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At least 55 records · Page 3

Information theory optimization of signals from small-angle scattering measurements

Small-angle X-ray scattering (SAXS) of particles in solution informs on the conformational states and assemblies of biological macromolecules (bioSAXS) outside of cryo- and solid-state conditions. In bioSAXS, the SAXS measurement under dilute conditions is resolution limited, and through an inverse Fourier transform, the measured SAXS intensities directly relate to the physical space occupied by the particles via the P (r)-distribution. Yet, this inverse transform of SAXS data has been historically cast as an ill-posed, ill-conditioned problem requiring an indirect approach. Here, we show that through the applications of matrix and information theories, the inverse transform of SAXS intensity data is a well-conditioned problem. The so-called ill-conditioning of the inverse problem is directly related to the Shannon number. By exploiting the oversampling enabled by modern detectors, a direct inverse Fourier transform of the SAXS data is possible, provided the recovered information does not exceed the Shannon number. The Shannon limit corresponds to the maximum number of significant singular values that can be recovered in a SAXS experiment, suggesting this relationship is a fundamental property of band-limited inverse integral transform problems. This correspondence reduces the complexity of the inverse problem to the Shannon limit and maximum dimension. We propose a hybrid scoring function using an information theory framework that assesses both the quality of the model-data fit as well as the quality of the recovered P (r)-distribution. The hybrid score utilizes the Akaike information criteria and Durbin-Watson statistic that considers parameter-model complexity, i.e., degrees of freedom, and the randomness of the model-data residuals. The described tests and findings extend the boundaries for bioSAXS by completing the information theory formalism initiated by Peter B. Moore to enable a quantitative measure of resolution in SAXS, robustly determine maximum dimension, and more precisely define the best parameter model appropriately representing the observed scattering data.

Rambo, Robert P. [Science and Technology Facilitie

A Centralized AI Lakehouse Framework for Brain Tumor MRI Classification and Segmentation, University KPI Forecasting, and Water Potability Prediction

In many university and healthcare projects, models are built for very different data types such as tables, institutional time series, and medical images, but they are deployed as separate applications. In this work, that separation made testing and maintenance difficult because each module had its own pipeline and runtime requirements. This paper presents an integrated AI lakehouse-style implementation that runs three model pipelines inside one containerized backend. For medical imaging, we used MRI datasets from IEEE DataPort: a four-class classification set with 7012 images (5708 train/1304 test) and a segmentation set with 3063 image–mask pairs. The classification model (ResNet50 transfer learning) is evaluated using a proper train–validation–test protocol across multiple splits (80/10/10, 70/10/20, 60/10/30, and 10/30/60), achieving a test accuracy of 99.00% under the standard 80/10/10 split. Additionally, a patient-level evaluation is conducted using an external glioma dataset to provide a more realistic assessment without data leakage. The segmentation model (DeepLabV3-ResNet50) achieved 83.09% validation mIoU and 88.79% Dice score. For university KPI forecasting, we used annual IPEDS and NSF HERD data from 2010 to 2023 for three universities (BSU, EOU, and UAB). To examine the effect of preprocessing on forecasting performance, two case studies are conducted. In the first case, linear interpolation is applied to generate semester-level data. In the second case, the original annual data is used directly without interpolation. Random Forest regression and ARIMA models are evaluated using MAE, RMSE, MAPE, and R 2 . The results showed that interpolation improved apparent forecasting performance due to smoothing, while evaluation on the original annual data provided a more realistic assessment of model behavior. To further validate the framework on a larger dataset, an additional case study is conducted using a student dropout dataset. For water potability, we trained and compared multiple tabular classifiers on a large dataset (1,048,575 samples). A Random Forest model (100 trees, max depth 10) achieved 85.86% test accuracy and high recall for unsafe samples (0.8447). All modules are served via FastAPI and deployed together using Docker, with workflow automation routing requests to the correct endpoint. System-level benchmarking indicates that the backend maintains stable throughput and latency under concurrent requests.

97 MATHEMATICS AND COMPUTING

A Probabilistic Model for Global EMIC Wave Activity Using Van Allen Probes Observations

Electromagnetic ion cyclotron (EMIC) waves play a key role in radiation belt dynamics through resonant interactions. However, their low occurrence probability, high variability, and spatial intermittency pose challenges for accurate modeling. In this study, we present a machine learning (ML)-based global EMIC wave model built on the entire data set from the Van Allen Probes mission. To capture the distinct statistical characteristics of wave occurrence and amplitude, the model is separated into two modules: an occurrence model trained using ML techniques, and a wave amplitude model sampled from observed probability distributions. The input parameters are limited to real-time or predictable variables to ensure practical applicability. Our model shows strong performance across the entire test set and demonstrates improved predictive capability over a baseline random occurrence model, particularly during quiet geomagnetic conditions. Evaluation during both quiet and active periods confirms the model's ability to represent the clustered and intermittent nature of EMIC wave activity. Furthermore, the model provides global estimates of wave power, enabling integration with radiation belt electron data and showing signatures consistent with wave-induced scattering. We found a good correlation between the global wave activity from the model and relativistic electron observation by Van Allen Probes, regardless of the availability of in situ wave observations. The modular structure of the model also allows for straightforward expansion for additional wave properties, such as wave frequency, which can be modeled independently. This flexible, event-sensitive approach offers a promising framework for data-driven radiation belt simulations and space weather applications.

79 ASTRONOMY AND ASTROPHYSICS

NEAR: Neural Embeddings for Amino acid Relationships

Protein language models (PLMs) have recently demonstrated potential to supplant classical protein database search methods based on sequence alignment, but are slower than common alignment-based tools and appear to be prone to a high rate of false labeling. Here, we present NEAR, a method based on neural representation learning that is designed to improve both speed and accuracy of search for likely homologs in a large protein sequence database. NEAR’s ResNet embedding model is trained using contrastive learning guided by trusted sequence alignments. It computes per-residue embeddings for target and query protein sequences, and identifies alignment candidates with a pipeline consisting of residue-level k-NN search and a simple neighbor aggregation scheme. Tests on a benchmark consisting of trusted remote homologs and randomly shuffled decoy sequences reveal that NEAR substantially improves accuracy relative to state-of-the-art PLMs, with lower memory requirements and faster embedding and search speed. While these results suggest that the NEAR model may be useful for standalone homology detection with increased sensitivity over standard alignment-based methods, in this manuscript we focus on a more straightforward analysis of the model’s value as a high-speed pre-filter for sensitive annotation. In that context, NEAR is at least 5x faster than the pre-filter currently used in the widely-used profile hidden Markov model (pHMM) search tool HMMER3, and also outperforms the pre-filter used in our fast pHMM tool, nail.

59 BASIC BIOLOGICAL SCIENCES

Efficient Training of Deep Neural Operator Networks via Randomized Sampling

Neural operators (NOs) employ deep neural networks to learn the mappings between infinitedimensional function spaces. Deep operator network (DeepONet), a popular NO architecture, has demonstrated success in the real-time prediction of complex dynamics across various scientific and engineering applications. In this work, we introduce a random sampling technique to be adopted during the training of DeepONet, aimed at improving the generalization ability of the model, while significantly reducing the computational time. The proposed approach targets the trunk network of the DeepONet model that outputs the basis functions corresponding to the spatiotemporal locations of the bounded domain on which the physical system is defined. While constructing the loss function, DeepONet training traditionally considers a uniform grid of spatiotemporal points at which all the output functions are evaluated for each iteration. This approach leads to a larger batch size, resulting in poor generalization and increased memory demands, due to the limitations of the stochastic gradient descent (SGD) optimizer. The proposed random sampling over the inputs of the trunk net mitigates these challenges, improving generalization and reducing the memory requirements during training, resulting in significant computational gains. We validate our hypothesis through three benchmark examples, demonstrating substantial reductions in training time while achieving comparable or lower overall test errors relative to the traditional training approach. Our results indicate that incorporating randomization in the trunk network inputs during training enhances the efficiency and robustness of DeepONet, offering a promising avenue for improving the framework’s performance in modeling complex physical systems.

Karumuri, Sharmila [Department of Civil & Systems

Karhunen–Loève deep learning method for surrogate modeling and approximate Bayesian parameter estimation

We evaluate the performance of the Karhunen-Loève Deep Neural Network (KL-DNN) framework for surrogate modeling and approximate Bayesian parameter estimation in partial differential equation models. In the surrogate model, the Karhunen-Loève (KL) expansions are used for the dimensionality reduction of the number of unknown parameters and variables, and a deep neural network is employed to relate the reduced space of parameters to that of the state variables. The KL-DNN surrogate model is used to formulate a maximum-a-posteriori-like least-squares problem, which is randomized to draw samples of the posterior distribution of the parameters. We test the proposed framework for a hypothetical unconfined aquifer via comparison with the forward MODFLOW and inverse PEST++ iterative ensemble smoother (IES) solutions as well as the state-of-the-art Fourier neural operator (FNO) and deep operator networks (DeepONets) operator learning surrogate models. Our results show that the KL-DNN surrogate model outperforms FNO and DeepONet for forward predictions. For solving inverse problems, the randomized algorithm provides the same or more accurate Bayesian predictions of the parameters than IES as evidenced by the higher log-predictive probability of both the estimated parameter field and the forecast hydraulic head. The posterior mean obtained from the randomized algorithm is closer to the reference parameter field than that obtained with FNO as the maximum a posteriori estimate.

Approximate Bayesian inference

Can the angular scale of cosmic homogeneity be used as a cosmological test?

Abstract In standard cosmology, the cosmic homogeneity scale is the transition scale above which the patterns arising from non-uniformities – such as groups and clusters of galaxies, voids, and filaments – become indistinguishable from a random distribution of sources. Recently, different groups have investigated the feasibility of using such a scale as a cosmological test and arrived at different conclusions. In this paper, we complement and extend these studies by exploring the evolution of the spatial ( $$R_{\textrm{H}}$$ R H ) and angular ( $$\theta _{\textrm{H}}$$ θ H ) homogeneity scales with redshift, assuming a spatially flat, $$\varLambda $$ Λ -Cold Dark Matter universe and linear cosmological perturbation theory. We confirm previous results concerning the non-monotonicity of $$R_{\textrm{H}}$$ R H with the matter density parameter $$\varOmega _{\textrm{m0}}$$ Ω m0 but also show that it exhibits a monotonical behavior with the Hubble constant $$H_{0}$$ H 0 within a large redshift interval. More importantly, we find that, for $$z \gtrsim 0.6$$ z ≳ 0.6 , $$\theta _{\textrm{H}}$$ θ H presents a monotonical behavior with $$\varOmega _{\textrm{m0}}$$ Ω m0 , as well as for $$H_0$$ H 0 the entire redshift interval analyzed. We find also that the angular homogeneity scale is sensitive to $$H_{0}$$ H 0 , especially at higher redshifts. Using the currently available $$\theta _{\textrm{H}}$$ θ H measurements, we illustrate the constraints on the $$\varOmega _{\textrm{m0}}$$ Ω m0 – $$H_{0}$$ H 0 plane through a MCMC analysis and show the feasibility of using the angular homogeneity scale as a new, model-independent way to constrain cosmological parameters.

Physics

The 3D Lyman- α forest power spectrum from eBOSS DR16

We measure the three-dimensional power spectrum (P3D) of the transmitted flux in the Lyman-α (Ly α) forest using the complete extended Baryon Oscillation Spectroscopic Survey data release 16 (eBOSS DR16). This sample consists of ~205 000 quasar spectra in the redshift range 2 ≤ z ≤ 4 at an effective redshift z = 2.334. We propose a pair-count spectral estimator in configuration space, weighting each pair by exp( i k ∙ r), for wave vector k and pixel pair separation r, effectively measuring the anisotropic power spectrum without the need for fast Fourier transforms. This accounts for the window matrix in a tractable way, avoiding artefacts found in Fourier-transform based power spectrum estimators due to the sparse sampling transverse to the line of sight of Ly α skewers. We extensively test our pipeline on two sets of mocks: (i) idealized Gaussian random fields with a sparse sampling of Ly α skewers, and (ii) log-normal LyaCoLoRe mocks including realistic noise levels, the eBOSS survey geometry and contaminants. On eBOSS DR16 data, the Kaiser formula with a non-linear correction term obtained from hydrodynamic simulations yields a good fit to the power spectrum data in the range $(0.02 ≤ k ≤ 0.35)$ h Mpc -1 at the 1–2σ level with a covariance matrix derived from LyaCoLoRe mocks. We demonstrate a promising new approach for full-shape cosmological analyses of Ly α forest data from cosmological surveys such as eBOSS, the currently observing Dark Energy Spectroscopic Instrument and future surveys such as the Prime Focus Spectrograph, WEAVE-QSO, and 4MOST.

79 ASTRONOMY AND ASTROPHYSICS

A scalable variational method for estimating the latent infection-rate field of an outbreak

In this paper, we explore whether the infection-rate of a disease can serve as a robust monitoring variable in epidemiological surveillance algorithms. The infection-rate is dependent on population mixing patterns that do not vary erratically day-to-day; in contrast, daily case-counts used in contemporary surveillance algorithms are corrupted by reporting errors. The technical challenge lies in estimating the latent infection-rate from case-counts. Here we devise a Bayesian method to estimate the infection-rate across multiple adjoining areal units, and then use it, via an anomaly detector, to discern a change in epidemiological dynamics. We extend an existing model for estimating the infection-rate in an areal unit by incorporating a Markov random field model, so that we may estimate infection-rates across multiple areal units, while preserving spatial correlations observed in the epidemiological dynamics. To carry out the high-dimensional Bayesian inverse problem, we develop an implementation of mean-field variational inference specific to the infection model and integrate it with the random field model to incorporate correlations across counties. The method is tested on estimating the COVID-19 infection-rates across all 33 counties in New Mexico using data from the summer of 2020, and then employing them to detect the arrival of the Fall 2020 COVID-19 wave. We perform the detection using a temporal algorithm that is applied county-by-county. We also show how the infection-rate field can be used to cluster counties with similar epidemiological dynamics.

60 APPLIED LIFE SCIENCES

Testing Classical Properties from Quantum Data

Many properties of Boolean functions can be tested far more efficiently than the function itself can be learned. However, this dramatic advantage often disappears when testers are limited to random samples of ƒ instead of adaptively chosen queries to f. In this work we investigate the quantum version of this restriction: quantum algorithms that test properties of a Boolean function f solely from copies of either the function state |ƒ⟩ ∝ ∑ x |x, ƒ(x)⟩ or the phase state |(-1) ƒ ⟩ ∝ ∑ x (-1) ƒ(x) |x⟩. For monotonicity, symmetry, and triangle-freeness, we show passive quantum testers are unboundedly or super-polynomially better than their classical passive testing counterparts. They are competitive with classic query -based testers in each case. Our new testers use techniques beyond quantum Fourier sampling, and it turns out this is necessary: we show a certain class of bent functions can be tested from 𝒪(1) function states but has a sample complexity lower bound of 2 Ω(n) for any tester relying exclusively on Fourier and classical samples. Our passive quantum testers are competitive with classical query -based testers, but this isn't universal: we exhibit a testing problem that can be solved from 𝒪(1) classical queries but requires Ω(2 n/2 ) function state copies. The Forrelation problem provides a separation of the same magnitude in the opposite direction, so we conclude that quantum data and classical queries are "maximally incomparable" resources for testing. We also begin the study of lower bounds for testing from quantum data. For quantum monotonicity testing, we prove that the ensembles of [Goldreich et al., 2000; Black, 2024], which give exponential lower bounds for classical sample-based testing, do not yield any nontrivial lower bounds for testing from quantum data. New insights specific to quantum data will be required for proving copy complexity lower bounds for testing in this model.

Boolean Functions

Biosynthesis of bioprivileged, linear molecules via novel carboligase reactions

Over the award period, we made progress on the three aims. We screened twenty-five carboligases for activity coupling twenty-one possible -keto acids (Aim 1). The carboligases were selected across a diverse set of protein sequences. Using Q-Exactive UHPLC-MS, we tested a total of 210 coupled products per enzyme and generated a dataset of 5250 enzyme-substrate activity relationships. We identified multiple enzymes that had activity for synthesizing suberic acid and heptanoic acid (Aim 2). We built a random forest model for predicting the activity of each enzyme toward substrates on which it was not tested using the data from Aim 1. Finally, we evaluated growth defects that occurred due to expression of different carboligases in E. coli (Aim 3). We were able to identify specific metabolites and putative pathways that, when supplemented in the media, recovered the growth defect associated with the presence of specific carboligases. We are in the process of publishing two manuscript describing the methods for high-throughput screening of enzyme promiscuity, using machine learning to predict activity on untested substrates, and enzyme activity data we collected. This project has produced enabling data for biosynthesis of a range of new-to-nature compounds to support biomanufacturing.

60 APPLIED LIFE SCIENCES

Beta-Decay Half-Lives beyond 54 Ca: A Systematic Survey of Decay Properties Approaching the Neutron Dripline

In an experiment performed at the Facility for Rare Isotope Beams (FRIB) using the FRIB Decay Station initiator, 15 new half-lives of isotopes near 54 Ca were measured. A new method of extracting lifetimes from experimental data, taking into account the unknown 𝛽-delayed neutron emission branches of very neutron-rich nuclei, was developed to enable systematic uncertainty analysis. The experiment observed a dramatic change in the half-life systematics for the isotopes with neutron number 𝑁 = 34. Beyond 𝑁 = 34, the decline of nuclear lifetime is much slower, leading to longer than anticipated lifetimes for near-dripline nuclei. State-of-the-art shell-model calculations can explain the experimental results, revealing the imprint of shell effects and the need for modification of single-particle neutron states. In conclusion, the results from a newly developed quasiparticle random phase approximation model with potential for making global predictions were also tested against the experimental results and good agreement was found.

Physics - Nuclear physics and radiation physics

Analysis Background & Noise in Stretched Wire Alignment Technique Measurements

The Stretched-Wire Alignment Technique (SWAT) is one method of magnet alignment for linear induction accelerators. The applications of SWAT have been implemented for aligning solenoid magnets on the Scorpius linear induction accelerator which will be sited at the Nevada National Security Site and the Flash X-Ray (FXR) linear induction accelerator at Lawrence Livermore National Laboratory’s Contained Firing Facility. This article describes both systematic (repeatable) and random sources of background and noise as well as practical ways to eliminate or reduce them to acceptable levels. Systematic sources include reflections from wire ends, rapid sag due to ohmic heating of the wire, magnetic materials, and shot rate. Random sources include air currents, vibration of nearby equipment, mechanical stability of test equipment, and the instruments used to measure the wire motion. Mitigations include curve fitting and adaptive noise signal cancellation, and mechanical damping. Finite Element Analysis (FEA) was used to identify and resolve a repeatable wire vibration frequency interfering with the signal resolution. Two stretched wire alignment technique set ups from Sandia National Labs and Lawrence Livermore National Lab have shown background noise sources and ways of mitigating them by either analysis methods or change of mechanical configuration. Conclusions that were drawn included the severe sensitivity of the deflection to even small external interferences of the SWAT wire such that it requires attention to detail in mechanical set up and analysis.

Linear Inductive Accelerator

Rapid Coal-Ash Characterization using Geophysical Methods & Machine Learning

Coal combustion products (CCP) are challenging to delineate in heterogeneous field settings. Conventional methods (test pits, coring, and laboratory analyses) are labor-intensive, slow, invasive, and provide sparse spatial coverage. This study evaluates whether rapid non-invasive geophysical screening methods—induced polarization (IP), magnetic susceptibility, and nuclear magnetic resonance (NMR) —combined with surface colorimetry (RGB_24), can discriminate CCP-soil mixtures and provide reliable estimates of CCP content. Laboratory measurements were collected on five CCP-soil mixtures (series) and modeled using (i) a linear baseline, (ii) a calibrated non-linear (power-mean) model, and (iii) a machine-learning (ML) Random Forest approach, with validation via leave-one-series-out and site-specific tests. Across the five series, individual signals—particularly IP and magnetic susceptibility—were strongly predictive of ash content but were consistently outperformed by combined models. The pooled calibrated non-linear and ML models captured the observed non-linearity and achieved high accuracy and precision, improving on linear fits. Colorimetry showed the weakest direct relationship with ash content for the tested samples but improved performance when included in multi-signal models. At pre-selected 3.5% decision threshold, calibrated and ML approaches yielded near-perfect classification (Matthews correlation coefficient ˜ 1), suggesting strong practical operability for field screening. Additionally, field-analog tests highlighted the role of endmembers—accuracy declined without access to end-member measurements but was largely recovered by collecting a minimal labeled pair for local recalibration. With end members, accuracy remained high. Globally trained models performed well on three operational unknowns; however, series-specific refits provided the most accurate predictions. Overall, these results highlight the potential of combining rapid geophysics and minimal local calibration for improved coal-ash delineation.

Peshtani, Klaudio

Hardware-in-the-Loop Testing of Wide-Area Damping Controller for Field Implementation in Large-scale Power Grid

In our previous work, an adaptive measurement-driven wide-area damping controller (WADC) for suppressing inter-area oscillations has been proposed and a hardware prototype was developed and validated through hardware-in-the-loop tests. As a continuation of the work, this paper introduces a WADC software prototype to handle the realistic challenges for field implementation in the control room of the power grid. The WADC software is developed and operated as an openPDC adapter with a graphical user interface (GUI) to monitor the WADC inputs and output, the communication delays and other variables. The software prototype has been fully tested through an enhanced hardware-in-the-loop (HIL) test setup. Its performance is verified under various realistic communication uncertainties, such as random time delays and data losses, with different communication protocols. The experiment results have proven the WADC software can deliver sufficient damping to suppress the targeted oscillation mode in handling various communication uncertainties for future field deployment.

Jia, Xinlan

Distributed Automatic Generation Control Considering DPV Using T&D Dynamic Co-Simulation

The increasing adoption of distributed energy resources (DERs) over the last decade warrants a reconsideration of control of generation resources. This paper proposes a distributed Automatic Generation Control (AGC) using transmission-and-distribution (T&D) dynamic co-simulation framework for the efficient DPV frequency regulation services. The co-simulation framework allows AGC units to exchange the information for distributed AGC, based on their adopted communication network topology. As a result, a cost-effective automatic generation control is achieved with DPV and conventional generators. The proposed distributed AGC is based on the gossip algorithm in which the neighboring AGC units share the relevant local information with each other and updates their share of AGC regulation signal. Distributed photovoltaics (DPV) unit contribute to AGC response based on their headroom capacity via DER aggregators. The algorithm is tested on IEEE-14 bus transmission system under conditions of generation failure and random load variation to observe effective frequency regulations service offered by DPVs and other AGC units. The study shows that DPV can effectively participate in AGC with the proposed distributed control framework.

automatic generation control

Highly Efficient Selection of High-redshift Emission-line Galaxies for Future DESI-like Surveys with Deep Multiband Imaging

Emission-line galaxies (ELGs) are an important tracer of baryon acoustic oscillations (BAOs) and large-scale structure at z > 1. In this work, we investigate the feasibility of using deep wide-area multiband imaging (e.g., from the Rubin Observatory) to efficiently select high-redshift ELGs. Using Hyper Suprime-Cam grizy photometry and COSMOS2020 many-band photometric redshifts, we design simple color cuts guided by a probabilistic random forest classifier to select galaxies at z = 1.1–1.6. We then empirically test and refine these color cuts using two samples of galaxies with deep spectroscopy and broad color coverage obtained with the Dark Energy Spectroscopic Instrument (DESI). Compared to DESI ELGs at z = 1.1–1.6, we achieve a higher redshift-measurement success rate (89% versus 69%), a much higher correct redshift-range success rate (84% versus 34%), and a far higher net surface density yield (1372 deg −2 versus 660 deg −2 ). Combining our sample with current DESI ELGs would increase the net ELG number density by a factor of ∼2.5, moving it out of the shot-noise limited regime and reducing the uncertainties on the BAO scale parameter at z = 1.1–1.6 by a factor of ∼2 at the highest redshifts. We also test selections using shallower photometry and obtain qualitatively similar results.

Salcedo Hernandez, Yoquelbin [University of Pittsb