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. ClimaQA’s source code is publicly available at https://github.com/Rose-STL-Lab/genie-climaqa

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 *do 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.

Large Language Models (LLMs) demonstrate promising capabilities in solving scientific problems but often suffer from the issue of hallucination. While integrating LLMs with tools can mitigate this issue, models fine-tuned on tool usage become overreliant on them and incur unnecessary costs. Inspired by how human experts assess problem complexity before selecting solutions, we propose a novel two-component fine-tuning method, Adapting while Learning (AWL). In the first component World Knowledge Learning (WKL), LLMs internalize scientific knowledge by learning from tool-generated solutions. In the second component Tool Usage Adaptation (TUA), we categorize problems as easy or hard based on the model’s accuracy, and train it to maintain direct reasoning for easy problems while switching to tools for hard ones. We validate our method on 6 scientific benchmark datasets across climate science, epidemiology, physics, and other domains. Compared to the original instruct model (8B), models post-trained with AWL achieve 29.11% higher answer accuracy and 12.72% better tool usage accuracy, even surpassing state-of-the-art models including GPT-4o and Claude-3.5 on 4 custom-created datasets. Our code is open-source at https://github.com/Rose-STL-Lab/Adapting-While-Learning.

Neural network minima are often connected by curves along which train and test loss remain nearly constant, a phenomenon known as mode connectivity. While this property has enabled applications such as model merging and fine-tuning, its theoretical explanation remains unclear. We propose a new approach to exploring the connectedness of minima using parameter space symmetry. By linking the topology of symmetry groups to that of the minima, we derive the number of connected components of the minima of linear networks and show that skip connections reduce this number. We then examine when mode connectivity and linear mode connectivity hold or fail, using parameter symmetries which account for a significant part of the minimum. Finally, we provide explicit expressions for connecting curves in the minima induced by symmetry. Using the curvature of these curves, we derive conditions under which linear mode connectivity approximately holds. Our findings highlight the role of continuous symmetries in understanding the neural network loss landscape.

Existing symmetry discovery methods predominantly focus on global transformations across the entire system or space, but they fail to consider the symmetries in local neighborhoods. This may result in the reported symmetry group being a misrepresentation of the true symmetry. In this paper, we formalize the notion of local symmetry as atlas equivariance. Our proposed pipeline, automatic local symmetry discovery (AtlasD), recovers the local symmetries of a function by training local predictor networks and then learning a Lie group basis to which the predictors are equivariant. We demonstrate AtlasD is capable of discovering local symmetry groups with multiple connected components in top-quark tagging and partial differential equation experiments. The discovered local symmetry is shown to be a useful inductive bias that improves the performance of downstream tasks in climate segmentation and vision tasks. Our code is publicly available at https://github.com/Rose-STL-Lab/AtlasD.

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 real-world 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. Using active learning, we train a surrogate model for each oracle and use these surrogates to guide generation of compounds with high predicted activity. 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. 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 ( 50% improvement in mean binding free energy score). The code is available at https://github.com/Rose-STL-Lab/MF-LAL.

Many important phenomena in scientific fields like climate, neuroscience, and epidemiology are naturally represented as spatiotemporal gridded data with complex interactions. 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 model latent time series and their causal relationships from spatiotemporal data. SPACY alleviates the high-dimensional challenge by discovering causal structures in the latent space. To aggregate spatially proximate, correlated grid points, we use spatial factors, parametrized by spatial kernel functions, to map observational time series to latent representations. Theoretically, we generalize the problem to a continuous spatial domain and establish identifiability when the observations arise from a nonlinear, invertible function of the product of latent series and spatial factors. Using this approach, we avoid assumptions that are often unverifiable, including those about instantaneous effects or sufficient variability. Empirically, SPACY outperforms state-of-the-art baselines on synthetic data, even in challenging settings where existing methods struggle, while remaining scalable for large grids. SPACY also identifies key known phenomena from real-world climate data. An implementation of SPACY is available at \url{https://github.com/Rose-STL-Lab/SPACY/}

Diffusion models are a powerful tool for probabilistic forecasting, yet most applications in high-dimensional complex systems predict future states individually. This approach struggles to model complex temporal dependencies and fails to explicitly account for the progressive growth of uncertainty inherent to the systems. While rolling diffusion frameworks, which apply increasing noise to forecasts at longer lead times, have been proposed to address this, their integration with state-of-the-art, high-fidelity diffusion techniques remains a significant challenge. We tackle this problem by introducing Elucidated Rolling Diffusion Models (ERDM), the first framework to successfully unify a rolling forecast structure with the principled, performant design of Elucidated Diffusion Models (EDM). To do this, we adapt the core EDM components--its noise schedule, network preconditioning, and Heun sampler--to the rolling forecast setting. The success of this integration is driven by three key contributions: $(i)$ a novel loss weighting scheme that focuses model capacity on the mid-range forecast horizons where determinism gives way to stochasticity; $(ii)$ an efficient initialization strategy using a pre-trained EDM for the initial window; and $(iii)$ a bespoke hybrid sequence architecture for robust spatiotemporal feature extraction under progressive denoising. On 2D Navier–Stokes simulations and ERA5 global weather forecasting at $1.5^\circ$ resolution, ERDM consistently outperforms key diffusion-based baselines, including conditional autoregressive EDM. ERDM offers a flexible and powerful general framework for tackling diffusion-based dynamics forecasting problems where modeling uncertainty propagation is paramount.

Conformal prediction has been explored as a general and efficient way to provide uncertainty quantification for time series. However, current methods struggle to handle time series data with change points — sudden shifts in the underlying data-generating process. In this paper, we propose a novel Conformal Prediction for Time-series with Change points (CPTC) algorithm, addressing this gap by integrating a model to predict the underlying state with online conformal prediction to model uncertainties in non-stationary time series. We prove CPTC's validity and improved adaptivity in the time series setting under minimum assumptions, and demonstrate CPTC's practical effectiveness on 6 synthetic and real-world datasets, showing improved validity and adaptivity compared to state-of-the-art baselines.

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 physics-ML simulations require domain-specific data and workflows that have been inaccessible to many ML experts. This paper is an extended version of our NeurIPS award-winning ClimSim dataset paper. The ClimSim dataset includes 5.7 billion pairs of multivariate input/output vectors spanning ten years at high temporal resolution, capturing the influence of high-resolution, high-fidelity physics on a host climate simulator's macro-scale state. In this extended version, we introduce a significant new contribution in Section 5, which provides a cross-platform, containerized pipeline to integrate ML models into operational climate simulators for hybrid testing. We also implement various baselines of ML models and hybrid simulators to highlight the ML challenges of building stable, skillful emulators. The data (https://huggingface.co/datasets/LEAP/ClimSim_high-res, also in a low-resolution version at https://huggingface.co/datasets/LEAP/ClimSim_low-res and an aquaplanet version at https://huggingface.co/datasets/LEAP/ClimSim_low-res_aqua-planet) 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 physics-ML and high-fidelity climate simulations.

We address the problem of learning Granger causality from asynchronous, interdependent, multi-type event sequences. In particular, we are interested in discovering instance-level causal structures in an unsupervised manner. Instance-level causality identifies causal relationships among individual events, providing more fine-grained information for decision-making. Existing work in the literature either requires strong assumptions, such as linearity in the intensity function, or heuristically defined model parameters that do not necessarily meet the requirements of Granger causality. We propose Instance-wise Self-Attentive Hawkes Processes (ISAHP), a novel deep learning framework that can directly infer the Granger causality at the event instance level. ISAHP is the first neural point process model that meets the requirements of Granger causality. It leverages the self-attention mechanism of the transformer to align with the principles of Granger causality. We empirically demonstrate that ISAHP is capable of discovering complex instance-level causal structures that cannot be handled by classical models. We also show that ISAHP achieves state-of-the-art performance in proxy tasks involving type-level causal discovery and instance-level event type prediction.

Graph transformers have recently received significant attention in graph learning, partly due to their ability to capture more global interaction via self-attention. Nevertheless, while higher-order graph neural networks have been reasonably well studied, the exploration of extending graph transformers to higher-order variants is just starting. Both theoretical understanding and empirical results are limited. In this paper, we provide a systematic study of the theoretical expressive power of order-$k$ graph transformers and sparse variants. We first show that, an order-$k$ graph transformer without additional structural information is less expressive than the $k$-Weisfeiler Lehman ($k$-WL) test despite its high computational cost. We then explore strategies to both sparsify and enhance the higher-order graph transformers, aiming to improve both their efficiency and expressiveness. Indeed, sparsification based on neighborhood information can enhance the expressive power, as it provides additional information about input graph structures. In particular, we show that a natural neighborhood-based sparse order-$k$ transformer model is not only computationally efficient, but also expressive – as expressive as $k$-WL test. We further study several other sparse graph attention models that are computationally efficient and provide their expressiveness analysis. Finally, we provide experimental results to show the effectiveness of the different sparsification strategies.

Accurate uncertainty measurement is a key step in building robust and reliable machine learning systems. Conformal prediction is a distribution-free uncertainty quantification framework popular for its ease of implementation, finite-sample coverage guarantees, and generality for underlying prediction algorithms. However, existing conformal prediction approaches for time series are limited to single-step prediction without considering the temporal dependency. In this paper, we propose the Copula Conformal Prediction algorithm for multivariate, multi-step Time Series forecasting, CopulaCPTS. We prove that CopulaCPTS has finite-sample validity guarantee. On four synthetic and real-world multivariate time series datasets, we show that CopulaCPTS produces more calibrated and efficient confidence intervals for multi-step prediction tasks than existing techniques. Our code is open-sourced at https://github.com/Rose-STL-Lab/CopulaCPTS.

In many neural networks, different values of the parameters may result in the same loss value. Parameter space symmetries are loss-invariant transformations that change the model parameters. Teleportation applies such transformations to accelerate optimization. However, the exact mechanism behind this algorithm's success is not well understood. In this paper, we show that teleportation not only speeds up optimization in the short-term, but gives overall faster time to convergence. Additionally, teleporting to minima with different curvatures improves generalization, which suggests a connection between the curvature of the minimum and generalization ability. Finally, we show that integrating teleportation into a wide range of optimization algorithms and optimization-based meta-learning improves convergence. Our results showcase the versatility of teleportation and demonstrate the potential of incorporating symmetry in optimization.

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

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. Implementation is available at [https://github.com/Rose-STL-Lab/MCD](https://github.com/Rose-STL-Lab/MCD).

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.

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. Code is available at [https://github.com/Rose-STL-Lab/spherical-dyffusion](https://github.com/Rose-STL-Lab/spherical-dyffusion).

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.

Graph Transformer (GT) recently has emerged as a new paradigm of graph learning algorithms, outperforming the previously popular Message Passing Neural Network (MPNN) on multiple benchmarks. Previous work shows that with proper position embedding, GT can approximate MPNN arbitrarily well, implying that GT is at least as powerful as MPNN. In this paper, we study the inverse connection and show that MPNN with virtual node (VN), a commonly used heuristic with little theoretical understanding, is powerful enough to arbitrarily approximate the self-attention layer of GT. In particular, we first show that if we consider one type of linear transformer, the so-called Performer/Linear Transformer, then MPNN + VN with only $\mathcal{O}(1)$ depth and $\mathcal{O}(1)$ width can approximate a self-attention layer in Performer/Linear Transformer. Next, via a connection between MPNN + VN and DeepSets, we prove the MPNN + VN with $\mathcal{O}(n^d)$ width and $\mathcal{O}(1)$ depth can approximate the self-attention layer arbitrarily well, where $d$ is the input feature dimension. Lastly, under some assumptions, we provide an explicit construction of MPNN + VN with $\mathcal{O}(1)$ width and $\mathcal{O}(n)$ depth approximating the self-attention layer in GT arbitrarily well. On the empirical side, we demonstrate that 1) MPNN + VN is a surprisingly strong baseline, outperforming GT on the recently proposed Long Range Graph Benchmark (LRGB) dataset, 2) our MPNN + VN improves over early implementation on a wide range of OGB datasets and 3) MPNN + VN outperforms Linear Transformer and MPNN on the climate modeling task.

To balance quality and cost, various domain areas of science and engineering run simulations at multiple levels of sophistication. Multi-fidelity active learning aims to learn a direct mapping from input parameters to simulation outputs at the highest fidelity by actively acquiring data from multiple fidelity levels. However, existing approaches based on Gaussian processes are hardly scalable to high-dimensional data. Deep learning-based methods often impose a hierarchical structure in hidden representations, which only supports passing information from low-fidelity to high-fidelity. These approaches can lead to the undesirable propagation of errors from low-fidelity representations to high-fidelity ones. We propose a novel framework called Disentangled Multi-fidelity Deep Bayesian Active Learning (D-MFDAL), which learns the surrogate models conditioned on the distribution of functions at multiple fidelities. On benchmark tasks of learning deep surrogates of partial differential equations including heat equation, Poisson’s equation and fluid simulations, our approach significantly outperforms state-of-the-art in prediction accuracy and sample efficiency.

Despite the success of equivariant neural networks in scientific applications, they require knowing the symmetry group a priori. However, it may be difficult to know which symmetry to use as an inductive bias in practice. Enforcing the wrong symmetry could even hurt the performance. In this paper, we propose a framework, LieGAN, to *automatically discover equivariances* from a dataset using a paradigm akin to generative adversarial training. Specifically, a generator learns a group of transformations applied to the data, which preserve the original distribution and fool the discriminator. LieGAN represents symmetry as interpretable Lie algebra basis and can discover various symmetries such as the rotation group $\mathrm{SO}(n)$, restricted Lorentz group $\mathrm{SO}(1,3)^+$ in trajectory prediction and top-quark tagging tasks. The learned symmetry can also be readily used in several existing equivariant neural networks to improve accuracy and generalization in prediction.

The Fragile Earth Workshop is a recurring event in ACM's KDD Conference on research in knowledge discovery and data mining that gathers the research community to find and explore how data science can measure and progress climate and social issues, fol- lowing the United Nations Sustainable Development Goals (SDGs) framework.

Stochastic simulations such as large-scale, spatiotemporal, age-structured epidemic models are computationally expensive at fine-grained resolution. While deep surrogate models can speed up the simulations, doing so for stochastic simulations and with active learning approaches is an underexplored area. We propose Interactive Neural Process (INP), a deep Bayesian active learning framework for learning deep surrogate models to accelerate stochastic simulations. INP consists of two components, a spatiotemporal surrogate model built upon Neural Process (NP) family and an acquisition function for active learning. For surrogate modeling, we develop Spatiotemporal Neural Process (STNP) to mimic the simulator dynamics. For active learning, we propose a novel acquisition function, Latent Information Gain (LIG), calculated in the latent space of NP based models. We perform a theoretical analysis and demonstrate that LIG reduces sample complexity compared with random sampling in high dimensions. We also conduct empirical studies on three complex spatiotemporal simulators for reaction diffusion, heat flow, and infectious disease. The results demonstrate that STNP outperforms the baselines in the offline learning setting and LIG achieves the state-of-the-art for Bayesian active learning.

While diffusion models can successfully generate data and make predictions, they are predominantly designed for static images. We propose an approach for training diffusion models for dynamics forecasting that leverages the temporal dynamics encoded in the data, directly coupling it with the diffusion steps in the network. We train a stochastic, time-conditioned interpolator and a backbone forecaster network that mimic the forward and reverse processes of conventional diffusion models, respectively. This design choice naturally encodes multi-step and long-range forecasting capabilities, allowing for highly flexible, continuous-time sampling trajectories and the ability to trade-off performance with accelerated sampling at inference time. In addition, the dynamics-informed diffusion process imposes a strong inductive bias, allowing for improved computational efficiency compared to traditional Gaussian noise-based diffusion models. Our approach performs competitively on probabilistic skill score metrics in complex dynamics forecasting of sea surface temperatures, Navier-Stokes flows, and spring mesh systems.

Modern climate projections lack adequate spatial and temporal resolution due to computational constraints. A consequence is inaccurate and imprecise predictions of critical processes such as storms. Hybrid methods that combine physics with machine learning (ML) have introduced a new generation of higher fidelity climate simulators that can sidestep Moore's Law by outsourcing compute-hungry, short, high-resolution simulations to ML emulators. However, this hybrid ML-physics simulation approach requires domain-specific treatment and has been inaccessible to ML experts because of lack of training data and relevant, easy-to-use workflows. We present ClimSim, the largest-ever dataset designed for hybrid ML-physics research. It comprises multi-scale climate simulations, developed by a consortium of climate scientists and ML researchers. It consists of 5.7 billion pairs of multivariate input and output vectors that isolate the influence of locally-nested, high-resolution, high-fidelity physics on a host climate simulator's macro-scale physical state.The dataset is global in coverage, spans multiple years at high sampling frequency, and is designed such that resulting emulators are compatible with downstream coupling into operational climate simulators. We implement a range of deterministic and stochastic regression baselines to highlight the ML challenges and their scoring. The data (https://huggingface.co/datasets/LEAP/ClimSim_high-res) and code (https://leap-stc.github.io/ClimSim) are released openly to support the development of hybrid ML-physics and high-fidelity climate simulations for the benefit of science and society.

Learning continuous-time point processes is essential to many discrete event forecasting tasks. However, integration poses a major challenge, particularly for spatiotemporal point processes (STPPs), as it involves calculating the likelihood through triple integrals over space and time. Existing methods for integrating STPP either assume a parametric form of the intensity function, which lacks flexibility; or approximating the intensity with Monte Carlo sampling, which introduces numerical errors. Recent work by Omi et al. proposes a dual network approach for efficient integration of flexible intensity function. However, their method only focuses on the 1D temporal point process. In this paper, we introduce a novel paradigm: `Auto-STPP` (Automatic Integration for Spatiotemporal Neural Point Processes) that extends the dual network approach to 3D STPP. While previous work provides a foundation, its direct extension overly restricts the intensity function and leads to computational challenges. In response, we introduce a decomposable parametrization for the integral network using ProdNet. This approach, leveraging the product of simplified univariate graphs, effectively sidesteps the computational complexities inherent in multivariate computational graphs. We prove the consistency of `Auto-STPP` and validate it on synthetic data and benchmark real-world datasets. `Auto-STPP` shows a significant advantage in recovering complex intensity functions from irregular spatiotemporal events, particularly when the intensity is sharply localized. Our code is open-source at https://github.com/Rose-STL-Lab/AutoSTPP.

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep generative models guided by Gaussian processes, which can be prohibitively slow when generating molecules with high binding affinity calculated by computationally-expensive physics-based methods. We present Latent Inceptionism on Molecules (LIMO), which significantly accelerates molecule generation with an inceptionism-like technique. LIMO employs a variational autoencoder-generated latent space and property prediction by two neural networks in sequence to enable faster gradient-based reverse-optimization of molecular properties. Comprehensive experiments show that LIMO performs competitively on benchmark tasks and markedly outperforms state-of-the-art techniques on the novel task of generating drug-like compounds with high binding affinity, reaching nanomolar range against two protein targets. We corroborate these docking-based results with more accurate molecular dynamics-based calculations of absolute binding free energy and show that one of our generated drug-like compounds has a predicted $K_D$ (a measure of binding affinity) of $6 \cdot 10^{-14}$ M against the human estrogen receptor, well beyond the affinities of typical early-stage drug candidates and most FDA-approved drugs to their respective targets. Code is available at https://github.com/Rose-STL-Lab/LIMO.

Incorporating symmetry as an inductive bias into neural network architecture has led to improvements in generalization, data efficiency, and physical consistency in dynamics modeling. Methods such as CNNs or equivariant neural networks use weight tying to enforce symmetries such as shift invariance or rotational equivariance. However, despite the fact that physical laws obey many symmetries, real-world dynamical data rarely conforms to strict mathematical symmetry either due to noisy or incomplete data or to symmetry breaking features in the underlying dynamical system. We explore approximately equivariant networks which are biased towards preserving symmetry but are not strictly constrained to do so. By relaxing equivariance constraints, we find that our models can outperform both baselines with no symmetry bias and baselines with overly strict symmetry in both simulated turbulence domains and real-world multi-stream jet flow.

The Fragile EarthWorkshop is a recurring event that gathers the research community to find and explore howdata science can measure and progress climate and social issues, following the framework of the United Nations Sustainable Development Goals (SDGs).

Science and engineering fields use computer simulation extensively. These simulations are often run at multiple levels of sophistication to balance accuracy and efficiency. Multi-fidelity surrogate modeling reduces the computational cost by fusing different simulation outputs. Cheap data generated from low-fidelity simulators can be combined with limited high-quality data generated by an expensive high-fidelity simulator. Existing methods based on Gaussian processes rely on strong assumptions of the kernel functions and can hardly scale to high-dimensional settings. We propose Multi-fidelity Hierarchical Neural Processes (MF-HNP), a unified neural latent variable model for multi-fidelity surrogate modeling. MF-HNP inherits the flexibility and scalability of Neural Processes. The latent variables transform the correlations among different fidelity levels from observations to latent space. The predictions across fidelities are conditionally independent given the latent states. It helps alleviate the error propagation issue in existing methods. MF-HNP is flexible enough to handle non-nested high dimensional data at different fidelity levels with varying input and output dimensions. We evaluate MF-HNP on epidemiology and climate modeling tasks, achieving competitive performance in terms of accuracy and uncertainty estimation. In contrast to deep Gaussian Processes with only low-dimensional (< 10) tasks, our method shows great promise for speeding up high-dimensional complex simulations (over 7000 for epidemiology modeling and 45000 for climate modeling).

Current deep learning models for dynamics forecasting struggle with generalization. They can only forecast in a specific domain and fail when applied to systems with different parameters, external forces, or boundary conditions. We propose a model-based meta-learning method called DyAd which can generalize across heterogeneous domains by partitioning them into different tasks. DyAd has two parts: an encoder that infers the time-invariant hidden features of the task with weak supervision, and a forecaster which learns the shared dynamics of the entire domain. The encoder adapts and controls the forecaster during inference using adaptive instance normalization and adaptive padding. Theoretically, we prove that the generalization error of such a procedure is related to the task relatedness in the source domain, as well as the domain differences between source and target. Experimentally, we demonstrate that our model outperforms state-of-the-art approaches on forecasting complex physical dynamics including turbulent flow, real-world sea surface temperature, and ocean currents.

Existing gradient-based optimization methods update parameters locally, in a direction that minimizes the loss function. We study a different approach, symmetry teleportation, that allows parameters to travel a large distance on the loss level set, in order to improve the convergence speed in subsequent steps. Teleportation exploits symmetries in the loss landscape of optimization problems. We derive loss-invariant group actions for test functions in optimization and multi-layer neural networks, and prove a necessary condition for teleportation to improve convergence rate. We also show that our algorithm is closely related to second order methods. Experimentally, we show that teleportation improves the convergence speed of gradient descent and AdaGrad for several optimization problems including test functions, multi-layer regressions, and MNIST classification.

The 4th [email protected] workshop is a forum to discuss new insights into how data mining can play a bigger role in epidemiology and public health research. While the integration of data science methods into epidemiology has significant potential, it remains under studied. We aim to raise the profile of this emerging research area of data-driven and computational epidemiology, and create a venue for presenting state-of-the-art and in-progress results-in particular, results that would otherwise be difficult to present at a major data mining conference, including lessons learnt in the 'trenches'. The current COVID-19 pandemic has only showcased the urgency and importance of this area. Our target audience consists of data mining and machine learning researchers from both academia and industry who are interested in epidemiological and public-health applications of their work, and practitioners from the areas of mathematical epidemiology and public health.

Deep learning is gaining increasing popularity for spatiotemporal forecasting. However, prior works have mostly focused on point estimates without quantifying the uncertainty of the predictions. In high stakes domains, being able to generate probabilistic forecasts with confidence intervals is critical to risk assessment and decision making. Hence, a systematic study of uncertainty quantification (UQ) methods for spatiotemporal forecasting is missing in the community. In this paper, we describe two types of spatiotemporal forecasting problems: regular grid-based and graph-based. Then we analyze UQ methods from both the Bayesian and the frequentist point of view, casting in a unified framework via statistical decision theory. Through extensive experiments on real-world road network traffic, epidemics, and air quality forecasting tasks, we reveal the statistical and computational trade-offs for different UQ methods: Bayesian methods are typically more robust in mean prediction, while confidence levels obtained from frequentist methods provide more extensive coverage over data variations. Computationally, quantile regression type methods are cheaper for a single confidence interval but require re-training for different intervals. Sampling based methods generate samples that can form multiple confidence intervals, albeit at a higher computational cost.

There is a great interest in scientific communities for harnessing the power of AI in applications ranging from climate science to quantum chemistry. The common theme in many of these applications is that the data are spatiotemporal with governing physics. Unfortunately, today's ML approaches are mostly purely data-driven, i.e., they solely rely on (labeled) data for learning statistical patterns. Collecting labeled data can be quite expensive in real-world applications. Moreover, the resulting black-box AI models are difficult to interpret for domain scientists.

Existing equivariant neural networks require prior knowledge of the symmetry group and discretization for continuous groups. We propose to work with Lie algebras (infinitesimal generators) instead of Lie groups. Our model, the Lie algebra convolutional network (L-conv) can automatically discover symmetries and does not require discretization of the group. We show that L-conv can serve as a building block to construct any group equivariant feedforward architecture. Both CNNs and Graph Convolutional Networks can be expressed as L-conv with appropriate groups. We discover direct connections between L-conv and physics: (1) group invariant loss generalizes field theory (2) Euler-Lagrange equation measures the robustness, and (3) equivariance leads to conservation laws and Noether current. These connections open up new avenues for designing more general equivariant networks and applying them to important problems in physical sciences.

Efficient and interpretable spatial analysis is crucial in many fields such as geology, sports, and climate science. Tensor latent factor models can describe higher-order correlations for spatial data. However, they are computationally expensive to train and are sensitive to initialization, leading to spatially incoherent, uninterpretable results. We develop a novel Multiresolution Tensor Learning (MRTL) algorithm for efficiently learning interpretable spatial patterns. MRTL initializes the latent factors from an approximate full-rank tensor model for improved interpretability and progressively learns from a coarse resolution to the fine resolution to reduce computation. We also prove the theoretical convergence and computational complexity of MRTL. When applied to two real-world datasets, MRTL demonstrates 4 5x speedup compared to a fixed resolution approach while yielding accurate and interpretable latent factors.

While deep learning has shown tremendous success in a wide range of domains, it remains a grand challenge to incorporate physical principles in a systematic manner to the design, training, and inference of such models. In this paper, we aim to predict turbulent flow by learning its highly nonlinear dynamics from spatiotemporal velocity fields of large-scale fluid flow simulations of relevance to turbulence modeling and climate modeling. We adopt a hybrid approach by marrying two well-established turbulent flow simulation techniques with deep learning. Specifically, we introduce trainable spectral filters in a coupled model of Reynolds-averaged Navier-Stokes (RANS) and Large Eddy Simulation (LES), followed by a specialized U-net for prediction. Our approach, which we call Turbulent-Flow Net, is grounded in a principled physics model, yet offers the flexibility of learned representations. We compare our model with state-of-the-art baselines and observe significant reductions in error for predictions 60 frames ahead. Most importantly, our method predicts physical fields that obey desirable physical characteristics, such as conservation of mass, whilst faithfully emulating the turbulent kinetic energy field and spectrum, which are critical for accurate prediction of turbulent flows.

We present a deep imitation learning framework for robotic bimanual manipulation in a continuous state-action space. A core challenge is to generalize the manipulation skills to objects in different locations. We hypothesize that modeling the relational information in the environment can significantly improve generalization. To achieve this, we propose to (i) decompose the multi-modal dynamics into elemental movement primitives, (ii) parameterize each primitive using a recurrent graph neural network to capture interactions, and (iii) integrate a high-level planner that composes primitives sequentially and a low-level controller to combine primitive dynamics and inverse kinematics control. Our model is a deep, hierarchical, modular architecture. Compared to baselines, our model generalizes better and achieves higher success rates on several simulated bimanual robotic manipulation tasks. We open source the code for simulation, data, and models at: https://github.com/Rose-STL-Lab/HDR-IL.

Missing data poses significant challenges while learning representations of video sequences. We present Disentangled Imputed Video autoEncoder (DIVE), a deep generative model that imputes and predicts future video frames in the presence of missing data. Specifically, DIVE introduces a missingness latent variable, disentangles the hidden video representations into static and dynamic appearance, pose, and missingness factors for each object, while it imputes each object trajectory where data is missing. On a moving MNIST dataset with various missing scenarios, DIVE outperforms the state of the art baselines by a substantial margin. We also present comparisons on a real-world MOTSChallenge pedestrian dataset, which demonstrates the practical value of our method in a more realistic setting. Our code can be found in https://github.com/Rose-STL-Lab/DIVE.

Precise near-ground trajectory control is difficult for multi-rotor drones, due to the complex aerodynamic effects caused by interactions between multi-rotor airflow and the environment. Conventional control methods often fail to properly account for these complex effects and fall short in accomplishing smooth landing. In this paper, we present a novel deep-learning-based robust nonlinear controller (Neural-Lander) that improves control performance of a quadrotor during landing. Our approach combines a nominal dynamics model with a Deep Neural Network (DNN) that learns high-order interactions. We apply spectral normalization (SN) to constrain the Lipschitz constant of the DNN. Leveraging this Lipschitz property, we design a nonlinear feedback linearization controller using the learned model and prove system stability with disturbance rejection. To the best of our knowledge, this is the first DNN-based nonlinear feedback controller with stability guarantees that can utilize arbitrarily large neural nets. Experimental results demonstrate that the proposed controller significantly outperforms a Baseline Nonlinear Tracking Controller in both landing and cross-table trajectory tracking cases. We also empirically show that the DNN generalizes well to unseen data outside the training domain.

To deepen our understanding of graph neural networks, we investigate the representation power of Graph Convolutional Networks (GCN) through the looking glass of graph moments, a key property of graph topology encoding path of various lengths. We find that GCNs are rather restrictive in learning graph moments. Without careful design, GCNs can fail miserably even with multiple layers and nonlinear activation functions. We analyze theoretically the expressiveness of GCNs, arriving at a modular GCN design, using different propagation rules. Our modular design is capable of distinguishing graphs from different graph generation models for surprisingly small graphs, a notoriously difficult problem in network science. Our investigation suggests that, depth is much more influential than width and deeper GCNs are more capable of learning higher order graph moments. Additionally, combining GCN modules with different propagation rules is critical to the representation power of GCNs.

Missing value imputation is a fundamental problem in spatiotemporal modeling, from motion tracking to the dynamics of physical systems. Deep autoregressive models suffer from error propagation which becomes catastrophic for imputing long-range sequences. In this paper, we take a non-autoregressive approach and propose a novel deep generative model: Non-AutOregressive Multiresolution Imputation (NAOMI) to impute long-range sequences given arbitrary missing patterns. NAOMI exploits the multiresolution structure of spatiotemporal data and decodes recursively from coarse to fine-grained resolutions using a divide-and-conquer strategy. We further enhance our model with adversarial training. When evaluated extensively on benchmark datasets from systems of both deterministic and stochastic dynamics. NAOMI demonstrates significant improvement in imputation accuracy (reducing average prediction error by 60% compared to autoregressive counterparts) and generalization for long range sequences.

Low-rank tensor regression, a new model class that learns high-order correlation from data, has recently received considerable attention. At the same time, Gaussian processes (GP) are well-studied machine learning models for structure learning. In this paper, we demonstrate interesting connections between the two, especially for multi-way data analysis. We show that low-rank tensor regression is essentially learning a multi-linear kernel in Gaussian processes, and the low-rank assumption translates to the constrained Bayesian inference problem. We prove the oracle inequality and derive the average case learning curve for the equivalent GP model. Our finding implies that low-rank tensor regression, though empirically successful, is highly dependent on the eigenvalues of covariance functions as well as variable correlations.

Traffic forecasting is a vital part of intelligent transportation systems. It becomes particularly challenging due to short-term (e.g., accidents, constructions) and long-term (e.g., peak-hour, seasonal, weather) traffic patterns. While most of the previously proposed techniques focus on normal condition forecasting, a single framework for extreme condition traffic forecasting does not exist. To address this need, we propose to take a deep learning approach. We build a deep neural network based on long short term memory (LSTM) units. We apply Deep LSTM to forecast peak-hour traffic and manage to identify unique characteristics of the traffic data. We further improve the model for post-accident forecasting with Mixture Deep LSTM model. It jointly models the normal condition traffic and the pattern of accidents. We evaluate our model on a real-world large-scale traffic dataset in Los Angeles. When trained end-to-end with suitable regularization, our approach achieves 30%–50% improvement over baselines. We also demonstrate a novel technique to interpret the model with signal stimulation. We note interesting observations from the trained neural network.

Tensor regression has shown to be advantageous in learning tasks with multi-directional relatedness. Given massive multiway data, traditional methods are often too slow to operate on or suffer from memory bottleneck. In this paper, we introduce subsampled tensor projected gradient to solve the problem. Our algorithm is impressively simple and efficient. It is built upon projected gradient method with fast tensor power iterations, leveraging randomized sketching for further acceleration. Theoretical analysis shows that our algorithm converges to the correct solution in fixed number of iterations. The memory requirement grows linearly with the size of the problem. We demonstrate superior empirical performance on both multi-linear multi-task learning and spatio-temporal applications.

Real-time traffic prediction from high-fidelity spatiotemporal traffic sensor datasets is an important problem for intelligent transportation systems and sustainability. However, it is challenging due to the complex topological dependencies and high dynamism associated with changing road conditions. In this paper, we propose a Latent Space Model for Road Networks (LSM-RN) to address these challenges holistically. In particular, given a series of road network snapshots, we learn the attributes of vertices in latent spaces which capture both topological and temporal properties. As these latent attributes are time-dependent, they can estimate how traffic patterns form and evolve. In addition, we present an incremental online algorithm which sequentially and adaptively learns the latent attributes from the temporal graph changes. Our framework enables real-time traffic prediction by 1) exploiting real-time sensor readings to adjust/update the existing latent spaces, and 2) training as data arrives and making predictions on-the-fly. By conducting extensive experiments with a large volume of real-world traffic sensor data, we demonstrate the superiority of our framework for real-time traffic prediction on large road networks over competitors as well as baseline graph-based LSM's.

Discovering latent structures in spatial data is of critical importance to understanding the user behavior of location-based services. In this paper, we study the problem of geographic segmentation of spatial data, which involves dividing a collection of observations into distinct geo-spatial regions and uncovering abstract correlation structures in the data. We introduce a novel, Latent Poisson Factor (LPF) model to describe spatial count data. The model describes the spatial counts as a Poisson distribution with a mean that factors over a joint item-location latent space. The latent factors are constrained with weak labels to help uncover interesting spatial dependencies. We study the LPF model on a mobile app usage data set and a news article readership data set. We empirically demonstrate its effectiveness on a variety of prediction tasks on these two data sets.

Low-rank tensor learning has many applications in machine learning. A series of batch learning algorithms have achieved great successes. However, in many emerging applications, such as climate data analysis, we are confronted with large-scale tensor streams, which poses significant challenges to existing solution in terms of computational costs and limited response time. In this paper, we propose an online accelerated low-rank tensor learning algorithm (ALTO) to solve the problem. At each iteration, we project the current tensor to the subspace of low-rank tensors in order to perform efficient tensor decomposition, then recover the decomposition of the new tensor. By randomly glancing at additional subspaces, we successfully avoid local optima at negligible extra computational cost. We evaluate our method on two tasks in streaming multivariate spatio-temporal analysis: online forecasting and multi-model ensemble, which shows that our method achieves comparable predictive accuracy with significant boost in run time.

Traditional anomaly detection on social media mostly focuses on individual point anomalies while anomalous phenomena usually occur in groups. Therefore, it is valuable to study the collective behavior of individuals and detect group anomalies. Existing group anomaly detection approaches rely on the assumption that the groups are known, which can hardly be true in real world social media applications. In this article, we take a generative approach by proposing a hierarchical Bayes model: Group Latent Anomaly Detection (GLAD) model. GLAD takes both pairwise and point-wise data as input, automatically infers the groups and detects group anomalies simultaneously. To account for the dynamic properties of the social media data, we further generalize GLAD to its dynamic extension d-GLAD. We conduct extensive experiments to evaluate our models on both synthetic and real world datasets. The empirical results demonstrate that our approach is effective and robust in discovering latent groups and detecting group anomalies.

Traditional anomaly detection on social media mostly focuses on individual point anomalies while anomalous phenomena usually occur in groups. Therefore it is valuable to study the collective behavior of individuals and detect group anomalies. Existing group anomaly detection approaches rely on the assumption that the groups are known, which can hardly be true in real world social media applications. In this paper, we take a generative approach by proposing a hierarchical Bayes model: Group Latent Anomaly Detection (GLAD) model. GLAD takes both pair-wise and point-wise data as input, automatically infers the groups and detects group anomalies simultaneously. To account for the dynamic properties of the social media data, we further generalize GLAD to its dynamic extension d-GLAD. We conduct extensive experiments to evaluate our models on both synthetic and real world datasets. The empirical results demonstrate that our approach is effective and robust in discovering latent groups and detecting group anomalies.

Variable selection problems are typically addressed under apenalized optimization framework. Nonconvex penalties such as the minimax concave plus (MCP) and smoothly clipped absolute deviation(SCAD), have been demonstrated to have the properties of sparsity practically and theoretically. In this paper we propose a new nonconvex penalty that we call exponential-type penalty. The exponential-type penalty is characterized by a positive parameter,which establishes a connection with the ell0 and ell1 penalties.We apply this new penalty to sparse supervised learning problems. To solve to resulting optimization problem, we resort to a reweighted ell1 minimization method. Moreover, we devise an efficient method for the adaptive update of the tuning parameter. Our experimental results are encouraging. They show that the exponential-type penalty is competitive with MCP and SCAD.