset and produce an ipywidget dashboard which can be displayed in a jupyter notebook or in jupyter lab.

Martindale, Nathan [Oak Ridge National Lab. (ORNL)↗

PyTorch Implementation of Log-Additive Convolutional Neural Networks

This code is a collection of python code that defines, trains, and tests Log-Additive Convolutional Neural Networks. The model components and training routine are based on the PyTorch python library. The code implements the Log-Additive Convolutional Neural Networks as described in Pagendam et al. 2023. In addition to the Log-Additive Convolutional Neural Networks, this library also defines the Log-Normal Density loss function as described in Pagendam et al. 2023. Code from this paper is not publicly available, so the Pytorch implementation of this type of model is unique to this library.

Callis, Skylar↗

Control Network Emulation Platform Software Package Description

The software package developed by Sandia National Laboratories is intended to allow the integration of Simulink models into emulations of control networks. To accomplish this, three programs are included: Simulink S-Function, Data Broker, and End Point

97 MATHEMATICS AND COMPUTING↗

Energy Resilient Recovery in Puerto Rico: Hurricane Maria Recovery Support

This report covers microgrids as a special application of distributed energy resources (DERs) in Puerto Rico. This is one of a series of reports describing the U.S. Department of Energy (DOE) multi-laboratory efforts undertaken. To ensure the sustainable, long-term recovery of Puerto Rico's electric power grid from hurricanes Maria and Irma and to build capacity to manage future potential natural disasters in the most secure and resilient way, DOE convened experts from multiple national laboratories to develop a comprehensive set of data, models, analytic tools, and studies, considering inputs from a wide variety of stakeholder groups, to support technically sound recommendations for Puerto Rico's energy investment decisions. In Phase 1 of the multi-laboratory effort to support Puerto Rico's recovery, the National Renewable Energy Laboratory (NREL) provided the utility company Puerto Rico Electric Power Authority (PREPA) recommendations for a new framework of interconnection standards to accelerate the integration of utility-scale, transmission-connected, renewable electrical generation and energy storage that ensure cross-technology compatibility and enable high deployment levels without compromising grid reliability, safety, or security (https://www.nrel.gov/docs/fy19osti/73848.pdf). In Phase 2, NREL published a report focused on the interconnection of distributed energy resources (DERs) to the electric distribution system in Puerto Rico (https://www.nrel.gov/docs/fy21osti/77127.pdf). This report familiarized the reader with Puerto Rico's distribution infrastructure and operational practices and procedures that are relevant to DER interconnection. The report also provided considerations for streamlining the interconnection process given the expected increase in deployments resulting from Puerto Rico's renewable portfolio standard goal of 100% renewables by 2050. Accordingly, the report identifies considerations and concerns associated with the increase in intermittent generation, strategies for DER interconnection best practices, and the potential use of the latest technological solutions identified in the latest revision of the Institute of Electrical and Electronics Engineers 1547-2018 interconnection standard. Additionally, the report identified ways to improve the physical resiliency of installed DERs. This task describes how distributed energy systems may participate in and contribute to improving the resiliency of Puerto Rico's energy infrastructure in the future. This report presents an analysis of the Puerto Rico grid to illustrate the possible different microgrid and minigrid scenarios. The capability to form sustained microgrids and minigrids has the potential to provide a high level of resiliency during disturbances on the grid. DERs, on the other hand, have the capability to aid in the microgrid operation by providing grid support as well as grid-forming functionality. Other tasks in Phase 3 include voltage regulation in distribution networks using DERs and transmission-and-distribution co-simulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

A Prototype Software to Demonstrate a Data Catalog for Hanford Environmental Datasets

Ensuring that data on long-term environmental remediation at the Hanford Site is high-quality, traceable, and easily accessible is an ongoing challenge, complicated by decades of data collection, multiple contractors maintaining data sources, and the wide range of data types. A centralized data catalog, known as the Hanford Environmental Information and Data Index (HEIDI), has been under development as part of the Hanford Environmental Data Management (HEDM) program to address these challenges. HEIDI fulfills a critical need to bring together a wide range of data types and sizes from multiple authoritative data sources, while documenting the data pedigree and quality information (i.e., traceable to the data source/originator). This document describes additional development and maturation of the HEIDI prototype. Key accomplishments included deploying the catalog software, Esri Geoportal Server, on a server accessible to Hanford Local Area Network users, conducting cybersecurity evaluations, investigating integrated authentication solutions, and conducting functional testing of the catalog prototype. The server-based deployment enabled targeted feedback, leading to enhancements including improved accessibility features and an expanded metadata schema. Specifications for the server-based deployment of the prototype catalog and the HEIDI metadata schema are provided in this document to support subsequent HEIDI deployment by the U.S. Department of Energy Richland Operations Office.

54 ENVIRONMENTAL SCIENCES↗

PSF–NET: A Nonparametric Point-spread Function Model for Ground-based Optical Telescopes

Ground-based optical telescopes are seriously affected by atmospheric turbulence induced aberrations. Understanding properties of these aberrations is important both for instrument design and image restoration method development. Because the point-spread function can reflect performance of the whole optic system, it is appropriate to use the point-spread function to describe atmospheric turbulence induced aberrations. Assuming point-spread functions induced by the atmospheric turbulence with the same profile belong to the same manifold space, we propose a nonparametric point-spread function—PSF–NET. The PSF–NET has a cycle convolutional neural network structure and is a statistical representation of the manifold space of PSFs induced by the atmospheric turbulence with the same profile. Testing the PSF–NET with simulated and real observation data, we find that a well trained PSF–NET can restore any short exposure images blurred by atmospheric turbulence with the same profile. Besides, we further use the impulse response of the PSF–NET, which can be viewed as the statistical mean PSF, to analyze interpretation properties of the PSF–NET. We find that variations of statistical mean PSFs are caused by variations of the atmospheric turbulence profile: as the difference of the atmospheric turbulence profile increases, the difference between statistical mean PSFs also increases. The PSF–NET proposed in this paper provides a new way to analyze atmospheric turbulence induced aberrations, which would benefit the development of new observation methods for ground-based optical telescopes.

79 ASTRONOMY AND ASTROPHYSICS↗

Neural network representations of multiphase Equations of State

Abstract Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general Equation of State model are adherence to the Laws of Thermodynamics, incorporation of phase transitions, and multiscale accuracy. Analytic models that adhere to all three are hard to develop and cumbersome to work with, often resulting in sacrificing one of these elements for the sake of efficiency. In this work, two deep-learning methods are proposed that provably satisfy the first and second conditions on a large-enough region of thermodynamic variable space. The first is based on learning the generating function (thermodynamic potential) while the second is based on structure-preserving, symplectic neural networks, respectively allowing modifications near or on phase transition regions. They can be used either “from scratch” to learn a full Equation of State, or in conjunction with a pre-existing consistent model, functioning as a modification that better adheres to experimental data. We formulate the theory and provide several computational examples to justify both approaches, highlighting their advantages and shortcomings.

Science & Technology - Other Topics↗

Elastomer Mechanics of Cross-Linked Linear-Ring Polymer Blends

Cross-linking a blend of linear and ring polymers creates a new topology-based dual-network elastomer in which the two components differ significantly in their topology. We use molecular simulations and topological analysis to examine key mechanical properties as functions of ring polymer volume fraction Φ R . For Φ R < Φ R *, where the rings begin to overlap, the network shear modulus G and the maximum stretch ratio λ p are weakly dependent on Φ R . For Φ R > Φ R *, entanglements trapped in the network are diluted as the rings overlap, leading to a significant decrease in G and an increase in λ p with increasing Φ R . Here, the peak tensile stress, σ p , exhibits a maximum around Φ R *, indicating an enhancement of network strength due to the stronger cohesion from the entanglements between linear and ring polymers.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Modeling Plant Metabolism: From Network Reconstruction to Mechanistic Models

Mathematical modeling of plant metabolism allows the plant science community to understand the organization of plant metabolism, obtain quantitative insights into metabolic functions, and derive engineering strategies for manipulation of metabolism. Among the various modeling approaches, metabolic pathway analysis can dissect the basic functional modes of subsections of core metabolism, such as photorespiration, and reveal how classical definitions of metabolic pathways have overlapping functionality. In current research using constraint-based modeling in plants, numerous computational tools are currently available to analyze large-scale and genome-scale metabolic networks. For 13 C-metabolic flux analysis, principles of isotopic steady state have been used to study heterotrophic plant tissues, while nonstationary isotope labeling approaches are amenable to the study of photoautotrophic and secondary metabolism. Enzyme kinetic models explore pathways in mechanistic detail, and we discuss different approaches to determine or estimate kinetic parameters. In this review, we describe recent advances and challenges in modeling plant metabolism.

59 BASIC BIOLOGICAL SCIENCES↗

Relaxations of the steady optimal gas flow problem for a non-Ideal gas

Natural gas ranks second in U.S. primary energy consumption. Because most production sites are remote, gas must be transported through pipeline networks equipped with compressors, valves, and other components. For both economic efficiency and system reliability, it is desirable to operate these networks optimally. The governing physics across pipeline components entails nonlinear, non-convex equality and inequality constraints, and the most general steady-flow operations problem is a Mixed-Integer Nonlinear Program (MINLP).This work focuses on one such steady-flow problem-the Optimal Gas Flow (OGF) for a natural gas pipeline network-which minimizes production cost subject to the steady-flow physics. For day-to-day operations, the ability to quickly compute a globally optimal solution and a strong lower bound for varying demand profiles is crucial. A promising strategy is to build tight relaxations of the OGF’s nonlinear constraints. However, many nonlinearities arising from non-ideal equations of state either lack relaxations or have relaxations that do not scale to realistic network sizes. We address this gap by combining recent advances in polyhedral relaxations for univariate functions to construct tight, computationally efficient relaxations of the OGF with a non-ideal equation of state. These relaxations solve within seconds on a standard laptop. In conclusion, we demonstrate their quality through extensive numerical experiments on very large-scale test networks from the literature and find that the proposed approach proves optimality in 92% of tested instances.

03 NATURAL GAS↗

Statistical and Neural Network for Real Sensor-Data-Driven Anomaly Detection in Nuclear Applications

Anomaly detection (AD) in sensor data is critical to ensure uninterrupted functionality of nuclear power plants (NPPs). Consequently, AD model validation through real-world sensor data is important for applications in nuclear facilities. In this paper, we propose an Autoencoder (AE)—a multi-layered neural network, for AD in sensor data from an operational NPP testbed. Since the dataset lacks labels for irregularities, we introduce random noise and label them to effectively train our model. The proposed AE model assigns a higher reconstruction error to the abnormal samples that deviate from those encountered during the training phase and uses the reconstruction loss to detect anomalies in a representative imbalanced dataset. We also introduce an analytical solution—seasonal trend decomposition (STD)—as another AD scheme for identifying irregularities withinthe same time-series dataset. In contrast to the AE model which relies on reconstruction loss, the STD scheme decomposes the entire dataset into its trend, seasonality, and residual components to pinpoint irregularities. Our findings indicate that the proposed AE and STD models individually achieve recall scores of 97% and 92%, respectively. We validate the performance of the two models on both balanced and imbalanced data. We further solidify the results by picking the combined selected anomalies of the two solutions with an "AND" operator for more reliable predictions.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Riverine organic matter functional diversity increases with catchment size

A large amount of dissolved organic matter (DOM) is transported to the ocean from terrestrial inputs each year (~0.95 Pg C per year) and undergoes a series of abiotic and biotic reactions, causing a significant release of CO 2 . Combined, these reactions result in variable DOM characteristics (e.g., nominal oxidation state of carbon, double-bond equivalents, chemodiversity) which have demonstrated impacts on biogeochemistry and ecosystem function. Despite this importance, however, comparatively few studies focus on the drivers for DOM chemodiversity along a riverine continuum. Here, we characterized DOM within samples collected from a stream network in the Yakima River Basin using ultrahigh-resolution mass spectrometry (i.e., FTICR-MS). To link DOM chemistry to potential function, we identified putative biochemical transformations within each sample. We also used various molecular characteristics (e.g., thermodynamic favorability, degradability) to calculate a series of functional diversity metrics. We observed that the diversity of biochemical transformations increased with increasing upstream catchment area and landcover. This increase was also connected to expanding functional diversity of the molecular formula. This pattern suggests that as molecular formulas become more diverse in thermodynamics or degradability, there is increased opportunity for biochemical transformations, potentially creating a self-reinforcing cycle where transformations in turn increase diversity and diversity increase transformations. We also observed that these patterns are, in part, connected to landcover whereby the occurrence of many landcover types (e.g., agriculture, urban, forest, shrub) could expand DOM functional diversity. For example, we observed that a novel functional diversity metric measuring similarity to common freshwater molecular formulas (i.e., carboxyl-rich alicyclic molecules) was significantly related to urban coverage. These results show that DOM diversity does not decrease along stream networks, as predicted by a common conceptual model known as the River Continuum Concept, but rather are influenced by the thermodynamic and degradation potential of molecular formula within the DOM, as well as landcover patterns.

54 ENVIRONMENTAL SCIENCES↗

Dual-function lignin monomers enable high-performance graphene electrodes via interface confinement and proton transfer enhancement

Graphene oxide (GO)-based energy storage faces dual bottlenecks: unsustainable reduction methods and sluggish proton transfer kinetics. Here, we introduce a groundbreaking green strategy using lignin-derived vanillyl alcohol (VA) as a dual-function monomer to simultaneously address these challenges. By thermally annealing GO/VA films at mild temperatures (<100 °C), VA triggers an interface-confined reduction of GO while self-polymerizing into redox-active oligomers (P-VA) that intercalate between graphene layers. This dual role-reducing agent and proton highway enables a 3D conductive network with minimized graphene restacking, abundant redox sites, and rapid H + transport pathways. Density Functional Theory (DFT) reveals how P-VA optimizes proton dynamics, while the resulting rGO-P-VA4-T90 electrode achieves a record volumetric capacitance of 311.1F/cm 3 (777.8F/cm 2 ) and retains 87.8 % capacity after 10,000 cycles. Flexible solid-state supercapacitors deliver 94.2 μWh/cm 2 energy density at 63.8 μW/cm 2 , rivaling state-of-the-art devices. Furthermore, this work redefines sustainable graphene engineering, merging biomass valorization with high-performance energy storage in a scalable, eco-friendly paradigm.

Graphene oxide reduction↗