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At least 649 records · Page 36

Baseflow Identification via Explainable AI With Kolmogorov‐Arnold Networks

Abstract Hydrological models often involve constitutive laws that may not be optimal in every application. We propose to replace such laws with the Kolmogorov‐Arnold networks (KANs), a class of neural networks designed to identify symbolic expressions. We demonstrate KAN's potential on the problem of baseflow identification, a notoriously challenging task plagued by significant uncertainty. KAN‐derived functional dependencies of the baseflow components on the aridity index outperform their original counterparts; they demonstrate that water availability, rather than potential evapotranspiration, drives baseflow by constraining actual evapotranspiration under arid conditions. On a test set, they increase the Nash‐Sutcliffe efficiency (NSE) by 65%, decrease the root mean squared error by 29%, and increase the Kling‐Gupta efficiency by 34%. This superior performance is achieved while reducing the number of fitting parameters from three to two. Next, we use data from 378 catchments across the continental United States to refine the water‐balance equation at the mean‐annual scale. The KAN‐derived equations based on the refined water balance outperform both the current aridity index model, with up to a 105% increase in NSE, and the KAN‐derived equations based on the original water balance. While the performance of our model and tree‐based machine learning methods is similar, KANs offer the advantage of simplicity and transparency and require no specific software or computational tools. This case study focuses on the aridity index formulation, but the approach is flexible and transferable to other hydrological processes. Plain Language Summary Equations used in hydrologic model are often suboptimal, resulting in reduced prediction accuracy and efficiency. We implemented Kolmogorov‐Arnold networks (KAN), a machine learning algorithm for deriving symbolic formulations, to estimate groundwater recharge and showed that it outperforms an existing state‐of‐the‐art semi‐empirical formulation. In hydrology, Nash‐Sutcliffe efficiency (NSE), root mean squared error (RMSE), and Kling‐Gupta efficiency (KGE) are commonly used to evaluate model performance. Higher NSE and KGE values indicate better performance, while lower RMSE values are preferable. Our results show that NSE increased by 71%, RMSE decreased by 32%, and KGE improved by 25%. In addition, KAN identifies an optimal functional form and can be used to derive new analytical formulas using the prior knowledge. The KAN‐inspired equation outperformed the original formulation and reduced the fitting parameters. Furthermore, we refined the water‐balance equation at the mean‐annual scale and showed that, based on the new water‐balance equation, KAN can derive new formulations that are superior to the original aridity index formulations (up to 105% increase in NSE) and KAN‐derived equations based on the original water balance. These findings highlight the significant potential of KAN to advance the scientific understanding of a wide range of hydrologic processes. Key Points Kolmogorov‐Arnold networks (KANs) enhance interpretability of machine‐learned hydrological models KAN‐derived symbolic formulations outperform state‐of‐the‐art semi‐empirical aridity indices KAN‐identified functional form yields an analytical index with fewer fitting parameters and improved performance

baseflow↗

Pyrocumulonimbus Events Over British Columbia in 2017: An Ensemble Model Study of Parameter Sensitivities and Climate Impacts of Wildfire Smoke in the Stratosphere

Abstract The Pyrocumulonimbus (pyroCb) events over British Columbia in 2017 were observed in the lower stratosphere for about 8–10 months after the smoke injections. Several previous studies used global climate models to investigate the physical parameters for the 2017 pyroCb events, but the conclusions show strong model dependency. In this study, we use the Energy Exascale Earth System Model (E3SM) and complete an ensemble of runs exploring three injection parameters: smoke aerosol mass, the percentage of black carbon within the smoke aerosols, and plume injection height. Additionally, we consider the heterogeneous reaction of ozone and primary organic matter. According to the satellite daily observed aerosol optical depth (AOD), we find that the best ensemble member is the simulation with 0.4 Tg of smoke, 3% of which is black carbon, a 13.5 km smoke injection height, and a 10 −5 probability factor of the heterogeneous reaction. Besides AOD, we examine the ensemble score based on the metrics used in previous studies: the metrics of the extinction coefficient at 18 km altitude and the maximum plume height. The conclusion of the best estimate of the injection parameters for 2017 pyroCb events shows strong not only model but also evaluation metric dependency. We use the Random Forest machine learning technique to quantify the relative importance of each parameter in accurately simulating the 2017 pyroCb events and find that the injection height is the most critical feature, no matter which metric is used to score the ensemble members.

54 ENVIRONMENTAL SCIENCES↗

Offshore Wind Farm Turbine and Energy Storage Optimization

Abstract This paper evaluates the technical and economic feasibility of repurposing decommissioned offshore oil and gas platforms as electrical substations for offshore wind projects in the U.S. Gulf of America, a region characterized by relatively low and highly variable wind speeds, extensive legacy offshore infrastructure, and exposure to merchant electricity markets. A unified techno-economic framework is developed using the Repurposing Offshore Infrastructure for Continued Energy (ROICE) Economic Model (REM) to integrate Gulfspecific wind resource assessment, commercial wind turbine performance, offshore infrastructure cost modeling, and wholesale electricity market exposure. Gulf wind speed data are vertically extrapolated to turbine hub height and combined with manufacturer power curves to compute annual energy production and capacity factors across a broad portfolio of commercial turbines, enabling identification of turbine designs best suited for low-wind offshore environments. Hourly electricity price data from the Midcontinent Independent System Operator (MISO) day-ahead market are incorporated to characterize revenue potential, price volatility, and the temporal alignment between wind generation and market conditions. In addition, a conceptual framework for offshore battery energy storage system (BESS) integration is developed to support future investigation of market-responsive energy shifting at repurposed platforms. Results from the turbine evaluation demonstrate that machines with lower cut-in wind speeds and earlier ‘rated-power’ characteristics significantly outperform larger, industry-standard offshore turbines for the same net power under Gulf wind conditions, underscoring the need for region-specific technology selection. Market analysis further reveals substantial price variability and limited intrinsic alignment between wind production and high-price periods, motivating consideration of operational flexibility mechanisms. While storage optimization is not implemented in this study, the REM framework establishes a transparent and replicable foundation for co-evaluating turbine selection, infrastructure constraints, and market exposure, providing a practical pathway for assessing the potential role of repurposed offshore platforms in enabling economically viable offshore wind development in the Gulf of America.

02 PETROLEUM↗

Development and construction status of the Mu2e electromagnetic calorimeter mechanical structures

Abstract The Mu2e experiment at Fermilab will search for the CLFV neutrino-less coherent conversion of a muon into an electron in the field of an aluminum nucleus. The observation of this process would be the evidence of physics beyond the Standard Model. Mu2e comprises a straw-tracker, an electromagnetic calorimeter and an external veto for cosmic rays. The calorimeter provides electron identification, a fast trigger and aids track reconstruction. It is a state-of-the-art crystal calorimeter and employs 1340 pure CsI crystals readout by UV-extended SiPM and fast electronics. The design consists of two identical annular disks positioned at the relative distance of 70 cm downstream the target.The hostile Mu2e conditions (total ionizing dose of 12 krad and a neutron fluence of 5 × 10 10 n/cm 2 @ 1 MeVeq (Si)/y, 1 T magnetic field and vacuum level of 10 −4 Torr) posed tight constraints on the mechanical structures and materials choice. The support structure of the two crystal matrices employs two aluminum hollow rings and parts made of open-cell vacuum-compatible carbon fiber. SiPMs and front-end electronics for each crystal are assembled in one mechanical unit inserted in a machined copper holder. The units are supported by a plate made of vacuum-compatible material. The plate integrates the cooling system made of a network of copper lines flowing a low temperature fluid and placed in thermal contact with the copper holders. The DAQ is hosted in aluminum crates positioned on the lateral surface of the disks. The crates also integrate the DAQ electronics cooling system. We review the constraints on the calorimeter structures design, the development of all the structural components, including the simulations that have determined the materials and technological choices and the specifications of the cooling station, components production and quality assurance tests, the procedures for detector assembly, transportation and installation in the experimental area.

Instruments & Instrumentation↗

Pile-up mitigation using attention

Abstract Particle production from secondary proton-proton collisions, commonly referred to as pile-up, impair the sensitivity of both new physics searches and precision measurements at large hadron collider (LHC) experiments. We propose a novel algorithm, Puma , for modeling pile-up with the help of deep neural networks based on sparse transformers. These attention mechanisms were developed for natural language processing but have become popular in other applications. In a realistic detector simulation, our method outperforms classical benchmark algorithms for pile-up mitigation in key observables. It provides a perspective for mitigating the effects of pile-up in the high luminosity era of the LHC, where up to 200 proton-proton collisions are expected to occur simultaneously.

47 OTHER INSTRUMENTATION↗

Improved detection of low-frequency within-host variants from deep sequencing: A case study with human papillomavirus

Abstract High-coverage sequencing allows the study of variants occurring at low frequencies within samples, but is susceptible to false-positives caused by sequencing error. Ion Torrent has a very low single nucleotide variant (SNV) error rate and has been employed for the majority of human papillomavirus (HPV) whole genome sequences. However, benchmarking of intrahost SNVs (iSNVs) has been challenging, partly due to limitations imposed by the HPV life cycle. We address this problem by deep sequencing three replicates for each of 31 samples of HPV type 18 (HPV18). Errors, defined as iSNVs observed in only one of three replicates, are dominated by C→T (G→A) changes, independently of trinucleotide context. True iSNVs, defined as those observed in all three replicates, instead show a more diverse SNV type distribution, with particularly elevated C→T rates in CCG context (CCG→CTG; CGG→CAG) and C→A rates in ACG context (ACG→AAG; CGT→CTT). Characterization of true iSNVs allowed us to develop two methods for detecting true variants: (1) VCFgenie, a dynamic binomial filtering tool which uses each variant’s allele count and coverage instead of fixed frequency cut-offs; and (2) a machine learning binary classifier which trains eXtreme Gradient Boosting models on variant features such as quality and trinucleotide context. Each approach outperforms fixed-cut-off filtering of iSNVs, and performance is enhanced when both are used together. Our results provide improved methods for identifying true iSNVs in within-host applications across sequencing platforms, specifically using HPV18 as a case study.

Virology↗

The entropy of galaxy spectra: how much information is encoded?

Abstract The inverse problem of extracting the stellar population content of galaxy spectra is analysed here from a basic standpoint based on information theory. By interpreting spectra as probability distribution functions, we find that galaxy spectra have high entropy, thus leading to a rather low effective information content. The highest variation in entropy is unsurprisingly found in regions that have been well studied for decades with the conventional approach. We target a set of six spectral regions that show the highest variation in entropy – the 4000 Å break being the most informative one. As a test case with real data, we measure the entropy of a set of high-quality spectra from the Sloan Digital Sky Survey, and contrast entropy-based results with the traditional method based on line strengths. The data are classified into star-forming (SF), quiescent (Q), and active galactic nucleus (AGN) galaxies, and show – independently of any physical model – that AGN spectra can be interpreted as a transition between SF and Q galaxies, with SF galaxies featuring a more diverse variation in entropy. The high level of entanglement complicates the determination of population parameters in a robust, unbiased way, and affects traditional methods that compare models with observations, as well as machine learning (especially deep learning) algorithms that rely on the statistical properties of the data to assess the variations among spectra. Entropy provides a new avenue to improve population synthesis models so that they give a more faithful representation of real galaxy spectra.

Ferreras, Ignacio (ORCID:0000000345843127)↗

Genome-Wide Analysis of RNA Decay in the Cyanobacterium Synechococcus sp. Strain PCC 7002

ABSTRACT RNA degradation is an important process that influences the ultimate concentration of individual proteins inside cells. While the main enzymes that facilitate this process have been identified, global maps of RNA turnover are available for only a few species. Even in these cases, there are few sequence elements that are known to enhance or destabilize a native transcript; even fewer confer the same effect when added to a heterologous transcript. To address this knowledge gap, we assayed genome-wide RNA degradation in the cyanobacterium Synechococcus sp. strain PCC 7002 by collecting total RNA samples after stopping nascent transcription with rifampin. We quantified the abundance of each position in the transcriptome as a function of time using RNA-sequencing data and later analyzed the global mRNA decay map using machine learning principles. Half-lives, calculated on a per-ORF (open reading frame) basis, were extremely short, with a median half-life of only 0.97 min. Despite extremely rapid turnover of most mRNA, transcripts encoding proteins involved in photosynthesis were both highly expressed and highly stable. Upon inspection of these stable transcripts, we identified an enriched motif in the 3′ untranslated region (UTR) that had similarity to Rho-independent terminators. We built statistical models for half-life prediction and used them to systematically identify sequence motifs in both 5′ and 3′ UTRs that correlate with stabilized transcripts. We found that transcripts linked to a terminator containing a poly(U) tract had a longer half-life than both those without a poly(U) tract and those without a terminator. IMPORTANCE RNA degradation is an important process that affects the final concentration of individual mRNAs, affecting protein expression and cellular physiology. Studies of how RNA is degraded increase our knowledge of this fundamental process as well as enable the creation of genetic tools to manipulate RNA stability. By studying global transcript turnover, we searched for sequence elements that correlated with transcript (in)stability and used these sequences to guide tool design. This study probes global RNA turnover in a cyanobacterium, Synechococcus sp. strain PCC 7002, that both has a unique array of RNases that facilitate RNA degradation and is an industrially relevant strain that could be used to convert CO 2 and sunlight into useful products.

59 BASIC BIOLOGICAL SCIENCES↗

Technical note: Uncertainties in eddy covariance CO 2 fluxes in a semiarid sagebrush ecosystem caused by gap-filling approaches

Abstract. Gap-filling eddy covariance CO2 fluxes is challenging at dryland sites due to small CO2 fluxes. Here, four machine learning (ML) algorithms including artificial neural network (ANN), k-nearest neighbors (KNNs), random forest (RF), and support vector machine (SVM) are employed and evaluated for gap-filling CO2 fluxes over a semiarid sagebrush ecosystem with different lengths of artificial gaps. The ANN and RF algorithms outperform the KNN and SVM in filling gaps ranging from hours to days, with the RF being more time efficient than the ANN. Performances of the ANN and RF are largely degraded for extremely long gaps of 2 months. In addition, our results suggest that there is no need to fill the daytime and nighttime net ecosystem exchange (NEE) gaps separately when using the ANN and RF. With the ANN and RF, the gap-filling-induced uncertainties in the annual NEE at this site are estimated to be within 16 g C m−2, whereas the uncertainties by the KNN and SVM can be as large as 27 g C m−2. To better fill extremely long gaps of a few months, we test a two-layer gap-filling framework based on the RF. With this framework, the model performance is improved significantly, especially for the nighttime data. Therefore, this approach provides an alternative in filling extremely long gaps to characterize annual carbon budgets and interannual variability in dryland ecosystems.

Yao, Jingyu↗

A representation-independent electronic charge density database for crystalline materials

Abstract In addition to being the core quantity in density-functional theory, the charge density can be used in many tertiary analyses in materials sciences from bonding to assigning charge to specific atoms. The charge density is data-rich since it contains information about all the electrons in the system. With the increasing prevalence of machine-learning tools in materials sciences, a data-rich object like the charge density can be utilized in a wide range of applications. The database presented here provides a modern and user-friendly interface for a large and continuously updated collection of charge densities as part of the Materials Project. In addition to the charge density data, we provide the theory and code for changing the representation of the charge density which should enable more advanced machine-learning studies for the broader community.

36 MATERIALS SCIENCE↗

MHD mode tracking using high-speed cameras and deep learning

Abstract We present a new algorithm to track the amplitude and phase of rotating magnetohydrodynamic (MHD) modes in tokamak plasmas using high speed imaging cameras and deep learning. This algorithm uses a convolutional neural network (CNN) to predict the amplitudes of the n = 1 sine and cosine mode components using solely optical measurements from one or more cameras. The model was trained and tested on an experimental dataset consisting of camera frame images and magnetic-based mode measurements from the High Beta Tokamak - Extended Pulse (HBT-EP) device, and it outperformed other, more conventional, algorithms using identical image inputs. The effect of different input data streams on the accuracy of the model’s predictions is also explored, including using a temporal frame stack or images from two cameras viewing different toroidal regions.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Offshore application of landslide susceptibility mapping using gradient-boosted decision trees: a Gulf of Mexico case study

Abstract Among natural hazards occurring offshore, submarine landslides pose a significant risk to offshore infrastructure installations attached to the seafloor. With the offshore being important for current and future energy production, there is a need to anticipate where future landslide events are likely to occur to support planning and development projects. Using the northern Gulf of Mexico (GoM) as a case study, this paper performs Landslide Susceptibility Mapping (LSM) using a gradient-boosted decision tree (GBDT) model to characterize the spatial patterns of submarine landslide probability over the United States Exclusive Economic Zone (EEZ) where water depths are greater than 120 m. With known spatial extents of historic submarine landslides and a Geographic Information System (GIS) database of known topographical, geomorphological, geological, and geochemical factors, the resulting model was capable of accurately forecasting potential locations of sediment instability. Results of a permutation modelling approach indicated that LSM accuracy is sensitive to the number of unique training locations with model accuracy becoming more stable as the number of training regions was increased. The influence that each input feature had on predicting landslide susceptibility was evaluated using the SHapely Additive exPlanations (SHAP) feature attribution method. Areas of high and very high susceptibility were associated with steep terrain including salt basins and escarpments. This case study serves as an initial assessment of the machine learning (ML) capabilities for producing accurate submarine landslide susceptibility maps given the current state of available natural hazard-related datasets and conveys both successes and limitations.

Dyer, Alec S. (ORCID:0000000219813904)↗

Nonequilibrium statistical mechanics and optimal prediction of partially-observed complex systems

Abstract Only a subset of degrees of freedom are typically accessible or measurable in real-world systems. As a consequence, the proper setting for empirical modeling is that of partially-observed systems. Notably, data-driven models consistently outperform physics-based models for systems with few observable degrees of freedom; e.g. hydrological systems. Here, we provide an operator-theoretic explanation for this empirical success. To predict a partially-observed system’s future behavior with physics-based models, the missing degrees of freedom must be explicitly accounted for using data assimilation and model parametrization. Data-driven models, in contrast, employ delay-coordinate embeddings and their evolution under the Koopman operator to implicitly model the effects of the missing degrees of freedom. We describe in detail the statistical physics of partial observations underlying data-driven models using novel maximum entropy and maximum caliber measures. The resulting nonequilibrium Wiener projections applied to the Mori–Zwanzig formalism reveal how data-driven models may converge to the true dynamics of the observable degrees of freedom. Additionally, this framework shows how data-driven models infer the effects of unobserved degrees of freedom implicitly, in much the same way that physics models infer the effects explicitly. This provides a unified implicit-explicit modeling framework for predicting partially-observed systems, with hybrid physics-informed machine learning methods combining both implicit and explicit aspects.

97 MATHEMATICS AND COMPUTING↗

Classifying metal‐binding sites with neural networks

Abstract To advance our ability to predict impacts of the protein scaffold on catalysis, robust classification schemes to define features of proteins that will influence reactivity are needed. One of these features is a protein's metal‐binding ability, as metals are critical to catalytic conversion by metalloenzymes. As a step toward realizing this goal, we used convolutional neural networks (CNNs) to enable the classification of a metal cofactor binding pocket within a protein scaffold. CNNs enable images to be classified based on multiple levels of detail in the image, from edges and corners to entire objects, and can provide rapid classification. First, six CNN models were fine‐tuned to classify the 20 standard amino acids to choose a performant model for amino acid classification. This model was then trained in two parallel efforts: to classify a 2D image of the environment within a given radius of the central metal binding site, either an Fe ion or a [2Fe‐2S] cofactor, with the metal visible (effort 1) or the metal hidden (effort 2). We further used two sub‐classifications of the [2Fe‐2S] cofactor: (1) a standard [2Fe‐2S] cofactor and (2) a Rieske [2Fe‐2S] cofactor. The accuracy for the model correctly identifying all three defined features was >95%, despite our perception of the increased challenge of the metalloenzyme identification. This demonstrates that machine learning methodology to classify and distinguish similar metal‐binding sites, even in the absence of a visible cofactor, is indeed possible and offers an additional tool for metal‐binding site identification in proteins.

59 BASIC BIOLOGICAL SCIENCES↗

Learning the Low Frequency Earthquake Activity on the Central San Andreas Fault

Abstract Low frequency earthquakes (LFEs) originating below the central San Andreas Fault are associated with slow‐slip beneath the seismogenic zone within the more ductile portion of the crust. Monitoring efforts over 15 years detected >1 million LFEs. We train a gradient boosted tree model using statistical features describing the seismic waveforms to estimate the hourly LFE event count. The burst‐like LFE behavior is reproduced, while lower amplitudes are predicted during the most active periods. The hourly event counts are up to 18% greater than the catalog. The ability to continuously monitor LFE activity provides insight to when geodetic measurements of slow slip are possible, without the need for developing a computational‐intensive template‐matching catalog. Similar waveform statistical features are found between detecting LFEs and tremors, which provides additional evidence tremors are composed of LFEs. The approach extracts information contained in continuous seismic waveforms that might benefit detecting precursory signals.

58 GEOSCIENCES↗

Ultra-fast interpretable machine-learning potentials

Abstract All-atom dynamics simulations are an indispensable quantitative tool in physics, chemistry, and materials science, but large systems and long simulation times remain challenging due to the trade-off between computational efficiency and predictive accuracy. To address this challenge, we combine effective two- and three-body potentials in a cubic B-spline basis with regularized linear regression to obtain machine-learning potentials that are physically interpretable, sufficiently accurate for applications, as fast as the fastest traditional empirical potentials, and two to four orders of magnitude faster than state-of-the-art machine-learning potentials. For data from empirical potentials, we demonstrate the exact retrieval of the potential. For data from density functional theory, the predicted energies, forces, and derived properties, including phonon spectra, elastic constants, and melting points, closely match those of the reference method. The introduced potentials might contribute towards accurate all-atom dynamics simulations of large atomistic systems over long-time scales.

36 MATERIALS SCIENCE↗

Explore Spatio‐Temporal Learning of Large Sample Hydrology Using Graph Neural Networks

Abstract Streamflow forecasting over gauged and ungauged basins play a vital role in water resources planning, especially under the changing climate. Increased availability of large sample hydrology data sets, together with recent advances in deep learning techniques, has presented new opportunities to explore temporal and spatial patterns in hydrological signatures for improving streamflow forecasting. The purpose of this study is to adapt and benchmark several state‐of‐the‐art graph neural network (GNN) architectures, including ChebNet, Graph Convolutional Network (GCN), and GraphWaveNet, for end‐to‐end graph learning. We explicitly represent river basins as nodes in a graph, learn the spatiotemporal nodal dependencies, and then use the learned relations to predict streamflow simultaneously across all nodes in the graph. The efficacy of the developed GNN models is investigated using the Catchment Attributes and MEteorology for Large‐sample Studies (CAMELS) data set under two settings, fixed graph topology (transductive learning), and variable graph topology (inductive learning), with the latter applicable to prediction in ungauged basins (PUB). Results indicate that GNNs are generally robust and computationally efficient, achieving similar or better performance than a baseline model trained using the long short‐term memory (LSTM) network. Further analyses are conducted to interpret the graph learning process at the edge and node levels and to investigate the effect of different model configurations. We conclude that graph learning constitutes a viable machine learning‐based method for aggregating spatiotemporal information from a multitude of sources for streamflow forecasting

Sun, Alexander Y.↗

Reliability-Informed Economic and Energy Evaluation for Bi-Level Design for Remanufacturing: A Case Study of Transmission and Hydraulic Manifold

Abstract Design for remanufacturing (DfRem) is one attractive strategy that encourages the reuse of a product and extends the product's life cycle. Traditional design processes often only consider product reliability at an early design stage. However, from the perspective of environmental sustainability, it is becoming increasingly important to evaluate the long-term economic and environmental impacts of design decisions during early-stage design. We propose a bi-level DfRem framework consisting of system-level reusability allocation and component-level design tradeoff analysis, considering reliability and product warranty policy. First, a system-level reusability allocation problem aims at a theoretical exploration of the design space where all the components comprising the system are allocated certain reuse rates to achieve target energy savings with minimum cost. Following the theoretical exploration at the system level, a component-level analysis looks at practical design options for each component and trades-off between the overall cost and energy consumption for multiple remanufacturing cycles. Both levels of the framework require modeling component reuse for multiple remanufacturing cycles, which we achieve by using a branched power-law model that provides probabilistic scenarios of reusing the component or replacing it with a new part. We demonstrate the utility of this framework with the case study of an infinitely variable transmission (IVT) used by some agricultural machines manufactured by John Deere and show snapshots of a prototype software tool that we developed for easy use by designers.

Engineering↗