arXiv subjects

Shirley Ho

Publications and source records attributed to Shirley Ho.

At least 37 records · Page 2Linked to original sources

arXiv2024

xVal: A Continuous Numerical Tokenization for Scientific Language Models

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.

stat.ML↗

arXiv2024

Multiple Physics Pretraining for Physical Surrogate Models

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.

cs.LG↗

arXiv2024

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

We present the MULTIMODAL UNIVERSE, a large-scale multimodal dataset of scientific astronomical data, compiled specifically to facilitate machine learning research. Overall, the MULTIMODAL UNIVERSE contains hundreds of millions of astronomical observations, constituting 100\,TB 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 MULTIMODAL UNIVERSE and a description of how to access the data is available at https://github.com/MultimodalUniverse/MultimodalUniverse

astro-ph.IM↗

arXiv2024

Accelerating Giant Impact Simulations with Machine Learning

Constraining planet formation models based on the observed exoplanet population requires generating large samples of synthetic planetary systems, which can be computationally prohibitive. A significant bottleneck is simulating the giant impact phase, during which planetary embryos evolve gravitationally and combine to form planets, which may themselves experience later collisions. To accelerate giant impact simulations, we present a machine learning (ML) approach to predicting collisional outcomes in multiplanet systems. Trained on more than 500,000 $N$-body simulations of three-planet systems, we develop an ML model that can accurately predict which two planets will experience a collision, along with the state of the post-collision planets, from a short integration of the system's initial conditions. Our model greatly improves on non-ML baselines that rely on metrics from dynamics theory, which struggle to accurately predict which pair of planets will experience a collision. By combining with a model for predicting long-term stability, we create an ML-based giant impact emulator, which can predict the outcomes of giant impact simulations with reasonable accuracy and a speedup of up to four orders of magnitude. We expect our model to enable analyses that would not otherwise be computationally feasible. As such, we release our training code, along with an easy-to-use API for our collision outcome model and giant impact emulator.

astro-ph.EP↗

arXiv2024

Field-level Emulation of Cosmic Structure Formation with Cosmology and Redshift Dependence

We present a field-level emulator for large-scale structure, capturing the cosmology dependence and the time evolution of cosmic structure formation. The emulator maps linear displacement fields to their corresponding nonlinear displacements from N-body simulations at specific redshifts. Designed as a neural network, the emulator incorporates style parameters that encode dependencies on $Ω_{\rm m}$ and the linear growth factor $D(z)$ at redshift $z$. We train our model on the six-dimensional N-body phase space, predicting particle velocities as the time derivative of the model's displacement outputs. This innovation results in significant improvements in training efficiency and model accuracy. Tested on diverse cosmologies and redshifts not seen during training, the emulator achieves percent-level accuracy on scales of $k\sim~1~{\rm Mpc}^{-1}~h$ at $z=0$, with improved performance at higher redshifts. We compare predicted structure formation histories with N-body simulations via merger trees, finding consistent merger event sequences and statistical properties.

astro-ph.CO↗

arXiv2024

Galaxy Clustering Analysis with SimBIG and the Wavelet Scattering Transform

The non-Gaussisan spatial distribution of galaxies traces the large-scale structure of the Universe and therefore constitutes a prime observable to constrain cosmological parameters. We conduct Bayesian inference of the $Λ$CDM parameters $Ω_m$, $Ω_b$, $h$, $n_s$, and $σ_8$ from the BOSS CMASS galaxy sample by combining the wavelet scattering transform (WST) with a simulation-based inference approach enabled by the ${\rm S{\scriptsize IM}BIG}$ forward model. We design a set of reduced WST statistics that leverage symmetries of redshift-space data. Posterior distributions are estimated with a conditional normalizing flow trained on 20,000 simulated ${\rm S{\scriptsize IM}BIG}$ galaxy catalogs with survey realism. We assess the accuracy of the posterior estimates using simulation-based calibration and quantify generalization and robustness to the change of forward model using a suite of 2,000 test simulations. When probing scales down to $k_{\rm max}=0.5~h/\text{Mpc}$, we are able to derive accurate posterior estimates that are robust to the change of forward model for all parameters, except $σ_8$. We mitigate the robustness issues with $σ_8$ by removing the WST coefficients that probe scales smaller than $k \sim 0.3~h/\text{Mpc}$. Applied to the BOSS CMASS sample, our WST analysis yields seemingly improved constraints obtained from a standard PT-based power spectrum analysis with $k_{\rm max}=0.25~h/\text{Mpc}$ for all parameters except $h$. However, we still raise concerns on these results. The observational predictions significantly vary across different normalizing flow architectures, which we interpret as a form of model misspecification. This highlights a key challenge for forward modeling approaches when using summary statistics that are sensitive to detailed model-specific or observational imprints on galaxy clustering.

astro-ph.CO↗

arXiv2024

AstroCLIP: A Cross-Modal Foundation Model for Galaxies

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.

astro-ph.IM↗

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

Latent Stochastic Differential Equations for Modeling Quasar Variability and Inferring Black Hole Properties

Quasars are bright and unobscured active galactic nuclei (AGN) thought to be powered by the accretion of matter around supermassive black holes at the centers of galaxies. The temporal variability of a quasar's brightness contains valuable information about its physical properties. The UV/optical variability is thought to be a stochastic process, often represented as a damped random walk described by a stochastic differential equation (SDE). Upcoming wide-field telescopes such as the Rubin Observatory Legacy Survey of Space and Time (LSST) are expected to observe tens of millions of AGN in multiple filters over a ten year period, so there is a need for efficient and automated modeling techniques that can handle the large volume of data. Latent SDEs are machine learning models well suited for modeling quasar variability, as they can explicitly capture the underlying stochastic dynamics. In this work, we adapt latent SDEs to jointly reconstruct multivariate quasar light curves and infer their physical properties such as the black hole mass, inclination angle, and temperature slope. Our model is trained on realistic simulations of LSST ten year quasar light curves, and we demonstrate its ability to reconstruct quasar light curves even in the presence of long seasonal gaps and irregular sampling across different bands, outperforming a multioutput Gaussian process regression baseline. Our method has the potential to provide a deeper understanding of the physical properties of quasars and is applicable to a wide range of other multivariate time series with missing data and irregular sampling.

astro-ph.GA↗

arXiv2024

{\sc SimBIG}: Cosmological Constraints using Simulation-Based Inference of Galaxy Clustering with Marked Power Spectra

We present the first $Λ$CDM cosmological analysis performed on a galaxy survey using marked power spectra. The marked power spectrum is the two-point function of a marked field, where galaxies are weighted by a function that depends on their local density. The presence of the mark leads these statistics to contain higher-order information of the original galaxy field, making them a good candidate to exploit the non-Gaussian information of a galaxy catalog. In this work we make use of \simbig, a forward modeling framework for galaxy clustering analyses, and perform simulation-based inference using normalizing flows to infer the posterior distribution of the $Λ$CDM cosmological parameters. We consider different mark configurations (ways to weight the galaxy field) and deploy them in the \simbig~pipeline to analyze the corresponding marked power spectra measured from a subset of the BOSS galaxy sample. We analyze the redshift-space mark power spectra decomposed in $\ell = 0, 2, 4$ multipoles and include scales up to the non-linear regime. Among the various mark configurations considered, the ones that give the most stringent cosmological constraints produce posterior median and $68\%$ confidence limits on the growth of structure parameters equal to $Ω_m=0.273^{+0.040}_{-0.030}$ and $σ_8=0.777^{+0.077}_{-0.071}$. Compared to a perturbation theory analysis using the power spectrum of the same dataset, the \simbig~marked power spectra constraints on $σ_8$ are up to $1.2\times$ tighter, while no improvement is seen for the other cosmological parameters.

astro-ph.CO↗

arXiv2024

${\rm S{\scriptsize IM}BIG}$: Cosmological Constraints from the Redshift-Space Galaxy Skew Spectra

Extracting the non-Gaussian information of the cosmic large-scale structure (LSS) is vital in unlocking the full potential of the rich datasets from the upcoming stage-IV galaxy surveys. Galaxy skew spectra serve as efficient beyond-two-point statistics, encapsulating essential bispectrum information with computational efficiency akin to power spectrum analysis. This paper presents the first cosmological constraints from analyzing the full set of redshift-space galaxy skew spectra of the data from the SDSS-III BOSS, accessing cosmological information down to nonlinear scales. Employing the ${\rm S{\scriptsize IM}BIG}$ forward modeling framework and simulation-based inference via normalizing flows, we analyze the CMASS-SGC sub-sample, which constitute approximately 10\% of the full BOSS data. Analyzing the scales up to $k_{\rm max}=0.5 \, {\rm Mpc}^{-1}h$, we find that the skew spectra improve the constraints on $Ω_{\rm m}, Ω_{\rm b}, h$, and $n_s$ by 34\%, 35\%, 18\%, 10\%, respectively, compared to constraints from previous ${\rm S{\scriptsize IM}BIG}$ power spectrum multipoles analysis, yielding $Ω_{\rm m}=0.288^{+0.024}_{-0.034}$, $Ω_{\rm b}= 0.043^{+0.005}_{-0.007}$, $h=0.759^{+0.104}_{-0.050}$, $n_{\rm s} = 0.918^{+0.041}_{-0.090}$ (at 68\% confidence limit). On the other hand, the constraints on $σ_8$ are weaker than from the power spectrum. Including the Big Bang Nucleosynthesis (BBN) prior on baryon density reduces the uncertainty on the Hubble parameter further, achieving $h=0.750^{+0.034}_{-0.032}$, which is a 38\% improvement over the constraint from the power spectrum with the same prior. Compared to the ${\rm S{\scriptsize IM}BIG}$ bispectrum (monopole) analysis, skew spectra offer comparable constraints on larger scales ($k_{\rm max}<0.3\, {\rm Mpc}^{-1}h$) for most parameters except for $σ_8$.

astro-ph.CO↗

arXiv2024

Particle clustering in turbulence: Prediction of spatial and statistical properties with deep learning

We investigate the utility of deep learning for modeling the clustering of particles that are aerodynamically coupled to turbulent fluids. Using a Lagrangian particle module within the Athena++ hydrodynamics code, we simulate the dynamics of particles in the Epstein drag regime within a periodic domain of isotropic forced hydrodynamic turbulence. This setup is an idealized model relevant to the collisional growth of micron to mm-sized dust particles in early stage planet formation. The simulation data are used to train a U-Net deep learning model to predict gridded three-dimensional representations of the particle density and velocity fields, given as input the corresponding fluid fields. The trained model qualitatively captures the filamentary structure of clustered particles in a highly non-linear regime. We assess model fidelity by calculating metrics of the density field (the radial distribution function) and of the velocity field (the relative velocity and the relative radial velocity between particles). Although trained only on the spatial fields, the model predicts these statistical quantities with errors that are typically <10%. Our results suggest that, given appropriately expanded training data, deep learning could complement direct numerical simulations in predicting particle clustering within turbulent flows.

astro-ph.EP↗

arXiv2023

Predicting the Initial Conditions of the Universe using a Deterministic Neural Network

Finding the initial conditions that led to the current state of the universe is challenging because it involves searching over an intractable input space of initial conditions, along with modeling their evolution via tools such as N-body simulations which are computationally expensive. Recently, deep learning has emerged as a surrogate for N-body simulations by directly learning the mapping between the linear input of an N-body simulation and the final nonlinear output from the simulation, significantly accelerating the forward modeling. However, this still does not reduce the search space for initial conditions. In this work, we pioneer the use of a deterministic convolutional neural network for learning the reverse mapping and show that it accurately recovers the initial linear displacement field over a wide range of scales ($<1$-$2\%$ error up to nearly $k\simeq0.8$-$0.9 \text{ Mpc}^{-1}h$), despite the one-to-many mapping of the inverse problem (due to the divergent backward trajectories at smaller scales). Specifically, we train a V-Net architecture, which outputs the linear displacement of an N-body simulation, given the nonlinear displacement at redshift $z=0$ and the cosmological parameters. The results of our method suggest that a simple deterministic neural network is sufficient for accurately approximating the initial linear states, potentially obviating the need for the more complex and computationally demanding backward modeling methods that were recently proposed.

astro-ph.CO↗

arXiv2023

Leaving No Branches Behind: Predicting Baryonic Properties of Galaxies from Merger Trees

Galaxies play a key role in our endeavor to understand how structure formation proceeds in the Universe. For any precision study of cosmology or galaxy formation, there is a strong demand for huge sets of realistic mock galaxy catalogs, spanning cosmologically significant volumes. For such a daunting task, methods that can produce a direct mapping between dark matter halos from dark matter-only simulations and galaxies are strongly preferred, as producing mocks from full-fledged hydrodynamical simulations or semi-analytical models is too expensive. Here we present a Graph Neural Network-based model that is able to accurately predict key properties of galaxies such as stellar mass, $g-r$ color, star formation rate, gas mass, stellar metallicity, and gas metallicity, purely from dark matter properties extracted from halos along the full assembly history of the galaxies. Tests based on the TNG300 simulation of the IllustrisTNG project show that our model can recover the baryonic properties of galaxies to high accuracy, over a wide redshift range ($z = 0-5$), for all galaxies with stellar masses more massive than $10^9\,M_\odot$ and their progenitors, with strong improvements over the state-of-the-art methods. We further show that our method makes substantial strides toward providing an understanding of the implications of the IllustrisTNG galaxy formation model.

astro-ph.GA↗

arXiv2023

Surrogate Modeling for Computationally Expensive Simulations of Supernovae in High-Resolution Galaxy Simulations

Some stars are known to explode at the end of their lives, called supernovae (SNe). The substantial amount of matter and energy that SNe release provides significant feedback to star formation and gas dynamics in a galaxy. SNe release a substantial amount of matter and energy to the interstellar medium, resulting in significant feedback to star formation and gas dynamics in a galaxy. While such feedback has a crucial role in galaxy formation and evolution, in simulations of galaxy formation, it has only been implemented using simple {\it sub-grid models} instead of numerically solving the evolution of gas elements around SNe in detail due to a lack of resolution. We develop a method combining machine learning and Gibbs sampling to predict how a supernova (SN) affects the surrounding gas. The fidelity of our model in the thermal energy and momentum distribution outperforms the low-resolution SN simulations. Our method can replace the SN sub-grid models and help properly simulate un-resolved SN feedback in galaxy formation simulations. We find that employing our new approach reduces the necessary computational cost to $\sim$ 1 percent compared to directly resolving SN feedback.

astro-ph.GA↗

arXiv2023

Reusability report: Prostate cancer stratification with diverse biologically-informed neural architectures

In Elmarakeby et al., "Biologically informed deep neural network for prostate cancer discovery", a feedforward neural network with biologically informed, sparse connections (P-NET) was presented to model the state of prostate cancer. We verified the reproducibility of the study conducted by Elmarakeby et al., using both their original codebase, and our own re-implementation using more up-to-date libraries. We quantified the contribution of network sparsification by Reactome biological pathways, and confirmed its importance to P-NET's superior performance. Furthermore, we explored alternative neural architectures and approaches to incorporating biological information into the networks. We experimented with three types of graph neural networks on the same training data, and investigated the clinical prediction agreement between different models. Our analyses demonstrated that deep neural networks with distinct architectures make incorrect predictions for individual patient that are persistent across different initializations of a specific neural architecture. This suggests that different neural architectures are sensitive to different aspects of the data, an important yet under-explored challenge for clinical prediction tasks.

cs.LG↗

arXiv2023

${\rm S{\scriptsize IM}BIG}$: The First Cosmological Constraints from the Non-Linear Galaxy Bispectrum

We present the first cosmological constraints from analyzing higher-order galaxy clustering on non-linear scales. We use ${\rm S{\scriptsize IM}BIG}$, a forward modeling framework for galaxy clustering analyses that employs simulation-based inference to perform highly efficient cosmological inference using normalizing flows. It leverages the predictive power of high-fidelity simulations and robustly extracts cosmological information from regimes inaccessible with current standard analyses. In this work, we apply ${\rm S{\scriptsize IM}BIG}$ to a subset of the BOSS galaxy sample and analyze the redshift-space bispectrum monopole, $B_0(k_1, k_2, k_3)$, to $k_{\rm max}=0.5\,h/{\rm Mpc}$. We achieve 1$σ$ constraints of $Ω_m=0.293^{+0.027}_{-0.027}$ and $σ_8= 0.783^{+0.040}_{-0.038}$, which are more than 1.2 and 2.4$\times$ tighter than constraints from standard power spectrum analyses of the same dataset. We also derive 1.4, 1.4, 1.7$\times$ tighter constraints on $Ω_b$, $h$, $n_s$. This improvement comes from additional cosmological information in higher-order clustering on non-linear scales and, for $σ_8$, is equivalent to the gain expected from a standard analysis on a $\sim$4$\times$ larger galaxy sample. Even with our BOSS subsample, which only spans 10% of the full BOSS volume, we derive competitive constraints on the growth of structure: $S_8 = 0.774^{+0.056}_{-0.053}$. Our constraint is consistent with results from both cosmic microwave background and weak lensing. Combined with a $ω_b$ prior from Big Bang Nucleosynthesis, we also derive a constraint on $H_0=67.6^{+2.2}_{-1.8}\,{\rm km\,s^{-1}\,Mpc^{-1}}$ that is consistent with early universe constraints.

astro-ph.CO↗

arXiv2023

${\rm S{\scriptsize IM}BIG}$: The First Cosmological Constraints from Non-Gaussian and Non-Linear Galaxy Clustering

The 3D distribution of galaxies encodes detailed cosmological information on the expansion and growth history of the Universe. We present the first cosmological constraints that exploit non-Gaussian cosmological information on non-linear scales from galaxy clustering, inaccessible with current standard analyses. We analyze a subset of the BOSS galaxy survey using ${\rm S{\scriptsize IM}BIG}$, a new framework for cosmological inference that leverages high-fidelity simulations and deep generative models. We use two clustering statistics beyond the standard power spectrum: the bispectrum and a convolutional neural network based summary of the galaxy field. We infer constraints on $Λ$CDM parameters, $Ω_b$, $h$, $n_s$, $Ω_m$, and $σ_8$, that are 1.6, 1.5, 1.7, 1.2, and 2.3$\times$ tighter than power spectrum analyses. With this increased precision, we derive constraints on the Hubble constant, $H_0$, and $S_8 = σ_8 \sqrt{Ω_m/0.3}$ that are competitive with other cosmological probes, even with a sample that only spans 10% of the full BOSS volume. Our $H_0$ constraints, imposing the Big Bang Nucleosynthesis prior on the baryon density, are consistent with the early time constraints from the cosmic microwave background (CMB). Meanwhile, our $S_8$ constraints are consistent with weak lensing experiments and similarly lie below CMB constraints. Lastly, we present forecasts to show that future work extending ${\rm S{\scriptsize IM}BIG}$ to upcoming spectroscopic galaxy surveys (DESI, PFS, Euclid) will produce leading $H_0$ and $S_8$ constraints that bridge the gap between early and late time measurements and shed light on current cosmic tensions.

astro-ph.CO↗