Helen Qu

Tatiana Acero-Cuellar, Federica Bianco, Gregory Dobler et al.

We present a study of the potential for Convolutional Neural Networks (CNNs) to enable separation of astrophysical transients from image artifacts, a task known as "real-bogus" classification without requiring a template subtracted (or difference) image which requires a computationally expensive process to generate, involving image matching on small spatial scales in large volumes of data. Using data from the Dark Energy Survey, we explore the use of CNNs to (1) automate the "real-bogus" classification, (2) reduce the computational costs of transient discovery. We compare the efficiency of two CNNs with similar architectures, one that uses "image triplets" (templates, search, and difference image) and one that takes as input the template and search only. We measure the decrease in efficiency associated with the loss of information in input finding that the testing accuracy is reduced from 96% to 91.1%. We further investigate how the latter model learns the required information from the template and search by exploring the saliency maps. Our work (1) confirms that CNNs are excellent models for "real-bogus" classification that rely exclusively on the imaging data and require no feature engineering task; (2) demonstrates that high-accuracy (> 90%) models can be built without the need to construct difference images, but some accuracy is lost. Since once trained, neural networks can generate predictions at minimal computational costs, we argue that future implementations of this methodology could dramatically reduce the computational costs in the detection of transients in synoptic surveys like Rubin Observatory's Legacy Survey of Space and Time by bypassing the Difference Image Analysis entirely.

Helen Qu, Rudy Morel, Michael McCabe et al.

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.

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.

Weiqiu You, Helen Qu, Marco Gatti et al.

Self-attributing neural networks (SANNs) present a potential path towards interpretable models for high-dimensional problems, but often face significant trade-offs in performance. In this work, we formally prove a lower bound on errors of per-feature SANNs, whereas group-based SANNs can achieve zero error and thus high performance. Motivated by these insights, we propose Sum-of-Parts (SOP), a framework that transforms any differentiable model into a group-based SANN, where feature groups are learned end-to-end without group supervision. SOP achieves state-of-the-art performance for SANNs on vision and language tasks, and we validate that the groups are interpretable on a range of quantitative and semantic metrics. We further validate the utility of SOP explanations in model debugging and cosmological scientific discovery. Our code is available at https://github.com/BrachioLab/sop

Helen Qu, Masao Sako, Anais Moller et al.

One of the brightest objects in the universe, supernovae (SNe) are powerful explosions marking the end of a star's lifetime. Supernova (SN) type is defined by spectroscopic emission lines, but obtaining spectroscopy is often logistically unfeasible. Thus, the ability to identify SNe by type using time-series image data alone is crucial, especially in light of the increasing breadth and depth of upcoming telescopes. We present a convolutional neural network method for fast supernova time-series classification, with observed brightness data smoothed in both the wavelength and time directions with Gaussian process regression. We apply this method to full duration and truncated SN time-series, to simulate retrospective as well as real-time classification performance. Retrospective classification is used to differentiate cosmologically useful Type Ia SNe from other SN types, and this method achieves >99% accuracy on this task. We are also able to differentiate between 6 SN types with 60% accuracy given only two nights of data and 98% accuracy retrospectively.

Shreya Havaldar, Helen Jin, Chaehyeon Kim et al.

As LLMs are deployed in knowledge-intensive settings (e.g., surgery, astronomy, therapy), users expect not just answers, but also meaningful explanations for those answers. In these settings, users are often domain experts (e.g., doctors, astrophysicists, psychologists) who require explanations that reflect expert-level reasoning. However, current evaluation schemes primarily emphasize plausibility or internal faithfulness of the explanation, which fail to capture whether the content of the explanation truly aligns with expert intuition. We formalize expert alignment as a criterion for evaluating explanations with T-FIX, a benchmark spanning seven knowledge-intensive domains. In collaboration with domain experts, we develop novel metrics to measure the alignment of LLM explanations with expert judgment.

Helen Jin, Shreya Havaldar, Chaehyeon Kim et al.

Feature-based methods are commonly used to explain model predictions, but these methods often implicitly assume that interpretable features are readily available. However, this is often not the case for high-dimensional data, and it can be hard even for domain experts to mathematically specify which features are important. Can we instead automatically extract collections or groups of features that are aligned with expert knowledge? To address this gap, we present FIX (Features Interpretable to eXperts), a benchmark for measuring how well a collection of features aligns with expert knowledge. In collaboration with domain experts, we propose FIXScore, a unified expert alignment measure applicable to diverse real-world settings across cosmology, psychology, and medicine domains in vision, language, and time series data modalities. With FIXScore, we find that popular feature-based explanation methods have poor alignment with expert-specified knowledge, highlighting the need for new methods that can better identify features interpretable to experts.

Helen Qu, Sang Michael Xie

Models trained on a labeled source domain (e.g., labeled images from wildlife camera traps) often generalize poorly when deployed on an out-of-distribution (OOD) target domain (e.g., images from new camera trap locations). In the domain adaptation setting where unlabeled target data is available, self-supervised pretraining (e.g., masked autoencoding or contrastive learning) is a promising method to mitigate this performance drop. Pretraining improves OOD error when the generic data augmentations used (e.g., masking or cropping) connect the source and target domains, which may be far apart in the input space. In this paper, we show on real-world tasks that standard fine-tuning after pretraining does not consistently improve OOD error over simply training from scratch on labeled source data. To better leverage pretraining for distribution shifts, we propose Connect Later: after pretraining with generic augmentations, fine-tune with targeted augmentations designed with knowledge of the distribution shift. Pretraining learns good representations within the source and target domains, while targeted augmentations connect the domains better during fine-tuning. Connect Later improves average OOD error over standard fine-tuning and supervised learning with targeted augmentations on 4 real-world datasets: Connect Later achieves the state-of-the-art on astronomical time-series classification (AstroClassification) by 2.5%, wildlife species identification (iWildCam-WILDS) with ResNet-50 by 0.9%, and tumor identification (Camelyon17-WILDS) with DenseNet121 by 1.1%; as well as best performance on a new dataset for astronomical time-series redshift prediction (Redshifts) by 0.03 RMSE (11% relative). Code and datasets are available at https://github.com/helenqu/connect-later.

Dimitrios Tanoglidis, Bhuvnesh Jain, Helen Qu

The deep learning architecture associated with ChatGPT and related generative AI products is known as transformers. Initially applied to Natural Language Processing, transformers and the self-attention mechanism they exploit have gained widespread interest across the natural sciences. The goal of this pedagogical and informal review is to introduce transformers to scientists. The review includes the mathematics underlying the attention mechanism, a description of the original transformer architecture, and a section on applications to time series and imaging data in astronomy. We include a Frequently Asked Questions section for readers who are curious about generative AI or interested in getting started with transformers for their research problem.

Helen Qu, Sang Michael Xie

CLIP and large multimodal models (LMMs) have better accuracy on examples involving concepts that are highly represented in the training data. However, the role of concept combinations in the training data on compositional generalization is largely unclear -- for instance, how does accuracy vary when a common object appears in an uncommon pairing with another object? In this paper, we investigate how word co-occurrence statistics in the pretraining dataset (a proxy for co-occurrence of visual concepts) impacts CLIP/LMM performance. To disentangle the effects of word co-occurrence frequencies from single-word frequencies, we measure co-occurrence with pointwise mutual information (PMI), which normalizes the joint probability of two words co-occurring by the probability of co-occurring independently. Using synthetically generated images with a variety of concept pairs, we show a strong correlation between PMI in the CLIP pretraining data and zero-shot accuracy in CLIP models trained on LAION-400M (r=0.97 and 14% accuracy gap between images in the top and bottom 5% of PMI values), demonstrating that even accuracy on common concepts is affected by the combination of concepts in the image. Leveraging this finding, we reproduce this effect in natural images by editing them to contain pairs with varying PMI, resulting in a correlation of r=0.75. Finally, we demonstrate that this behavior in CLIP transfers to LMMs built on top of CLIP (r=0.70 for TextVQA, r=0.62 for VQAv2). Our findings highlight the need for algorithms and architectures that improve compositional generalization in multimodal models without scaling the training data combinatorially. Our code is available at https://github.com/helenqu/multimodal-pretraining-pmi.

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.

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.

Raheem Karim Hashmani, Garrett W. Merz, Helen Qu et al.

We introduce a framework for generating highly multimodal datasets with explicitly calculable mutual information between modalities. This enables the construction of benchmark datasets that provide a novel testbed for systematic studies of mutual information estimators and multimodal self-supervised learning techniques. Our framework constructs realistic datasets with known mutual information using a flow-based generative model and a structured causal framework for generating correlated latent variables.

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.

Helen Qu, Masao Sako

Upcoming photometric surveys will discover tens of thousands of Type Ia supernovae (SNe Ia), vastly outpacing the capacity of our spectroscopic resources. In order to maximize the science return of these observations in the absence of spectroscopic information, we must accurately extract key parameters, such as SN redshifts, with photometric information alone. We present Photo-zSNthesis, a convolutional neural network-based method for predicting full redshift probability distributions from multi-band supernova lightcurves, tested on both simulated Sloan Digital Sky Survey (SDSS) and Vera C. Rubin Legacy Survey of Space and Time (LSST) data as well as observed SDSS SNe. We show major improvements over predictions from existing methods on both simulations and real observations as well as minimal redshift-dependent bias, which is a challenge due to selection effects, e.g. Malmquist bias. Specifically, we show a 61x improvement in prediction bias <Delta z> on PLAsTiCC simulations and 5x improvement on real SDSS data compared to results from a widely used photometric redshift estimator, LCFIT+Z. The PDFs produced by this method are well-constrained and will maximize the cosmological constraining power of photometric SNe Ia samples.