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At least 37 records · Page 2

Machine learning approaches for integrating multi-omics data to expand microbiome annotation (Final Technical Report)

We fulfilled all original three aims of the proposal. Following the earlier release (during the first phase of the project at Montana) of software that identifies and fills gaps in the annotation of metabolic proteins within bacterial genomes, we have nearly completed a second gap-filling tool that improves accuracy and explainability. We completed software for alignment-based annotation of protein coding DNA, allowing for coding frameshifts caused by sequencing error. Finally, we completed a neural embedding model for identifying similarities between protein sequences based on amino-wise latent vectors.

59 BASIC BIOLOGICAL SCIENCES

A Finite Element Method for Compressible and Turbulent Multiphase Flow Instabilities with Heat Transfer

We present a new finite element framework for modeling compressible, turbulent multiphase flows with heat transfer. For two-fluid systems with a free surface, the Volume of Fluid (VOF) method is implemented without the need for interface reconstruction, while turbulence is resolved using a dynamic Vreman large eddy simulation (LES) model. Unlike most two-phase VOF studies, which neglect heat transfer, the present approach incorporates energy transport equations within the VOF formulation to account for heat exchange, an effect particularly important in turbulent flows. Conjugate heat transfer is often challenging in finite volume methods, which require explicit specification of heat fluxes at the solid–fluid interface, limiting accuracy and predictive capability. By contrast, the finite element formulation does not require heat flux inputs, allowing more accurate and robust simulation of heat transfer between solids and fluids. The method is demonstrated through three representative cases. First, a two-fluid instability with a single-mode perturbation is simulated and validated against analytical growth rates. Second, conjugate heat transfer is examined in a high-temperature flow over a cold metal cylinder, with validation performed both quantitatively—via pressure coefficient comparisons with experimental data—and qualitatively using vector field topology. Finally, compressible spray injection and breakup are modeled, demonstrating the ability of the framework to capture interfacial dynamics and atomization under turbulent, high-speed conditions. In the compressible spray injection and breakup case, the results indicate that the finite element formulation achieved higher predictive accuracy and robustness than the finite-volume method. With the same mesh resolution, the FEM reduced the root mean square error (RMSE) and mean absolute percentage error (MAPE) from 6.96 mm and 26.0% (for the FVM) to 4.85 mm and 12.7%, respectively, demonstrating improved accuracy and robustness in capturing interfacial dynamics and heat transfer. The study also introduced vector field topology to visualize and interpret coherent flow structures and instabilities, offering insights beyond conventional scalar-field analyses.

97 MATHEMATICS AND COMPUTING

Reinforcement Learning for Anomaly Detection in Nuclear Power Plant Operation and Maintenance

In nuclear power plants (NPPs), timely identification of sensor and human errors is critical to ensure safe and efficient plant operations. Anomaly detection models can be employed for this task. However, traditional anomaly detection approaches may have high dependency on labeled datasets and struggle with adaptability in complex, dynamic environments. Reinforcement learning (RL) has demonstrated significant potential in fault diagnosis and anomaly detection; however, its application to anomaly detection in NPPs remains a relatively underexplored research direction. Hence, to address this gap, in this study, we present a novel physics-informed reinforcement learning model, PIRL-AD: Physics-Informed Reinforcement Learning for Anomaly Detection, that integrates domain knowledge from calorimetric equations into the RL framework for enhanced sensor and human error anomaly detection. We evaluate the performance of PIRL-AD against a non-physics informed RL benchmark and a support vector machine (SVM) on data collected from a forced flow loop testbed. Experimental results suggest that PIRL-AD outperforms other baselines on a range of anomalous datasets that include both sensor and human-induced anomalies across key performance metrics, statistically outperforming the RL and SVM benchmarks with respect to geometric mean (respectively, 92.96% vs. 91.06% vs. 83.01%) and F1-score (respectively, 89.23% vs. 86.98% vs. 77.01%). Furthermore, the findings suggest the potential of physics-integrated reinforcement learning models for enhanced anomaly detection performance in NPPs.

Reinforcement learning

Secure Wireless Communication Using Distributed Coherent Transmission and Spatial Signal Decomposition

We present a new approach to secure wireless communications using coherent distributed transmission of signals that are spatially decomposed between a two-element distributed antenna array. High-accuracy distributed coordination of microwave wireless systems supports the ability to transmit different parts of a signal from separate transmitters such that they combine coherently at a designated destination. In this article, we explore this concept using a two-element coherent distributed phased array where each of the two transmitters sends a separate component of a communication signal, where each symbol is decomposed into a sum of two pseudorandom signal vectors, the coherent summation of which yields the intended symbol. By directing the transmission to an intended receiver using distributed beamforming, the summation of the two vector components is largely confined to a spatial region at the destination receiver. We implement the technique in a $50−λ$ array operating at 3 GHz. We evaluate the symbol error rate (SER) in 2-D space through simulation and measurement, showing that the approach yields a spatially confined secure region where the information is recoverable (i.e., the received signal has low SER), and outside of which the information is unrecoverable (high SER). The proposed system is also compared against a traditional beamforming system where each node sends the same data. We validate experimentally that our approach achieves a low SER of 0.0082 at broadside and an SER above 0.25 at all other locations compared to a traditional beamforming approach that achieves a SER of 0 at all locations measured.

Engineering - Electronic and electrical engineerin

Efficient Simulation of Logical Magic State Preparation Protocols

Developing space- and time-efficient logical magic state preparation (MSP) protocols will likely be an essential step toward building a large-scale fault-tolerant quantum computer. Motivated by this need, we introduce a scalable method for simulating logical MSP protocols under the standard circuit-level noise model. When applied to protocols based on code-switching, magic state cultivation, and magic state distillation, our method yields a complexity polynomial in (i) the number of qubits and (ii) the nonstabilizerness, e.g., stabilizer rank or Pauli rank, of the target encoded magic state. The efficiency of our simulation method is rooted in a curious fact: every circuit-level Pauli error in these protocols propagates to a Clifford error at the end. This property is satisfied by a large family of protocols, including those that repeatedly measure a transversal Clifford that squares to a Pauli. We provide a proof-of-principle numerical simulation that prepares a magic state using such logical Clifford measurements. Our work enables practical simulation of logical MSP protocols without resorting to approximations or resource-intensive state-vector simulations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Representativity error scaling of models of the high temperature test facility

Error scaling is a critical step toward the validation of modeling capabilities for high-temperature gas-cooled reactors (HTGRs). Extensive effort is being made to bring HTGRs into the validation basis of numerous thermal-hydraulics codes. Here, this paper demonstrates how systems-level codes can be leveraged to perform error scaling analyses between an experimental facility and a plant-to-be facility. Specifically, we focus on two conduction cooldown experiments from the High Temperature Test Facility (HTTF) and the General Atomics 350 MW th modular high-temperature gas-cooled reactor (MHTGR-350). The error scaling methodology employed in this study is representativity, which in the context of this work was used to quantify how well experiments captured the physics of the plant facility by comparing sensitivity vectors between the two facilities. In addition, two different RELAP5–3D models of the HTTF were included in the comparison to determine if modeling methodologies notably impact the representativity results. The key figures of merit are the maximum block temperature and the coolant outlet temperature. The time-dependent maximum block temperature had a low representativity of below 0.1 for both models across both transients. The coolant outlet temperature had a higher representativity of around 0.6 for both models during the pressurized conduction cooldown, but it was below 0.2 for the depressurized conduction cooldown. Overall, the HTTF experiments were not representative of the transients in the MHTGR-350. However, these results can play a significant role in informing future potential experiments for HTGR systems that iterate on what the HTTF accomplished.

22 - GENERAL STUDIES OF NUCLEAR REACTORS

Ground state energy and magnetization curve of a frustrated magnetic system from real-time evolution on a digital quantum processor

Models of interacting many-body quantum systems that may realize new exotic phases of matter, notably quantum spin liquids, are challenging to study using even state-of-the-art classical methods such as tensor network simulations. Quantum computing provides a promising route for overcoming these difficulties to find ground states, dynamics, and more. In this paper, we argue that recently developed hybrid quantum-classical algorithms based on real-time evolution are promising methods for solving a particularly important model in the search for spin liquids, the antiferromagnetic Heisenberg model on the two-dimensional kagome lattice. We show how to construct efficient quantum circuits to implement time evolution for the model and to evaluate key observables on the quantum computer, and we argue that the method has favorable scaling with increasing system size. We then restrict to a 12-spin star plaquette from the kagome lattice and a related 8-spin system, and we give an empirical demonstration on these small systems that the hybrid algorithms can efficiently find the ground state energy and the magnetization curve. For these demonstrations, we use four levels of approximation: exact state vectors, exact state vectors with statistical noise from sampling, noisy classical emulators, and (for the 8-spin system only) real quantum hardware, specifically the Quantinuum H1-1 processor; for the noisy simulations and hardware demonstration, we also employ error mitigation strategies based on the symmetries of the Hamiltonian. Our results strongly suggest that these hybrid algorithms present a promising direction for studying quantum spin liquids and more generally for resolving important unsolved problems in condensed matter theory and beyond.

97 MATHEMATICS AND COMPUTING

DESI DR2 Baryon Acoustic Oscillations from the Lyman Alpha Forest Multipoles

We present an alternative measurement of the Baryon Acoustic Oscillation (BAO) using the Legendre multipole representation of the Ly$α$ forest correlation functions from the second data release (DR2) of the Dark Energy Spectroscopic Instrument survey. Compressing the auto- and cross-correlation functions into Legendre multipoles yields a positive-definite covariance matrix without any smoothing -- unlike the baseline DR2 analysis -- thanks to a significantly reduced data vector size. We introduce the statistical corrections required to debias the finite-sample covariance matrix estimate and demonstrate that monopole and quadrupole terms for both auto- and cross-correlations can be used even when the correlation functions are distorted by continuum errors and contaminated by metals. This formalism has slightly diminished the constraining power of the BAO scale, while considerably weakening constraints on nuisance parameters. We measure the isotropic BAO scale with $0.93\%$ precision at $z_\mathrm{eff}=2.35$, the Hubble parameter $H(z_\mathrm{eff})=(239.5\pm3.4)~(147.09~\mathrm{Mpc}/r_d) ~\mathrm{km~s}^{-1}~\text{Mpc}^{-1}$, and the transverse comoving distance $D_M(z_\mathrm{eff})=(5.80 \pm 0.10)~(r_d/147.09~\mathrm{Mpc})$~Gpc for a given value of the sound horizon ($r_d$). Our BAO results are entirely consistent with the baseline DR2 analysis.

Karaçaylı, Naim Göksel [Chicago U., KICP; Ohio Sta

Single-qubit multi-party transmission using universal symmetric quantum cloning

This study considers the hypothetical quantum network case where Alice wishes to transmit one qubit of information (specifically a pure quantum state) to M parties, where M is some large number. The remote receivers locally perform single-qubit quantum state tomography on the transmitted qubits in order to compute the quantum state within some error rate (dependent on the tomography technique and the number of transmitted qubits). We show that with the use of an intermediate optimal symmetric universal quantum cloning machine (between Alice and the remote receivers) as a repeater-type node in a hypothetical quantum network, Alice can send significantly fewer qubits compared to direct transmission of the message qubits to each of the M remote receivers. This is possible due to two properties of quantum cloning. The first is that single qubit quantum clones retain the same Bloch angle as the initial quantum state. This means that if the mixed state of the quantum clone can be computed to high enough accuracy, the original pure quantum state can be inferred by extrapolating that vector to the surface of the Bloch sphere. The second property is that the state overlap of approximate quantum clones, with respect to the original pure quantum state, quickly converges (specifically for 1 → M , the limit of the fidelity as M goes to infinity is $\frac{2}{3}$). This means that Alice can prepare a constant number of qubits (which are then passed through the quantum cloning machine) in order to achieve a desired error rate if M is large enough. Combined, these two properties mean that for a large M , Alice can prepare many orders of magnitude fewer qubits in order to achieve the same single qubit transmission accuracy compared to the naive direct qubit transmission approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Uncertainty propagation in feed-forward neural network models

We develop new uncertainty propagation methods for feed-forward neural network architectures with leaky ReLU activation functions subject to random perturbations in the input vectors. In particular, we derive analytical expressions for the probability density function (PDF) of the neural network output and its statistical moments as a function of the input uncertainty and the parameters of the network, i.e., weights and biases. A key finding is that an appropriate linearization of the leaky ReLU activation function yields accurate statistical results even for large perturbations in the input vectors. This can be attributed to the way information propagates through the network. We also propose new analytically tractable Gaussian copula surrogate models to approximate the full joint PDF of the neural network output. To validate our theoretical results, we conduct Monte Carlo simulations and a thorough error analysis on a multi-layer neural network representing a nonlinear integro-differential operator between two polynomial function spaces. Our findings demonstrate excellent agreement between the theoretical predictions and Monte Carlo simulations.

MLP networks

Wireless Patch Antenna Characterization for Live Health Monitoring Using Machine Learning

Temperature monitoring in extreme environments, such as coal-fired power plants, was addressed by designing and testing wireless patch antennas for use in machine learning-aided temperature estimation. The sensors were designed to monitor the temperature and health of boiler systems. Wireless interrogation of the sensor was performed using a Vector Network Analyzer (VNA) and a pair of interrogation antennas to capture resonance behavior under varying thermal and spatial conditions with sensitivities ranging from 0.052 to 0.20 $\frac{𝑀𝐻𝑧}{°C}$. Sensor calibration was conducted using a Long Short-Term Memory (LSTM) model, which leveraged temporal patterns to account for hysteresis effects. The calibration method demonstrated improved performance when combined with an LSTM model, achieving up to a 76% improvement in temperature estimation error when compared with Linear Regression (LR). The experiments highlighted an innovative solution for patch antenna-based non-contact temperature measurement, which addresses limitations with conventional methods such as RFID-based systems, infrared, and thermocouples.

20 FOSSIL-FUELED POWER PLANTS

PIP-II LLRF Master Oscillator and Precision Reference Line- Station Level Design and Testing

The PIP-II superconducting linac at Fermilab requires a highly stable RF Reference Line to maintain phase synchronization throughout the accelerator. Temperature-induced changes in the electrical length of long coaxial cables can introduce phase drift and measurement errors. The reference-line architecture mitigates these effects by phase averaging the forward and reflected RF signals, while a phase-locked loop anchors the system to the master oscillator. This work focuses on the characterization, validation, and mechanical integration of station-level RF assemblies using CAD modeling, vector network analyzer measurements, and spectrum analyzer testing. PID-controlled thermal plates will stabilize critical RF components and further reduce temperature-dependent phase and amplitude variations. These methods support repeatable, standardized designs that can be reliably integrated across the different reference-line stations.

Mosher, Alexander [U. Illinois, Chicago; Fermilab]

A Machine Learning based Approach of Estimating Equivalent Circuit Model Parameters at Different SoCs of Li-ion Batteries from Voltage Relaxation

Abstract: In this study, an approach of estimating the equivalent circuit model (ECM) parameters for Li-ion batteries (LIBs) is proposed based on the voltage value at different intervals while relaxing the LIB after discharge. The typical approach for estimating ECM parameters of a LIB is to conduct electrochemical impedance spectroscopy (EIS) measurements at different frequencies and fit them to a predefined circuit model, which requires additional measuring arrangements and specialized devices. The proposed methodology utilizes four different voltages at 0s, 60s, 360s, and 1800s alongside the specific state of charge (SoC) value for a specific constant discharge current value of ~1C until the relaxation stage to train and evaluate three regression-based machine learning models— Support Vector Regression (SVR), Extreme Gradient Boosting (XGBoost), and Gaussian Process Regression (GPR)—for estimating the ECM parameters of the selected model. Bayesian optimization is employed for hyperparameter tuning to achieve optimal performance for all the regressor models, among which, the GPR provided the best performance with the root-mean-squared error (RMSE) of less than 4x10-4 on average for the resistive components and less than 0.27 for capacitive components with excellent R2 scores. The simplicity of the approach enables it to eliminate the need for sophisticated measuring equipment and computation power.

Sagar, Md. Samiul [The University of Alabama (UA)]

PIP-II LLRF Master Oscillator and Precision Reference Line - Station Level Design and Testing

The PIP-II superconducting linac at Fermilab requires a highly stable RF Reference Line to maintain phase syn- chronization throughout the accelerator. Temperature- induced changes in the electrical length of long coaxial cables can introduce phase drift and measurement errors. The reference-line architecture mitigates these effects by phase averaging the forward and reflected RF signals, while a phase-locked loop anchors the system to the mas- ter oscillator. This work focuses on the characterization, validation, and mechanical integration of station-level RF assemblies using CAD modeling, vector network analyzer measurements, and spectrum analyzer testing. PID-controlled thermal plates will stabilize critical RF components and further reduce temperature-dependent phase and amplitude variations. These methods sup- port repeatable, standardized designs that can be reliably integrated across the different reference-line stations.

Mosher, Alexander [U. Illinois, Chicago]

Reduced Order Modeling conditioned on monitored features for response and error bounds estimation in engineered systems

Reduced Order Models (ROMs) form essential tools across engineering domains by virtue of their function as surrogates for computationally intensive digital twinning simulators. Although purely data-driven methods are available for ROM construction, schemes that allow to retain a portion of the physics tend to enhance the interpretability and generalization of ROMs. However, physics-based techniques can adversely scale when dealing with nonlinear systems that feature parametric dependencies. This study introduces a generative physics-based ROM that is suited for nonlinear systems with parametric dependencies and is additionally able to provide numerical error bounds associated with the respective estimates. A main contribution of this work is the conditioning of these parametric ROMs to features that can be derived from monitoring measurements, feasibly in an online fashion. This is contrary to most existing ROM schemes, which remain restricted to the prescription of the physics-based, and usually a priori unknown, system parameters. Our work utilizes conditional Variational Autoencoders to continuously map the required reduction bases to a feature vector extracted from limited output measurements, while additionally allowing for a probabilistic assessment of the ROM-estimated Quantities of Interest. An auxiliary task using a neural network-based parametrization of suitable probability distributions is introduced to re-establish the link with physical model parameters. We verify the proposed scheme on a series of simulated case studies incorporating effects of geometric and material nonlinearity under parametric dependencies related to system properties and input load characteristics.

Conditional VAEs

Transplatformer: translating toxicogenomic profiles between generations of platforms

Background Transcriptomic profiling technologies have advanced the analysis of biological and toxicological responses. However, substantial differences in probe design, dynamic range, gene coverage, and preprocessing pipelines across platforms introduce artifacts that limit cross-study integration and hinder the reuse of historical datasets. We aim to develop computational methods for accurate cross-platform translation to maximize the value of legacy resources. Results We present TransPlatformer a deep learning framework for translating gene expression profiles across heterogeneous toxicogenomics platforms. TransPlatformer employs a novel attention-based architecture to map high-dimensional fold-change vectors from legacy microarray technologies to current platforms. Models are trained and evaluated using DrugMatrix, spanning three technological generations. We investigate mixed-tissue, single-tissue, and cross-tissue training paradigms and benchmark performance against multilayer perceptron and matrix-completion baselines. In mixed-tissue training, TransPlatformer achieves a greater than 50% reduction in mean absolute error (0.043 vs. 0.09) and nearly doubles Pearson correlation ( ≈ 0.71 vs. 0.37) relative to baseline methods. Importantly, TransPlatformer preserves rare but biologically meaningful over- and under-expressed signals, with mean absolute error below 0.22. Single-tissue models yield further improvements for well-represented organs, such as a 10% reduction in liver mean absolute error, while underscoring the need for data augmentation strategies in low-sample tissues.ra Conclusions TransPlatformer provides an effective and scalable computational solution for cross-platform transcriptomic translation. By enabling biologically faithful harmonization of gene expression data, the proposed approach facilitates the reuse of legacy toxicogenomics datasets, enhances downstream biomarker discovery, and supports more reproducible predictive modeling in toxicology.

59 BASIC BIOLOGICAL SCIENCES

More buck-per-shot: Why learning trumps mitigation in noisy quantum sensing

Quantum sensing is one of the most promising applications for quantum technologies. However, reaching the ultimate sensitivities enabled by the laws of quantum mechanics can be a challenging task in realistic scenarios where noise is present. While several strategies have been proposed to deal with the detrimental effects of noise, these come at the cost of an extra shot budget. Given that shots are a precious resource for sensing – as infinite measurements could lead to infinite precision – care must be taken to truly guarantee that any shot not being used for sensing is actually leading to some metrological improvement. In this work, we study whether investing shots in error-mitigation, inference techniques, or combinations thereof, can improve the sensitivity of a noisy quantum sensor on a (shot) budget. We present a detailed bias–variance error analysis for various sensing protocols. Our results show that the costs of zero-noise extrapolation techniques outweigh their benefits. We also find that pre-characterizing a quantum sensor via inference techniques leads to the best performance, under the assumption that the sensor is sufficiently stable.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC

Light and Strange Vector Resonances from Lattice QCD at Physical Quark Masses

We present the first ab initio calculation at physical quark masses of scattering amplitudes describing the lightest pseudoscalar mesons interacting via the strong force in the vector channel. Using lattice quantum chromodynamics, we postdict the defining parameters for two short-lived resonances, the ρ(770) and K*(892) which manifest as complex energy poles in ππ and Kπ scattering amplitudes, respectively. The calculation proceeds by first computing the finite-volume energy spectrum of the two-hadron systems and then determining the amplitudes from the energies using the Lüscher formalism. The error budget includes a data-driven systematic error, obtained by scanning possible fit ranges and fit models to extract the spectrum from Euclidean correlators, as well as the scattering amplitudes from the latter. The final results, obtained by analytically continuing multiple parametrizations into the complex energy plane, are M ρ = 796(5)(50)MeV, Γ ρ = 192(10)(31) MeV, M K* = 893(2)(54) MeV, and Γ K = 51(2)(11) MeV, where the subscript indicates the resonance and M and Γ stand for the mass and width, respectively, and where the first bracket indicates the statistical and the second bracket the systematic uncertainty.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS