Scientific ML

Scientific machine learning reports predictive performance. It does not report whether the same prediction would survive a different draw of training data. Across $9$ chemistry benchmarks, two classifiers trained on independent bootstraps of the same training set agree on aggregate accuracy to within $1.3\text{--}4.2$ percentage points but disagree on the class label of $8.0\text{--}21.8\%$ of test molecules. We call this gap \emph{cross-sample prediction churn}. The standard parameter-side techniques (deep ensembles, MC dropout, stochastic weight averaging) do not reduce this gap; two data-side methods do. The first is $K$-bootstrap bagging, which cuts the rate $40\text{--}54\%$ on every dataset at no accuracy cost ($K{\times}$-ERM compute). The second is \emph{twin-bootstrap}, our proposal: two networks trained jointly on independent bootstraps with a sym-KL consistency loss between their predictions, which at matched $2{\times}$-ERM compute reduces churn a further median $45\%$ beyond bagging-$K{=}2$. Cross-sample prediction churn deserves a column alongside predictive performance in scientific-ML benchmark reports, because without it the parameter-side and data-side methods are indistinguishable on the metric they actually differ on.

Scientific Machine Learning (SciML) faces unique challenges for extreme-resolution data, with mitigations that often fail to scale or degrade the accuracy of trained models. While some specialized methods have achieved remarkable results in training models or performing inference on massive spatial datasets with bespoke techniques, there is no generalized framework for parallelization over input data below batch size one per device. In this work we introduce ShardTensor: a novel paradigm of domain parallelism that enables flexible scaling of input data to arbitrary sizes. By decoupling the spatial dimensionality of input data from hardware constraints, ShardTensor enables scientific machine learning workloads to reach new levels of high fidelity training and inference. We demonstrate both strong and weak scaling of workloads during training and inference, showing improved latency with strong scaling and demonstrating the capacity to process higher data sizes with weak scaling. Additionally, we demonstrate multiple dimensions of parallelization, removing barriers to SciML on extreme-scale inputs.

Mirroring its ubiquity in popular media and all human activities, the use of deep learning (DL) is rapidly growing in scientific imaging modalities. However, unlike everyday RGB pictures, pixels encode precise physicochemical properties in scientific imaging across potentially thousands of channels. While DL is well validated on human-centric RGB perceptual tasks, its effectiveness for scientific imaging remains uncertain. Here, we show that the naive application of DL frameworks to scientific images can lead to critical failures. We evaluate the use of DL for pathology, comparing RGB images of stained tissue with the quantitative and information-rich biochemical signatures of infrared (IR) imaging. Despite this informational advantage, DL models trained on IR data paradoxically underperform. We investigate this discrepancy to find that IR data priors interact poorly with the simplicity bias of DL, causing models to collapse to one-dimensional predictions. This constitutes a catastrophic DL failure because the model's representational capacity remains largely unused, while furthermore raising AI safety concerns and undermining the advantages of such scientific modalities. Notably, this problem persists even with state-of-the-art DL robustification strategies, which are primarily designed and validated for RGB imagery and thus inherit the same prior-bias mismatch. This work establishes a framework for understanding the limitations of generic DL in science and advocates for the study of modality-specific failure modes to guide the development of specialized, safe AI algorithms.

Probabilistic super-resolution of high-dimensional spatial fields using diffusion models is often computationally prohibitive due to the cost of operating directly in pixel space. We propose PODiff, a structured conditional generative framework that performs diffusion in a fixed, variance-ordered Proper Orthogonal Decomposition (POD) coefficient space, exploiting the orthogonality of POD modes to impose an interpretable, variance-ordered latent geometry. This design enables efficient ensemble generation, preserves dominant spatial structure, and yields spatially interpretable, well-calibrated uncertainty at substantially lower computational cost. We evaluate PODiff on sea surface temperature downscaling over the West Australian coast and on a controlled advection-diffusion benchmark. PODiff achieves reconstruction accuracy comparable to pixel-space diffusion while requiring significantly less memory and producing more reliable uncertainty estimates than deterministic and Monte Carlo Dropout baselines.

We present AdaGraph, a graph-native clustering algorithm born from the Structure-Centric Machine Learning (SC-ML) paradigm -- a new field of unsupervised learning that replaces geometry-centric (distance-based) computation with structure-centric (topology-based) computation, fundamentally dissolving the curse of dimensionality. AdaGraph operates entirely within the kNN graph topology, a representation that retains meaningful relational structure in arbitrarily high dimensions where Euclidean distance metrics become uninformative. AdaGraph requires no a priori specification of the number of clusters k, handles noise natively, and scales via the SLCD (Sample-Learn-Calibrate-Deploy) prototype-deployment framework. As its unsupervised tuning objective, AdaGraph pairs with Graph-SCOPE, the topology-based cluster validity index introduced as a separate SC-ML contribution. On 10 synthetic benchmarks spanning d=10 to d=5000, Graph-SCOPE achieves mean ARI=0.900 and correctly selects k on 9/10 datasets -- outperforming Silhouette, Davies-Bouldin, and Calinski-Harabasz -- while maintaining Kendall tau >= 0.92 with ground-truth cluster quality across all dimensionalities (Silhouette: tau ~= 0.46). We validate AdaGraph across three scientific domains: (1) gene co-expression discovery in hepatocellular carcinoma (GSE14520, 10,000 genes, 488 patients, no dimensionality reduction), where AdaGraph identifies condition-specific gene modules that WGCNA, ICA, NMF, and Spectral Biclustering fail to resolve; (2) natural language text clustering, where AdaGraph achieves ARI=0.751 on 20NG-6cat versus HDBSCAN's 0.464 (62% relative improvement); (3) materials science clustering of superconductors (145-dimensional Magpie features), perovskites, and JARVIS-DFT materials, where AdaGraph achieves the highest Graph-SCOPE on all three datasets.

Machine Learning (ML) has transformed many scientific fields, yet key applications still lack standardized benchmarks. Raman spectroscopy, a widely used technique for non-invasive molecular analysis, is one such field where progress is limited by fragmented datasets, inconsistent evaluation, and models that fail to capture the structure of spectral data. We introduce RamanBench, the first large-scale, fully reproducible benchmark for ML on Raman spectroscopy, consisting of streamlined data access, evaluation protocols and code, as well as a live leaderboard. It unifies 74 datasets (including 16 first released with this benchmark) across four domains, comprising 325,668 spectra and spanning classification and regression tasks under diverse experimental conditions. We benchmark 28 models under a standardized protocol, including classical methods (e.g., PLS), Raman-specific (e.g., RamanNet), Tabular Foundation Model (TFM) (e.g., TabPFN), and time-series approaches (e.g., ROCKET). TFM consistently outperform domain-specific and gradient boosting baselines, while time-series models remain competitive. However, no method generalizes across datasets, revealing a fundamental gap. Therefore, we invite the community to contribute new approaches to our living benchmark, with the potential to accelerate advances in critical applications such as medical diagnostics, biological research, and materials science.

We present Mesh Field Theory (MeshFT) and its neural realization, MeshFT-Net: a structure-preserving framework for mesh-based continuum physics that cleanly separates the physics' topological structure from its metric structure. Imposing minimal physical principles (locality, permutation equivariance, orientation covariance, and energy balance/dissipation inequality), we prove a reduction theorem for mesh-based physics. Under these conditions, the physical dynamics admit a local factorization into a port-Hamiltonian form: the conservative interconnection is fixed uniquely by mesh topology, whereas metric effects enter only through constitutive relations and dissipation. This reduction clarifies what must be fixed and what should be learned, directly informing MeshFT-Net's design. Across evaluations on analytic and realistic datasets, physics-consistency tests, and out-of-distribution validation, MeshFT-Net achieves near-zero energy drift and strong physical fidelity (correct dispersion and momentum conservation) along with robust extrapolation and high data efficiency. By eliminating non-physical degrees of freedom and learning only metric-dependent structure, MeshFT provides a principled inductive bias for stable, faithful, and data-efficient learning-based physical simulation.

Protein dynamics underlie many biological functions, yet remain difficult to characterize due to the high computational cost of molecular dynamics simulations and the scarcity of dynamic structural data. This survey reviews recent advances in artificial intelligence for protein dynamics from three perspectives: learning from structural ensembles and trajectories, learning from physical energy signals, and learning to accelerate molecular simulations. We summarize representative methods for conformation ensemble generation, trajectory generation, Boltzmann generators, physics-aware adaptation, machine learning potentials, coarse-grained modeling, and collective variable discovery. We further discuss available datasets and key open challenges, such as scalability, thermodynamic consistency, kinetic fidelity, and integration with experimental constraints.

The cost of Kohn-Sham density functional theory (KS-DFT) calculations scales with the number of solver iterations, which depends on the quality of the initial guess. Machine learning methods that predict initial guesses from molecular geometry can reduce this cost, but matrix-prediction models fail when extrapolating to larger molecules, degrading rather than accelerating convergence [Liu et al., 2025]. We show that this failure is a supervision problem, not an extrapolation problem: models trained on ground-state targets fit those targets well out of distribution, yet produce initial guesses that slow convergence. Solver-Aligned Initialization Learning (SAIL) resolves this for both Hamiltonian and density matrix models by differentiating through the self-consistent field (SCF) solver end-to-end. We introduce the Effective Relative Iteration Count (ERIC), a correction to the commonly used RIC that accounts for hidden Fock-build overhead. On QM40, which contains molecules up to 4$\times$ larger than the training distribution, SAIL reduces ERIC by 37% (PBE), 33% (SCAN), and 28% (B3LYP), more than doubling the previous state-of-the-art reduction on B3LYP. On QMugs molecules 10$\times$ larger than the training set, SAIL delivers a 1.35$\times$ wall-time speedup at the hybrid level of theory, extending ML SCF acceleration to large drug-like molecules.

Toward the goal of using Scientific Machine Learning (SciML) emulators to improve the numerical representation of aerosol processes in global atmospheric models, we explore the emulation of aerosol microphysics processes under cloud-free conditions in the 4-mode Modal Aerosol Module (MAM4) within the Energy Exascale Earth System Model version 2 (E3SMv2). To develop an in-depth understanding of the challenges and opportunities in applying SciML to aerosol processes, we begin with a simple feedforward neural network architecture that has been used in earlier studies, but we systematically examine key emulator design choices, including architecture complexity and variable normalization, while closely monitoring training convergence behavior. Our results show that optimization convergence, scaling strategy, and network complexity strongly influence emulation accuracy. When effective scaling is applied and convergence is achieved, the relatively simple architecture, used together with a moderate network size, can reproduce key features of the microphysics-induced aerosol concentration changes with promising accuracy. These findings provide practical clues for the next stages of emulator development; they also provide general insights that are likely applicable to the emulation of other aerosol processes, as well as other atmospheric physics involving multi-scale variability.

We report the first systematic evidence of hallucination in AI models of fluid dynamics, demonstrated in the canonical problem of hydrodynamically unstable transport known as viscous fingering. AI-based modeling of flow with instabilities remains challenging because rapidly evolving, multiscale fingering patterns are difficult to resolve accurately. We identify solutions that appear visually realistic yet are physically implausible, analogous to hallucinations in large language models. These hallucinations manifest as spurious fluid interfaces and reverse diffusion that violate conservation laws. We show that their origin lies in the spectral bias of AI models, which becomes dominant at high flow rates and viscosity contrasts. Guided by this insight, we introduce DeepFingers, a new framework for AI-driven fluid dynamics that enforces balanced learning across the full spectrum of spatial modes by combining the Fourier Neural Operator with a Deep Operator Network to predict the spatiotemporal evolution of viscous fingers. By conditioning on both time and viscosity contrast, DeepFingers learns mappings between successive concentration fields across regimes. The framework accurately captures tip splitting, finger merging, and channel formation while preserving global metrics of mixing. The results open a new research direction to investigate fundamental limitations in AI models of physical systems.

This is our fourth work in the series on machine learning (ML) moment closure models for the radiative transfer equation (RTE). In the first three papers of this series, we considered the RTE in slab geometry in 1D1V (i.e. one dimension in physical space and one dimension in angular space), and introduced a gradient-based ML moment closure [1], then enforced the hyperbolicity through a symmetrizer [2], or together with physical characteristic speeds by learning the eigenvalues of the Jacobian matrix [3]. Here, we extend our framework to the RTE in 2D2V (i.e. two dimensions in physical space and two dimensions in angular space). The main idea is to preserve the leading part of the classical $P_N$ model and modify only the highest-order block row. By analyzing the structural properties of the $P_N$ model, we show that its coefficient matrices are symmetric and admit a block-tridiagonal structure. Then we use this property to introduce a block-diagonal symmetrizer for the ML moment model and derive explicit algebraic conditions on the closure blocks which guarantee the symmetrizable hyperbolicity of the resulting ML system. These conditions lead to a natural parametrization of the closure in terms of a symmetric positive definite matrix together with symmetric closure blocks, which can be learned from data while automatically enforcing symmetrizable hyperbolicity by construction. The numerical results show that the proposed framework improves upon the classical $P_N$ model while maintaining hyperbolicity.

Extreme-edge scientific applications use machine learning models to analyze sensor data and make real-time decisions. Their stringent latency and throughput requirements demand small batch sizes and require that model weights remain fully on-chip. Spatial dataflow implementations are common for extreme-edge applications. Spatial dataflow works well for small networks, but it fails to scale to larger models due to inherent resource scaling limitations. AI Engines on modern FPGA SoCs offer a promising alternative with high compute density and additional on-chip memory. However, the architecture, programming model, and performance-scaling behavior of AI Engines differ fundamentally from those of the programmable logic, making direct comparison non-trivial and the benefits of using AI Engines unclear. This work addresses how and when extreme-edge scientific neural networks should be implemented on AI Engines versus programmable logic. We provide systematic architectural characterization and micro-benchmarking and introduce a latency-adjusted resource equivalence (LARE) metric that identifies when AI Engine implementations outperform programmable logic designs. We further propose spatial and API-level dataflow optimizations tailored to low-latency scientific inference. Finally, we demonstrate the successful deployment of end-to-end neural networks on AI Engines that cannot fit on programmable logic when using the hlsml toolchain.

We propose a self-supervised physics-informed neural network (PINN) framework that adaptively balances physics-based and data-driven supervision for scientific machine learning under data scarcity. Unlike prior PINNs that rely on fixed or heuristic weighting of physics residuals and data loss, our approach introduces a learnable blending neuron that dynamically adjusts the relative contribution of each term based on their uncertainties. This mechanism enables stable training and improved generalization without manual tuning. To further enhance efficiency, we integrate a transfer learning strategy that reuses representations from related domains and adapts them to new physical systems with limited data. We validate the framework for the prediction of heat transfer in liquid-metal miniature heat sinks using only 87 CFD datapoints, where the adaptive PINN achieves an error <8%, outperforming shallow neural networks, kernel methods, and physics-only baselines. Our framework provides a general recipe for embedding physics adaptively into neural networks, offering a robust and reproducible approach for data-scarce problems across various scientific domains, including fluid dynamics and material modeling.

For decades, physics-based climate models have been used to provide insights for climate decision-making. Their application is, however, constrained by significant computational and technical demands. Machine learning (ML) emulators offer a way to reduce these high computational costs; yet, it remains challenging to use ML emulators effectively in climate research. In practice, climate scientists often bypass emulators altogether, and machine learning researchers frequently develop them as methodological showcases without proving their practical utility. The reasons are diverse, ranging from limited accessibility and a lack of specialized knowledge to broader concerns about the physical grounding of ML methods. Here, we discuss limitations and introduce a framework for guiding emulator development, considering both climate science and machine learning perspectives. We argue that designing easy-to-adopt emulators that address clearly defined tasks and demonstrate their reliability is essential. This offers a promising path towards making machine-learning approaches more relevant and usable for applied climate research.

We introduce Clifford Kolmogorov-Arnold Network (ClKAN), a flexible and efficient architecture for function approximation in arbitrary Clifford Algebra spaces. We propose the use of Randomized Quasi-Monte Carlo grid generation as a solution to the exponential scaling associated with higher-dimensional algebras. Our ClKAN also introduces new batch normalization strategies to deal with variable domain input. ClKAN finds application in scientific discovery and engineering, and is validated in synthetic and physics-inspired tasks.

Machine learning models for climate and Earth science are becoming increasingly capable, yet model deployment into operational use remains a largely unaddressed challenge: general-purpose model-serving tools, such as MLflow and KServe, assume input data availability at the inference node, while data acquisition, failure handling, and preprocessing are trusted to a separate workflow. We present OpFML: Operational Forecasting with Machine Learning - a configurable pipeline integrating the four steps of operational inference into a single TOML-configured workflow: data consumption, contingency handling, preprocessing, and model inference. By consolidating these steps, OpFML removes the significant boilerplate code required for each new deployment. We demonstrate the pipeline on the operational forecasting of daily fire activity over southern Italy.

Progress in computational science depends on complex numerical workflows that must faithfully encode physical laws, yet translating conceptual insight into reliable code remains a major bottleneck. Although large language models can generate isolated code fragments, they lack the structured reasoning required to design, verify, and iteratively refine complete scientific pipelines. Here we introduce ATHENA, an agentic framework explicitly designed to emulate scientific research modeled as a knowledge-driven contextual bandit process. Its core loop separates conceptual policy from numerical realization through expert-derived conceptual scaffolding, enabling principled diagnosis, reformulation, and repair of computational strategies. Across scientific computing and scientific machine learning tasks, ATHENA autonomously derives and correctly applies exact analytical solutions, constructs stable numerical solvers, diagnoses ill-posed formulations, and orchestrates hybrid symbolic-numeric workflows. Quantitatively, ATHENA matches and frequently surpasses the accuracy of expert-authored reference solutions reported in the literature on canonical benchmarks. By reframing computation as an object of agentic reasoning, our framework enables autonomous orchestration of heterogeneous algorithms across scientific domains.

Predicting critical phenomena from limited labeled data remains a challenging task in statistical physics. As percolation theory provides a canonical model for phase transitions with well-established critical exponents, it serves as an ideal benchmark for validating new machine learning frameworks. Here, we introduce a label-efficient learning framework based on a Siamese Neural Network (SNN) to identify phase transitions in three-dimensional site and bond percolation models. Using only 22 labeled probability points drawn entirely from non-critical regions, the method locates percolation thresholds with percent-level accuracy and yields estimates of the critical exponent $ν$ consistent with literature values within statistical uncertainty. Analysis of the learned representations clarifies what the network learns: although trained solely on binary similarity labels, the network autonomously converges to a statistic that coincides quantitatively with the normalized largest-cluster size $S_{max}/L^3$ ($r > 0.99$), the finite-size order parameter of percolation. This underlies the framework's most distinctive capability -- a model trained solely on simple cubic lattices identifies the phase transition in face-centered cubic lattices without retraining. The framework thus offers a complementary route to criticality detection in settings where no quantitative order parameter is explicitly defined or labeled data is scarce.

While there are many applications of ML to scientific problems that look promising, visuals can be deceiving. Using numerical analysis techniques, we rigorously quantify the accuracy, convergence rates, and generalization bounds of certain ML models applied to linear differential equations for parameter discovery or solution finding. Beyond the quantity and discretization of data, we identify that the function space of the data is critical to the generalization of the model. A similar lack of generalization is empirically demonstrated for commonly used models, including physics-specific techniques. Counterintuitively, we find that different classes of models can exhibit opposing generalization behaviors. Based on our theoretical analysis, we also introduce a new mechanistic interpretability lens on scientific models whereby Green's function representations can be extracted from the weights of black-box models. Our results inform a new cross-validation technique for measuring generalization in physical systems, which can serve as a benchmark.

The characterization of Hamiltonians and other components of open quantum dynamical systems plays a crucial role in quantum computing and other applications. Scientific machine learning techniques have been applied to this problem in a variety of ways, including by modeling with deep neural networks. However, the majority of mathematical models describing open quantum systems are linear, and the natural nonlinearities in learnable models have not been incorporated using physical principles. We present a data-driven model for open quantum systems that includes learnable, thermodynamically consistent terms. The trained model is interpretable, as it directly estimates the system Hamiltonian and linear components of coupling to the environment. We validate the model on synthetic two and three-level data, as well as experimental two-level data collected from a quantum device at Lawrence Livermore National Laboratory.

Autoencoders have found widespread application in both their original deterministic form and in their variational formulation (VAEs). In scientific applications and in image processing it is often of interest to consider data that are viewed as functions; while discretisation (of differential equations arising in the sciences) or pixellation (of images) renders problems finite dimensional in practice, conceiving first of algorithms that operate on functions, and only then discretising or pixellating, leads to better algorithms that smoothly operate between resolutions. In this paper function-space versions of the autoencoder (FAE) and variational autoencoder (FVAE) are introduced, analysed, and deployed. Well-definedness of the objective governing VAEs is a subtle issue, particularly in function space, limiting applicability. For the FVAE objective to be well defined requires compatibility of the data distribution with the chosen generative model; this can be achieved, for example, when the data arise from a stochastic differential equation, but is generally restrictive. The FAE objective, on the other hand, is well defined in many situations where FVAE fails to be. Pairing the FVAE and FAE objectives with neural operator architectures that can be evaluated on any mesh enables new applications of autoencoders to inpainting, superresolution, and generative modelling of scientific data.