Ke Zhang, Yankang Liu, Roya Zandi +1cs.AI cs.MS cs.SE
Scientific benchmarks are commonly built by domain experts who write tasks and cross-check one another's work, or who adapt existing material from textbooks, published papers, and online resources. These routes can produce strong evaluations, but they require substantial per-item labor. Language models can reduce this repeated work by proposing candidates quickly. The remaining problem is acceptance. We target scientific questions whose answers require computations with specialist software rather than unaided reasoning alone. A candidate is invalid if its script fails or returns a different answer, or trivial if a model answers it without the software. We present ToolGate, which treats every generated item as a proposal and keeps it only if three gates pass. First, an executable solution script must reproduce the proposed answer when run with the scientific software. Second, randomized no-tool screening rejects candidates that models can already solve from the prompt alone. Third, a tool-using agent must solve each survivor within a fixed time limit. We instantiate ToolGate in FEniCSx with 500 generation attempts. The local-verification gate retains 478 candidates. For final reporting, we rescreen this pool after generation: two randomized no-tool screens exclude 222 from the reported pool, and direct GPT-5.5 API calls at medium reasoning (the API default) exclude another 121. Of the remaining 135, a GPT-5.5 Codex CLI agent with access to FEniCSx solves 130; exact deduplication leaves 128 unique protocol survivors. ToolGate turns repeated answer checking and difficulty screening into an auditable process while leaving domain design and final review to experts.
Sparse representations are often expected to make models smaller and also reduce inference cost. For Fourier Neural Operators (FNOs), these objectives are not equivalent or do not always align: removing parts of the learned operator can leave the underlying transforms and dense computations unchanged, while changing the grid on which the model is evaluated can introduce overhead of its own. We therefore distinguish sparsity in the representation, in the stored parameters, in the theoretical operation count, and in measured runtime, and present an empirical study of several routes toward sparse FNOs that tests each transition between them separately. Coarsening the execution grid reduces the theoretical cost without reducing measured latency, and adding a correction term recovers accuracy at the cost of making the model slower. Even an 83\% parameter reduction remains slower than the dense baseline under ordinary execution. These results motivate a stricter definition of useful sparsity: the deployed operator must preserve solution accuracy and map its reduced support to a genuinely cheaper execution path.
L. Thümmler, T. Kurodaastro-ph.IM astro-ph.HE cs.LG physics.comp-ph
Learned surrogates for expensive inner solver blocks are a widely pursued route to faster multiphysics simulation. We report a controlled, end-to-end negative result and identify three structural barriers, none of them a deficiency of the network we trained. The testbed is the implicit Newton solve coupling energy-dependent neutrino radiation to matter in a general-relativistic radiation-hydrodynamics code, its most expensive physics routine per call. First, per-call cost and share of runtime are different quantities, and only the second bounds acceleration. An exclusive self-time profile puts the target block at 16.9% of critical-rank wall clock, capping any surrogate at ~1.2x by Amdahl's law. A surrogate 5.8x cheaper per call merely ties the solver, and the configuration stable enough to run without fallback reaches only parity. Second, offline accuracy cannot rank surrogates for deployment: across fourteen networks the pooled Spearman error-versus-survival correlation (rho = +0.73) is a between-family confound that vanishes under control (rho = -0.04). Third, a correct out-of-distribution gate cannot accelerate a loop that leaves its training distribution. We give the break-even deferral fraction in closed form: because the visited states sit 73x off the data manifold, the gate defers 96.8 to 99.7% of cells, almost invariant to surrogate quality. Including its own cost, the gated loop is a 0.94 to 0.96x slowdown. We further separate stability from fidelity: a never-crashing gated run accumulates a linear -19.9% density bias over 6000 steps. The error is a directed, ballistically accumulating bias, not the variance-driven divergence the autoregressive literature targets.
Heyang Thomas Li, Alexander Pletzer, Yuan Tian +2cs.SE cs.AI cs.NE
Python is widely used in scientific research because it enables rapid development and provides rich ecosystems for data analysis, artificial intelligence (AI), and machine learning. However, customized research code can become prohibitively slow as experiments scale. This challenge is particularly acute in discrete-event project-scheduling simulations, where sequential state updates, nested loops, conditional evaluations, and object-oriented structures limit the benefits of compiled numerical and GPU-accelerated libraries. Addressing these bottlenecks typically requires iterative profiling, refactoring, testing, and validation, yet researchers may lack the time or specialized software-engineering expertise for low-level optimization. This paper presents a systematic refactoring approach using Claude agentic AI on real-world project-scheduling workloads in a high-performance computing (HPC) environment. Guided by representative benchmarks and correctness checks, the agent identifies bottlenecks, implements targeted optimizations, and evaluates their effects, while the researcher retains final control. Testing runtime reduced from 1,298 seconds to under 200 seconds without changing outputs, saving four million core-hours (NZ\$320,000) annually.
Daniel Musekamp, Boshra Ariguib, Andrei Manolache +1cs.LG
Foundation models for time-dependent partial differential equations (PDEs) are trained on large and diverse collections of physical systems and can generalize effectively to new downstream tasks. After fine-tuning on only a few trajectories from a target domain, they can achieve strong accuracy in low-data regimes. However, these models are typically large and computationally intensive, limiting their usefulness as fast surrogates for numerical solvers. We propose Teacher Rollout Extension (TREX), a knowledge distillation framework that transfers the predictive capability of a pretrained foundation model into a compact and efficient student. Starting from a fine-tuned teacher, TREX augments limited downstream data by generating long synthetic trajectories through teacher rollouts, optionally with periodic noise injection. This procedure samples from the teacher-induced rollout distribution without requiring explicit knowledge of the initial-condition distribution, while exposing the student to long-horizon states and local recovery behavior around states encountered during autoregressive prediction. The student can further incorporate task-specific inductive biases, such as equivariance, that the teacher does not necessarily enforce. We evaluate TREX on multiple PDE benchmarks. The resulting students can match or surpass the teacher's accuracy while reducing the number of parameters by several orders of magnitude and achieving more than an order-of-magnitude speedup in inference.
Fortran has been the cornerstone of high-performance computing for decades and remains unmatched in many domains. Yet the language faces an expertise gap: a new generation of scientists is barely familiar with it, while many experienced Fortran developers are only now transitioning to modern ecosystems such as JAX. This gap often results in "Fython" - Python code written with a Fortran mindset - that fails to leverage modern frameworks. We present FGPT, a transpiler framework designed to bridge this gap. It provides a systematic pipeline that transpiles Fortran into GPU-adapted Fortran, auto-differentiable Fortran via Tapenade, or NumPy and JAX scripts. Its architecture comprises three stages: (i) a frontend that parses Fortran and extracts target procedures along with all their dependencies; (ii) a middle-end that lowers the code into an intermediate representation, then into GPU-adapted or auto-differentiable Fortran, or a NumPy class; and (iii) a backend that transforms NumPy scripts into JAX modules optimized for GPU acceleration and automatic differentiation. Large language models fail when applied to the scale of community scientific codes-often spanning hundreds of thousands of lines-where consistent transformations, strict numerical fidelity, and validation against production tests are non-negotiable. FGPT addresses these challenges by preserving program semantics throughout the entire translation. We verified the framework on representative climate modeling kernels and demonstrated that it produces correct, differentiable Python implementations without requiring manual intervention. By combining rigorous compiler techniques with modern accelerator support, FGPT offers a scalable, trustworthy path for modernizing legacy Fortran code.
Solving large, sparse linear systems is a core task in scientific computing, and efficient iterative solvers rely critically on effective and robust preconditioning. While classical methods such as algebraic multigrid (AMG) are highly scalable, their robustness can degrade on indefinite or nonsymmetric systems where heuristics originally developed for elliptic PDEs are less reliable. Recently, Graph Neural Networks (GNNs) have emerged as data-driven preconditioners; yet, the practical impact of imposing an AMG-style hierarchy remains underexplored for general sparse matrices. In this work, we propose a Graph Neural Multilevel Preconditioner (GMP) that adopts an AMG hierarchy as a structural prior and learns smoothing, restriction, and interpolation operators in a unified framework. Our method targets general sparse systems and is instantiated as a drop-in preconditioner for standard Krylov solvers. On a benchmark of over 800 sparse matrices, we compare against classical AMG, single-level ILUT, and state-of-the-art GNN preconditioners, and characterize the regimes where multilevel graph neural preconditioning improves convergence or, conversely, introduces overhead relative to strong single-level baselines. These results highlight both the promise and the limitations of enforcing AMG-style multilevel structure in learned preconditioners for large-scale scientific simulations.
Large language models increasingly solve scientific-computing tasks, but executable feedback from one problem rarely becomes durable capability on subsequent problems. We study scientific-computing experience consolidation: converting verified runtime experience into transferable procedural knowledge and persistent model improvement. This setting presents two challenges: trajectory-derived artifacts may encode source-specific repairs rather than cross-task computational mechanisms; and a weaker target model may be unable to operationalize an otherwise valid abstract procedure - an abstraction-execution gap. We introduce SciConsolidate, which contrasts verified successes and failures to induce cross-task procedures, selects them through a development-validation gate, and uses failure-informed, answer-free query synthesis to expand the consolidation data without requiring pre-existing reference answers. Because the target model may not directly execute these abstractions, a stronger model concretizes them into executable code supervision for standard, procedure-free SFT; a matched no-procedure teacher branch isolates the value of procedural guidance. On SciCode, runtime procedure injection improves Qwen3.6-27B by +3.85/+6.26 sub-step/main-problem points, but yields almost no aggregate main-problem gain for Qwen3.5-9B, providing operational evidence of the abstraction-execution gap. After procedure-guided concretization, the 9B student improves under procedure-free deployment by +3.89/+6.25 points over the no-procedure SFT control and by +5.62/+11.25 over the original 9B model. These results establish an experience-to-capability pathway for scientific computing and provide a practical starting point for scaling self-improving scientific assistance.
The coupled ghost and gluon Dyson--Schwinger equations (DSEs) of four-dimensional Landau-gauge Yang--Mills (YM) theory are solved with a neural representation trained only from renormalized equation residuals. The neural and fixed-point solutions agree at the percent level and remain stable under changes of initialization, network size, integration grid, and infrared boundary condition. Variations of the three-gluon vertex model produce substantially larger effects than the neural error. The MiniMOM ultraviolet running and the sign change of the gluon Schwinger function are also reproduced within the limitations of the truncation.
Haofei Gao, Tingjia Miao, Wenkai Jin +12hep-lat cs.AI hep-ph
Lattice quantum chromodynamics (LQCD) provides a first-principles framework for computing hadronic observables, but its practical use remains limited by the substantial expertise required to turn research motivation into reliable computing workflows. Here we present \textsc{LQCDMaster}, a tool-augmented, skill-guided and domain-specialized scientific computing agent that converts natural-language LQCD research tasks into executable PyQUDA computing workflows, including measurement scripts, job-submission artifacts, execution logs and numerical outputs. The system combines agentic planning, expert-annotated LQCD skills and a deterministic Wick-contraction tool to constrain the algebraically fragile components of code generation. We evaluate \textsc{LQCDMaster} on a benchmark at the forefront of scientific research, comprising 70 LQCD computing tasks, with observables covering local and nonlocal two-point functions, Wilson loops, meson and baryon three-point functions. The generated workflows exactly reproduce expert-written implementations in 63 of 70 tasks at machine precision, with three additional discrepancies attributable to convention mismatches. Across representative observables, the agent reduces implementation time from hours to minutes while preserving end-to-end numerical validation. Further, we present a typical case of \textsc{LQCDMaster}-driven exploration: a lattice computation of light-cone distribution amplitudes with diagonal Wilson-line, a quantity accessible with standard methods but never before computed, and computation of the spectrum of proton, deuteron, triton, hyperon, hyperdeuteron and hypertriton. This work pioneers the paradigm of agentic scientific computing by automating the end-to-end scientific computing workflows in lattice QCD research, lowering its barrier and facilitating the exploration and verification of non-standard scientific ideas.
Computational imaging, which recovers hidden signals from indirect, noisy measurements, underpins quantitative discovery across scientific disciplines, yet building a correct reconstruction pipeline demands deep domain expertise and remains laborious even for domain scientists. We introduce Imaging-101, a benchmark of 57 expert-verified computational imaging tasks spanning six scientific domains, each grounded in a peer-reviewed paper and canonicalized into a standardized four-stage pipeline (preprocessing, forward physics modeling, inverse solver, and visualization) Three evaluation tracks (planning, function-level unit tests, and end-to-end reconstruction) probe distinct agent capabilities across the full pipeline. Evaluating seven frontier LLMs uncovers systematic challenges in applying coding agents to computational imaging that go beyond those exposed by general coding benchmarks, spanning algorithm selection, physical convention handling, and pipeline integration. These findings highlight concrete capability gaps and point toward skill-augmented, domain-specialized agents as a practical path to reliable computational imaging assistance.
We present PDEFlow, an autonomous agentic framework that turns user-level ODE and PDE descriptions into solver-backed neural-operator pipelines. The workflow links problem specification, data generation, operator training, and checkpoint-based inference. A stateful input graph converts multi-turn natural-language input and user edits into validated problem specifications. The data-generation module then samples parameters, solves the configured governing-equation with FEniCSx finite-element backend, and stores the solutions as operator-ready tensors. The training and inference stages use a registry-based interface, allowing different neural operators to be trained and deployed without changing the surrounding pipeline. In the current implementation, we instantiate this interface with a multi-branch Bayesian DeepONet. Experiments on benchmark ODE and PDE tasks show that PDEFlow can construct valid specifications, generate solver-backed datasets, train neural operators across steady and transient problem classes, and provide solver-free predictions from saved checkpoints. The framework is designed for repeatable scientific and engineering workflows where many related physics configurations must be specified, simulated, learned, and queried with minimal manual intervention.
Scientists increasingly rely on open-source tools to support their research workflows, yet discovering relevant software among over 600 million GitHub repositories remains challenging. Existing code search benchmarks focus on general software engineering tasks and fail to capture the domain-specific vocabulary and needs of scientific computing. We present a curated corpus of 5,264 high-quality, domain-classified scientific repositories spanning five NASA Science Mission Directorate divisions -- Earth Science, Astrophysics, Planetary Science, Heliophysics, and Biological & Physical Sciences -- enriched with cleaned READMEs, extracted topics, and additional context from crawled links. Building on this corpus, we introduce two novel information retrieval benchmarks: (1) a repository search benchmark with 219 expert-curated queries designed by domain scientists, and (2) a large-scale code snippet retrieval benchmark containing 117,950 code snippets and 119,720 queries across seven programming languages. Baseline evaluations on repository search reveal significant performance variation across scientific domains. Code snippet retrieval proves equally challenging, with substantial variation driven by differing documentation practices, coding standards, and programming language conventions across scientific communities. All datasets and benchmarks are publicly released on HuggingFace to support research on scientific tool discovery.
Max Kreider, John Harlim, Daning Huangcs.LG math.DS
Accurate prediction of complex dynamical systems from noisy measurements remains a significant challenge in scientific computing. Kernel ridge regression learning strategies are often effective when applied to clean data, but have limited success with noisy data. Recent work has observed that a weak formulation can act to filter noisy data, and different learning strategies have achieved increased noise robustness with a weak-form framework. In this manuscript, we give an overview of the filtering mechanism behind the weak formulation and provide a bias-variance error decomposition. Using these insights, we combine a weak formulation with a kernel learning strategy to propose Weak-form Kernel Ridge Regression (WKRR) for learning dynamical systems. The proposed framework is simple to implement, effective for both clean and noisy data, and outperforms several baseline methods. We demonstrate the performance of WKRR on chaotic benchmark systems in up to 64 dimensions, as well as 15,000-dimensional real-world fluid data.
Jiwei Jia, Xinliang Liu, Juntao Wang +1math.NA cs.AI math-ph
Solving heterogeneous Helmholtz equations at high wavenumbers remains challenging because the discretized operator is indefinite, pollution degrades phase accuracy, and scalar coarse-grid correction can discard the local phase and propagation-direction information carried by oscillatory errors. We propose Multi-channel Multigrid (McMg), a learned phase-space multigrid preconditioner for heterogeneous Helmholtz equations. Rather than predicting the solution directly, McMg maps residuals to corrections within an iterative framework. Its central idea is to coarsen physical space while retaining unresolved local wave information in the channel dimension: each coarse node carries a learned packet of amplitude, phase, direction, and scattering coefficients rather than a single scalar unknown. The architecture combines linear multi-channel transfer operators with locally adaptive stencils, neural PDE operators, and medium-dependent smoothers whose coefficients are generated from the wave speed. For a fixed medium, the V-cycle is linear in the residual; nonlinear physical features are computed once in a setup phase and cached, so each online iteration reduces to convolutions with fixed coefficients. We further study generalization across scales. Models trained on small domains transfer directly to larger domains and higher effective wavenumbers, and a Layer-by-Layer Progressive Finetuning (LLPF) strategy extends the support of the learned Green's operator by adding and finetuning only new coarse levels. Numerical experiments on high-frequency, high-contrast, and large-scale three-dimensional problems demonstrate that McMg requires substantially fewer iterations and less wall-clock time than strong classical baselines, while consistently outperforming existing neural preconditioners.
Andrin Rehmann, Heiko Zimmermann, Dion Häfnerphysics.comp-ph cs.LG
Differentiable partial differential equation (PDE) solvers underpin solver-in-the-loop ML training, gradient-based optimal control, and inverse problems, yet the practical cost of obtaining correct, usable gradients from a given solver on a given problem is largely undocumented. Integration effort, computational cost, gradient accuracy, and numerical conditioning vary widely across solvers and are discoverable only by trial and error. We introduce Mosaic, an extensible benchmarking framework for differentiable PDE solvers that standardizes access to solver gradients. Each solver is packaged as a containerized component (Tesseract) exposing a uniform gradient API regardless of language or automatic differentiation (AD) strategy, enabling researchers to evaluate, compare, and build on non-trivial physical solvers. Our evaluation of 14 solvers across fluid dynamics, structural mechanics, and heat transfer demonstrates that the benchmark surfaces practically relevant differences: order-of-magnitude variation in computational cost and Jacobian conditioning, alongside structural incompatibilities that eliminate solvers from realistic tasks entirely. Despite this variation, all solvers that produce gradients converge to similar optima, indicating that the practical barriers are memory limits, numerical stability, and setup compatibility rather than gradient accuracy alone. Mosaic is open-source and available at https://github.com/pasteurlabs/mosaic.
Reza T Batley, Andrew Kichline, Sourav Sahacs.LG cs.AI
This work introduces the Separable Neural Architecture (SNA), a function representational class combining neural approximation with tensor decomposition. The SNA decouples localized coordinate functions (atoms) from global interactions governed by a sparse, low-rank interaction object. This architecture possesses a compact and smooth inductive bias well-suited for solving partial differential equations (PDEs). When viewed as a Galerkin trial space under the variational SNA (VSNA) framework, the formulation satisfies classical variational guarantees under Lax-Milgram: well-posedness, quasi-optimality, convergence, and stability. In high-dimensional spatiotemporal--parametric PDEs, the VSNA mitigates the curse of dimensionality by scaling algebraically rather than exponentially. Exploiting an entirely factorized, tensor-native alternating least squares (ALS) optimization framework reduces this cost to linear in dimension. The VSNA is validated across elliptic, hyperbolic, and parabolic systems, demonstrating close alignment with predicted algebraic and spectral scaling rates. We showcase the SNA as a "solve once, query anywhere" physical world model via two engineering case studies: a 7D parametric manufacturing simulation and an experimental thermal-to-property inversion pipeline for Inconel 718. The VSNA executes a 1,000,000-query Monte Carlo sweep in 102s on a standard laptop CPU, yielding a 150,000x speedup over a full-grid finite element baseline hosted on an NVIDIA A100 GPU. It further enables real-time generative inverse-mode reconstructions under 100ms. These results demonstrate that the SNA serves as a compact mathematical substrate for continuous parameter manifolds to enable real-time inversion, optimization loops, and rapid uncertainty propagation.
In science and engineering, Lagrangian simulation methods such as Smooth Particle Hydrodynamics (SPH) or Material Point Method (MPM) are often employed to study the behavior of dynamic systems. However, these methods can be prohibitively computationally expensive, particularly when simulating multi-scale spatial or temporal phenomena, e.g., void growth and coalescence within macro-scale geometries, structural failure of spacecraft components resulting from hypervelocity impact of space debris particles, etc. In contrast to graph-based methods, where the state of the system is understood as a discrete set of particles, we propose a learning framework for scalable representation and dynamics modeling of massive particle systems by treating the system state as a function and its evolution as a trajectory in Hilbert space. Rather than representing the state as a discrete set of particles or embedding it in a nonlinear latent manifold, we approximate the state space with a linear subspace spanned by learned neural basis functions. This parameterization enables direct projection to obtain latent coefficients and explicit access to the basis functions, avoiding optimization over a nonlinear latent space. The resulting representation admits a natural interpretation: latent variables correspond to coefficients in Hilbert space, and basis functions correspond to spatial modes, analogous to Proper Orthogonal Decomposition. The framework thus unifies classical projection-based reduced-order modeling with modern deep learning, while remaining invariant to the number of discretization points. Experiments on large-scale SPH simulations with over one million particles, including dynamic events with extreme deformation and fragmentation, demonstrate that the proposed method accurately reconstructs and predicts dynamics, achieving an R$^2$ score above $0.99$ with as few as $32$ basis functions.
Sebastian Neumayer, Daniel Potts, Fabian Taubertmath.NA cs.LG
We investigate the approximation of solution operators for partial differential equations (PDEs) using sparse high-dimensional techniques. Building on a dimension-incremental framework, we combine product basis expansions with sparse recovery methods, specifically orthogonal matching pursuit (OMP), to substantially reduce the required sample size compared with a previously considered cubature-based approach. We evaluate the resulting method numerically on several examples, comparing it against both cubature-based sparse approximation and Fourier neural operators in terms of accuracy, runtime, and sample size. The experiments show that our approach considerably reduces the number of required PDE solves relative to its predecessor while maintaining competitive accuracy, particularly when the solution admits a sparse representation in the chosen basis. Furthermore, the recovered sparse index sets yield interpretable insights into the relevant variables and parameter interactions.
Neural operators have achieved significant success in modern scientific computing due to their flexibility and strong generalization capabilities. Existing models, however, primarily rely on first-order kernel integral approximations, which severely limit their expressivity. To address this, we propose the Infinite-order Kernel Neural Operator (IKNO), which constructs neural operators via infinite-order kernel integrals and admits an elegant closed-form finite approximation. We develop two complementary infinite-order neural operator constructions: IKNO-Vanilla, which applies the full-kernel resolvent on the product grid via Kronecker eigendecomposition, and IKNO-TP, an alternative tensor-product operator that composes per-axis resolvents. Furthermore, we develop fast computation schemes for both variants of IKNO, which achieve outstanding global information aggregation while maintaining high computational efficiency. Empirically, we evaluate our IKNO on both time-dependent and time-independent benchmarks with arbitrary input shapes, including large-scale industrial datasets. Extensive experiments demonstrate that the IKNO method consistently achieves the SOTA accuracy with significant improvements on nearly all benchmark datasets while maintaining scalability to very large point clouds.
Computing pseudospectra of non-normal matrices is essential for understanding the stability and transient behavior of dynamical systems. Such analysis is critical in applications including fluid dynamics, control systems, and differential operators, where non-normality can lead to significant transient amplification and sensitivity to perturbations that are not captured by eigenvalue analysis alone. At large scales, commonly used numerical approaches for pseudospectra computation can become computationally demanding, as they require repeated auxiliary computations to identify spectrally sensitive regions in the complex plane. We present a neural network-based approach that predicts sensitive regions directly from matrix features, thereby avoiding exhaustive pseudospectra evaluation across the entire complex plane. We calibrate the prediction threshold on validation data to ensure reliable coverage of sensitive regions. The trained neural network guides the selection of grid points requiring full computation, enabling focused computation only where necessary. The approach provides a practical preprocessing strategy for efficient pseudospectra computation. Numerical experiments on non-normal banded matrices demonstrate substantial speedup compared to full grid-based numerical evaluation while maintaining high accuracy in identifying sensitive regions.