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At least 19 records

Interpretable Models for Workflow Differentiation in High-Performance Scientific Networks

Scientific workflows in high-performance networks spawn hundreds of interdependent flows that must be managed collectively—yet existing network classifiers treat each flow in isolation, leading to fragmented QoS decisions and missed interflow patterns. We present a novel traffic classification solution that operates at the workflow level, distinguishing entire filetransfer operations from streaming analytics by capturing how concurrent flows interact and burst together. We introduce a workflow identification window (WIW) that ingests raw packet headers from parallel flows into unified tensors, preserving the spatial-temporal patterns that differentiate scientific workflows. This approach achieves 98.7% accuracy using CNN, LSTM, and hybrid architectures, while maintaining 84% accuracy on production traffic collected a week later—demonstrating robustness to temporal drift. By integrating SHAP and GradCAM explainability, we reveal that early-packet timing patterns and cross-flow correlations drive classification decisions, providing operators with interpretable insights. Our system enables coherent workflow-level QoS enforcement and dynamic bandwidth allocation in scientific networks, eliminating manual per-flow configuration while maintaining classification latency at millisecond level.

Giannakou, Anna [LBL, Berkeley]

Data for A Role for Differential Rubisco Activase Isoform Expression in C4 Bioenergy Grasses at High Temperature

Rubisco activase (Rca) facilitates the release of sugar-phosphate inhibitors at Rubisco catalytic sites during CO2 fixation. Most plant species express two Rca isoforms, the larger Rca-α and the shorter Rca-β, either by alternative splicing from a single gene or expression from separate genes. The mechanism of Rubisco activation by Rca isoforms has been intensively studied in C3 plants. However, the functional role of Rca in C4 plants where Rubisco and Rca are located in a much higher [CO2] compartment is less clear. In this study, we selected four C4 bioenergy grasses and the model C4 grass setaria ( Setaria viridis ) to investigate the role of Rca in C4 photosynthesis. All five C4 grass species contained two Rca genes, one encoding Rca-α and the other Rca-β, which were positioned closely together in the genomes. A variety of abiotic stress-related motifs were identified in the Rca-α promoter of each grass, and while the Rca-β gene was constantly highly expressed at ambient temperature, Rca-α isoforms were expressed only at high temperature but never surpassed 30% of Rca-β content. The pattern of Rca-α induction on transition to high temperature and reduction on return to ambient temperature was the same in all five C4 grasses. In sorghum ( Sorghum bicolor ), sugarcane ( Saccharum officinarum ), and setaria, the induction rate of Rca-α was similar to the recovery rate of photosynthesis and Rubisco activation at high temperature. This association between Rca-α isoform expression and maintenance of Rubisco activation at high temperature suggests that Rca-α has a functional thermo-protective role in carbon fixation in C4 grasses by sustaining Rubisco activation at high temperature.

Genomics

APOLLO: a facility-scale differentiable virtual accelerator at Fermilab FAST/IOTA

As the design complexity of modern accelerators grows, there is more interest in using advanced simulations that have fast execution time or yield additional insights like gradients. The FAST/IOTA facility has been working on implementing and experimentally validating an end-to-end digital twin that is both fast and gradient-aware, allowing for rapid prototyping of new software and experiments with minimal beam time costs. Our framework integrates physics and ML codes for linac and ring simulation through a set of generic interfaces between surrogate and physics-based sections. To reproduce device inputs and outputs, system state is exposed as a deterministic event loop in a specialized discrete event simulator architecture. Because Fermilab is undergoing control system transition, several APIs were implemented as final user interfaces - a fully asynchronous EPICS soft IOC, a gRPC-based Data Pool Manager (DPM), and legacy ACNET protocols. We discuss implementation details as well as challenges handling live data assimilation and future plans to extend modelling to main complex proton accelerators like PIPII and Booster.

Kuklev, Nikita [Fermilab]

Identifying Differential Equations in Fourier Domain (FourierIdent)

We investigate identifying differential equations in the frequency domain. Fourier analysis is an important tool in theoretical analysis and numerical solvers of differential equations, yet there is limited work in exploring this connection in the identification of differential equations. This paper aims to identify the underlying differential equation in the frequency domain, from a given single realization of the differential equation perturbed by noise. Such setting imposes difficulties which are different from other identification methods where computation is carried out in the physical domain. We propose several ways to mitigate the challenges arising from noise in data and large differences in the magnitudes of frequency responses. The main takeaways are that identifying differential equations solely in the frequency domain is challenging, the method we propose is based on a form of domain partitions in the frequency domain, and this method shows benefits for complex data even with high level of noise. We introduce a Fourier feature denoising, and define the meaningful data region and the core regions of features to reduce the effect of noise in the frequency domain and to enhance the accuracy in coefficient identification. The proposed method is tested on various differential equations with linear, nonlinear, and high-order derivative feature terms, and shows advantages on complex data with many frequency modes, even under high level of noise.

97 MATHEMATICS AND COMPUTING

Differential equations for cosmological correlators

Cosmological fluctuations retain a memory of the physics that generated them in their spatial correlations. The strength of correlations varies smoothly as a function of external kinematics, which is encoded in differential equations satisfied by cosmological correlation functions. In this work, we provide a broader perspective on the origin and structure of these differential equations. As a concrete example, we study conformally coupled scalar fields in a power-law cosmology. The wavefunction coefficients in this model have integral representations, with the integrands being the product of the corresponding flat-space results and “twist factors” that depend on the cosmological evolution. Similar twisted integrals arise for loop amplitudes in dimensional regularization, and their recent study has led to the discovery of rich mathematical structures and powerful new tools for computing multi-loop Feynman integrals in quantum field theory. The integrals of interest in cosmology are also part of a finite-dimensional basis of master integrals, which satisfy a system of first-order differential equations. We develop a formalism to derive these differential equations for arbitrary tree graphs. The results can be represented in graphical form by associating the singularities of the differential equations with a set of graph tubings. Upon differentiation, these tubings grow in a local and predictive fashion. In fact, a few remarkably simple rules allow us to predict — by hand — the equations for all tree graphs. While the rules of this “kinematic flow” are defined purely in terms of data on the boundary of the spacetime, they reflect the physics of bulk time evolution. We also study the analogous structures in tr ϕ 3 theory, and see some glimpses of hidden structure in the sum over planar graphs. This suggests that there is an autonomous combinatorial or geometric construction from which cosmological correlations, and the associated spacetime, emerge.

Cosmological models

Study of fully coupled three-dimensional envelope instability using automatic differentiation

Automatic differentiation is a powerful tool for computing derivatives of simulation results with respect to given parameters. In this Letter, we have applied this tool to investigate the instability of a dynamical system governed by 21 ordinary differential equations. This second-order instability (named envelope instability) is driven by space-charge effects and has a significant impact on the operational regimes of particle accelerators. Our study delves into the three-dimensional envelope instability, incorporating both transverse and longitudinal coupling. Conventionally, analyzing this complex system would necessitate solving 441 ordinary differential equations, which is computationally intractable. However, by employing automatic differentiation, we were able to track only 21 equations. This approach allowed us to uncover an additional instability stopband, which arises from space-charge-induced coupling and has not been reported in previous studies. This research highlights the significant advantages of automatic differentiation in analyzing complicated dynamical systems involving a large number of ordinary differential equations.

Qiang, Ji [Lawrence Berkeley National Laboratory (

The Memory Scaling of Reverse-Mode Differentiation in Particle Accelerator Simulations with Space Charge

The recent development of differentiable simulation codes for particle accelerators has enabled gradient-based workflows that promise finer control and more realistic modeling of accelerator facilities. However, when using reverse-mode automatic differentiation, the memory usage continuously increases during the simulation, and can potentially exceed the available hardware memory - especially when costly space charge computation is included. To study the memory requirements for differentiable simulations, we have implemented space charge in Cheetah, a PyTorch-based beam tracking code that supports reverse-mode differentiation. We find that the memory usage for reverse-mode differentiation grows linearly with the number of macroparticles and cells, and that it is proportional to the number of space charge kicks involved in the simulation. This general scaling can be used to evaluate whether a given differentiable simulation is feasible given hardware memory constraints.

Dhamrait, Arjun

Chapter 4 - Recent Advances in Identification of Differential Equations from Noisy Data: IDENT Review

Differential equations and numerical methods are extensively used to model various real-world phenomena in science and engineering. With modern developments, we aim to find the underlying differential equation from a single observation of time-dependent data. If we assume that the differential equation is a linear combination of various linear and nonlinear differential terms, then the identification problem can be formulated as solving a linear system. The goal then reduces to finding the optimal coefficient vector that best represents the time derivative of the given data. We review some recent works on the identification of differential equations. We find some common themes for the improved accuracy: (i) The formulation of linear system with proper denoising is important, (ii) how to utilize sparsity and model selection to find the correct coefficient support needs careful attention, and (iii) there are ways to improve the coefficient recovery. We present an overview and analysis of recent developments on the topic.

97 MATHEMATICS AND COMPUTING

Differentiable hybrid neural network approach for enhancing reactor dynamics simulations

Reactor dynamics simulations provide essential insights into the time-dependent behavior of nuclear reactors under various operating conditions. However, high-fidelity simulations can be computationally intensive, requiring significant computational resources. Here, to address this challenge, this study employs a differentiable hybrid model that utilizes neural networks as a corrector to enhance the performance of a low-fidelity simulation, aligning its predictions with those of a high-fidelity simulation. Low-fidelity and high-fidelity simulations were obtained by adjusting the mesh size in the System Dynamics Analysis Tool. The differentiable hybrid model was trained in two approaches: time-step-wise and sequence-wise. It was then applied to simulate various transients in a molten salt reactor. Its performance was evaluated by comparing its responses to transients against those of the high-fidelity simulation. An additional approach was performed using a data-driven model to correct the low-fidelity simulation. In comparison, the differentiable hybrid model showed significant improvements in transient prediction, effectively addressing the limitations of the low-fidelity simulations. The results highlighted the robustness of the differentiable hybrid model in both training approaches. It delivered simulations that were at least 3.8 times faster than high-fidelity models. In the time-step-wise approach, it achieved at least a 39% improvement in accuracy. In the sequence-wise approach, it showed at least an 81% accuracy improvement over the full transient. This approach offers a promising path for improving computational efficiency without compromising accuracy in nuclear reactor simulations, making it suitable for real-time digital twin applications.

42 - ENGINEERING

JAX-CanVeg: A Differentiable Land Surface Model

Land surface models consider the exchange of water, energy, and carbon along the soil-canopy-atmosphere continuum, which is challenging to model due to their complex interdependency and associated challenges in representing and parameterizing them. Differentiable modeling provides a new opportunity to capture these complex interactions by seamlessly hybridizing process-based models with deep neural networks (DNNs), benefiting both worlds, that is, the physical interpretation of process-based models and the learning power of DNNs. Here, we developed a differentiable land model, JAX-CanVeg. The new model builds on the legacy CanVeg by incorporating advanced functionalities through JAX in the graphic processing unit support, automatic differentiation, and integration with DNNs. We demonstrated JAX-CanVeg's hybrid modeling capability by applying the model at four flux tower sites with varying aridity. To this end, we developed a hybrid version of the Ball-Berry equation that emulates the water stress impact on stomatal closure to explore the capability of the hybrid model in (a) improving the simulations of latent heat fluxes (LE) and net ecosystem exchange (NEE), (b) improving the optimization trade-off when learning observations of both LE and NEE, and (c) benefiting a multi-layer canopy model setup. Our results show that the proposed hybrid model improved the simulations of LE and NEE at all sites, with an improved optimization trade-off over the process-based model. Additionally, the multi-layer canopy set benefited hybrid modeling at some sites. Anchored in differentiable modeling, our study provides a new avenue for modeling land-atmosphere interactions by leveraging the benefits of both data-driven learning and process-based modeling.

54 ENVIRONMENTAL SCIENCES

Differential Privacy in Grid Kitchen: Implementation & Software Documentation

Sharing of power grid feeder models faces significant challenges due to the potential risk of exposing sensitive operational information. Traditional anonymization techniques have shown notable limitations in other sensitive domains, as evidenced by documented re-identification attacks that combine supposedly anonymized datasets with auxiliary information, raising concerns that similar vulnerabilities could affect power grid data. Consequently, there is a pressing need for a more rigorous privacy protection strategy that not only delivers formal mathematical guarantees but also preserves the analytical value of the shared models. To address this challenge, we have enhanced the Grid Kitchen framework by implementing differential privacy mechanisms within the distribution model dehydration pipeline. This implementation carefully calibrates and applies noise to sensitive attributes in feeder models according to configurable privacy levels—low, moderate, and high—each offering different balances between data utility and privacy protection. Our approach uses established noise functions (Gaussian for continuous data and Discrete Laplace for integer values) with parameters carefully calibrated so that the impact of individual data points is effectively masked in the final output. The integration leverages our Noise Catalog, which we developed to categorize feeder model properties by component type, data type, and sensitivity. This catalog guides the application of appropriate noise functions and privacy parameters ($\varepsilon$ and $\delta$) to each attribute, ensuring consistent privacy protection across the model while maintaining its structural integrity and analytical usefulness. This implementation also includes evaluation tools that allow model owners to assess the impact of privacy-preserving transformations before sharing data with external parties. This report provides documentation for the differential privacy capabilities added to the Grid Kitchen project. It includes a primer on differential privacy concepts and their importance in modern data sharing, details the architecture of our implementation, explains the privacy modes and parameter configurations, and offers practical guidance on using the code for applying differential privacy to grid feeder models. Through examples and code snippets, we demonstrate the effective application of these privacy-enhancing technologies, enabling utility operators and researchers to confidently share grid data while protecting sensitive information.

24 POWER TRANSMISSION AND DISTRIBUTION

Combination and interpretation of differential Higgs boson production cross sections in proton-proton collisions at $ \sqrt{s}=13 $ TeV

Precision measurements of Higgs boson differential production cross sections are a key tool to probe the properties of the Higgs boson and test the standard model. New physics can affect both Higgs boson production and decay, leading to deviations from the distributions that are expected in the standard model. In this paper, combined measurements of differential spectra in a fiducial region matching the experimental selections are performed, based on analyses of four Higgs boson decay channels (γγ, ZZ$^{(*)}$, WW$^{(*)}$, and ττ) using proton-proton collision data recorded with the CMS detector at $ \sqrt{s}=13 $ TeV, corresponding to an integrated luminosity of 138 fb$^{−1}$. The differential measurements are extrapolated to the full phase space and combined to provide the differential spectra. A measurement of the total Higgs boson production cross section is also performed using the γγ and ZZ decay channels, with a result of $ {53.4}_{-2.9}^{+2.9}{\left(\textrm{stat}\right)}_{-1.8}^{+1.9}\left(\textrm{syst}\right) $ pb, consistent with the standard model prediction of 55.6 ± 2.5 pb. The fiducial measurements are used to compute limits on Higgs boson couplings using the κ-framework and the SM effective field theory.[graphic not available: see fulltext]

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS

Use of differential plasma rotation to prevent disruptive tearing mode onset from 3-wave coupling

Abstract Plasma differential rotation is found to be capable of preventing disruptive neoclassical tearing modes (NTMs) seeded by nonlinear three-wave coupling. As tearing modes degrade confinement and can lead to disruptions, stabilization strategies are crucial to the successful operation of future devices. In ITER-relevant scenarios on DIII-D, rotationally coupled m / n = 1/1 and 3/2 modes have been observed to drive 2/1 islands through three-wave coupling. The frequency of the driven 2/1 mode is set by matching conditions and the frequencies of the driving modes. When the driven mode frequency matches the local plasma rotation frequency, e.g. at low differential rotation, the driven 2/1 island can grow into a disruptive NTM. Using neutral beam torque as an actuator to scan the differential rotation, these experiments demonstrate that a sufficiently large frequency mismatch prevents destabilization of disruptive 2/1 NTMs by three-wave coupling. This work indicates that differential rotation can be used as an actuator to prevent NTMs seeded by three-wave coupling.

Richner, N. J. (ORCID:0000000155443915)

Differentiable vertex fitting for jet flavor tagging

This work explores the use of differentiable programming to integrate domain knowledge, in the form of domain specific software, into neural networks to develop scientific machine learning systems. We propose a differentiable vertex fitting algorithm that estimates the crossing point of multiple curves. In the high energy physics setting, these curves are defined by particle equations of motion and the crossing point represents the origin of particle production. This differentiable vertex fitting algorithm can be seamlessly integrated into neural networks, and we show its utility and efficacy in the high energy physics application of the classification of jets, i.e., collimated streams of particles in particle detectors whose originating parent particle we aim to classify. We demonstrate how differentiable vertex fitting can be integrated into larger transformer-based models for jet flavor tagging and show improvements in heavy flavor jet classification when compared to baseline models. Published by the American Physical Society 2024

Smith, Rachel E. C. (ORCID:0000000335851262)

scikit-SUNDAE ((SUN)DIALS Differential Algebraic Equations) [SWR-24-137]

Scikit-SUNDAE provides Python bindings to SUNDIALS integrators. The implicit differential algebraic (IDA) solver and C-based variable-coefficient ordinary differential equations (CVODE) solver are both included. The name SUNDAE combines (SUN)DIALS and DAE, which stands for differential algebraic equations. Solvers specific to DAE problems are not frequently available in Python. An ordinary differential equation (ODE) solver is also included for completeness. ODEs can be categorized as a subset of DAEs (i.e., DAEs with no algebraic constraints). https://pypi.org/project/scikit-sundae

Randall, Corey

Identification of Differential Equations by Dynamics-Guided Weighted Weak Form with Voting

In the identification of differential equations from data, significant progresses have been made with the weak/integral formulation. In this paper, we explore the direction of finding more efficient and robust test functions adaptively given the observed data. While this is a difficult task, we propose weighting a collection of localized test functions for better identification of differential equations from a single trajectory of noisy observations on the differential equation. We find that using high dynamic regions is effective in finding the equation as well as the coefficients, and propose a dynamics indicator per differential term and weight the weak form accordingly. For stable identification against noise, we further introduce a voting strategy to identify the active features from an ensemble of recovered results by selecting the features that frequently occur in different weighting of test functions. Systematic numerical experiments are provided to demonstrate the robustness of our method.

97 MATHEMATICS AND COMPUTING

Cysteine Rich Intestinal Protein 2 is a copper-responsive regulator of skeletal muscle differentiation and metal homeostasis

Copper (Cu) is essential for respiration, neurotransmitter synthesis, oxidative stress response, and transcription regulation, with imbalances leading to neurological, cognitive, and muscular disorders. Here we show the role of a novel Cu-binding protein (Cu-BP) in mammalian transcriptional regulation, specifically on skeletal muscle differentiation using murine primary myoblasts. Utilizing synchrotron X-ray fluorescence-mass spectrometry, we identified murine cysteine-rich intestinal protein 2 (mCrip2) as a key Cu-BP abundant in both nuclear and cytosolic fractions. mCrip2 binds two to four Cu + ions with high affinity and presents limited redox potential. CRISPR/Cas9-mediated deletion of mCrip2 impaired myogenesis, likely due to Cu accumulation in cells. CUT&RUN and transcriptome analyses revealed its association with gene promoters, including MyoD1 and metallothioneins, suggesting a novel Cu-responsive regulatory role for mCrip2. Our work describes the significance of mCrip2 in skeletal muscle differentiation and metal homeostasis, expanding understanding of the Cu-network in myoblasts. Copper (Cu) is essential for various cellular processes, including respiration and stress response, but imbalances can cause serious health issues. This study reveals a new Cu-binding protein (Cu-BP) involved in muscle development in primary myoblasts. Using unbiased metalloproteomic techniques and high throughput sequencing, we identified mCrip2 as a key Cu-BP found in cell nuclei and cytoplasm. mCrip2 binds up to four Cu + ions and has a limited redox potential. Deleting mCrip2 using CRISPR/Cas9 disrupted muscle formation due to Cu accumulation. Further analyses showed that mCrip2 regulates the expression of genes like MyoD1, essential for muscle differentiation, and metallothioneins in response to copper supplementation. This research highlights the importance of mCrip2 in muscle development and metal homeostasis, providing new insights into the Cu-network in cells.

59 BASIC BIOLOGICAL SCIENCES

A taxonomy of automatic differentiation pitfalls

Automatic differentiation is a popular technique for computing derivatives of computer programs. While automatic differentiation has been successfully used in countless engineering, science, and machine learning applications, it can sometimes nevertheless produce surprising results. In this paper, we categorize problematic usages of automatic differentiation, and illustrate each category with examples such as chaos, time-averages, discretizations, fixed-point loops, lookup tables, linear solvers, and probabilistic programs, in the hope that readers may more easily avoid or detect such pitfalls. We also review debugging techniques and their effectiveness in these situations.

Autodiff