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Shirley Ho

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11 papers

2 author rows

NeurIPS Conference 2025 Conference Paper

AION-1: Omnimodal Foundation Model for Astronomical Sciences

Liam Parker
Francois Lanusse
Jeff Shen
Ollie Liu
Tom Hehir
Leopoldo Sarra
Lucas Meyer
Micah Bowles

While foundation models have shown promise across a variety of fields, astronomy lacks a unified framework for joint modeling across its highly diverse data modalities. In this paper, we present AION-1, the first large-scale multimodal foundation family of models for astronomy. AION-1 enables arbitrary transformations between heterogeneous data types using a two-stage architecture: modality-specific tokenization followed by transformer-based masked modeling of cross-modal token sequences. Trained on over 200M astronomical objects, AION-1 demonstrates strong performance across regression, classification, generation, and object retrieval tasks. Beyond astronomy, AION-1 provides a scalable blueprint for multimodal scientific foundation models that can seamlessly integrate heterogeneous combinations of real-world observations. Our model release is entirely open source, including the dataset, training script, and weights.

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NeurIPS Conference 2025 Conference Paper

Lost in Latent Space: An Empirical Study of Latent Diffusion Models for Physics Emulation

François Rozet
Ruben Ohana
Michael McCabe
Gilles Louppe
Francois Lanusse
Shirley Ho

The steep computational cost of diffusion models at inference hinders their use as fast physics emulators. In the context of image and video generation, this computational drawback has been addressed by generating in the latent space of an autoencoder instead of the pixel space. In this work, we investigate whether a similar strategy can be effectively applied to the emulation of dynamical systems and at what cost. We find that the accuracy of latent-space emulation is surprisingly robust to a wide range of compression rates (up to 1000x). We also show that diffusion-based emulators are consistently more accurate than non-generative counterparts and compensate for uncertainty in their predictions with greater diversity. Finally, we cover practical design choices, spanning from architectures to optimizers, that we found critical to train latent-space emulators.

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NeurIPS Conference 2025 Conference Paper

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

Rudy Morel
Francesco Ramunno
Jeff Shen
Alberto Bietti
Kyunghyun Cho
Miles Cranmer
Siavash Golkar
OLEXANDR GUGNIN

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.

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NeurIPS Conference 2024 Conference Paper

Multiple Physics Pretraining for Spatiotemporal Surrogate Models

Michael McCabe
Bruno Régaldo-Saint Blancard
Liam Parker
Ruben Ohana
Miles Cranmer
Alberto Bietti
Michael Eickenberg
Siavash Golkar

We introduce multiple physics pretraining (MPP), an autoregressive task-agnostic pretraining approach for physical surrogate modeling of spatiotemporal systems with transformers. In MPP, rather than training one model on a specific physical system, we train a backbone model to predict the dynamics of multiple heterogeneous physical systems simultaneously in order to learn features that are broadly useful across systems and facilitate transfer. In order to learn effectively in this setting, we introduce a shared embedding and normalization strategy that projects the fields of multiple systems into a shared embedding space. We validate the efficacy of our approach on both pretraining and downstream tasks over a broad fluid mechanics-oriented benchmark. We show that a single MPP-pretrained transformer is able to match or outperform task-specific baselines on all pretraining sub-tasks without the need for finetuning. For downstream tasks, we demonstrate that finetuning MPP-trained models results in more accurate predictions across multiple time-steps on systems with previously unseen physical components or higher dimensional systems compared to training from scratch or finetuning pretrained video foundation models. We open-source our code and model weights trained at multiple scales for reproducibility.

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NeurIPS Conference 2024 Conference Paper

The Multimodal Universe: Enabling Large-Scale Machine Learning with 100 TB of Astronomical Scientific Data

Eirini Angeloudi
Jeroen Audenaert
Micah Bowles
Benjamin M. Boyd
David Chemaly
Brian Cherinka
Ioana Ciucă
Miles Cranmer

We present the Multimodal Universe, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, our dataset contains hundreds of millions of astronomical observations, constituting 100TB of multi-channel and hyper-spectral images, spectra, multivariate time series, as well as a wide variety of associated scientific measurements and metadata. In addition, we include a range of benchmark tasks representative of standard practices for machine learning methods in astrophysics. This massive dataset will enable the development of large multi-modal models specifically targeted towards scientific applications. All codes used to compile the dataset, and a description of how to access the data is available at https: //github. com/MultimodalUniverse/MultimodalUniverse

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NeurIPS Conference 2024 Conference Paper

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

Ruben Ohana
Michael McCabe
Lucas Meyer
Rudy Morel
Fruzsina J. Agocs
Miguel Beneitez
Marsha Berger
Blakesley Burkhart

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.

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ICLR Conference 2022 Conference Paper

Learned Simulators for Turbulence

Kimberly L. Stachenfeld
Drummond Buschman Fielding
Dmitrii Kochkov
Miles D. Cranmer
Tobias Pfaff
Jonathan Godwin
Can Cui
Shirley Ho

Turbulence simulation with classical numerical solvers requires high-resolution grids to accurately resolve dynamics. Here we train learned simulators at low spatial and temporal resolutions to capture turbulent dynamics generated at high resolution. We show that our proposed model can simulate turbulent dynamics more accurately than classical numerical solvers at the comparably low resolutions across various scientifically relevant metrics. Our model is trained end-to-end from data and is capable of learning a range of challenging chaotic and turbulent dynamics at low resolution, including trajectories generated by the state-of-the-art Athena++ engine. We show that our simpler, general-purpose architecture outperforms various more specialized, turbulence-specific architectures from the learned turbulence simulation literature. In general, we see that learned simulators yield unstable trajectories; however, we show that tuning training noise and temporal downsampling solves this problem. We also find that while generalization beyond the training distribution is a challenge for learned models, training noise, added loss constraints, and dataset augmentation can help. Broadly, we conclude that our learned simulator outperforms traditional solvers run on coarser grids, and emphasize that simple design choices can offer stability and robust generalization.

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NeurIPS Conference 2020 Conference Paper

Discovering Symbolic Models from Deep Learning with Inductive Biases

Miles Cranmer
Alvaro Sanchez Gonzalez
Peter Battaglia
Rui Xu
Kyle Cranmer
David Spergel
Shirley Ho

We develop a general approach to distill symbolic representations of a learned deep model by introducing strong inductive biases. We focus on Graph Neural Networks (GNNs). The technique works as follows: we first encourage sparse latent representations when we train a GNN in a supervised setting, then we apply symbolic regression to components of the learned model to extract explicit physical relations. We find the correct known equations, including force laws and Hamiltonians, can be extracted from the neural network. We then apply our method to a non-trivial cosmology example—a detailed dark matter simulation—and discover a new analytic formula which can predict the concentration of dark matter from the mass distribution of nearby cosmic structures. The symbolic expressions extracted from the GNN using our technique also generalized to out-of-distribution-data better than the GNN itself. Our approach offers alternative directions for interpreting neural networks and discovering novel physical principles from the representations they learn.

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ICML Conference 2016 Conference Paper

Estimating Cosmological Parameters from the Dark Matter Distribution

Siamak Ravanbakhsh
Junier B. Oliva
Sebastian Fromenteau
Layne Price
Shirley Ho
Jeff G. Schneider
Barnabás Póczos

A grand challenge of the 21st century cosmology is to accurately estimate the cosmological parameters of our Universe. A major approach in estimating the cosmological parameters is to use the large scale matter distribution of the Universe. Galaxy surveys provide the means to map out cosmic large-scale structure in three dimensions. Information about galaxy locations is typically summarized in a "single" function of scale, such as the galaxy correlation function or power-spectrum. We show that it is possible to estimate these cosmological parameters directly from the distribution of matter. This paper presents the application of deep 3D convolutional networks to volumetric representation of dark matter simulations as well as the results obtained using a recently proposed distribution regression framework, showing that machine learning techniques are comparable to, and can sometimes outperform, maximum-likelihood point estimates using "cosmological models". This opens the way to estimating the parameters of our Universe with higher accuracy.

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ICML Conference 2015 Conference Paper

Finding Galaxies in the Shadows of Quasars with Gaussian Processes

Roman Garnett
Shirley Ho
Jeff G. Schneider

We develop an automated technique for detecting damped Lyman-αabsorbers (DLAs) along spectroscopic sightlines to quasi-stellar objects (QSOs or quasars). The detection of DLAs in large-scale spectroscopic surveys such as SDSS–III is critical to address outstanding cosmological questions, such as the nature of galaxy formation. We use nearly 50000 QSO spectra to learn a tailored Gaussian process model for quasar emission spectra, which we apply to the DLA detection problem via Bayesian model selection. We demonstrate our method’s effectiveness with a large-scale validation experiment on over 100000 spectra, with excellent performance.

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NeurIPS Conference 2015 Conference Paper

Optimal Ridge Detection using Coverage Risk

Yen-Chi Chen
Christopher Genovese
Shirley Ho
Larry Wasserman

We introduce the concept of coverage risk as an error measure for density ridge estimation. The coverage risk generalizes the mean integrated square error to set estimation. We propose two risk estimators for the coverage risk and we show that we can select tuning parameters by minimizing the estimated risk. We study the rate of convergence for coverage risk and prove consistency of the risk estimators. We apply our method to three simulated datasets and to cosmology data. In all the examples, the proposed method successfully recover the underlying density structure.

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