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DOE OSTI2026

Latent Twins

Over the past decade, scientific machine learning has transformed the development of mathematical and computational frameworks for analyzing, modeling, and predicting complex systems. From inverse problems to numerical partial differential equations (PDEs), dynamical systems, and model reduction, these advances have pushed the boundaries of what can be simulated. Yet they have often progressed in parallel, with representation learning and algorithmic solution methods evolving largely as separate pipelines. With Latent Twins, we propose a unifying mathematical framework that creates a hidden surrogate in latent space for the underlying equations. Whereas digital twins mirror physical systems in the digital world, Latent Twins mirror mathematical systems in a learned latent space governed by operators. Through this lens, classical modeling, inversion, model reduction, and operator approximation all emerge as special cases of a single principle. We establish the fundamental approximation properties of Latent Twins for both ordinary differential equations (ODEs) and PDEs and demonstrate the framework across three representative settings: (i) canonical ODEs, capturing diverse dynamical regimes; (ii) a PDE benchmark using the shallow-water equations, contrasting Latent Twin simulations with deep operator network and forecasts with a four-dimensional variational method baseline; and (iii) a challenging real-data geopotential reanalysis dataset, reconstructing and forecasting from sparse, noisy observations. Latent Twins provide a compact, interpretable surrogate for solution operators that evaluate across arbitrary time gaps in a single-shot, while remaining compatible with scientific pipelines such as assimilation, control, and uncertainty quantification. Looking forward, this framework offers scalable, theory-grounded surrogates that bridge data-driven representation learning and classical scientific modeling across disciplines.

Latent Twins↗
DOE OSTI2022

A mixed, unified forward/inverse framework for earthquake problems: fault implementation and coseismic slip estimate

SUMMARY We introduce a new finite-element (FE) based computational framework to solve forward and inverse elastic deformation problems for earthquake faulting via the adjoint method. Based on two advanced computational libraries, FEniCS and hIPPYlib for the forward and inverse problems, respectively, this framework is flexible, transparent and easily extensible. We represent a fault discontinuity through a mixed FE elasticity formulation, which approximates the stress with higher order accuracy and exposes the prescribed slip explicitly in the variational form without using conventional split node and decomposition discrete approaches. This also allows the first order optimality condition, that is the vanishing of the gradient, to be expressed in continuous form, which leads to consistent discretizations of all field variables, including the slip. We show comparisons with the standard, pure displacement formulation and a model containing an in-plane mode II crack, whose slip is prescribed via the split node technique. We demonstrate the potential of this new computational framework by performing a linear coseismic slip inversion through adjoint-based optimization methods, without requiring computation of elastic Green’s functions. Specifically, we consider a penalized least squares formulation, which in a Bayesian setting—under the assumption of Gaussian noise and prior—reflects the negative log of the posterior distribution. The comparison of the inversion results with a standard, linear inverse theory approach based on Okada’s solutions shows analogous results. Preliminary uncertainties are estimated via eigenvalue analysis of the Hessian of the penalized least squares objective function. Our implementation is fully open-source and Jupyter notebooks to reproduce our results are provided. The extension to a fully Bayesian framework for detailed uncertainty quantification and non-linear inversions, including for heterogeneous media earthquake problems, will be analysed in a forthcoming paper.

58 GEOSCIENCES↗
DOE OSTI2022

Automatic information extraction from childhood cancer pathology reports

The International Classification of Childhood Cancer (ICCC) facilitates the effective classification of a heterogeneous group of cancers in the important pediatric population. However, there has been no development of machine learning models for the ICCC classification. We developed deep learning-based information extraction models from cancer pathology reports based on the ICD-O-3 coding standard. In this article, we describe extending the models to perform ICCC classification. We developed 2 models, ICD-O-3 classification and ICCC recoding (Model 1) and direct ICCC classification (Model 2), and 4 scenarios subject to the training sample size. We evaluated these models with a corpus consisting of 29206 reports with age at diagnosis between 0 and 19 from 6 state cancer registries. Our findings suggest that the direct ICCC classification (Model 2) is substantially better than reusing the ICD-O-3 classification model (Model 1). Applying the uncertainty quantification mechanism to assess the confidence of the algorithm in assigning a code demonstrated that the model achieved a micro-F1 score of 0.987 while abstaining (not sufficiently confident to assign a code) on only 14.8% of ambiguous pathology reports. Our experimental results suggest that the machine learning-based automatic information extraction from childhood cancer pathology reports in the ICCC is a reliable means of supplementing human annotators at state cancer registries by reading and abstracting the majority of the childhood cancer pathology reports accurately and reliably.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Large-scale deep learning for metastasis detection in pathology reports

Objectives No existing algorithm can reliably identify metastasis from pathology reports across multiple cancer types and the entire US population. In this study, we develop a deep learning model that automatically detects patients with metastatic cancer by using pathology reports from many laboratories and of multiple cancer types. Materials and Methods We use 60 471 unstructured pathology reports from 4 Surveillance, Epidemiology, and End Results (SEER) registries. The reports were coded into 1 of 3 labels: metastasis negative, metastases positive, or metastasis undetermined. We utilize a task-specific deep neural network trained from scratch and compare its performance with a widely used large language model (LLM). Results Our deep learning architecture trained on task-specific data outperforms a general-purpose LLM, with a recall of 0.894 compared to 0.824. We quantified model uncertainty and used it to defer reports for human review. We found that retaining 72.9% of reports increased recall from 0.894 to 0.969. Discussion A smaller deep learning architecture trained on task-specific data outperforms a general LLM. Equally critical to model performance is the incorporation of uncertainty quantification, achieved here through an abstention mechanism. Conclusions This study’s finding demonstrate the feasibility of developing algorithms to automatically identify metastatic cancer cases from unstructured pathology reports.

machine learning↗
DOE OSTI2024

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong

Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.

Evolutionary Biology↗
DOE OSTI2026

Determination of nuclear PDFs using Markov chain Monte Carlo methods

Global QCD analyses of nuclear parton distribution functions (nPDFs) have traditionally relied on the Hessian method for uncertainty estimation. However, the inherent Gaussian approximation and reliance on local curvature often prove insufficient for nPDF fits, which are frequently characterized by limited data constraints and non-Gaussian likelihoods. In this paper, we present the first nPDF determination based on Markov Chain Monte Carlo (MCMC) techniques, implemented within the nCTEQ framework using an adaptive Metropolis-Hastings algorithm. The MCMC approach enables a direct mapping of the posterior distribution and reveals a highly nontrivial parameter-space structure, including multiple modes and pronounced non-Gaussian behavior, particularly for the valence PDFs. We perform the first single-nucleus global analysis of lead PDFs using exclusively lead data and compare it to a multi-nuclei fit employing a standard analytic A dependence. The inclusion of lighter nuclei reduces quark uncertainties and modifies the shape of the lead PDFs, while leaving the gluon distribution largely unaffected. A complementary Hessian analysis exposes systematic limitations of the Gaussian approximation. Our results demonstrate that MCMC methods provide a more reliable framework for uncertainty quantification in nPDF determinations.

Derakhshanian, N. [Institute of Nuclear Physics Po↗
DOE OSTI2025

Bayesian inference of nuclear-matter density from proton scattering

Background: Proton elastic scattering at intermediate energy is widely employed as a tool for determining the matter radius of atomic nuclei. Here, the sensitivity of the approach relies on high-resolution measurements at small scattering angles and low-momentum transfer. Under these conditions, the Glauber multiple scattering theory accurately describes the proton-nucleus elastic cross section. Purpose: Investigate the sensitivity of the Glauber multiple scattering theory to uncertainties associated with input parameters such as the nuclear-matter density distribution and nucleon-nucleon data. Method: A joint Bayesian inference was performed using 12 angular distributions of elastic scattering at different energies on 58 Ni, 90 Zr, and 208 Pb targets. A Metropolis-Hastings algorithm was implemented to make an uncertainty quantification analysis for the input parameters used in the Glauber multiple scattering theory. Results: The experimental cross sections were fitted simultaneously using a joint Bayesian inference approach. Posterior probability density distributions of 42 input parameters were obtained from the analysis. A moderate correlation between the nuclear density parameters and the nucleon-nucleon cross sections was found. This correlation impacts the extraction of the nuclear-matter radius. Conclusions: The present analysis provided a consistent method for extracting the nuclear-matter density distribution of 58 Ni, 90 Zr, and 208 Pb from data across different incident energies. Due to the correlation of the nucleon-nucleon cross sections with the other input parameters, a constrained Bayesian inference using free nucleon-nucleon cross section data was performed. The nuclear-matter radii obtained from the analysis are in good agreement with multiple results reported in the literature.

190 ≤ A ≤ 219↗
DOE OSTI2020

Benchmarking noise extrapolation with the OpenPulse control framework

Distilling precise estimates from noisy intermediate scale quantum (NISQ) data has recently attracted considerable attention Kandala et al., Nature (London) 567, 491 (2019). In order to augment digital qubit metrics, such as gate fidelity, we discuss analog error mitigability, i.e., the ability to accurately distill precise observable estimates, as a hybrid quantum classical computing benchmarking task. Specifically, using Rabi oscillations as a test program, we characterize single qubit error rates on IBM's Poughkeepsie superconducting quantum hardware, incorporate control-mediated noise dependence into a generalized rescaling protocol, and analyze how noise characteristics influence Richardson extrapolation-based error mitigation. Finally, our results identify regions in the space of Hamiltonian control fields and circuit depth which are most amenable to reliable noise extrapolation, as well as shed light on how low-level hardware characterization can be used as a predictive tool for uncertainty quantification in error-mitigated NISQ computations.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

Bayesian inference for plasmonic nanometrology

Here, we introduce a Bayesian method for the characterization of plasmonic nanoparticles, which is applicable to both near- and far-field problems. Designed to combine data generated from any photon-plasmon interaction experiment with physically motivated theoretical models, our approach leverages state-of-the-art Markov chain Monte Carlo sampling techniques and returns parameter estimates on nanometric scales. Simulated spectral data sets, describing resonant scattering of photons from ellipsoidal and toroidal nanoparticles, are explored as concrete examples of our approach, with the resulting Bayesian estimates showing excellent agreement with the ground truth, even under conditions of high statistical noise. By incorporating Bayes factors into the method as well, we reveal how model selection can determine which one of competing geometric shapes better explains the observed data. Our comprehensive nanometrology procedure can be tailored to a variety of light-particle interaction models, and its reliance on Bayesian inference furnishes automatic uncertainty quantification. In addition to applicability to a host of plasmonic configurations such as nanoparticle dimers, trimers, and array studies, it is proposed that the presented analysis can be extended to the quantum regime, where nonclassical photon statistics may provide additional insight for inference of scatterer properties.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2025

Data-driven gradient optimization for field emission management in a superconducting radio-frequency linac

Field emission can cause significant problems in superconducting radio-frequency linear accelerators (linacs). When cavity gradients are pushed higher, radiation levels within the linacs may rise exponentially, causing degradation of many nearby systems. This research aims to utilize machine learning with uncertainty quantification to predict radiation levels at multiple locations throughout the linacs and ultimately optimize cavity gradients to reduce field emission-induced radiation while maintaining the total linac energy gain necessary for the experimental physics program. The optimized solutions show over 40% reductions for both neutron and gamma radiation from the standard operational settings. Published by the American Physical Society 2025

43 PARTICLE ACCELERATORS↗
DOE OSTI2020

Beyond the proton drip line: Bayesian analysis of proton-emitting nuclei

The limits of the nuclear landscape are determined by nuclear binding energies. Beyond the proton drip lines, where the separation energy becomes negative, there is not enough binding energy to prevent protons from escaping the nucleus. Predicting properties of unstable nuclear states in the vast territory of proton emitters poses an appreciable challenge for nuclear theory as it often involves far extrapolations. In addition, significant discrepancies between nuclear models in the proton-rich territory call for quantified predictions. With the help of Bayesian methodology, we mix a family of nuclear mass models corrected with statistical emulators trained on the experimental mass measurements, in the proton-rich region of the nuclear chart. Separation energies were computed within nuclear density functional theory using several Skyrme and Gogny energy density functionals. We also considered mass predictions based on two models used in astrophysical studies. Quantified predictions were obtained for each model using Bayesian Gaussian processes trained on separation-energy residuals and combined via Bayesian model averaging. Here, we obtained a good agreement between averaged predictions of statistically corrected models and experiment. In particular, we quantified model results for one- and two-proton separation energies and derived probabilities of proton emission. This information enabled us to produce a quantified landscape of proton-rich nuclei. The most promising candidates for two-proton decay studies have been identified. Finally, the methodology used in this work has broad applications to model-based extrapolations of various nuclear observables. It also provides a reliable uncertainty quantification of theoretical predictions.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Efficient emulation of relativistic heavy ion collisions with transfer learning

Measurements from the Large Hadron Collider (LHC) and the Relativistic Heavy Ion Collider (RHIC) can be used to study the properties of quark-gluon plasma. Systematic constraints on these properties must combine measurements from different collision systems and methodically account for experimental and theoretical uncertainties. Such studies require a vast number of costly numerical simulations. While computationally inexpensive surrogate models (“emulators”) can be used to efficiently approximate the predictions of heavy ion simulations across a broad range of model parameters, training a reliable emulator remains a computationally expensive task. We use transfer learning to map the parameter dependencies of one model emulator onto another, leveraging similarities between different simulations of heavy ion collisions. By limiting the need for large numbers of simulations to only one of the emulators, this technique reduces the numerical cost of comprehensive uncertainty quantification when studying multiple collision systems and exploring different models.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2022

Training and projecting: A reduced basis method emulator for many-body physics

Here, we present the reduced basis method as a tool for developing emulators for equations with tun able parameters within the context of the nuclear many-body problem. The method uses a basis expansion informed by a set of solutions for a few values of the model parameters and then projects the equations over a well-chosen low-dimensional subspace. We connect some of the results in the eigenvector continuation literature to the formalism of reduced basis methods and show how these methods can be applied to a broad set of problems. As we illustrate, the possible success of the formalism on such problems can be diagnosed beforehand by a principal component analysis. We apply the reduced basis method to the one-dimensional Gross-Pitaevskii equation with a harmonic trap ping potential and to nuclear density functional theory for 48 Ca, achieving speed-ups of more than x150 and x250, respectively, when compared to traditional solvers. The outstanding performance of the approach, together with its straightforward implementation, show promise for its application to the emulation of computationally demanding calculations, including uncertainty quantification.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2023

Wave-function-based emulation for nucleon-nucleon scattering in momentum space

Emulators for low-energy nuclear physics can provide fast and accurate predictions of bound-state and scattering observables for applications that require repeated calculations with different parameters, such as Bayesian uncertainty quantification. In this paper, we extend a scattering emulator based on the Kohn variational principle (KVP) to momentum space (including coupled channels) with arbitrary boundary conditions, which enable the mitigation of spurious singularities known as Kohn anomalies. We test it on a modern chiral nucleon-nucleon (N N) interaction, including emulation of the coupled channels. We provide comparisons between a Lippmann-Schwinger equation emulator and our KVP momentum-space emulator for a representative set of neutron-proton (n p) scattering observables, and also introduce a quasi-spline-based approach for the KVP-based emulator. Furthermore, our findings show that while there are some trade-offs between accuracy and speed, all three emulators perform well. Self-contained Jupyter notebooks that generate the results and figures in this paper are publicly available.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2024

Relativistic effects in Green's function Monte Carlo calculations of neutrino-nucleus scattering

Here, microscopic calculations of neutrino-nucleus scattering cross sections are critical for the success of the neutrino-oscillation program. In addition to retaining nuclear correlations in the initial and final state of the reaction, they are based on consistent nuclear interactions and transition current operators, thereby enabling robust uncertainty quantification. In this work, we address a significant limitation of these microscopic methods, which arises from their nonrelativistic nature. By performing the calculations in a reference frame that minimizes nucleon momenta and utilizing the so-called two-fragment model, we extend the applicability of Green's function Monte Carlo calculations of neutrino-nucleus scattering to higher momenta than currently possible. To validate this approach, we compare our theoretical predictions against inclusive data measured by the MiniBooNE, T2K, and MINER ν A experiments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

Nuclear-matter saturation and symmetry energy within Δ -full chiral effective field theory

Nuclear saturation and the symmetry energy are key properties of low-energy nuclear physics that depend on fine details of the nuclear interaction. The equation of state around saturation is also an important anchor for extrapolations to higher densities and studies of neutron stars. Here we develop a unified statistical framework that uses realistic nuclear forces to link the theoretical modeling of finite nuclei and infinite nuclear matter. We construct fast and accurate emulators for nuclear-matter observables and employ an iterative history-matching approach to explore and reduce the enormous parameter domain of Δ -full chiral interactions. We perform rigorous uncertainty quantification and find that model calibration including O 16 observables gives saturation predictions that are more precise than those that only use few-body data. Published by the American Physical Society 2024

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Learning PDFs through interpretable latent representations in Mellin space

Representing the parton distribution functions (PDFs) of the proton and other hadrons through flexible, high-fidelity parametrizations has been a long-standing goal of particle physics phenomenology. This is particularly true since the chosen parametrization methodology can play an influential role in the ultimate PDF uncertainties as extracted in QCD global analyses; these, in turn, are often determinative of the reach of experiments at the LHC and other facilities to nonstandard physics, including at large 𝑥, where parametrization effects can be significant. In this study, we explore a series of encoder-decoder machine-learning (ML) models with various neural-network topologies as efficient means of reconstructing PDFs from meaningful information stored in an interpretable latent space. Given recent effort to pioneer synergies between QCD analyses and lattice-gauge calculations, we formulate a latent representation based on the behavior of PDFs in Mellin space, i.e., their integrated moments, and test the ability of various models to decode PDFs from this information faithfully. We introduce a numerical package, PDFdecoder, which implements several encoder-decoder models to reconstruct PDFs with high fidelity and use this end-to-end tool to explore how such neural-network-based models might connect PDF parametrizations to underlying properties like their Mellin moments. We additionally dissect patterns of learned correlations between encoded Mellin moments and reconstructed PDFs that suggest opportunities for further improvements to ML-based approaches to PDF parametrizations and uncertainty quantification.

Machine learning↗
DOE OSTI2025

Observation of the singly Cabibbo-suppressed decay Λ c + → p π 0

Utilizing 4.5 fb − 1 of e + e − annihilation data collected with the BESIII detector at the BEPCII collider at center-of-mass energies between 4.600 and 4.699 GeV, the first observation of the singly Cabibbo-suppressed decay Λ c + → p π 0 is presented, with a statistical significance of 5.4 σ . The ratio of the branching fractions of Λ c + → p π 0 and Λ c + → p η is measured as B ( Λ c + → p π 0 ) / B ( Λ c + → p η ) = ( 0.120 ± 0.02 6 stat ± 0.00 7 syst ) . This result resolves the longstanding discrepancy between earlier experimental searches, providing both a decisive conclusion and valuable input for QCD-inspired theoretical models. A sophisticated deep learning approach using a Transformer-based architecture is employed to distinguish the signal from the prevalent hadronic backgrounds, complemented by thorough validation and systematic uncertainty quantification. Published by the American Physical Society 2025

Ablikim, M.↗