Liam Parker

Michael McCabe, Bruno Régaldo-Saint Blancard, Liam Holden Parker et al. · cambridge

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.

Siavash Golkar, Mariel Pettee, Michael Eickenberg et al. · cambridge

Due in part to their discontinuous and discrete default encodings for numbers, Large Language Models (LLMs) have not yet been commonly used to process numerically-dense scientific datasets. Rendering datasets as text, however, could help aggregate diverse and multi-modal scientific data into a single training corpus, thereby potentially facilitating the development of foundation models for science. In this work, we introduce xVal, a strategy for continuously tokenizing numbers within language models that results in a more appropriate inductive bias for scientific applications. By training specially-modified language models from scratch on a variety of scientific datasets formatted as text, we find that xVal generally outperforms other common numerical tokenization strategies on metrics including out-of-distribution generalization and computational efficiency.

Pablo Lemos, Liam Parker, ChangHoon Hahn et al.

We present the first simulation-based inference (SBI) of cosmological parameters from field-level analysis of galaxy clustering. Standard galaxy clustering analyses rely on analyzing summary statistics, such as the power spectrum, $P_\ell$, with analytic models based on perturbation theory. Consequently, they do not fully exploit the non-linear and non-Gaussian features of the galaxy distribution. To address these limitations, we use the {\sc SimBIG} forward modelling framework to perform SBI using normalizing flows. We apply SimBIG to a subset of the BOSS CMASS galaxy sample using a convolutional neural network with stochastic weight averaging to perform massive data compression of the galaxy field. We infer constraints on $Ω_m = 0.267^{+0.033}_{-0.029}$ and $σ_8=0.762^{+0.036}_{-0.035}$. While our constraints on $Ω_m$ are in-line with standard $P_\ell$ analyses, those on $σ_8$ are $2.65\times$ tighter. Our analysis also provides constraints on the Hubble constant $H_0=64.5 \pm 3.8 \ {\rm km / s / Mpc}$ from galaxy clustering alone. This higher constraining power comes from additional non-Gaussian cosmological information, inaccessible with $P_\ell$. We demonstrate the robustness of our analysis by showcasing our ability to infer unbiased cosmological constraints from a series of test simulations that are constructed using different forward models than the one used in our training dataset. This work not only presents competitive cosmological constraints but also introduces novel methods for leveraging additional cosmological information in upcoming galaxy surveys like DESI, PFS, and Euclid.

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.

Nolan Koblischke, Liam Parker, Francois Lanusse et al.

Finding scientifically interesting phenomena through slow, manual labeling campaigns severely limits our ability to explore the billions of galaxy images produced by telescopes. In this work, we develop a pipeline to create a semantic search engine from completely unlabeled image data. Our method leverages Vision-Language Models (VLMs) to generate descriptions for galaxy images, then contrastively aligns a pre-trained multimodal astronomy foundation model with these embedded descriptions to produce searchable embeddings at scale. We find that current VLMs provide descriptions that are sufficiently informative to train a semantic search model that outperforms direct image similarity search. Our model, AION-Search, achieves state-of-the-art zero-shot performance on finding rare phenomena despite training on randomly selected images with no deliberate curation for rare cases. Furthermore, we introduce a VLM-based re-ranking method that nearly doubles the recall for our most challenging targets in the top-100 results. For the first time, AION-Search enables flexible semantic search scalable to 140 million galaxy images, enabling discovery from previously infeasible searches. More broadly, our work provides an approach for making large, unlabeled scientific image archives semantically searchable, expanding data exploration capabilities in fields from Earth observation to microscopy. The code, data, and app are publicly available at https://github.com/NolanKoblischke/AION-Search

Liam Parker, Emre Onal, Anton Stengel et al.

Neural Collapse (NC) gives a precise description of the representations of classes in the final hidden layer of classification neural networks. This description provides insights into how these networks learn features and generalize well when trained past zero training error. However, to date, (NC) has only been studied in the final layer of these networks. In the present paper, we provide the first comprehensive empirical analysis of the emergence of (NC) in the intermediate hidden layers of these classifiers. We examine a variety of network architectures, activations, and datasets, and demonstrate that some degree of (NC) emerges in most of the intermediate hidden layers of the network, where the degree of collapse in any given layer is typically positively correlated with the depth of that layer in the neural network. Moreover, we remark that: (1) almost all of the reduction in intra-class variance in the samples occurs in the shallower layers of the networks, (2) the angular separation between class means increases consistently with hidden layer depth, and (3) simple datasets require only the shallower layers of the networks to fully learn them, whereas more difficult ones require the entire network. Ultimately, these results provide granular insights into the structural propagation of features through classification neural networks.

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.

Liam Parker, Francois Lanusse, Siavash Golkar et al.

We present AstroCLIP, a single, versatile model that can embed both galaxy images and spectra into a shared, physically meaningful latent space. These embeddings can then be used - without any model fine-tuning - for a variety of downstream tasks including (1) accurate in-modality and cross-modality semantic similarity search, (2) photometric redshift estimation, (3) galaxy property estimation from both images and spectra, and (4) morphology classification. Our approach to implementing AstroCLIP consists of two parts. First, we embed galaxy images and spectra separately by pretraining separate transformer-based image and spectrum encoders in self-supervised settings. We then align the encoders using a contrastive loss. We apply our method to spectra from the Dark Energy Spectroscopic Instrument and images from its corresponding Legacy Imaging Survey. Overall, we find remarkable performance on all downstream tasks, even relative to supervised baselines. For example, for a task like photometric redshift prediction, we find similar performance to a specifically-trained ResNet18, and for additional tasks like physical property estimation (stellar mass, age, metallicity, and sSFR), we beat this supervised baseline by 19\% in terms of $R^2$. We also compare our results to a state-of-the-art self-supervised single-modal model for galaxy images, and find that our approach outperforms this benchmark by roughly a factor of two on photometric redshift estimation and physical property prediction in terms of $R^2$, while remaining roughly in-line in terms of morphology classification. Ultimately, our approach represents the first cross-modal self-supervised model for galaxies, and the first self-supervised transformer-based architectures for galaxy images and spectra.