Jeff Shen

Payel Mukhopadhyay, Stefan S. Nixon, Romain Watteaux et al.

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, $α$, 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 $α$. 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.

Ruben Ohana, Michael McCabe, Lucas Meyer et al. · cambridge

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.

Jeff Shen, Peter Melchior

Machine learning techniques can automatically identify outliers in massive datasets, much faster and more reproducible than human inspection ever could. But finding such outliers immediately leads to the question: which features render this input anomalous? We propose a new feature attribution method, Inverse Multiscale Occlusion, that is specifically designed for outliers, for which we have little knowledge of the type of features we want to identify and expect that the model performance is questionable because anomalous test data likely exceed the limits of the training data. We demonstrate our method on outliers detected in galaxy spectra from the Dark Energy Survey Instrument and find its results to be much more interpretable than alternative attribution approaches.

Siavash Golkar, Jake Kovalic, Irina Espejo Morales et al.

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.

Michael McCabe, Payel Mukhopadhyay, Tanya Marwah et al. · cambridge

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.

Rudy Morel, Francesco Pio Ramunno, Jeff Shen et al.

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.

Jeff Shen, Francois Lanusse, Liam Holden Parker et al. · cambridge

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.

Jeff Shen, Lindsay M. Smith · princeton

We present cryptogram solving as an ideal testbed for studying neural network reasoning and generalization; models must decrypt text encoded with substitution ciphers, choosing from 26! possible mappings without explicit access to the cipher. We develop ALICE (an Architecture for Learning Interpretable Cryptogram dEcipherment), a simple encoder-only Transformer that sets a new state-of-the-art for both accuracy and speed on this decryption problem. Surprisingly, ALICE generalizes to unseen ciphers after training on only ${\sim}1500$ unique ciphers, a minute fraction ($3.7 \times 10^{-24}$) of the possible cipher space. To enhance interpretability, we introduce a novel bijective decoding head that explicitly models permutations via the Gumbel-Sinkhorn method, enabling direct extraction of learned cipher mappings. Through early exit and probing experiments, we reveal how ALICE progressively refines its predictions in a way that appears to mirror common human strategies -- early layers place greater emphasis on letter frequencies, while later layers form word-level structures. Our architectural innovations and analysis methods are applicable beyond cryptograms and offer new insights into neural network generalization and interpretability.