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DOE OSTI2026

Learning genetic perturbation effects with variational causal inference

Advances in sequencing technologies have enhanced the understanding of gene regulation in cells. In particular, Perturb-seq has enabled high-resolution profiling of the transcriptomic response to genetic perturbations at the single-cell level. This understanding has implications in functional genomics and potentially for identifying therapeutic targets. Various computational models have been developed to predict perturbational effects. While deep learning models excel at interpolating observed perturbational data, they tend to overfit in the lack of enough data and may not generalize well to unseen perturbations. In contrast, mechanistic models, such as linear causal models based on gene regulatory networks, hold greater potential for extrapolation, as they encapsulate regulatory information that can predict responses to unseen perturbations. However, their application has been limited to small studies due to overly simplistic assumptions, making them less effective in handling noisy, large-scale single-cell data. We propose a hybrid approach that combines a mechanistic causal model with variational deep learning, termed Single Cell Causal Variational Autoencoder (SCCVAE). The mechanistic model employs a learned regulatory network to represent perturbational changes as shift interventions that propagate through the learned network. SCCVAE integrates this mechanistic causal model into a variational autoencoder, generating rich, comprehensive transcriptomic responses. Our results indicate that SCCVAE exhibits superior performance over current state-of-the-art baselines for extrapolating to predict unseen perturbational responses. Additionally, for the observed perturbations, the latent space learned by SCCVAE allows for the identification of functional perturbation modules and simulation of single-gene knockdown experiments of varying penetrance, presenting a robust tool for interpreting and interpolating perturbational responses at the single-cell level.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Forecasting Commercial Building Electricity Consumption, Zone Airflow and Zone Temperature: Update - Development of a Generalized Machine Learning Approach

The U.S. power grid is being transformed to make it smarter, more efficient, and cleaner. This transformation is leading to the addition of a significant of energy generated by distributed, variable, and renewable resources. Because of the variable nature of renewable generation, the short- and long-term supply and demand imbalances are less predictable, and conventional approaches to mitigating the imbalances will be less efficient or cost effective. To address this challenge and to support the mission and the vision of the U.S. Department of Energy’s (DOE’s) Office of Energy Efficiency and Renewable Energy (EERE) Building Technologies Office has developed a Grid-Interactive Efficient Building Strategy. The strategy focuses on simultaneously improving building energy efficiency and supporting reliability and resilience of the electric grid more efficiently and at a lower cost. In addition, EERE and DOE’s Office of Electricity created an initiative led by DOE and supported by the national laboratories under the Grid Modernization Lab Consortium structure to enhance grid modernization. The work reported in this document is part of the first set of projects funded under the initiative to design, develop, and validate scalable transactive control technologies for the commercial buildings sector. Transactive controls requires the ability of individual end-use loads to express flexibility as a function of a transactive signal (e.g., price). Empirical grey- and black-box models have been widely used to express flexibility. Although this approach is generally easy to construct and simple to use, it does not capture non-linear behavior that some end-use loads represent. Therefore, Pacific Northwest National Laboratory (PNNL) with support from Western Washington University conducted this research to explore the use of deep machine learning (ML) techniques. The work reported in this document is limited to forecasting whole building electricity consumption, the zone airflow and the zone temperature predictions.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2020

Analytic marginalization of N(z) uncertainties in tomographic galaxy surveys

In this paper, we present a new method to marginalize over uncertainties in redshift distributions, N(z), within tomographic cosmological analyses applicable to current and upcoming photometric galaxy surveys. We allow for arbitrary deviations from the best-guess N(z) governed by a general covariance matrix describing the uncertainty in our knowledge of redshift distributions. In principle, this is marginalization over hundreds or thousands of new parameters describing potential deviations as a function of redshift and tomographic bin. However, by linearly expanding the theory predictions around a fiducial model, this marginalization can be performed analytically, resulting in a modified data covariance matrix that effectively downweights the modes of the data vector that are more sensitive to redshift distribution variations. We showcase this method by applying it to the galaxy clustering measurements from the Hyper Suprime-Cam first data release. We illustrate how to marginalize over sample variance of the calibration sample and a large general systematic uncertainty in photometric estimation methods, and explore the impact of priors imposing smoothness in the redshift distributions.

79 ASTRONOMY AND ASTROPHYSICS↗

DOE OSTI2025

Scattering neutrinos, spin models, and permutations

We consider a class of Heisenberg all-to-all coupled spin models inspired by neutrino interactions in a supernova with N degrees of freedom. These models are characterized by a coupling matrix that is relatively simple in the sense that there are only a few, relative to N , nontrivial eigenvalues, in distinction to the classic Heisenberg spin-glass models, leading to distinct behavior in both the high-temperature and low-temperature regimes. When the momenta of the neutrinos are uniform and random in directions, we can calculate the large- N partition function for the quantum Heisenberg model. In particular, the high-temperature partition function predicts a non-Gaussian density of states, providing interesting counterexamples showing the limits of general theorems on the density of states for quantum spin models. We can repeat the same argument for classical Heisenberg models, also known as rotor models, and we find the high-temperature expansion is completely controlled by the eigenvalues of the coupling matrix, and again predicts non-Gaussian behavior for the density of states as long as the number of eigenvalues does not scale linearly with N . Indeed, we derive the amusing fact that these partition functions are essentially the generating function for counting permutations in the high-temperature regime. Finally, for the case relevant to neutrinos in a supernova, we identify the low-temperature phase as a unique state with the direction of the momenta of the neutrino dictating its coherent state in flavor-space, a state we dub the “flavor-momentum-locked” state. Published by the American Physical Society 2025

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2020

Sequence-to-sequence neural networks for short-term electrical load forecasting in commercial office buildings

The U.S. power grid is transforming to become smarter, cleaner, and more effi- cient. This is leading to the addition of significant distributed variable renew- able generation. Due to the variable nature of renewable generation, the short- and long-term supply-demand imbalances are less predictable, and conventional approaches to mitigating the imbalance will not be efficient or cost-effective. To address this challenge, transactive control technologies have been proposed which balance energy generation and consumption with market activity and in- frastructural limitations. Transactive control requires the ability of individual end-use loads to express flexibility as a function of a transactive signal (e.g., price). Empirical gray- and black-box models have been widely used to express flexibility, and although these approaches are generally easy to construct and simple to use, they do not capture the non-linear behavior that some end-use loads represent . Machine learning approaches have been proposed to address this limitation. Although deep learning approaches for forecasting end-use loads have been explored, certain aspects of the application of deep models to load forecasting are not well understood. These aspects include how much training data is required, and how models should be structured and trained. To that end, this work explores how to approach applying deep recurrent neural networks to short-term electrical load forecasting with a case study of four commercial office buildings. We identify data requirements for training accurate models of whole building electricity use conditioned on outdoor temperature, provide insight into model hyperparameter sensitivity, and demonstrate how readily models can be generalized to unseen buildings.

Skomski, Elliott↗

DOE OSTI2021

Constructing tensor network influence functionals for general quantum dynamics

Here, we describe an iterative formalism to compute influence functionals that describe the general quantum dynamics of a subsystem beyond the assumption of linear coupling to a quadratic bath. We use a space-time tensor network representation of the influence functional and investigate its approximability in terms of its bond dimension and time-like entanglement in the tensor network description. We study two numerical models, the spin-boson model and a model of interacting hard-core bosons in a 1D harmonic trap. We find that the influence functional and the intermediates involved in its construction can be efficiently approximated by low bond dimension tensor networks in certain dynamical regimes, which allows the quantum dynamics to be accurately computed for longer times than with direct time evolution methods. However, as one iteratively integrates out the bath, the correlations in the influence functional can first increase before decreasing, indicating that the final compressibility of the influence functional is achieved via non-trivial cancellation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2021

Pyomo.GDP: an ecosystem for logic based modeling and optimization development

We present three core principles for engineering-oriented integrated modeling and optimization tool sets—intuitive modeling contexts, systematic computer-aided reformulations, and flexible solution strategies—and describe how new developments in Pyomo.GDP for Generalized Disjunctive Programming (GDP) advance this vision. We describe a new logical expression system implementation for Pyomo.GDP allowing for a more intuitive description of logical propositions. The logical expression system supports automated reformulation of these logical constraints to linear constraints. We also describe two new logic-based global optimization solver implementations built on Pyomo.GDP that exploit logical structure to avoid “zero-flow” numerical difficulties that arise in nonlinear network design problems when nodes or streams disappear. These new solvers also demonstrate the capability to link to external libraries for expanded functionality within an integrated implementation. We present these new solvers in the context of a flexible array of solution paths available to GDP models. Finally, we present results on a new library of GDP models demonstrating the value of multiple solution approaches.

42 ENGINEERING↗

DOE OSTI2019

Quasi-Stochastic Approximation and Off-Policy Reinforcement Learning: Preprint

The Robbins-Monro stochastic approximation algorithm is a foundation of many algorithmic frameworks for reinforcement learning and often an efficient approach to solving (or approximating the solution to) complex optimal control problems. In many cases, however, practitioners are unable to apply these techniques because of an inherent high variance. This paper aims to provide a general foundation for 'quasi-stochastic approximation,' in which all of the processes under consideration are deterministic, much like quasi-Monte Carlo for variance reduction in simulation. The variance reduction can be substantial, subject to tuning of pertinent parameters in the algorithm. This paper introduces a new coupling argument to establish the optimal rate of convergence provided the gain is sufficiently large. These results are established for linear models and tested also in nonideal settings. A major application of these general results is a new class of reinforcement learning algorithms for deterministic state space models. In this setting, the main contribution is a class of algorithms for approximating the value function for a given policy, using a different policy designed to introduce exploration.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2022

Exploring Structure-Sensitive Relations for Small Species Adsorption Using Machine Learning

Accurate prediction of adsorption energies on heterogeneous catalyst surfaces is crucial to predicting reactivity and screening materials. Adsorption linear scaling relations have been developed extensively but often lack accuracy and apply to one adsorbate and a single binding site type at a time. These facts undermine their ability to predict structure sensitivity and optimal catalyst structure. Using machine learning on nearly 300 density functional theory calculations, we demonstrate that generalized coordination number scaling relations hold well for oxygen- and high-valency carbon-binding species but fail for others. Here we reveal that the valency and the electronic coupling of a species with the surface, along with the site type and its coordination environment, are critical for small species adsorption. The model simultaneously predicts the adsorption energy and preferred site and significantly outperforms linear scalings in accuracy. It can expose the structure sensitivity of chemical reactions and enable enhanced catalyst activity via engineering particle shape and facet defects. The generality of our methodology is validated by training the model with transition metal data and transferring it to predict adsorption energies on single-atom alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Hybrid programming-model strategies for GPU offloading of electronic structure calculation kernels

To address the challenge of performance portability and facilitate the implementation of electronic structure solvers, we developed the basic matrix library (BML) and Parallel, Rapid O(N), and Graph-based Recursive Electronic Structure Solver (PROGRESS) library. The BML implements linear algebra operations necessary for electronic structure kernels using a unified user interface for various matrix formats (dense and sparse) and architectures (CPUs and GPUs). Focusing on density functional theory and tight-binding models, PROGRESS implements several solvers for computing the single-particle density matrix and relies on BML. In this paper, we describe the general strategies used for these implementations on various computer architectures, using OpenMP target functionalities on GPUs, in conjunction with third-party libraries to handle performance critical numerical kernels. In this study, we demonstrate the portability of this approach and its performance in benchmark problems.

36 MATERIALS SCIENCE↗

DOE OSTI2021

A new method for obtaining model-free viscoelastic material properties from atomic force microscopy experiments using discrete integral transform techniques

Viscoelastic characterization of materials at the micro- and the nanoscale is commonly performed with the aid of force–distance relationships acquired using atomic force microscopy (AFM). The general strategy for existing methods is to fit the observed material behavior to specific viscoelastic models, such as generalized viscoelastic models or power-law rheology models, among others. Here we propose a new method to invert and obtain the viscoelastic properties of a material through the use of the Z-transform, without using a model. We present the rheological viscoelastic relations in their classical derivation and their z-domain correspondence. We illustrate the proposed technique on a model experiment involving a traditional ramp-shaped force–distance AFM curve, demonstrating good agreement between the viscoelastic characteristics extracted from the simulated experiment and the theoretical expectations. We also provide a path for calculating standard viscoelastic responses from the extracted material characteristics. The new technique based on the Z-transform is complementary to previous model-based viscoelastic analyses and can be advantageous with respect to Fourier techniques due to its generality. Additionally, it can handle the unbounded inputs traditionally used to acquire force–distance relationships in AFM, such as ramp functions, in which the cantilever position is displaced linearly with time for a finite period of time.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Time Evolution of Correlation Functions in Quantum Many-Body Systems

We give rigorous analytical results on the temporal behavior of two-point correlation functions—also known as dynamical response functions or Green’s functions—in closed many-body quantum systems. We show that in a large class of translation-invariant models the correlation functions factorize at late times $\langle$A ( t ) B$\rangle$ β → $\langle$ A$\rangle$ β $\langle$ B$\rangle$ β , thus proving that dissipation emerges out of the unitary dynamics of the system. We also show that for systems with a generic spectrum the fluctuations around this late-time value are bounded by the purity of the thermal ensemble, which generally decays exponentially with system size. For autocorrelation functions we provide an upper bound on the timescale at which they reach the factorized late time value. Remarkably, this bound is only a function of local expectation values and does not increase with system size. We give numerical examples that show that this bound is a good estimate in nonintegrable models, and argue that the timescale that appears can be understood in terms of an emergent fluctuation-dissipation theorem. Our study extends to further classes of two point functions such as the symmetrized ones and the Kubo function that appears in linear response theory, for which we give analogous results.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

A symbolic framework to obtain mid-fidelity models of flexible multibody systems with application to horizontal-axis wind turbines

Abstract. The article presents a symbolic framework (also called computer algebra program) that is used to obtain, in symbolic mathematical form, the linear and nonlinear equations of motion of a mid-fidelity multibody system including rigid and flexible bodies. Our approach is based on Kane's method and a nonlinear shape function representation for flexible bodies. The shape function approach does not represent the state of the art for flexible multibody dynamics but is an effective trade-off to obtain mid-fidelity models with few degrees of freedom, taking advantage of the separation of space and time. The method yields compact symbolic equations of motion with implicit account of the constraints. The general and automatic framework facilitates the creation and manipulation of models with various levels of complexity by adding or removing degrees of freedom. The symbolic treatment allows for analytical gradients and linearized equations of motion. The linear and nonlinear equations can be exported to Python code or dedicated software. There are multiple applications, such as time domain simulation, stability analyses, frequency domain analyses, advanced controller design, state observers, and digital twins. In this article, we describe the method we used to systematically generate the equations of motion of multibody systems and present the implementation of the framework using the Python package SymPy. We apply the framework to generate illustrative land-based and offshore wind turbine models. We compare our results with OpenFAST simulations and discuss the advantages and limitations of the method. The Python implementation is provided as an open-source project.

Branlard, Emmanuel (ORCID:0000000277506128)↗

DOE OSTI2021

Direct numerical simulation of supercritical oxy-methane mixing layers with CO 2 substituted counterparts

Direct numerical simulations (DNS) of temporally developing, three dimensional, CH 4 /CO 2 , CH 4 /O 2 and CO 2 /O 2 mixing layers, are conducted at a supercritical pressure of 300 atm. To effectively model the supercritical regime, the employed formulation includes the compressible form of the governing equations, the cubic Peng-Robinson equation of state and a generalized formulation for heat and mass flux vectors derived from non-equilibrium thermodynamics and fluctuation theory. A linear inviscid stability analysis is also performed for each case, to determine its most unstable wavelength. Flow visualizations reveal the presence of high density gradient magnitude regions for all three mixing layers, with conditional averages indicating increased presence of heavier fluid species within these regions. No significant departures are observed from perfect gas behavior, with compressibility factors very close to unity for all three mixing cases. Applicability of presumed probability density function methods (PDF) is examined for the three supercritical mixing layers. An a priori analysis is also conducted to investigate various simplifying assumptions employed in modeling various subgrid scale (SGS) flux models. Two additional terms are identified in the large eddy simulations (LES) equations, the gradient of SGS contribution of pressure in the momentum equation and the gradient of SGS contribution of heat flux in energy equation, whose magnitudes are similar and comparable with their respective resolved terms. The performance of the scale similarity model to represent these additional terms is investigated. Lastly, the performance of Smagorinsky, gradient and scale similarity models are also investigated.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2020

Elevation distributed micro-climatology data in a coastal glaciated watershed

Air temperature, ground temperature and relative humidity data were collected in a longitudinal transect of the Nooksack watershed at varying elevations from 500 to 1800 m above sea level. Data were collected by anchoring sensors from trees above winter snow levels and shaded from direct solar radiation. Paired sensors were also buried 3 cm under ground near each air temperature sensor to determine snow absence or presence. Select sites included relative humidity sensors to indicate whether precipitation was occurring. Data were collected every 3-4 h from December 2015 to Sept 2018 (with ongoing collection). Code for analysis of daily mean, minimum, maximum, and temperature change with elevation (lapse rates) are available on Github (https://doi.org/10.5281/zenodo.3239539). The sensor download and intermediate data products are available on HydroShare at (http://www.hydroshare.org/resource/222e832d3df24dea9bae9bbeb6f4219d) with publicly accessible visualization available from the Nooksack Observatory at data.cuahsi.org. Hydrologic models are generally structured with a single annual average lapse rate parameter which assumes a linear temperature gradient with elevation. The daily data (2016-2018) is used as part of ongoing studies on the non-linear dynamics and temporal variability of temperature with elevation to improve assessments of watershed function and salmon habitat.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2021

Electric and magnetic black holes in a new nonlinear electrodynamics model

Highlights: • We introduce a new NED model which is comparable with the BI model in the weak-field limit. • We find an electric black hole solution in the context of Einstein’s gravity minimally coupled with the new NED model. • We study the thermal stability of the electric black hole solution. • Modified Smarr’s formula consistent with the first law of black hole thermodynamics is obtained. A new nonlinear electrodynamics (NED) model is introduced in the form of a nonpolynomial Lagrangian which admits static spherical and also plane wave solutions in a flat space. Upon coupling with gravity the electric field is finite and comparable with the Born–Infeld counterpart. The electric and magnetic black hole solutions in the Einstein’s gravity coupled with this NED model are presented. The solutions give both asymptotically and in the weak field limit Reissner–Nordström (RN) black hole and unlike the other known models our electric solution is expressed in terms of elementary functions in a closed form. We study the first law and derive the modified Smarr’s formula for the electric type extension of our model. Considerable rich structure, especially thermodynamic ones, ranging from first to the second order phase transitions are added to the RN black hole of linear electrodynamics with this NED model. Having the exact solution for the metric function at our disposal we investigate the stability of the electric black hole from both the thermodynamical and causal points of view.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2022

Changes in polarization dictate necessary approximations for modeling electronic deexcitation intensity: Application to x-ray emission

Accurate simulation of electronic excitations and deexcitations are critical for complementing complex spectroscopic experiments and can provide validation to theoretical approaches. Here, using a generalized framework, we contrast the accuracy and validity of orbital-constrained and linear-response approaches that build upon Kohn-Sham density functional theory (DFT) to simulate emission spectra of electronic origin and propose an efficient approximation, named many-body x-ray emission spectroscopy or MBXES, for simulating such processes. We show analytically as well as with computed examples that for electronic (de)excitation leading to an appreciable change in polarization (i.e., density rearrangement), the adiabatic approximation in a response-based formalism will be inadequate for the calculation of oscillator strength. Thus, such a change (e.g., in the net electrostatic dipole moment of a finite system) can be used as a metric for evaluating the applicability of the adiabatic response-based approach and can be particularly valuable in x-ray emission spectroscopy. On the other hand, MBXES, the flexible method introduced in this paper, can compute oscillator strengths accurately at a much lower computational expense on the basis of two DFT-based self-consistent field calculations. Using illustrative examples of emission spectra, the efficacy of the MBXES method is demonstrated by comparison with its parent theory, orbital-optimized DFT, and with experiments.

74 ATOMIC AND MOLECULAR PHYSICS↗

DOE OSTI2026

Neural Scaling Laws of Deep ReLU and Deep Operator Network: A Theoretical Study

Neural scaling laws play a pivotal role in the performance of deep neural networks and have been observed in a wide range of tasks. However, a complete theoretical framework for understanding these scaling laws remains underdeveloped. In this paper, we explore the neural scaling laws for deep operator networks, which involve learning mappings between function spaces, with a focus on the Chen and Chen style architecture. These approaches, which include the popular Deep Operator Network (DeepONet), approximate the output functions using a linear combination of learnable basis functions and coefficients that depend on the input functions. We establish a theoretical framework to quantify the neural scaling laws by analyzing its approximation and generalization errors. We articulate the relationship between the approximation and generalization errors of deep operator networks and key factors such as network model size and training data size. Moreover, we address cases where input functions exhibit low-dimensional structures, allowing us to derive tighter error bounds. These results also hold for deep ReLU networks and other similar structures. Our results offer a partial explanation of the neural scaling laws in operator learning and provide a theoretical foundation for their applications.

97 MATHEMATICS AND COMPUTING↗