arXiv subjects

Rose Yu

Publications and source records attributed to Rose Yu.

At least 55 records · Page 3Linked to original sources

arXiv2025

Can LLMs Understand Time Series Anomalies?

Large Language Models (LLMs) have gained popularity in time series forecasting, but their potential for anomaly detection remains largely unexplored. Our study investigates whether LLMs can understand and detect anomalies in time series data, focusing on zero-shot and few-shot scenarios. Inspired by conjectures about LLMs' behavior from time series forecasting research, we formulate key hypotheses about LLMs' capabilities in time series anomaly detection. We design and conduct principled experiments to test each of these hypotheses. Our investigation reveals several surprising findings about LLMs for time series: (1) LLMs understand time series better as images rather than as text, (2) LLMs do not demonstrate enhanced performance when prompted to engage in explicit reasoning about time series analysis. (3) Contrary to common beliefs, LLMs' understanding of time series does not stem from their repetition biases or arithmetic abilities. (4) LLMs' behaviors and performance in time series analysis vary significantly across different models. This study provides the first comprehensive analysis of contemporary LLM capabilities in time series anomaly detection. Our results suggest that while LLMs can understand trivial time series anomalies, we have no evidence that they can understand more subtle real-world anomalies. Many common conjectures based on their reasoning capabilities do not hold. All synthetic dataset generators, final prompts, and evaluation scripts have been made available in https://github.com/rose-stl-lab/anomllm.

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arXiv2025

ClimaQA: An Automated Evaluation Framework for Climate Question Answering Models

The use of Large Language Models (LLMs) in climate science has recently gained significant attention. However, a critical issue remains: the lack of a comprehensive evaluation framework capable of assessing the quality and scientific validity of model outputs. To address this issue, we develop ClimaGen (Climate QA Generator), an adaptive learning framework that generates question-answer pairs from graduate textbooks with climate scientists in the loop. As a result, we present ClimaQA-Gold, an expert-annotated benchmark dataset alongside ClimaQA-Silver, a large-scale, comprehensive synthetic QA dataset for climate science. Finally, we develop evaluation strategies and compare different LLMs on our benchmarks. Our results offer novel insights into various approaches used to enhance knowledge of climate LLMs. The source code is publicly available at https://github.com/Rose-STL-Lab/genie-climaqa

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arXiv2025

Diffusion-BBO: Diffusion-Based Inverse Modeling for Online Black-Box Optimization

Online black-box optimization (BBO) aims to optimize an objective function by iteratively querying a black-box oracle in a sample-efficient way. While prior studies focus on forward approaches such as Gaussian Processes (GPs) to learn a surrogate model for the unknown objective function, they struggle with steering clear of out-of-distribution and invalid designs in scientific discovery tasks. Recently, inverse modeling approaches that map the objective space to the design space with conditional diffusion models have demonstrated impressive capability in learning the data manifold. However, these approaches proceed in an offline fashion with pre-collected data. How to design inverse approaches for online BBO to actively query new data and improve the sample efficiency remains an open question. In this work, we propose Diffusion-BBO, a sample-efficient online BBO framework leveraging the conditional diffusion model as the inverse surrogate model. Diffusion-BBO employs a novel acquisition function Uncertainty-aware Exploration (UaE) to propose scores in the objective space for conditional sampling. We theoretically prove that Diffusion-BBO with UaE achieves a near-optimal solution for online BBO. We also empirically demonstrate that Diffusion-BBO with UaE outperforms existing online BBO baselines across 6 scientific discovery tasks.

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arXiv2024

Neural Point Process for Learning Spatiotemporal Event Dynamics

Learning the dynamics of spatiotemporal events is a fundamental problem. Neural point processes enhance the expressivity of point process models with deep neural networks. However, most existing methods only consider temporal dynamics without spatial modeling. We propose Deep Spatiotemporal Point Process (\ours{}), a deep dynamics model that integrates spatiotemporal point processes. Our method is flexible, efficient, and can accurately forecast irregularly sampled events over space and time. The key construction of our approach is the nonparametric space-time intensity function, governed by a latent process. The intensity function enjoys closed form integration for the density. The latent process captures the uncertainty of the event sequence. We use amortized variational inference to infer the latent process with deep networks. Using synthetic datasets, we validate our model can accurately learn the true intensity function. On real-world benchmark datasets, our model demonstrates superior performance over state-of-the-art baselines. Our code and data can be found at the https://github.com/Rose-STL-Lab/DeepSTPP.

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arXiv2024

VICON: Vision In-Context Operator Networks for Multi-Physics Fluid Dynamics Prediction

In-Context Operator Networks (ICONs) have demonstrated the ability to learn operators across diverse partial differential equations using few-shot, in-context learning. However, existing ICONs process each spatial point as an individual token, severely limiting computational efficiency when handling dense data in higher spatial dimensions. We propose Vision In-Context Operator Networks (VICON), which integrates vision transformer architectures to efficiently process 2D data through patch-wise operations while preserving ICON's adaptability to multiphysics systems and varying timesteps. Evaluated across three fluid dynamics benchmarks, VICON significantly outperforms state-of-the-art baselines: DPOT and MPP, reducing the averaged last-step rollout error by 37.9% compared to DPOT and 44.7% compared to MPP, while requiring only 72.5% and 34.8% of their respective inference times. VICON naturally supports flexible rollout strategies with varying timestep strides, enabling immediate deployment in imperfect measurement systems where sampling frequencies may differ or frames might be dropped - common challenges in real-world settings - without requiring retraining or interpolation. In these realistic scenarios, VICON exhibits remarkable robustness, experiencing only 24.41% relative performance degradation compared to 71.37%-74.49% degradation in baseline methods, demonstrating its versatility for deploying in realistic applications. Our scripts for processing datasets and code are publicly available at https://github.com/Eydcao/VICON.

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arXiv2024

Multi-Modal Forecaster: Jointly Predicting Time Series and Textual Data

Current forecasting approaches are largely unimodal and ignore the rich textual data that often accompany the time series due to lack of well-curated multimodal benchmark dataset. In this work, we develop TimeText Corpus (TTC), a carefully curated, time-aligned text and time dataset for multimodal forecasting. Our dataset is composed of sequences of numbers and text aligned to timestamps, and includes data from two different domains: climate science and healthcare. Our data is a significant contribution to the rare selection of available multimodal datasets. We also propose the Hybrid Multi-Modal Forecaster (Hybrid-MMF), a multimodal LLM that jointly forecasts both text and time series data using shared embeddings. However, contrary to our expectations, our Hybrid-MMF model does not outperform existing baselines in our experiments. This negative result highlights the challenges inherent in multimodal forecasting. Our code and data are available at https://github.com/Rose-STL-Lab/Multimodal_ Forecasting.

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arXiv2024

Probabilistic Emulation of a Global Climate Model with Spherical DYffusion

Data-driven deep learning models are transforming global weather forecasting. It is an open question if this success can extend to climate modeling, where the complexity of the data and long inference rollouts pose significant challenges. Here, we present the first conditional generative model that produces accurate and physically consistent global climate ensemble simulations by emulating a coarse version of the United States' primary operational global forecast model, FV3GFS. Our model integrates the dynamics-informed diffusion framework (DYffusion) with the Spherical Fourier Neural Operator (SFNO) architecture, enabling stable 100-year simulations at 6-hourly timesteps while maintaining low computational overhead compared to single-step deterministic baselines. The model achieves near gold-standard performance for climate model emulation, outperforming existing approaches and demonstrating promising ensemble skill. This work represents a significant advance towards efficient, data-driven climate simulations that can enhance our understanding of the climate system and inform adaptation strategies.

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arXiv2024

Symmetry-Informed Governing Equation Discovery

Despite the advancements in learning governing differential equations from observations of dynamical systems, data-driven methods are often unaware of fundamental physical laws, such as frame invariance. As a result, these algorithms may search an unnecessarily large space and discover less accurate or overly complex equations. In this paper, we propose to leverage symmetry in automated equation discovery to compress the equation search space and improve the accuracy and simplicity of the learned equations. Specifically, we derive equivariance constraints from the time-independent symmetries of ODEs. Depending on the types of symmetries, we develop a pipeline for incorporating symmetry constraints into various equation discovery algorithms, including sparse regression and genetic programming. In experiments across diverse dynamical systems, our approach demonstrates better robustness against noise and recovers governing equations with significantly higher probability than baselines without symmetry. Our codebase is available at https://github.com/Rose-STL-Lab/symmetry-ode-discovery.

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arXiv2024

MORL-Prompt: An Empirical Analysis of Multi-Objective Reinforcement Learning for Discrete Prompt Optimization

RL-based techniques can be employed to search for prompts that, when fed into a target language model, maximize a set of user-specified reward functions. However, in many target applications, the natural reward functions are in tension with one another -- for example, content preservation vs. style matching in style transfer tasks. Current techniques focus on maximizing the average of reward functions, which does not necessarily lead to prompts that achieve balance across rewards -- an issue that has been well-studied in the multi-objective and robust optimization literature. In this paper, we conduct an empirical comparison of several existing multi-objective optimization techniques adapted to this new setting: RL-based discrete prompt optimization. We compare two methods optimizing the volume of the Pareto reward surface and one method that chooses an update direction that benefits all rewards simultaneously. We evaluate performance on two NLP tasks: style transfer and machine translation, each using three competing reward functions. Our experiments demonstrate that multi-objective methods that directly optimize the volume of the Pareto reward surface perform better and achieve a better balance of all rewards than those that attempt to find monotonic update directions.

cs.CL↗

arXiv2024

Functional-level Uncertainty Quantification for Calibrated Fine-tuning on LLMs

Accurate uncertainty quantification in large language models (LLMs) is essential for reliable confidence estimation, yet fine-tuned LLMs often become overconfident under limited adaptation data. Existing uncertainty methods for PEFT-based LLMs are largely post hoc, estimating uncertainty after fine-tuning rather than improving how adapters specialize to task-specific input-output relationships. We propose Functional-Level Uncertainty Quantification for Calibrated Fine-Tuning (UQ4CT), which calibrates uncertainty over the functional space induced by prompt-dependent mixtures of LoRA experts. UQ4CT implements this perspective through a mixture-of-experts fine-tuning framework, where a calibration loss aligns functional-level confidence with predictive correctness during training. Across four multiple-choice benchmarks and two open-ended generative QA tasks, UQ4CT reduces Expected Calibration Error (ECE) by over $25\%$ while preserving high accuracy. Under distribution shift, UQ4CT maintains superior calibration and competitive accuracy, demonstrating improved reliability and generalization for fine-tuned LLMs.

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arXiv2024

Back to Bayesics: Uncovering Human Mobility Distributions and Anomalies with an Integrated Statistical and Neural Framework

Existing methods for anomaly detection often fall short due to their inability to handle the complexity, heterogeneity, and high dimensionality inherent in real-world mobility data. In this paper, we propose DeepBayesic, a novel framework that integrates Bayesian principles with deep neural networks to model the underlying multivariate distributions from sparse and complex datasets. Unlike traditional models, DeepBayesic is designed to manage heterogeneous inputs, accommodating both continuous and categorical data to provide a more comprehensive understanding of mobility patterns. The framework features customized neural density estimators and hybrid architectures, allowing for flexibility in modeling diverse feature distributions and enabling the use of specialized neural networks tailored to different data types. Our approach also leverages agent embeddings for personalized anomaly detection, enhancing its ability to distinguish between normal and anomalous behaviors for individual agents. We evaluate our approach on several mobility datasets, demonstrating significant improvements over state-of-the-art anomaly detection methods. Our results indicate that incorporating personalization and advanced sequence modeling techniques can substantially enhance the ability to detect subtle and complex anomalies in spatiotemporal event sequences.

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arXiv2024

Latent Space Symmetry Discovery

Equivariant neural networks require explicit knowledge of the symmetry group. Automatic symmetry discovery methods aim to relax this constraint and learn invariance and equivariance from data. However, existing symmetry discovery methods are limited to simple linear symmetries and cannot handle the complexity of real-world data. We propose a novel generative model, Latent LieGAN (LaLiGAN), which can discover symmetries of nonlinear group actions. It learns a mapping from the data space to a latent space where the symmetries become linear and simultaneously discovers symmetries in the latent space. Theoretically, we show that our model can express nonlinear symmetries under some conditions about the group action. Experimentally, we demonstrate that our method can accurately discover the intrinsic symmetry in high-dimensional dynamical systems. LaLiGAN also results in a well-structured latent space that is useful for downstream tasks including equation discovery and long-term forecasting.

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arXiv2024

Technical report: Improving the properties of molecules generated by LIMO

This technical report investigates variants of the Latent Inceptionism on Molecules (LIMO) framework to improve the properties of generated molecules. We conduct ablative studies of molecular representation, decoder model, and surrogate model training scheme. The experiments suggest that an autogressive Transformer decoder with GroupSELFIES achieves the best average properties for the random generation task.

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arXiv2024

ClimSim-Online: A Large Multi-scale Dataset and Framework for Hybrid ML-physics Climate Emulation

Modern climate projections lack adequate spatial and temporal resolution due to computational constraints, leading to inaccuracies in representing critical processes like thunderstorms that occur on the sub-resolution scale. Hybrid methods combining physics with machine learning (ML) offer faster, higher fidelity climate simulations by outsourcing compute-hungry, high-resolution simulations to ML emulators. However, these hybrid ML-physics simulations require domain-specific data and workflows that have been inaccessible to many ML experts. As an extension of the ClimSim dataset (Yu et al., 2024), we present ClimSim-Online, which also includes an end-to-end workflow for developing hybrid ML-physics simulators. The ClimSim dataset includes 5.7 billion pairs of multivariate input/output vectors, capturing the influence of high-resolution, high-fidelity physics on a host climate simulator's macro-scale state. The dataset is global and spans ten years at a high sampling frequency. We provide a cross-platform, containerized pipeline to integrate ML models into operational climate simulators for hybrid testing. We also implement various ML baselines, alongside a hybrid baseline simulator, to highlight the ML challenges of building stable, skillful emulators. The data (https://huggingface.co/datasets/LEAP/ClimSim_high-res) and code (https://leap-stc.github.io/ClimSim and https://github.com/leap-stc/climsim-online) are publicly released to support the development of hybrid ML-physics and high-fidelity climate simulations.

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arXiv2024

Multi-Fidelity Residual Neural Processes for Scalable Surrogate Modeling

Multi-fidelity surrogate modeling aims to learn an accurate surrogate at the highest fidelity level by combining data from multiple sources. Traditional methods relying on Gaussian processes can hardly scale to high-dimensional data. Deep learning approaches utilize neural network based encoders and decoders to improve scalability. These approaches share encoded representations across fidelities without including corresponding decoder parameters. This hinders inference performance, especially in out-of-distribution scenarios when the highest fidelity data has limited domain coverage. To address these limitations, we propose Multi-fidelity Residual Neural Processes (MFRNP), a novel multi-fidelity surrogate modeling framework. MFRNP explicitly models the residual between the aggregated output from lower fidelities and ground truth at the highest fidelity. The aggregation introduces decoders into the information sharing step and optimizes lower fidelity decoders to accurately capture both in-fidelity and cross-fidelity information. We show that MFRNP significantly outperforms state-of-the-art in learning partial differential equations and a real-world climate modeling task. Our code is published at: https://github.com/Rose-STL-Lab/MFRNP

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arXiv2024

Discovering Mixtures of Structural Causal Models from Time Series Data

Discovering causal relationships from time series data is significant in fields such as finance, climate science, and neuroscience. However, contemporary techniques rely on the simplifying assumption that data originates from the same causal model, while in practice, data is heterogeneous and can stem from different causal models. In this work, we relax this assumption and perform causal discovery from time series data originating from a mixture of causal models. We propose a general variational inference-based framework called MCD to infer the underlying causal models as well as the mixing probability of each sample. Our approach employs an end-to-end training process that maximizes an evidence-lower bound for the data likelihood. We present two variants: MCD-Linear for linear relationships and independent noise, and MCD-Nonlinear for nonlinear causal relationships and history-dependent noise. We demonstrate that our method surpasses state-of-the-art benchmarks in causal discovery tasks through extensive experimentation on synthetic and real-world datasets, particularly when the data emanates from diverse underlying causal graphs. Theoretically, we prove the identifiability of such a model under some mild assumptions.

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arXiv2024

Understanding the Difficulty of Solving Cauchy Problems with PINNs

Physics-Informed Neural Networks (PINNs) have gained popularity in scientific computing in recent years. However, they often fail to achieve the same level of accuracy as classical methods in solving differential equations. In this paper, we identify two sources of this issue in the case of Cauchy problems: the use of $L^2$ residuals as objective functions and the approximation gap of neural networks. We show that minimizing the sum of $L^2$ residual and initial condition error is not sufficient to guarantee the true solution, as this loss function does not capture the underlying dynamics. Additionally, neural networks are not capable of capturing singularities in the solutions due to the non-compactness of their image sets. This, in turn, influences the existence of global minima and the regularity of the network. We demonstrate that when the global minimum does not exist, machine precision becomes the predominant source of achievable error in practice. We also present numerical experiments in support of our theoretical claims.

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arXiv2024

Data-Driven Simulator for Mechanical Circulatory Support with Domain Adversarial Neural Process

Mechanical Circulatory Support (MCS) devices, implemented as a probabilistic deep sequence model. Existing mechanical simulators for MCS rely on oversimplifying assumptions and are insensitive to patient-specific behavior, limiting their applicability to real-world treatment scenarios. To address these shortcomings, our model Domain Adversarial Neural Process (DANP) employs a neural process architecture, allowing it to capture the probabilistic relationship between MCS pump levels and aortic pressure measurements with uncertainty. We use domain adversarial training to combine simulation data with real-world observations, resulting in a more realistic and diverse representation of potential outcomes. Empirical results with an improvement of 19% in non-stationary trend prediction establish DANP as an effective tool for clinicians to understand and make informed decisions regarding MCS patient treatment.

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