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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

Hamiltonian formulations for perturbed dissipationless plasma equations

The Hamiltonian formulations for the perturbed Vlasov–Maxwell equations and the perturbed ideal magnetohydrodynamics (MHD) equations are expressed in terms of the perturbation derivative ∂ F / ∂ ϵ ≡ [ F , S ] of an arbitrary functional F [ ψ ] of the Vlasov–Maxwell fields ψ = ( f , E , B ) or the ideal MHD fields ψ = ( ρ , u , s , B ) , which are assumed to depend continuously on the (dimensionless) perturbation parameter ϵ . In this study, [ , ] denotes the functional Poisson bracket for each set of plasma equations and the perturbation action functional S is said to generate dynamically accessible perturbations of the plasma fields. The new Hamiltonian perturbation formulation introduces a framework for functional perturbation methods in plasma physics and highlights the crucial roles played by polarization and magnetization in Vlasov–Maxwell and ideal MHD perturbation theories. One application considered in this paper is a formulation of plasma stability that guarantees dynamical accessibility and leads to a natural generalization to higher-order perturbation theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

NASA NTRS1989

A hybrid-perturbation-Galerkin technique which combines multiple expansions

A two-step hybrid perturbation-Galerkin method for the solution of a variety of differential equations type problems is found to give better results when multiple perturbation expansions are employed. The method assumes that there is parameter in the problem formulation and that a perturbation method can be sued to construct one or more expansions in this perturbation coefficient functions multiplied by computed amplitudes. In step one, regular and/or singular perturbation methods are used to determine the perturbation coefficient functions. The results of step one are in the form of one or more expansions each expressed as a sum of perturbation coefficient functions multiplied by a priori known gauge functions. In step two the classical Bubnov-Galerkin method uses the perturbation coefficient functions computed in step one to determine a set of amplitudes which replace and improve upon the gauge functions. The hybrid method has the potential of overcoming some of the drawbacks of the perturbation and Galerkin methods as applied separately, while combining some of their better features. The proposed method is applied, with two perturbation expansions in each case, to a variety of model ordinary differential equations problems including: a family of linear two-boundary-value problems, a nonlinear two-point boundary-value problem, a quantum mechanical eigenvalue problem and a nonlinear free oscillation problem. The results obtained from the hybrid methods are compared with approximate solutions obtained by other methods, and the applicability of the hybrid method to broader problem areas is discussed.

Geer, James F.↗

NASA NTRS1990

A hybrid perturbation-Galerkin technique that combines multiple expansions

A two-step hybrid perturbation-Galerkin method for the solution of a variety of differential equations type problems is found to give better results when multiple perturbation expansions are employed. The method assumes that there is parameter in the problem formulation and that a perturbation method can be used to construct one or more expansions in this perturbation coefficient functions multiplied by computed amplitudes. In step one, regular and/or singular perturbation methods are used to determine the perturbation coefficient functions. The results of step one are in the form of one or more expansions each expressed as a sum of perturbation coefficient functions multiplied by a priori known gauge functions. In step two the classical Bubnov-Galerkin method uses the perturbation coefficient functions computed in step one to determine a set of amplitudes which replace and improve upon the gauge functions. The hybrid method has the potential of overcoming some of the drawbacks of the perturbation and Galerkin methods as applied separately, while combining some of their better features. The proposed method is applied, with two perturbation expansions in each case, to a variety of model ordinary differential equations problems including: a family of linear two-boundary-value problems, a nonlinear two-point boundary-value problem, a quantum mechanical eigenvalue problem and a nonlinear free oscillation problem. The results obtained from the hybrid methods are compared with approximate solutions obtained by other methods, and the applicability of the hybrid method to broader problem areas is discussed.

Geer, James F.↗

DOE OSTI2024

A simulation study of the ability to detect power distribution perturbations in the texas A&M TRIGA reactor with self-powered neutron detectors

Given the variety of ways that nuclear reactor core power may be perturbed, reactor operators and developers are keen on understanding the accuracy and convergence time during which perturbations in reactor power distribution may be synthesized (i.e., inferred) from an array of in-core radiation detectors. A simulation study was conducted as described herein using a highly detailed model of the Texas A&M Training, Research, Isotopes, General Atomics Reactor, in which an array of self-powered neutron detectors (SPNDs) was considered for input to the power synthesis methodology. The core power synthesis is conducted using a point-based iterative method with an iterative loop built in to ensure working equation consistency. The forward problem of SPND response to simulated perturbations in reactor power was solved for Gaussian peak-type perturbations in the reactor power distribution. These perturbations varied in variance, amplitude, and core location to assess their impact on synthesis error and to determine the number of iterations required for convergence. A relation between the unique resolvability limit and perturbation width was identified such that the maximum synthesis error increased rapidly when the peak width went beneath this limit (a width approximating half the reactor’s fuel pin-to-pin pitch); this resolvability limit is specific to the SPND configuration and fuel segmentation considered herein. The synthesis error increased linearly with perturbation peak amplitude, whereas the convergence time increased nonlinearly. Perturbations located closer to the center of the core were synthesized more accurately, albeit with a higher number of required iterations. These findings provide a qualitative and quantitative understanding of the accuracy and speed at which different types of spatial power perturbations can be resolved in light-water reactors.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2023

Diffusion–convection model of runaway electrons due to large magnetohydrodynamic perturbations in post-thermal quench plasmas

Systematic test particle tracing simulations for runaway electrons (REs) are performed for six post-thermal quench equilibria from DIII-D and ITER, where large scale, kink-like n = 1 (n is the toroidal mode number) magnetohydrodynamic (MHD) instabilities are found. The modeled particle guiding center orbits allow extraction of the effective diffusion–convection coefficients of REs in the presence of large three-dimensional (3D) perturbations up to 10% of the equilibrium toroidal field. With a fixed spatial distribution of the field perturbation, the RE transport coefficients along the plasma radial coordinate track reasonably well with the surface-averaged perturbation level. A substantial variation in the value of the transport coefficients—by three orders of magnitude in most cases, however, occurs with varying launching location of REs along the plasma radius. Large 3D perturbations almost always lead to comparable diffusion and convection processes, meaning that diffusion alone is insufficient to describe the particle motion. At lower (but still high) level of perturbation, the RE convection is found to be dominant over diffusion. A similar observation is made when the perturbation is too strong. In the presence of large perturbation, the dependence of the RE transport on the particle energy is sensitive to the spatial distribution of the perturbation. Based on numerically obtained RE transport coefficients, an analytic fitting model is proposed to quantify the particle diffusion and convection processes due to large MHD events in post-thermal quench plasmas. The model is shown to reasonably well reproduce the direct test particle tracing results for the RE loss fraction and can, thus, be useful for incorporating into other kinetic RE codes in order to simulate the RE beam evolution in the presence of large 3D perturbations.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS1996

Waveform Perturbations os Spherical Transiet Waves Propagating in a Random Medium

Of those aspects of sonic-boom propagation that are not yet fully understood, one of the more important is that which relates to the perturbations of the waveform. This phenomenon, which arises also in connection with the propagation of other types of transient waves in real media, generally take the form, in the case of sonic-boom N-waves, of a random high-frequency structure (sometimes called fine structure) that is most prominent in the regions immediately behind each of the shocks. The perturbations in those regions can be large, occasionally attaining magnitudes comparable to that of th incident wave itself. Such magnitudes, in combination with the high-frequency character of the perturbations, can lead to a considerable increase in the perceived noisiness of the sonic boom. Waveform perturbations are consequently an important factor as regards the question of sonic-boom acceptability. On the basis of observations, and some early theoretical studies, it is now generally accepted that perturbations of sonic-boom waveforms are a manifestation of the effect on the propagating wave of relatively small-scale variations in the acoustic properties of the atmosphere- variations that are usually associated with turbulence. Although the mechanism underlying perturbations of sonic-boom waveforms seems thus to be well understood, no fully-satisfactory theory of such perturbations has emerged. Indeed, even for the relatively simple case of an incident step-function pulse, no theory of waveform perturbations, formulated in a realistic three-dimensional context, has been advanced that is valid in the region of strongest perturbations; viz., the region immediately behind, and including, the wave front. The work reported herein represents an attempt to develop such a theory.

Wenzel, Alan R.↗

DOE OSTI2024

Flowing plasma rearrangement in the presence of static perturbing fields

Charged particles interacting with electromagnetic waves have a portion of their energy tied up in wave-driven oscillations. When these waves are localized to the exhaust of linear magnetic confinement systems, this ponderomotive effect can be utilized to enhance particle confinement. The same effect can be derived for particles moving via an E×B drift into a region of a static perturbation to the electromagnetic fields which has a large wave vector component in the direction of the motion. In this work, we use a simplified slab model to self-consistently solve for the electromagnetic fields within the fluid flowing plasma of a static flute-like (k∥=0) perturbation and evaluate the resulting ponderomotive potential. We find that two types of perturbations can exist within the flowing plasma, which are an O wave and an X wave in the frame moving with the fluid. In the case of tenuous plasma, these perturbations are magnetostatic or electrostatic multipole-analog perpendicular to the guiding magnetic field in the lab frame, respectfully. For denser plasmas, the O wave-like perturbation is screened at the electron skin depth scale, and the X wave-like perturbation is a combination of a similar perpendicular electric perturbation and parallel magnetic perturbation. The ponderomotive potential generated in the X wave-like case is gyrofrequency-dependent and can be used as either potential barriers or potential wells, depending on the direction of the flow velocity.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2023

Quantifying the robustness of deep multispectral segmentation models against natural perturbations and data poisoning

In overhead image segmentation tasks, including additional spectral bands beyond the traditional RGB channels can improve model performance. However, it is still unclear how incorporating this additional data impacts model robustness to adversarial attacks and natural perturbations. For adversarial robustness, the additional in-formation could improve the model’s ability to distinguish malicious inputs, or simply provide new attack avenues and vulnerabilities. For natural perturbations, the additional information could better inform model decisions and weaken perturbation effects or have no significant influence at all. In this work, we seek to characterize the performance and robustness of a multispectral (RGB and near infrared) image segmentation model subjected to adversarial attacks and natural perturbations. While existing adversarial and natural robustness research has focused primarily on digital perturbations, we prioritize on creating realistic perturbations designed with physical world conditions in mind. For adversarial robustness, we focus on data poisoning attacks whereas for natural robustness, we focus on extending ImageNet-C common corruptions for fog and snow that coherently and self-consistently perturbs the input data. Overall, we find both RGB and multispectral models are vulnerable to data poisoning attacks regardless of input or fusion architectures and that while physically-realizable natural perturbations still degrade model performance, the impact differs based on fusion architecture and input data.

Deep learning, multispectral images, multimodal fu↗

NASA NTRS1980

Evaluation of a strained-coordinate perturbation procedure - Nonlinear subsonic and transonic flows

An evaluation is made of a perturbation method devised to obtain highly accurate approximations to families of strongly nonlinear solutions which are either continuous or discontinuous, and which represent variations in some arbitrary parameter. The method first defines a unit perturbation by using two nonlinear solutions which differ from one another by a nominal change in some geometric or flow parameter, then employs this unit perturbation to predict a family of related nonlinear solutions over a range of parameter variation. Coordinate straining is incorporated into this perturbation method for determining the unit perturbation to account for the movement of discontinuities and maxima of high-gradient regions due to the perturbation. Attention is given to transonic and subsonic flows. Comparisons of the perturbation results with the corresponding 'exact' nonlinear solutions show a remarkable accuracy and range of validity of the perturbation method across the spectrum of examples considered.

Stahara, S. S.↗

NASA NTRSDate not supplied

Perturbation Modeling and Navigation Tuning for a Crewed Station in Near Rectilinear Halo Orbit

NASA's Gateway program will build a crew-tended station in an Earth-Moon Near Rectilinear Halo Orbit (NRHO) to support deep space missions to the lunar surface and heliocentric space. The station in the NRHO will be visited by crewed vehicles including lunar landers that are high mass relative to Gateway. Docking events with large vehicles induce significant thruster plume and docking contact velocity perturbations. Crewed vehicles induce significant venting perturbations that can stress the navigation filter's ability to remain converged about an estimated state. The torques that arise from venting and lunar gravity gradient require reaction control system (RCS) thruster intervention, which themselves induce a velocity perturbation. The best method to model RCS thruster perturbations is currently in development. This paper simulates different RCS perturbation models, schedules, and an increasing magnitude to investigate the navigation sensitivity to different RCS perturbation models. From the RCS perturbation models simulated, a worst-case scenario is chosen for further scrutiny. The navigation filter is further tuned to handle the most disruptive perturbation modeling and the resulting performance is analyzed.

Navigation↗

DOE OSTI2022

Process-oriented stochastic perturbations applied to the parametrization of turbulence and shallow convection for ensemble prediction

Weather forecasting nowadays often requires some estimation of uncertainties associated with the output of meteorological models, in order to better inform decision making, especially in the context of intense weather events. Ensemble prediction systems provide such information through sets of possible scenarios which are designed to represent various uncertainty sources, including model uncertainties. A wide variety of methods have been proposed to estimate model uncertainties, among which perturbation methods targeting uncertain processes are a promising research field. Here, we focus on the representation of small-scale variability by process-oriented perturbation schemes applied to two key physical processes, namely turbulence and shallow convection. The perturbations are applied to a single-column version of the convection-permitting AROME model, in three idealized boundary-layer cases. Large-eddy simulations (LESs) of the same cases serve as a reference for the subgrid variability that has to be represented, and the results are also compared to those given by the Stochastically Perturbed Parametrization Tendencies (SPPT) method, which is a method commonly used by weather forecast centres to represent model uncertainty. The spread produced by our process-oriented perturbations of turbulence and shallow convection does not represent all the small-scale variability implied by the LESs for temperature and humidity. However, it is of a similar order of magnitude for the wind, thanks to perturbations generated by the stochastic turbulence scheme. The dispersion is structurally different from what is obtained with SPPT. It is non-negligible in the lower levels, where SPPT perturbations are usually suppressed because of numerical instabilities, indicating a possible complementarity between the schemes.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2025

Breakdown of superdiffusion in perturbed quantum integrable spin chains and ladders

Superdiffusive transport with dynamical exponent z=3/2 has been firmly established at finite temperature for a class of integrable systems with a non-Abelian global symmetry G. On the inclusion of integrability-breaking perturbations, diffusive transport with z=2 is generically expected to hold in the limit of late time. Recent studies of the classical Haldane-Ishimori-Skylanin model have found that perturbations that preserve the global symmetry lead to a much slower time scale for the onset of diffusion, albeit with uncertainty over the exact scaling exponent. That is, for perturbations of strength λ, the characteristic timescale for diffusion goes as t*∼λ−α for some α. Using large-scale matrix product state simulations, we investigate this behavior for perturbations to the canonical quantum model showing superdiffusion: the S=1/2 quantum Heisenberg chain. We consider a ladder configuration and look at various perturbations that either break or preserve the SU(2) symmetry, leading to scaling exponents consistent with those observed in one classical study [McCarthy , Phys. Rev. B 110, L180301 (2024)2469-995010.1103/PhysRevB.110.L180301]: α=2 for symmetry-breaking terms and α=6 for symmetry-preserving terms. We also consider perturbations from another integrable point of the ladder model with G=SU(4) and find consistent results. Finally, we consider a generalization to an SU(3) ladder and find that the α=6 scaling appears to be universal across superdiffusive systems when the perturbations preserve the non-Abelian symmetry G.

Wang, Kevin↗

DOE OSTI2020

Perturbation-Based Diagnosis of False Data Injection Attack Using Distributed Energy Resources

Modern smart grid relies on various sensor measurements for its operational control. In a successful false data injection attack, the attacker manipulates the measurements from the grid sensors such that undetected errors are introduced into the estimates of the system parameters leading to catastrophic situations. This paper proposes a novel perturbation based false data injection attack detection mechanism that utilizes inverter based distributed energy resources (DERs) to create low magnitude perturbation signal in the distribution system voltage that is inconsequential to the normal grid operation. Two voltage sensitivity analysis based algorithms are designed to identify the optimal set of DERs that can create the voltage perturbation signal of desired magnitude. An analytical method of voltage sensitivity analysis is used to compute the magnitude of voltage perturbation signal at each node in a computationally efficient manner. Then, a detection mechanism is developed that checks for the presence of the perturbation sequence in each sensor measurement. A sensor measurement is deemed authentic if the voltage perturbation signal is present in the data. In case of sensor malfunction or cyber-attack, the perturbation signal will not be present in the measurement data. Performance of the proposed attack detection mechanism is validated via simulation of the IEEE 69 bus test system.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2021

Attribute-Guided Adversarial Training for Robustness to Natural Perturbations

We report while existing work in robust deep learning has focused on small pixel-level norm-based perturbations, this may not account for perturbations encountered in several real world settings. In many such cases although test data might not be available, broad specifications about the types of perturbations (such as an unknown degree of rotation) may be known. We consider a setup where robustness is expected over an unseen test domain that is not i.i.d. but deviates from the training domain. While this deviation may not be exactly known, its broad characterization is specified a priori, in terms of attributes. We propose an adversarial training approach which learns to generate new samples so as to maximize exposure of the classifier to the attributes-space, without having access to the data from the test domain. Our adversarial training solves a min-max optimization problem, with the inner maximization generating adversarial perturbations, and the outer minimization finding model parameters by optimizing the loss on adversarial perturbations generated from the inner maximization. We demonstrate the applicability of our approach on three types of naturally occurring perturbations --- object-related shifts, geometric transformations, and common image corruptions. Our approach enables deep neural networks to be robust against a wide range of naturally occurring perturbations. We demonstrate the usefulness of the proposed approach by showing the robustness gains of deep neural networks trained using our adversarial training on MNIST, CIFAR-10, and a new variant of the CLEVR dataset.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Implementation of Perturbation Theory and Sensitivity Capabilities in Griffin

Griffin is a Multiphysics Object-Oriented Simulation Environment (MOOSE) based reactor Multiphysics analysis application, jointly developed by Argonne and Idaho National Laboratories under the DOE-NE NEAMS program. This fiscal year, capabilities for reactivity and sensitivity evaluation using perturbation methods were implemented and verified. The First Order Perturbation Method (FOPT) was employed to compute reactivity worth resulting from small perturbations in input parameters, while the Generalized Perturbation Theory (GPT) was used to evaluate sensitivities of a range of response types, including reaction rate ratio, k-eigenvalue, neutron generation time, and effective delayed neutron fraction. These perturbation methods enable users to quantify how response quantities change due to a perturbation in a input parameter without explicitly performing an additional transport simulation for each perturbed state. In particular, the GPT formulation accounts for indirect effects arising from flux changes by solving generalized inhomogeneous equations, for which a Neumann series-based iterative solution method was developed and implemented in Griffin. The implemented reactivity and sensitivity evaluation capabilities were verified using two test problems: an infinite homogeneous system and a two-dimensional hexagonal core. The results showed excellent agreement with reference solutions obtained by a direct method based on finite difference approximation as well as GPT-based results from the PERSENT code, confirming the accuracy of both reactivity and sensitivity evaluations. Additionally, preliminary uncertainty quantification (UQ) results were obtained by combining the sensitivity values computed using GPT and external covariance data, demonstrating that the implemented sensitivity results can be reliably used for uncertainty calculations. To further demonstrate the generality and practical strength of the implementation, the sensitivity evaluation capability was successfully applied to the Empire microreactor with a geometrically complex design that poses significant modeling challenges. The results confirm that Griffin enables sensitivity evaluations even for irregular and highly heterogeneous reactor configurations, thereby establishing a foundation for UQ applications in advanced reactor designs and analyses.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

Axion Perturbations: A General Analytical Treatment

Cosmological data provides us two key constraints on dark matter (DM): it must have a particular abundance, and it must have an adiabatic spectrum of density perturbations in the early universe. Many different cosmological scenarios have been proposed that establish the abundance of axion DM in qualitatively different ways. In this paper we emphasize that, despite this variety of backgrounds, the perturbations in axion DM can be understood from universal principles. How does a feebly interacting axion field acquire perturbations proportional to those of photons? How do the isocurvature power spectrum and non-Gaussianity depend on the background evolution of the universe? We answer these questions for a completely general choice of cosmological background and temperature-dependent axion potential. We show that the most general solution to the axion field equation on super-horizon scales is entirely determined by the family of background solutions for different initial field values . This holds for both the component in the field perturbation solution contributing to the DM isocurvature perturbation (enhanced at late times by the sensitivity of the DM abundance to the initial condition, , which can be large for initial conditions near the hilltop), and the other component that contributes to the DM curvature perturbation. In particular, we explain that an unperturbed axion field in the early universe evolving into one with nontrivial adiabatic perturbations is guaranteed by Weinberg's theorem on adiabatic modes. These results have been derived before with various assumptions, such as a radiation dominated background or a quadratic potential. Our aim is to give a clear, simple derivation that is manifestly independent of those assumptions, and thus can be applied to any cosmological axion scenario.

Cosmology and Nongalactic Astrophysics (astro-ph.C↗

NASA NTRS1976

The global reference atmospheric model, mod 2 (with two scale perturbation model)

The Global Reference Atmospheric Model was improved to produce more realistic simulations of vertical profiles of atmospheric parameters. A revised two scale random perturbation model using perturbation magnitudes which are adjusted to conform to constraints imposed by the perfect gas law and the hydrostatic condition is described. The two scale perturbation model produces appropriately correlated (horizontally and vertically) small scale and large scale perturbations. These stochastically simulated perturbations are representative of the magnitudes and wavelengths of perturbations produced by tides and planetary scale waves (large scale) and turbulence and gravity waves (small scale). Other new features of the model are: (1) a second order geostrophic wind relation for use at low latitudes which does not "blow up" at low latitudes as the ordinary geostrophic relation does; and (2) revised quasi-biennial amplitudes and phases and revised stationary perturbations, based on data through 1972.

Justus, C. G.↗