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At least 19 records

The Sensitivity of Variational Bayesian Neural Network Performance to Hyperparameters

In scientific applications, predictive modeling is often of limited use without accurate uncertainty quantification (UQ) to indicate when a model may be extrapolating or when more data needs to be collected. Bayesian Neural Networks (BNNs) produce predictive uncertainty by propagating uncertainty in neural network (NN) weights and offer the promise of obtaining not only an accurate predictive model but also accurate UQ. However, in practice, obtaining accurate UQ with BNNs is difficult due in part to the approximations used for model training (such as those made in variational inference) and in part to the need to choose a suitable set of hyperparameters; these hyperparameters outnumber those needed for traditional NNs and often have opaque effects on the results. We aim to shed light on the effects of hyperparameter choices for variational BNNs by performing a global sensitivity analysis of variational BNN performance under varying hyperparameter settings. Our results indicate that many of the hyperparameters interact with each other to affect both predictive accuracy and UQ. For improved usage of variational BNNs in real-world applications, we suggest that thorough hyperparameter tuning, including tuning of prior hyperparameters and loss function parameters, is essential for accurate UQ in variational BNNs.

97 MATHEMATICS AND COMPUTING

SIDDA: SInkhorn Dynamic Domain Adaptation

Modern neural networks (NNs) often do not generalize well in the presence of a "covariate shift"; that is, in situations where the training and test data distributions differ, but the conditional distribution of classification labels remains unchanged. In such cases, NN generalization can be reduced to a problem of learning more domain-invariant features. Domain adaptation (DA) methods include a range of techniques aimed at achieving this; however, these methods have struggled with the need for extensive hyperparameter tuning, which then incurs significant computational costs. In this work, we introduce SIDDA, an out-of-the-box DA training algorithm built upon the Sinkhorn divergence, that can achieve effective domain alignment with minimal hyperparameter tuning and computational overhead. We demonstrate the efficacy of our method on multiple simulated and real datasets of varying complexity, including simple shapes, handwritten digits, and real astronomical observations. SIDDA is compatible with a variety of NN architectures, and it works particularly well in improving classification accuracy and model calibration when paired with equivariant neural networks (ENNs). We find that SIDDA enhances the generalization capabilities of NNs, achieving up to a ≈40% improvement in classification accuracy on unlabeled target data. We also study the efficacy of DA on ENNs with respect to the varying group orders of the dihedral group DN, and find that the model performance improves as the degree of equivariance increases. Finally, we find that SIDDA enhances model calibration on both source and target data--achieving over an order of magnitude improvement in the ECE and Brier score. SIDDA's versatility, combined with its automated approach to domain alignment, has the potential to advance multi-dataset studies by enabling the development of highly generalizable models.

Pandya, Sneh [Northeastern U.]

SIDDA: SInkhorn Dynamic Domain Adaptation for image classification with equivariant neural networks

Modern neural networks (NNs) often do not generalize well in the presence of a ‘covariate shift’; that is, in situations where the training and test data distributions differ, but the conditional distribution of classification labels given the data remains unchanged. In such cases, NN generalization can be reduced to a problem of learning more robust, domain-invariant features. Domain adaptation (DA) methods include a broad range of techniques aimed at achieving this; however, these methods have struggled with the need for extensive hyperparameter tuning, which then incurs significant computational costs. In this work, we introduce SInkhorn Dynamic Domain Adaptation (SIDDA), an out-of-the-box DA training algorithm built upon the Sinkhorn divergence, that can achieve effective domain alignment with minimal hyperparameter tuning and computational overhead. We demonstrate the efficacy of our method on multiple simulated and real datasets of varying complexity, including simple shapes, handwritten digits, real astronomical observations, and remote sensing data. These datasets exhibit covariate shifts due to noise, blurring, differences between telescopes, and variations in imaging wavelengths. SIDDA is compatible with a variety of NN architectures, and it works particularly well in improving classification accuracy and model calibration when paired with symmetry-aware equivariant NNs (ENNs). We find that SIDDA consistently enhances the generalization capabilities of NNs, achieving up to a ${\approx}40\%$ improvement in classification accuracy on unlabeled target data, while also providing a more modest performance gain of $\lesssim 1\%$ on labeled source data. We also study the efficacy of DA on ENNs with respect to the varying group orders of the dihedral group DN, and find that the model performance improves as the degree of equivariance increases. Finally, if SIDDA achieves proper domain alignment, it also enhances model calibration on both source and target data, with the most significant gains in the unlabeled target domain—achieving over an order of magnitude improvement in the expected calibration error and Brier score. SIDDA’s versatility across various NN models and datasets, combined with its automated approach to domain alignment, has the potential to significantly advance multi-dataset studies by enabling the development of highly generalizable models.

79 ASTRONOMY AND ASTROPHYSICS

When does global attention help: a unified empirical study on atomistic graph learning

Graph neural networks (GNNs) are widely used as surrogates for costly experiments and first-principles simulations to study the behavior of compounds at atomistic scale, and their architectural complexity is constantly increasing to enable the modeling of complex physics. While most recent GNNs combine more traditional message passing neural networks (MPNNs) layers to model short-range interactions with more advanced graph transformers (GTs) with global attention mechanisms to model long-range interactions, it is still unclear when global attention mechanisms provide real benefits over well-tuned MPNN layers due to inconsistent implementations, features, or hyperparameter tuning. We introduce the first unified, reproducible benchmarking framework–built on HydraGNN–that enables seamless switching among four controlled model classes: MPNN, MPNN with chemistry/topology encoders, GPS-style hybrids of MPNN with global attention, and fully fused localglobal models with encoders. Using seven diverse open-source datasets for benchmarking across regression and classification tasks, we systematically isolate the contributions of message passing, global attention, and encoder-based feature augmentation. Our study shows that encoder-augmented MPNNs form a robust baseline, while fused localglobal models yield the clearest benefits for properties governed by long-range interaction effects. We further quantify the accuracycompute trade-offs of attention, reporting its overhead in memory. Together, these results establish the first controlled evaluation of global attention in atomistic graph learning and provide a reproducible testbed for future model development.

Equivariant graph neural networks

G2PDeep-v2: A Web-Based Deep-Learning Framework for Phenotype Prediction and Biomarker Discovery for All Organisms Using Multi-Omics Data

Multi-omics data offers rich insights into complex traits across organisms, yet integrating and analyzing these datasets for phenotype prediction and marker discovery remains challenging. Researchers need accessible tools that combine deep learning, hyperparameter optimization, visualization, and downstream analysis in a unified web platform. To address this, we developed G2PDeep-v2, a web-based platform powered by deep learning for phenotype prediction and marker discovery from multi-omics data across a wide range of organisms, including humans and plants. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

59 BASIC BIOLOGICAL SCIENCES

Self-adaptive weights based on balanced residual decay rate for physics-informed neural networks and deep operator networks

Physics-informed deep learning has emerged as a promising alternative for solving partial differential equations. However, for complex problems, training these networks can still be challenging, often resulting in unsatisfactory accuracy and efficiency. In this work, we demonstrate that the failure of plain physics-informed neural networks arises from the significant discrepancy in the convergence rate of residuals at different training points, where the slowest convergence rate dominates the overall solution convergence. Based on these observations, we propose a pointwise adaptive weighting method that balances the residual decay rate across different training points. The performance of our proposed adaptive weighting method is compared with current state-of-the-art adaptive weighting methods on benchmark problems for both physics-informed neural networks and physics-informed deep operator networks. In conclusion, through extensive numerical results we demonstrate that our proposed approach of balanced residual decay rates offers several advantages, including bounded weights, high prediction accuracy, fast convergence rate, low training uncertainty, low computational cost, and ease of hyperparameter tuning.

Balanced convergence rate

Online LIBS–ML Framework for Dynamic Characterization of Heterogeneous Waste-Derived Gasification Feedstocks

LIBS−ML framework for real time feedstock characterization during continuous conveyor transport Heterogeneous waste derived feedstocks (e.g., waste coal, biomass and blends) introduce rapid variability in heating value and ash chemistry that affect gasifier operation, yet conventional laboratory characterization techniques are too slow to support proactive control. To address this gap, this study reports on an online, in situ, dynamic characterization framework that couple’s laser-induced breakdown spectroscopy (LIBS) with leakage safe machine learning (ML) regression to deliver real time, decision quality predictions of gasifier relevant properties. A controlled sample matrix spanning two different waste coals, two different biomasses, and engineered blends under two particle size conditions were constructed and benchmarked using standardized laboratory analyses for proximate/ultimate properties and ash composition. LIBS spectra were acquired dynamically as material flowed on a conveyor belt, using high energy 1064 nm laser ablation and shot averaging to improve repeatability and precision. Supervised regression models (multi layer perceptron (MLP) /artificial neural network (ANN), random forest (RF), and support vector regression (SVR)) and an optimized weighted ensemble were trained on emission line feature sets using nested cross validation with Bayesian hyperparameter tuning and validated against an independent hold out set. The proposed LIBS−ML workflow achieves near laboratory predictive fidelity across parametric targets (including higher heating value (HHV), ash content, fixed carbon, sulfur, major ash forming oxides, and initial deformation temperature (IDT)), with the weighted ensemble providing a robust default predictor under dynamic measurement conditions. These results demonstrate a practical pathway for real time feedstock characterization that can enable feedforward adjustments and more resilient gasifier operation for variable quality waste derived fuels.

Biomass

ON-OFF neuromorphic ISING machines using Fowler-Nordheim annealers

We introduce NeuroSA, a neuromorphic architecture specifically designed to ensure asymptotic convergence to the ground state of an Ising problem using a Fowler-Nordheim quantum mechanical tunneling based threshold-annealing process. The core component of NeuroSA consists of a pair of asynchronous ON-OFF neurons, which effectively map classical simulated annealing dynamics onto a network of integrate-and-fire neurons. The threshold of each ON-OFF neuron pair is adaptively adjusted by an FN annealer and the resulting spiking dynamics replicates the optimal escape mechanism and convergence of SA, particularly at low-temperatures. To validate the effectiveness of our neuromorphic Ising machine, we systematically solved benchmark combinatorial optimization problems such as MAX-CUT and Max Independent Set. Across multiple runs, NeuroSA consistently generates distribution of solutions that are concentrated around the state-of-the-art results (within 99%) or surpass the current state-of-the-art solutions for Max Independent Set benchmarks. Furthermore, NeuroSA is able to achieve these superior distributions without any graph-specific hyperparameter tuning. For practical illustration, we present results from an implementation of NeuroSA on the SpiNNaker2 platform, highlighting the feasibility of mapping our proposed architecture onto a standard neuromorphic accelerator platform.

42 ENGINEERING

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)]

Enhancing Gaussian Process Surrogates for Optimization and Posterior Approximation via Random Exploration

This paper proposes novel noise-free Bayesian optimization strategies that rely on a random exploration step to enhance the accuracy of Gaussian process surrogate models. The new algorithms retain the ease of implementation of the classical GP-UCB algorithm, but the additional random exploration step accelerates their convergence, nearly achieving the optimal convergence rate. Furthermore, to facilitate Bayesian inference with intractable likelihoods, we propose to utilize optimization iterates for maximum a posteriori estimation to build a Gaussian process surrogate model for the unnormalized log-posterior density. We provide bounds for the Hellinger distance between the true and the approximate posterior distributions in terms of the number of design points. We demonstrate the effectiveness of our Bayesian optimization algorithms in nonconvex benchmark objective functions, in a machine learning hyperparameter tuning problem, and in a black-box engineering design problem. The effectiveness of our posterior approximation approach is demonstrated in two Bayesian inference problems for parameters of dynamical systems.

Bayesian inference

GP Cosmology Surrogate v1.0

GP Cosmology Surrogate is a Python library for building and training a generalized multi-output Gaussian process (GP) framework of @takhtaganov2021cosmic. In this approach, the surrogate is constructed sequentially, guided by a Bayesian optimization acquisition function that targets reduction of emulation error in the regions most consistent with the observational data. This adaptive design concentrates computational resources where they have the greatest impact on inference accuracy. The library supports efficient training for separable GP kernels, which allows the use of Kronecker algebra to handle high-dimensional input spaces and large numbers of correlated outputs. This makes it well suited for applications such as modeling cosmological power spectra, large-scale physical simulations, and multi-output hyperparameter tuning. By combining scalable multi-output GP modeling with data-driven adaptive sampling, GPsurrogate enables parameter inference and optimization with substantially fewer simulations than conventional space-filling designs.

Lukic, Zarija [Lawrence Berkeley National Laborato

Data Agnostic Feature-Target Analysis & Ranking Machine Learning Pipeline (DAFTAR-ML) v0.1.0

DAFTAR-ML is a specialized machine-learning pipeline that identifies relevant features based on their relationship to a target variable. Many ML pipelines focus solely on prediction, and feature ranking is often absent or lacks robust statistical methods. DAFTAR-ML performs its tasks with this outcome in mind. Model training is robust, using nested cross-validation and hyperparameter tuning. Instead of relying on native feature-importance scores, it employs SHAP (SHapley Additive exPlanations) to quantify feature importance. The pipeline also produces comprehensive results, including publication-quality visualizations.

Melie, Tina [Lawrence Berkeley National Laboratory

Analyzing and Exploring Training Recipes for Large-Scale Transformer-Based Weather Prediction

Abstract The rapid rise of deep learning (DL) in numerical weather prediction (NWP) has led to a proliferation of models which forecast atmospheric variables with comparable or superior skill than traditional physics-based NWP. However, among these leading DL models, there is a wide variance in both the training settings and architecture used. Further, the lack of thorough ablation studies makes it hard to discern which components are most critical to success. In this work, we show that it is possible to attain high forecast skill even with relatively off-the-shelf architectures, simple training procedures, and moderate compute budgets. Specifically, we train a minimally modified Swin Transformer V2 (SwinV2) on ERA5 data and find that it attains superior skill in terms of mean-square errors of deterministic forecasts when compared against the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS). Almost all DL–NWP systems share a core set of hyperparameters and design decisions. To aid and expedite future DL–NWP research, we present an in-depth, systematic exploration of different loss functions, model sizes and depths, patch sizes, and multistep training objectives. We also examine the model performance with metrics beyond the typical accuracy (ACC) and RMSE and investigate how the performance scales with model size. Through our open-source code, scoring pipelines, and models, we share our findings on key aspects of the training pipeline. These ablations reduce the necessity for expensive hyperparameter tuning and lower the barrier to entry for future DL–NWP research. Significance Statement This study investigates the potential of using large-scale transformer-based models for weather prediction, showing that it is possible to achieve high forecast accuracy with simpler, off-the-shelf architectures. By training a minimally modified SwinV2 transformer on ERA5 data, we show that the model achieves competitive forecast skill in terms of mean-square error for key variables, outperforming the European Centre for Medium-Range Weather Forecasts’ Integrated Forecasting System (IFS) at all lead times. Our findings suggest that effective training strategies, such as multistep fine-tuning and channel-weighted losses, significantly enhance the model’s performance. However, we also highlight that these improvements come with trade-offs in other areas, such as ensemble spread and high-frequency spatial detail. This work highlights the promise of deep learning in improving weather forecasts, which could lead to better preparedness and response to weather events, ultimately benefiting society by providing more reliable weather predictions.

Willard, Jared D. [Lawrence Berkeley National Labo

CUDO: closed-form universal dwell-time optimization for computer-controlled optical surfacing

Precision optical figuring demands fast and accurate dwell time optimization to reach nanometer- and sub-nanometer-level accuracy in next-generation optical systems. We introduce CUDO (closed-form universal dwell-time optimization), the first, to the best of our knowledge, unified closed-form analytical framework that supports both function-form and matrix-form dwell time models in computer-controlled optical surfacing (CCOS). In contrast to traditional methods, which rely on iterative optimization and hyperparameter tuning, our framework derives direct analytical solutions with no adjustable parameters. This approach unifies the solution principles of existing methods within a single mathematical model, delivering three key advantages: (1) accuracy on par with, or superior to, iterative solvers, (2) substantial reduction in computation time, and (3) numerical robustness. Comparative studies with prior art confirm that closed-form solutions achieve equivalent residual error while removing runtime bottlenecks. By simplifying the implementation and enabling real-time, scalable deployment, CUDO establishes a practical foundation for future deterministic fabrication of large-aperture and high-performance optics.

36 MATERIALS SCIENCE

Predicting initial trans-membrane pressure across cycles in the ultrafiltration process using random forest

With growing freshwater scarcity, direct potable reuse (DPR) systems that reclaim wastewater for drinking are becoming increasingly important for sustainable water supply. Reliable operation requires minimizing downtime in ultrafiltration (UF) units, where membrane fouling leads to elevated trans-membrane pressure (TMP). This study develops data-driven regression models based on random forest (RF) and autoregressive (AR) approaches to forecast the initial TMP at the start of each UF filtration cycle in a pilot-scale DPR system. The RF model consistently outperforms baseline methods, including historical mean, last observation carried forward, and AR models, across multiple forecast horizons, achieving the lowest root mean square error. To evaluate how different classes of process variables contribute to TMP dynamics over time, we examine the feature importance of independent input variables across multiple forecast horizons. This analysis provides insight into the temporal relevance of operational and sensor-derived features, guiding control and monitoring strategies. Additionally, the impact of hyperparameter tuning on TMP prediction performance is assessed for both direct and recursive RF modelling approaches. The proposed RF framework establishes a robust foundation for predictive monitoring and real-time optimization of UF operations, supporting sustainable and reliable water reuse.

direct potable reuse

Recent Progress on Surface Water Quality Models Utilizing Machine Learning Techniques

Surface waterbodies are heavily exposed to pollutants caused by natural disasters and human activities. Empowering sensor technologies in water quality monitoring, sufficient measurements have become available to develop machine learning (ML) models. Numerous ML models have quickly been adopted to predict water quality indicators in various surface waterbodies. This paper reviews 78 recent articles from 2022 to October 2024, categorizing water quality models utilizing ML into three groups: Point-to-Point (P2P), which estimates the current target value based on other measurements at the same time point; Sequence-to-Point (S2P), which utilizes previous time series data to predict the target value at one time point ahead; and Sequence-to-Sequence (S2S), which uses previous time series data to forecast sequential target values in the future. The ML models used in each group are classified and compared according to water quality indicators, data availability, and model performance. Widely used strategies for improving performance, including feature engineering, hyperparameter tuning, and transfer learning, are recognized and described to enhance model effectiveness. The interpretability limitations of ML applications are discussed. This review provides a perspective on emerging ML for surface water quality models.

machine learning (ML)

Xanthos-Lake Model Source Code

This repository contains the source code for Xanthos-Lake, a lake-modeling extension of the Xanthos framework that introduces a coupled lake component comprising the Xanthos-Lake Snow and Ice Model (xLSIM) and the Xanthos-Lake Water Balance Model (xLWBM). xLSIM is a basin-aware machine-learning model for lake snow, ice, and thermal conditions. It predicts monthly lake ice thickness, snow depth, snow-cover fraction, mixing-layer temperature, and lake ice fraction from meteorological forcing and lake surface-area information. It uses sequence-based deep-learning architectures, including Transformer and hybrid Long Short-Term Memory–Transformer (LSTM–Transformer) models, together with seasonal encoding, multi-lake learning, physical masking, and basin-level cryospheric and non-cryospheric classification. The training workflow uses Ray for scalable execution and includes optional Ray Tune hyperparameter optimization. Model predictions, observations, diagnostics, and feature-importance outputs are written in NetCDF. xLWBM is the water-balance component of the new lake framework. It simulates monthly lake storage, surface area, evaporation, inflow, outflow, and lake–groundwater exchange. It combines physical water-balance equations with calibrated bathymetric relationships, weir-based outlet flow, modified Penman open-water evaporation, groundwater head relaxation, Penman–Monteith snow and ice sublimation, and snow, ice, and thermal conditions supplied by xLSIM. The model calibrates lake parameters against satellite-derived surface-area data, using evaporation-based calibration where surface-area data are unavailable, and supports small, medium, and large lake classes. For large lakes, xLWBM is integrated with the managed-routing workflow so that lake storage and outflow interact directly with downstream river routing and reservoir operations. Together, xLSIM and xLWBM provide Xanthos with a coupled lake-modeling capability. xLSIM supplies the snow, ice, and thermal conditions that affect lake evaporation and snow- and ice-related water exchanges, while xLWBM translates those conditions into dynamic lake storage, surface area, evaporation, and discharge. In return, xLWBM supplies evolving lake surface area to xLSIM. This coupling enables Xanthos to represent lakes as active hydrologic components within basin-scale water-availability and routing simulations.

Machine Learning

Neural Network Analysis of Nuclear Magnetic Resonance and Infrared Spectra

Nuclear magnetic resonance (NMR) spectroscopy and infrared (IR) spectroscopy are powerful chemical characterization techniques with broad general usage. However, the manual evaluation of the resulting spectra is time-consuming and requires significant expertise, preventing insights from being used in real-time applications. With recent advances in computation and artificial intelligence (AI), new tools are available for automating spectral interpretation. In this work, machine learning (ML) algorithms using 1-dimensional convolutional neural networks (CNNs) were applied to identify common functional groups from spectral information. Raw spectra were collected virtually from the Human Metabolome Database (HMDB) and National Institute of Standards and Technology (NIST) Chemistry WebBook and processed into a suitable standard. Algorithm design was tailored to best fit the nature of the problem, with built-in flexibility to accommodate relevant parameters beyond the raw spectral input, specifically solvent identity and magnetic frequency for NMR. The predictive capability of the algorithm in identifying functional groups is displayed in several examples. This methodology has been compiled into a code repository and could easily be modified to adapt alternative data sources, including other spectrum types. To mitigate overfitting, a common problem in mathematical modeling where overfamiliarity with training data produces trends that are not representative of the general data, a novel metric was developed, referred to as Accufit. Accufit includes a parameter that penalizes substantial differences in the training accuracy and the accuracy of an independent validation set. Examples are presented showing the effectiveness of Accufit in maintaining the model’s predictive capability while controlling the overfitting when used as a custom metric for hyperparameter tuning.

Sturgill, James