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

In-Context Operator Networks (ICONs) are models that learn operators across different types of PDEs using a few-shot, in-context approach. Although they show successful generalization to various PDEs, existing methods treat each data point as a single token, and suffer from computational inefficiency when processing dense data, limiting their application in higher spatial dimensions. In this work, we propose Vision In-Context Operator Networks (VICON), incorporating a vision transformer architecture that efficiently processes 2D functions through patch-wise operations. We evaluated our method on three fluid dynamics datasets, demonstrating both superior performance (reducing scaled $L^2$ error by $40\%$ and $61.6\%$ for two benchmark datasets for compressible flows, respectively) and computational efficiency (requiring only one-third of the inference time per frame) in long-term rollout predictions compared to the current state-of-the-art sequence-to-sequence model with fixed timestep prediction: Multiple Physics Pretraining (MPP). Compared to MPP, our method preserves the benefits of in-context operator learning, enabling flexible context formation when dealing with insufficient frame counts or varying timestep values.

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.

Discovering Latent Structural Causal Models from Spatio-Temporal Data

Many important phenomena in scientific fields such as climate, neuroscience, and epidemiology are naturally represented as spatiotemporal gridded data with complex interactions. For example, in climate science, researchers aim to uncover how large-scale events, such as the North Atlantic Oscillation (NAO) and the Antarctic Oscillation (AAO), influence other global processes. Inferring causal relationships from these data is a challenging problem compounded by the high dimensionality of such data and the correlations between spatially proximate points. We present SPACY (SPAtiotemporal Causal discoverY), a novel framework based on variational inference, designed to explicitly model latent time-series and their causal relationships from spatially confined modes in the data. Our method uses an end-to-end training process that maximizes an evidence-lower bound (ELBO) for the data likelihood. Theoretically, we show that, under some conditions, the latent variables are identifiable up to transformation by an invertible matrix. Empirically, we show that SPACY outperforms state-of-the-art baselines on synthetic data, remains scalable for large grids, and identifies key known phenomena from real-world climate data.

Adapting While Learning: Grounding LLMs for Scientific Problems with Intelligent Tool Usage Adaptation

Large Language Models (LLMs) demonstrate promising capabilities in solving simple scientific problems but often produce hallucinations for complex ones. While integrating LLMs with tools can increase reliability, this approach typically results in over-reliance on tools, diminishing the model's ability to solve simple problems through basic reasoning. In contrast, human experts first assess problem complexity using domain knowledge before choosing an appropriate solution approach. Inspired by this human problem-solving process, we propose a novel two-component fine-tuning method. In the first component World Knowledge Distillation (WKD), LLMs learn directly from solutions generated using tool's information to internalize domain knowledge. In the second component Tool Usage Adaptation (TUA), we partition problems into easy and hard categories based on the model's direct answering accuracy. While maintaining the same alignment target for easy problems as in WKD, we train the model to intelligently switch to tool usage for more challenging problems. We validate our method on six scientific benchmark datasets, spanning mathematics, climate science and epidemiology. On average, our models demonstrate a 28.18% improvement in answer accuracy and a 13.89% increase in tool usage precision across all datasets, surpassing state-of-the-art models including GPT-4o and Claude-3.5.

ClimaQA: An Automated Evaluation Framework for Climate Foundation Models

The use of foundation models 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 automated algorithmic 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 Large Language Models (LLMs) on our benchmarks. Our results offer novel insights into various approaches used to enhance climate foundation models.

MF-LAL: Drug Compound Generation Using Multi-Fidelity Latent Space Active Learning

Current generative models for drug discovery primarily use molecular docking as an oracle to guide the generation of active compounds. However, such models are often not useful in practice because even compounds with high docking scores do not consistently show experimental activity. More accurate methods for activity prediction exist, such as molecular dynamics based binding free energy calculations, but they are too computationally expensive to use in a generative model. To address this challenge, we propose Multi-Fidelity Latent space Active Learning (MF-LAL), a generative modeling framework that integrates a set of oracles with varying cost-accuracy tradeoffs. Unlike previous approaches that separately learn the surrogate model and generative model, MF-LAL combines the generative and multi-fidelity surrogate models into a single framework, allowing for more accurate activity prediction and higher quality samples. We train MF-LAL with a novel active learning algorithm to further reduce computational cost. Our experiments on two disease-relevant proteins show that MF-LAL produces compounds with significantly better binding free energy scores than other single and multi-fidelity approaches.

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

From common-sense reasoning to domain-specific tasks, parameter-efficient fine tuning (PEFT) methods for large language models (LLMs) have showcased significant performance improvements on downstream tasks. However, fine-tuned LLMs often struggle with overconfidence in uncertain predictions, particularly due to sparse training data. This overconfidence reflects poor epistemic uncertainty calibration, which arises from limitations in the model's ability to generalize with limited data. Existing PEFT uncertainty quantification methods for LLMs focus on the post fine-tuning stage and thus have limited capability in calibrating epistemic uncertainty. To address these limitations, we propose Functional-Level Uncertainty Quantification for Calibrated Fine-Tuning (UQ4CT), which captures and calibrates functional-level epistemic uncertainty during the fine-tuning stage via a mixture-of-expert framework. We show that UQ4CT reduces Expected Calibration Error (ECE) by more than $25\%$ while maintaining high accuracy across $5$ benchmarks. Furthermore, UQ4CT maintains superior ECE performance with high accuracy under distribution shift, showcasing improved generalizability.

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 did not demonstrate enhanced performance when prompted to engage in *explicit reasoning* about time series analysis 3. Contrary to common beliefs, LLM's understanding of time series *do not* stem from their repetition biases or arithmetic abilities 4. LLMs' behaviors and performance in time series analysis *vary significantly* across different model architectures This study provides the first comprehensive analysis of contemporary LLM capabilities in time series anomaly detection. Our results suggest that while LLMs can understand time series anomalies, many common conjectures based on their reasoning capabilities do not hold. These insights pave the way for more effective LLM-based approaches in time series analysis, bridging the gap between forecasting and anomaly detection applications.

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.

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.