arXiv subjects

Rudy Morel

Publications and source records attributed to Rudy Morel.

18 recordsLinked to original sources

arXiv2026

Emergent Transfer of a Physics Foundation Model from Simulation to Laboratory Turbulence

Whether physics foundation models can be usefully deployed on laboratory experiments remains an open question for scientific machine learning (ML). We test this question on the Rayleigh-Taylor instability (RTI), a ubiquitous and demanding fluid instability seen from tabletop flows to supernova explosions, in which small perturbations at a density interface grow into chaotic, multiscale mixing as a lighter fluid accelerates into a heavier one. Standard ML models struggle with RTI, and despite over a century of theoretical, numerical, and experimental work, it carries an unresolved discrepancy between simulation and experiment: the late-time mixing growth rate, $\alpha$, measured in most laboratory experiments ($\sim$ 0.06-0.07), is roughly three times the value from idealized direct numerical simulations (DNS, $\sim$ 0.02). The gap's origin remains debated. These properties make RTI a stringent test for a question that matters well beyond RTI: can foundation models trained only on simulations generalise to sparse, messy, and noisy laboratory settings? We finetune Walrus, a foundation model for continuum dynamics, on three or fewer DNS realizations and recover key RTI physics over long rollouts. Applied zero-shot to sliding-barrier laboratory data, the finetuned model leaves the DNS-like regime and enters the observed growth band, having never seen a single experimental sample. These results provide independent, data-driven evidence that initial conditions play a crucial role in the longstanding sim-experiment gap in $\alpha$. The model also generalises zero-shot to stable stratification, a buoyancy regime absent from training, correctly slowing mixing-layer growth. Together, our results show that foundation models can generalise well beyond their training data, predicting laboratory behavior and unseen physical regimes, opening new ways to probe longstanding simulation-experiment gaps.

physics.flu-dyn↗

arXiv2026

MIMIC: A Generative Multimodal Foundation Model for Biomolecules

Biological function emerges from coupled constraints across sequence, structure, regulation, evolution, and cellular context, yet most foundation models in biology are trained within one modality or for a fixed forward task. We present MIMIC, a generative multimodal foundation model trained on our newly curated and aligned dataset, LORE, linking nucleic acid, protein, evolutionary, structural, regulatory, and semantic/contextual modalities within partially observed biomolecular states. MIMIC uses a split-track encoder-decoder architecture to condition on arbitrary subsets of observed modalities and reconstruct or generate missing components of molecular state across the genome, transcriptome, and proteome. Multimodal conditioning consistently improves MIMIC's sequence reconstruction relative to sequence-only inputs, while its learned representations enable state-of-the-art performance on RNA and protein downstream tasks. MIMIC achieves state-of-the-art splicing prediction, and its joint generative formulation enables isoform-aware inference that further improves performance. Beyond prediction, the same generative framework supports constrained design. For RNA, MIMIC identifies corrective edits in a clinically relevant HBB splice-disrupting mutation without reverting it by using evolutionary and structural signals. For proteins, jointly conditioning on shape and surface chemistry of PD-L1 and hACE2 binding sites produces diverse, high-confidence sequences with strong in silico support for target binding. Finally, MIMIC uses experimental context as semantic conditioning to model assay-dependent RNA chemical probing, rather than treating context as a fixed output. Together, these results position MIMIC's aligned multimodal generative modeling as a strong foundation for unifying representation learning, conditional prediction, and constrained biomolecular design within a single model.

cs.AI↗

arXiv2026

Representation Learning for Spatiotemporal Physical Systems

Machine learning approaches to spatiotemporal physical systems have primarily focused on next-frame prediction, with the goal of learning an accurate emulator for the system's evolution in time. However, these emulators are computationally expensive to train and are subject to performance pitfalls, such as compounding errors during autoregressive rollout. In this work, we take a different perspective and look at scientific tasks further downstream of predicting the next frame, such as estimation of a system's governing physical parameters. Accuracy on these tasks offers a uniquely quantifiable glimpse into the physical relevance of the representations of these models. We evaluate the effectiveness of general-purpose self-supervised methods in learning physics-grounded representations that are useful for downstream scientific tasks. Surprisingly, we find that not all methods designed for physical modeling outperform generic self-supervised learning methods on these tasks, and methods that learn in the latent space (e.g., joint embedding predictive architectures, or JEPAs) outperform those optimizing pixel-level prediction objectives. Code is available at https://github.com/helenqu/physical-representation-learning.

cs.LG↗

arXiv2026

Test-time Generalization for Physics through Neural Operator Splitting

Neural operators have shown promise in learning solution maps of partial differential equations (PDEs), but they often struggle to generalize when test inputs lie outside the training distribution, such as novel initial conditions, unseen PDE coefficients or unseen physics. Prior works address this limitation with large-scale multiple physics pretraining followed by fine-tuning, but this still require examples from the new dynamics, falling short of true zero-shot generalization. In this work, we propose a method to enhance generalization at test time, i.e., without modifying pretrained weights. Building on DISCO, which provides a dictionary of neural operators trained across different dynamics, we introduce a neural operator splitting strategy that, at test time, searches over compositions of training operators to approximate unseen dynamics.On challenging out-of-distribution tasks including parameter extrapolation and novel combinations of physics phenomena, our approach achieves state-of-the-art zero-shot generalization results, while being able to recover the underlying PDE parameters. These results underscore test-time computation as a key avenue for building flexible, compositional, and generalizable neural operators.

cs.LG↗

arXiv2025

Predicting partially observable dynamical systems via diffusion models with a multiscale inference scheme

Conditional diffusion models provide a natural framework for probabilistic prediction of dynamical systems and have been successfully applied to fluid dynamics and weather prediction. However, in many settings, the available information at a given time represents only a small fraction of what is needed to predict future states, either due to measurement uncertainty or because only a small fraction of the state can be observed. This is true for example in solar physics, where we can observe the Sun's surface and atmosphere, but its evolution is driven by internal processes for which we lack direct measurements. In this paper, we tackle the probabilistic prediction of partially observable, long-memory dynamical systems, with applications to solar dynamics and the evolution of active regions. We show that standard inference schemes, such as autoregressive rollouts, fail to capture long-range dependencies in the data, largely because they do not integrate past information effectively. To overcome this, we propose a multiscale inference scheme for diffusion models, tailored to physical processes. Our method generates trajectories that are temporally fine-grained near the present and coarser as we move farther away, which enables capturing long-range temporal dependencies without increasing computational cost. When integrated into a diffusion model, we show that our inference scheme significantly reduces the bias of the predicted distributions and improves rollout stability.

cs.LG↗

arXiv2025

Walrus: A Cross-Domain Foundation Model for Continuum Dynamics

Foundation models have transformed machine learning for language and vision, but achieving comparable impact in physical simulation remains a challenge. Data heterogeneity and unstable long-term dynamics inhibit learning from sufficiently diverse dynamics, while varying resolutions and dimensionalities challenge efficient training on modern hardware. Through empirical and theoretical analysis, we incorporate new approaches to mitigate these obstacles, including a harmonic-analysis-based stabilization method, load-balanced distributed 2D and 3D training strategies, and compute-adaptive tokenization. Using these tools, we develop Walrus, a transformer-based foundation model developed primarily for fluid-like continuum dynamics. Walrus is pretrained on nineteen diverse scenarios spanning astrophysics, geoscience, rheology, plasma physics, acoustics, and classical fluids. Experiments show that Walrus outperforms prior foundation models on both short and long term prediction horizons on downstream tasks and across the breadth of pretraining data, while ablation studies confirm the value of our contributions to forecast stability, training throughput, and transfer performance over conventional approaches. Code and weights are released for community use.

cs.LG↗

arXiv2025

Universal Spectral Tokenization via Self-Supervised Panchromatic Representation Learning

Sequential scientific data span many resolutions and domains, and unifying them into a common representation is a key step toward developing foundation models for the sciences. Astronomical spectra exemplify this challenge: massive surveys have collected millions of spectra across a wide range of wavelengths and resolutions, yet analyses remain fragmented across spectral domains (e.g., optical vs. infrared) and object types (e.g., stars vs. galaxies), limiting the ability to pool information across datasets. We present a deep learning model that jointly learns from heterogeneous spectra in a self-supervised manner. Our universal spectral tokenizer processes spectra from a variety of object types and resolutions directly on their native wavelength grids, producing intrinsically aligned, homogeneous, and physically meaningful representations that can be efficiently adapted to achieve competitive performance across a range of downstream tasks. For the first time, we demonstrate that a single model can unify spectral data across resolutions and domains, suggesting that our model can serve as a powerful building block for foundation models in astronomy -- and potentially extend to other scientific domains with heterogeneous sequential data, such as climate and healthcare.

astro-ph.IM↗

arXiv2025

AION-1: Omnimodal Foundation Model for Astronomical Sciences

While foundation models have shown promise across a variety of fields, astronomy still lacks a unified framework for joint modeling across its highly diverse data modalities. In this paper, we present AION-1, a family of large-scale multimodal foundation models for astronomy. AION-1 integrates heterogeneous imaging, spectroscopic, and scalar data using a two-stage architecture: modality-specific tokenization followed by transformer-based masked modeling of cross-modal token sequences. The model is pretrained on five large-scale surveys: Legacy Survey, Hyper Suprime-Cam (HSC), Sloan Digital Sky Survey (SDSS), Dark Energy Spectroscopic Instrument (DESI), and Gaia. These span more than 200 million observations of stars, galaxies, and quasars. With a single frozen encoder, AION-1 achieves strong results on a broad suite of downstream tasks, including galaxy and stellar property estimation, galaxy morphology classification, similarity-based retrieval, galaxy image segmentation, and spectral super-resolution. We release AION-1 model variants ranging from 300 M to 3.1 B parameters. Beyond astronomy, AION-1 provides a scalable blueprint for multimodal scientific foundation models that can seamlessly integrate noisy, instrument-specific observations. All code, tokenizers, pretrained weights, and a lightweight evaluation suite are released under an open-source license.

astro-ph.IM↗

arXiv2025

Neutral gas phase distribution from HI morphology: phase separation with scattering spectra and variational autoencoders

Unraveling the multi-phase structure of the diffuse interstellar medium (ISM) as traced by neutral hydrogen (HI) is essential to understanding the lifecycle of the Milky Way. However, HI phase separation is a challenging and under-constrained problem. The neutral gas phase distribution is often inferred from the spectral line structure of HI emission. In this work, we develop a data-driven phase separation method that extracts HI phase structure solely from the spatial morphology of HI emission intensity structures. We combine scattering spectra (SS) statistics with a Gaussian-mixture variational autoencoder (VAE) model to: 1. derive an interpretable statistical model of different HI phases from their multi-scale morphological structures; 2. use this model to decompose the 2D channel maps of GALFA-HI emission in diffuse high latitude ($|b|>30$\degree) regions over narrow velocity channels ($\Delta v=3$ km/s) into cold neutral medium (CNM), warm neutral medium (WNM), and noise components. We integrate our CNM map over velocity channels to compare it to an existing map produced by a spectrum-based method, and find that the two maps are highly correlated, while ours recovers more spatially coherent structures at small scales. Our work illustrates and quantifies a clear physical connection between the HI morphology and HI phase structure, and unlocks a new avenue for improving future phase separation techniques by making use of both HI spectral and spatial information to decompose HI in 3D position-position-velocity (PPV) space. These results are consistent with a physical picture where processes that drive HI phase transitions also shape the morphology of HI gas, imprinting a sparse, filamentary CNM that forms out of a diffuse, extended WNM.

astro-ph.GA↗

arXiv2025

DISCO: learning to DISCover an evolution Operator for multi-physics-agnostic prediction

We address the problem of predicting the next state of a dynamical system governed by unknown temporal partial differential equations (PDEs) using only a short trajectory. While standard transformers provide a natural black-box solution to this task, the presence of a well-structured evolution operator in the data suggests a more tailored and efficient approach. Specifically, when the PDE is fully known, classical numerical solvers can evolve the state accurately with only a few parameters. Building on this observation, we introduce DISCO, a model that uses a large hypernetwork to process a short trajectory and generate the parameters of a much smaller operator network, which then predicts the next state through time integration. Our framework decouples dynamics estimation (i.e., DISCovering an evolution operator from a short trajectory) from state prediction (i.e., evolving this operator). Experiments show that pretraining our model on diverse physics datasets achieves state-of-the-art performance while requiring significantly fewer epochs. Moreover, it generalizes well and remains competitive when fine-tuned on downstream tasks.

cs.LG↗

arXiv2024

The Well: a Large-Scale Collection of Diverse Physics Simulations for Machine Learning

Machine learning based surrogate models offer researchers powerful tools for accelerating simulation-based workflows. However, as standard datasets in this space often cover small classes of physical behavior, it can be difficult to evaluate the efficacy of new approaches. To address this gap, we introduce the Well: a large-scale collection of datasets containing numerical simulations of a wide variety of spatiotemporal physical systems. The Well draws from domain experts and numerical software developers to provide 15TB of data across 16 datasets covering diverse domains such as biological systems, fluid dynamics, acoustic scattering, as well as magneto-hydrodynamic simulations of extra-galactic fluids or supernova explosions. These datasets can be used individually or as part of a broader benchmark suite. To facilitate usage of the Well, we provide a unified PyTorch interface for training and evaluating models. We demonstrate the function of this library by introducing example baselines that highlight the new challenges posed by the complex dynamics of the Well. The code and data is available at https://github.com/PolymathicAI/the_well.

cs.LG↗

arXiv2024

Contextual Counting: A Mechanistic Study of Transformers on a Quantitative Task

Transformers have revolutionized machine learning across diverse domains, yet understanding their behavior remains crucial, particularly in high-stakes applications. This paper introduces the contextual counting task, a novel toy problem aimed at enhancing our understanding of Transformers in quantitative and scientific contexts. This task requires precise localization and computation within datasets, akin to object detection or region-based scientific analysis. We present theoretical and empirical analysis using both causal and non-causal Transformer architectures, investigating the influence of various positional encodings on performance and interpretability. In particular, we find that causal attention is much better suited for the task, and that no positional embeddings lead to the best accuracy, though rotary embeddings are competitive and easier to train. We also show that out of distribution performance is tightly linked to which tokens it uses as a bias term.

cs.LG↗

arXiv2024

Riding Wavelets: A Method to Discover New Classes of Price Jumps

Cascades of events and extreme occurrences have garnered significant attention across diverse domains such as financial markets, seismology, and social physics. Such events can stem either from the internal dynamics inherent to the system (endogenous), or from external shocks (exogenous). The possibility of separating these two classes of events has critical implications for professionals in those fields. We introduce an unsupervised framework leveraging a representation of jump time-series based on wavelet coefficients and apply it to stock price jumps. In line with previous work, we recover the fact that the time-asymmetry of volatility is a major feature. Mean-reversion and trend are found to be two additional key features, allowing us to identify new classes of jumps. Furthermore, thanks to our wavelet-based representation, we investigate the reflexive properties of co-jumps, which occur when multiple stocks experience price jumps within the same minute. We argue that a significant fraction of co-jumps results from an endogenous contagion mechanism.

q-fin.GN↗

arXiv2023

Path Shadowing Monte-Carlo

We introduce a Path Shadowing Monte-Carlo method, which provides prediction of future paths, given any generative model. At any given date, it averages future quantities over generated price paths whose past history matches, or `shadows', the actual (observed) history. We test our approach using paths generated from a maximum entropy model of financial prices, based on a recently proposed multi-scale analogue of the standard skewness and kurtosis called `Scattering Spectra'. This model promotes diversity of generated paths while reproducing the main statistical properties of financial prices, including stylized facts on volatility roughness. Our method yields state-of-the-art predictions for future realized volatility and allows one to determine conditional option smiles for the S\&P500 that outperform both the current version of the Path-Dependent Volatility model and the option market itself.

q-fin.MF↗

arXiv2023

Scattering Spectra Models for Physics

Physicists routinely need probabilistic models for a number of tasks such as parameter inference or the generation of new realizations of a field. Establishing such models for highly non-Gaussian fields is a challenge, especially when the number of samples is limited. In this paper, we introduce scattering spectra models for stationary fields and we show that they provide accurate and robust statistical descriptions of a wide range of fields encountered in physics. These models are based on covariances of scattering coefficients, i.e. wavelet decomposition of a field coupled with a point-wise modulus. After introducing useful dimension reductions taking advantage of the regularity of a field under rotation and scaling, we validate these models on various multi-scale physical fields and demonstrate that they reproduce standard statistics, including spatial moments up to 4th order. These scattering spectra provide us with a low-dimensional structured representation that captures key properties encountered in a wide range of physical fields. These generic models can be used for data exploration, classification, parameter inference, symmetry detection, and component separation.

physics.data-an↗

arXiv2023

Scale Dependencies and Self-Similar Models with Wavelet Scattering Spectra

We introduce the wavelet scattering spectra which provide non-Gaussian models of time-series having stationary increments. A complex wavelet transform computes signal variations at each scale. Dependencies across scales are captured by the joint correlation across time and scales of wavelet coefficients and their modulus. This correlation matrix is nearly diagonalized by a second wavelet transform, which defines the scattering spectra. We show that this vector of moments characterizes a wide range of non-Gaussian properties of multi-scale processes. We prove that self-similar processes have scattering spectra which are scale invariant. This property can be tested statistically on a single realization and defines a class of wide-sense self-similar processes. We build maximum entropy models conditioned by scattering spectra coefficients, and generate new time-series with a microcanonical sampling algorithm. Applications are shown for highly non-Gaussian financial and turbulence time-series.

physics.data-an↗

arXiv2023

Unearthing InSights into Mars: Unsupervised Source Separation with Limited Data

Source separation involves the ill-posed problem of retrieving a set of source signals that have been observed through a mixing operator. Solving this problem requires prior knowledge, which is commonly incorporated by imposing regularity conditions on the source signals, or implicitly learned through supervised or unsupervised methods from existing data. While data-driven methods have shown great promise in source separation, they often require large amounts of data, which rarely exists in planetary space missions. To address this challenge, we propose an unsupervised source separation scheme for domains with limited data access that involves solving an optimization problem in the wavelet scattering covariance representation space$\unicode{x2014}$an interpretable, low-dimensional representation of stationary processes. We present a real-data example in which we remove transient, thermally-induced microtilts$\unicode{x2014}$known as glitches$\unicode{x2014}$from data recorded by a seismometer during NASA's InSight mission on Mars. Thanks to the wavelet scattering covariances' ability to capture non-Gaussian properties of stochastic processes, we are able to separate glitches using only a few glitch-free data snippets.

cs.LG↗

arXiv2023

Multi-scale clustering and source separation of InSight mission seismic data

Unsupervised source separation involves unraveling an unknown set of source signals recorded through a mixing operator, with limited prior knowledge about the sources, and only access to a dataset of signal mixtures. This problem is inherently ill-posed and is further challenged by the variety of timescales exhibited by sources in time series data from planetary space missions. As such, a systematic multi-scale unsupervised approach is needed to identify and separate sources at different timescales. Existing methods typically rely on a preselected window size that determines their operating timescale, limiting their capacity to handle multi-scale sources. To address this issue, we propose an unsupervised multi-scale clustering and source separation framework by leveraging wavelet scattering spectra that provide a low-dimensional representation of stochastic processes, capable of distinguishing between different non-Gaussian stochastic processes. Nested within this representation space, we develop a factorial variational autoencoder that is trained to probabilistically cluster sources at different timescales. To perform source separation, we use samples from clusters at multiple timescales obtained via the factorial variational autoencoder as prior information and formulate an optimization problem in the wavelet scattering spectra representation space. When applied to the entire seismic dataset recorded during the NASA InSight mission on Mars, containing sources varying greatly in timescale, our approach disentangles such different sources, e.g., minute-long transient one-sided pulses (known as "glitches") and structured ambient noises resulting from atmospheric activities that typically last for tens of minutes, and provides an opportunity to conduct further investigations into the isolated sources.

cs.LG↗