Data-driven benchmarks have led to significant progress in key scientific modeling domains including weather and structural biology. Here, we introduce the Zebrafish Activity Prediction Benchmark (ZAPBench) to measure progress on the problem of predicting cellular-resolution neural activity throughout an entire vertebrate brain. The benchmark is based on a novel dataset containing 4d light-sheet microscopy recordings of over 70,000 neurons in a larval zebrafish brain, along with motion stabilized and voxel-level cell segmentations of these data that facilitate development of a variety of forecasting methods. Initial results from a selection of time series and volumetric video modeling approaches achieve better performance than naive baseline methods, but also show room for further improvement. The specific brain used in the activity recording is also undergoing synaptic-level anatomical mapping, which will enable future integration of detailed structural information into forecasting methods.
Spatiotemporal forecasting is critical in applications such as traffic prediction, climate modeling, and environmental monitoring. However, the prevalence of missing data in real-world sensor networks significantly complicates this task. In this paper, we introduce the Temporal Graph MLP-Mixer (T-GMM), a novel architecture designed to address these challenges. The model combines node-level processing with patch-level subgraph encoding to capture localized spatial dependencies while leveraging a three-dimensional MLP-Mixer to handle temporal, spatial, and feature-based dependencies. Experiments on the AQI, ENGRAD, PV-US and METR-LA datasets demonstrate the model's ability to effectively forecast even in the presence of significant missing data. While not surpassing state-of-the-art models in all scenarios, the T-GMM exhibits strong learning capabilities, particularly in capturing long-range dependencies. These results highlight its potential for robust, scalable spatiotemporal forecasting.
In many problem settings that require spatio-temporal forecasting, the values in the time-series not only exhibit spatio-temporal correlations but are also influenced by spatial diffusion across locations. One such example is forecasting the concentration of fine particulate matter (PM2.5) in the atmosphere which is influenced by many complex factors, the most important ones being diffusion due to meteorological factors as well as transport across vast distances over a period of time. We present a novel Spatio-Temporal Graph Neural Network architecture, that specifically captures these dependencies to forecast the PM2.5 concentration. Our model is based on an encoder-decoder architecture where the encoder and decoder parts leverage gated recurrent units (GRU) augmented with a graph neural network (TransformerConv) to account for spatial diffusion. Our model can also be seen as a generalization of various existing models for time-series or spatio-temporal forecasting. We demonstrate the model's effectiveness on two real-world PM2.5 datasets: (1) data collected by us using a recently deployed network of low-cost PM$_{2.5}$ sensors from 511 locations spanning the entirety of the Indian state of Bihar over a period of one year, and (2) another publicly available dataset that covers severely polluted regions from China for a period of 4 years. Our experimental results show our model's impressive ability to account for both spatial as well as temporal dependencies precisely.
Next-generation reservoir computing (NG-RC) has attracted much attention due to its excellent performance in spatio-temporal forecasting of complex systems and its ease of implementation. This paper shows that NG-RC can be encoded as a kernel ridge regression that makes training efficient and feasible even when the space of chosen polynomial features is very large. Additionally, an extension to an infinite number of covariates is possible, which makes the methodology agnostic with respect to the lags into the past that are considered as explanatory factors, as well as with respect to the number of polynomial covariates, an important hyperparameter in traditional NG-RC. We show that this approach has solid theoretical backing and good behavior based on kernel universality properties previously established in the literature. Various numerical illustrations show that these generalizations of NG-RC outperform the traditional approach in several forecasting applications.
Large-scale human mobility exhibits spatial and temporal patterns that can assist policymakers in decision making. Although traditional prediction models attempt to capture these patterns, they often interfered by non-periodic public events, such as disasters and occasional celebrations. Since regular human mobility patterns are heavily affected by these events, estimating their causal effects is critical to accurate mobility predictions. Although news articles provide unique perspectives on these events in an unstructured format, processing is a challenge. In this study, we propose a causality-augmented prediction model, called CausalMob, to analyze the causal effects of public events. We first utilize large language models (LLMs) to extract human intentions from news articles and transform them into features that act as causal treatments. Next, the model learns representations of spatio-temporal regional covariates from multiple data sources to serve as confounders for causal inference. Finally, we present a causal effect estimation framework to ensure event features remain independent of confounders during prediction. Based on large-scale real-world data, the experimental results show that the proposed model excels in human mobility prediction, outperforming state-of-the-art models.
Spatiotemporal forecasting of traffic flow data represents a typical problem in the field of machine learning, impacting urban traffic management systems. In general, spatiotemporal forecasting problems involve complex interactions, nonlinearities, and long-range dependencies due to the interwoven nature of the temporal and spatial dimensions. Due to this, traditional statistical and machine learning methods cannot adequately handle the temporal and spatial dependencies in these complex traffic flow datasets. A prevalent approach in the field combines graph convolutional networks and multi-head attention mechanisms for spatiotemporal processing. This paper proposes a wavelet-based temporal attention model, namely a wavelet-based dynamic spatiotemporal aware graph neural network (W-DSTAGNN), for tackling the traffic forecasting problem. Wavelet decomposition can help by decomposing the signal into components that can be analyzed independently, reducing the impact of non-stationarity and handling long-range dependencies of traffic flow datasets. Benchmark experiments using three popularly used statistical metrics confirm that our proposal efficiently captures spatiotemporal correlations and outperforms ten state-of-the-art models (including both temporal and spatiotemporal benchmarks) on three publicly available traffic datasets. Our proposed ensemble method can better handle dynamic temporal and spatial dependencies and make reliable long-term forecasts. In addition to point forecasts, our proposed model can generate interval forecasts that significantly enhance probabilistic forecasting for traffic datasets.
Advances in medical imaging technologies have enabled the collection of longitudinal images, which involve repeated scanning of the same patients over time, to monitor disease progression. However, predictive modeling of such data remains challenging due to high dimensionality, irregular sampling, and data sparsity. To address these issues, we propose ImageFlowNet, a novel model designed to forecast disease trajectories from initial images while preserving spatial details. ImageFlowNet first learns multiscale joint representation spaces across patients and time points, then optimizes deterministic or stochastic flow fields within these spaces using a position-parameterized neural ODE/SDE framework. The model leverages a UNet architecture to create robust multiscale representations and mitigates data scarcity by combining knowledge from all patients. We provide theoretical insights that support our formulation of ODEs, and motivate our regularizations involving high-level visual features, latent space organization, and trajectory smoothness. We validate ImageFlowNet on three longitudinal medical image datasets depicting progression in geographic atrophy, multiple sclerosis, and glioblastoma, demonstrating its ability to effectively forecast disease progression and outperform existing methods. Our contributions include the development of ImageFlowNet, its theoretical underpinnings, and empirical validation on real-world datasets. The official implementation is available at https://github.com/KrishnaswamyLab/ImageFlowNet.
Marine fog poses a significant hazard to global shipping, necessitating effective detection and forecasting to reduce economic losses. In recent years, several machine learning (ML) methods have demonstrated superior detection accuracy compared to traditional meteorological methods. However, most of these works are developed on proprietary datasets, and the few publicly accessible datasets are often limited to simplistic toy scenarios for research purposes. To advance the field, we have collected nearly a decade's worth of multi-modal data related to continuous marine fog stages from four series of geostationary meteorological satellites, along with meteorological observations and numerical analysis, covering 15 marine regions globally where maritime fog frequently occurs. Through pixel-level manual annotation by meteorological experts, we present the most comprehensive marine fog detection and forecasting dataset to date, named M4Fog, to bridge ocean and atmosphere. The dataset comprises 68,000 "super data cubes" along four dimensions: elements, latitude, longitude and time, with a temporal resolution of half an hour and a spatial resolution of 1 kilometer. Considering practical applications, we have defined and explored three meaningful tracks with multi-metric evaluation systems: static or dynamic marine fog detection, and spatio-temporal forecasting for cloud images. Extensive benchmarking and experiments demonstrate the rationality and effectiveness of the construction concept for proposed M4Fog. The data and codes are available to whole researchers through cloud platforms to develop ML-driven marine fog solutions and mitigate adverse impacts on human activities.
Accuracy and timeliness are indeed often conflicting goals in prediction tasks. Premature predictions may yield a higher rate of false alarms, whereas delaying predictions to gather more information can render them too late to be useful. In applications such as wildfires, crimes, and traffic jams, timely forecasting are vital for safeguarding human life and property. Consequently, finding a balance between accuracy and timeliness is crucial. In this paper, we propose an early spatio-temporal forecasting model based on Multi-Objective reinforcement learning that can either implement an optimal policy given a preference or infer the preference based on a small number of samples. The model addresses two primary challenges: 1) enhancing the accuracy of early forecasting and 2) providing the optimal policy for determining the most suitable prediction time for each area. Our method demonstrates superior performance on three large-scale real-world datasets, surpassing existing methods in early spatio-temporal forecasting tasks.
The objective of traffic prediction is to accurately forecast and analyze the dynamics of transportation patterns, considering both space and time. However, the presence of distribution shift poses a significant challenge in this field, as existing models struggle to generalize well when faced with test data that significantly differs from the training distribution. To tackle this issue, this paper introduces a simple and universal spatio-temporal prompt-tuning framework-FlashST, which adapts pre-trained models to the specific characteristics of diverse downstream datasets, improving generalization in diverse traffic prediction scenarios. Specifically, the FlashST framework employs a lightweight spatio-temporal prompt network for in-context learning, capturing spatio-temporal invariant knowledge and facilitating effective adaptation to diverse scenarios. Additionally, we incorporate a distribution mapping mechanism to align the data distributions of pre-training and downstream data, facilitating effective knowledge transfer in spatio-temporal forecasting. Empirical evaluations demonstrate the effectiveness of our FlashST across different spatio-temporal prediction tasks using diverse urban datasets. Code is available at https://github.com/HKUDS/FlashST.
Multi-modality spatio-temporal (MoST) data extends spatio-temporal (ST) data by incorporating multiple modalities, which is prevalent in monitoring systems, encompassing diverse traffic demands and air quality assessments. Despite significant strides in ST modeling in recent years, there remains a need to emphasize harnessing the potential of information from different modalities. Robust MoST forecasting is more challenging because it possesses (i) high-dimensional and complex internal structures and (ii) dynamic heterogeneity caused by temporal, spatial, and modality variations. In this study, we propose a novel MoST learning framework via Self-Supervised Learning, namely MoSSL, which aims to uncover latent patterns from temporal, spatial, and modality perspectives while quantifying dynamic heterogeneity. Experiment results on two real-world MoST datasets verify the superiority of our approach compared with the state-of-the-art baselines. Model implementation is available at https://github.com/beginner-sketch/MoSSL.
Spatio-temporal forecasting is crucial in real-world dynamic systems, predicting future changes using historical data from diverse locations. Existing methods often prioritize the development of intricate neural networks to capture the complex dependencies of the data, yet their accuracy fails to show sustained improvement. Besides, these methods also overlook node heterogeneity, hindering customized prediction modules from handling diverse regional nodes effectively. In this paper, our goal is not to propose a new model but to present a novel low-rank adaptation framework as an off-the-shelf plugin for existing spatial-temporal prediction models, termed ST-LoRA, which alleviates the aforementioned problems through node-level adjustments. Specifically, we first tailor a node adaptive low-rank layer comprising multiple trainable low-rank matrices. Additionally, we devise a multi-layer residual fusion stacking module, injecting the low-rank adapters into predictor modules of various models. Across six real-world traffic datasets and six different types of spatio-temporal prediction models, our approach minimally increases the parameters and training time of the original models by less than 4%, still achieving consistent and sustained performance enhancement.
Graph Neural Networks (GNNs) and Transformer-based models have been increasingly adopted to learn the complex vector representations of spatio-temporal graphs, capturing intricate spatio-temporal dependencies crucial for applications such as traffic datasets. Although many existing methods utilize multi-head attention mechanisms and message-passing neural networks (MPNNs) to capture both spatial and temporal relations, these approaches encode temporal and spatial relations independently, and reflect the graph's topological characteristics in a limited manner. In this work, we introduce the Cycle to Mixer (Cy2Mixer), a novel spatio-temporal GNN based on topological non-trivial invariants of spatio-temporal graphs with gated multi-layer perceptrons (gMLP). The Cy2Mixer is composed of three blocks based on MLPs: A temporal block for capturing temporal properties, a message-passing block for encapsulating spatial information, and a cycle message-passing block for enriching topological information through cyclic subgraphs. We bolster the effectiveness of Cy2Mixer with mathematical evidence emphasizing that our cycle message-passing block is capable of offering differentiated information to the deep learning model compared to the message-passing block. Furthermore, empirical evaluations substantiate the efficacy of the Cy2Mixer, demonstrating state-of-the-art performances across various spatio-temporal benchmark datasets. The source code is available at \url{https://github.com/leemingo/cy2mixer}.
Spatio-temporal forecasting is crucial in various fields and requires a careful balance between identifying subtle patterns and filtering out noise. Vector quantization (VQ) appears well-suited for this purpose, as it quantizes input vectors into a set of codebook vectors or patterns. Although VQ has shown promise in various computer vision tasks, it surprisingly falls short in enhancing the accuracy of spatio-temporal forecasting. We attribute this to two main issues: inaccurate optimization due to non-differentiability and limited representation power in hard-VQ. To tackle these challenges, we introduce Differentiable Sparse Soft-Vector Quantization (SVQ), the first VQ method to enhance spatio-temporal forecasting. SVQ balances detail preservation with noise reduction, offering full differentiability and a solid foundation in sparse regression. Our approach employs a two-layer MLP and an extensive codebook to streamline the sparse regression process, significantly cutting computational costs while simplifying training and improving performance. Empirical studies on five spatio-temporal benchmark datasets show SVQ achieves state-of-the-art results, including a 7.9% improvement on the WeatherBench-S temperature dataset and an average mean absolute error reduction of 9.4% in video prediction benchmarks (Human3.6M, KTH, and KittiCaltech), along with a 17.3% enhancement in image quality (LPIPS). Code is publicly available at https://github.com/Pachark/SVQ-Forecasting.
Air quality forecasting has garnered significant attention recently, with data-driven models taking center stage due to advancements in machine learning and deep learning models. However, researchers face challenges with complex data acquisition and the lack of open-sourced datasets, hindering efficient model validation. This paper introduces PurpleAirSF, a comprehensive and easily accessible dataset collected from the PurpleAir network. With its high temporal resolution, various air quality measures, and diverse geographical coverage, this dataset serves as a useful tool for researchers aiming to develop novel forecasting models, study air pollution patterns, and investigate their impacts on health and the environment. We present a detailed account of the data collection and processing methods employed to build PurpleAirSF. Furthermore, we conduct preliminary experiments using both classic and modern spatio-temporal forecasting models, thereby establishing a benchmark for future air quality forecasting tasks.
Modelling spatio-temporal processes on road networks is a task of growing importance. While significant progress has been made on developing spatio-temporal graph neural networks (Gnns), existing works are built upon three assumptions that are not practical on real-world road networks. First, they assume sensing on every node of a road network. In reality, due to budget-constraints or sensor failures, all locations (nodes) may not be equipped with sensors. Second, they assume that sensing history is available at all installed sensors. This is unrealistic as well due to sensor failures, loss of packets during communication, etc. Finally, there is an assumption of static road networks. Connectivity within networks change due to road closures, constructions of new roads, etc. In this work, we develop FRIGATE to address all these shortcomings. FRIGATE is powered by a spatio-temporal Gnn that integrates positional, topological, and temporal information into rich inductive node representations. The joint fusion of this diverse information is made feasible through a novel combination of gated Lipschitz embeddings with Lstms. We prove that the proposed Gnn architecture is provably more expressive than message-passing Gnns used in state-of-the-art algorithms. The higher expressivity of FRIGATE naturally translates to superior empirical performance conducted on real-world network-constrained traffic data. In addition, FRIGATE is robust to frugal sensor deployment, changes in road network connectivity, and temporal irregularity in sensing.
Machine learning approaches for solving partial differential equations require learning mappings between function spaces. While convolutional or graph neural networks are constrained to discretized functions, neural operators present a promising milestone toward mapping functions directly. Despite impressive results they still face challenges with respect to the domain geometry and typically rely on some form of discretization. In order to alleviate such limitations, we present CORAL, a new method that leverages coordinate-based networks for solving PDEs on general geometries. CORAL is designed to remove constraints on the input mesh, making it applicable to any spatial sampling and geometry. Its ability extends to diverse problem domains, including PDE solving, spatio-temporal forecasting, and inverse problems like geometric design. CORAL demonstrates robust performance across multiple resolutions and performs well in both convex and non-convex domains, surpassing or performing on par with state-of-the-art models.
Environmental monitoring is crucial to our understanding of climate change, biodiversity loss and pollution. The availability of large-scale spatio-temporal data from sources such as sensors and satellites allows us to develop sophisticated models for forecasting and understanding key drivers. However, the data collected from sensors often contain missing values due to faulty equipment or maintenance issues. The missing values rarely occur simultaneously leading to data that are multivariate misaligned sparse time series. We propose two models that are capable of performing multivariate spatio-temporal forecasting while handling missing data naturally without the need for imputation. The first model is a transformer-based model, which we name SERT (Spatio-temporal Encoder Representations from Transformers). The second is a simpler model named SST-ANN (Sparse Spatio-Temporal Artificial Neural Network) which is capable of providing interpretable results. We conduct extensive experiments on two different datasets for multivariate spatio-temporal forecasting and show that our models have competitive or superior performance to those at the state-of-the-art.
There is a recent surge in the development of spatio-temporal forecasting models in the transportation domain. Long-range traffic forecasting, however, remains a challenging task due to the intricate and extensive spatio-temporal correlations observed in traffic networks. Current works primarily rely on road networks with graph structures and learn representations using graph neural networks (GNNs), but this approach suffers from over-smoothing problem in deep architectures. To tackle this problem, recent methods introduced the combination of GNNs with residual connections or neural ordinary differential equations (ODE). However, current graph ODE models face two key limitations in feature extraction: (1) they lean towards global temporal patterns, overlooking local patterns that are important for unexpected events; and (2) they lack dynamic semantic edges in their architectural design. In this paper, we propose a novel architecture called Graph-based Multi-ODE Neural Networks (GRAM-ODE) which is designed with multiple connective ODE-GNN modules to learn better representations by capturing different views of complex local and global dynamic spatio-temporal dependencies. We also add some techniques like shared weights and divergence constraints into the intermediate layers of distinct ODE-GNN modules to further improve their communication towards the forecasting task. Our extensive set of experiments conducted on six real-world datasets demonstrate the superior performance of GRAM-ODE compared with state-of-the-art baselines as well as the contribution of different components to the overall performance. The code is available at https://github.com/zbliu98/GRAM-ODE
Graph neural networks (GNNs), especially dynamic GNNs, have become a research hotspot in spatio-temporal forecasting problems. While many dynamic graph construction methods have been developed, relatively few of them explore the causal relationship between neighbour nodes. Thus, the resulting models lack strong explainability for the causal relationship between the neighbour nodes of the dynamically generated graphs, which can easily lead to a risk in subsequent decisions. Moreover, few of them consider the uncertainty and noise of dynamic graphs based on the time series datasets, which are ubiquitous in real-world graph structure networks. In this paper, we propose a novel Dynamic Diffusion-Variational Graph Neural Network (DVGNN) for spatio-temporal forecasting. For dynamic graph construction, an unsupervised generative model is devised. Two layers of graph convolutional network (GCN) are applied to calculate the posterior distribution of the latent node embeddings in the encoder stage. Then, a diffusion model is used to infer the dynamic link probability and reconstruct causal graphs in the decoder stage adaptively. The new loss function is derived theoretically, and the reparameterization trick is adopted in estimating the probability distribution of the dynamic graphs by Evidence Lower Bound during the backpropagation period. After obtaining the generated graphs, dynamic GCN and temporal attention are applied to predict future states. Experiments are conducted on four real-world datasets of different graph structures in different domains. The results demonstrate that the proposed DVGNN model outperforms state-of-the-art approaches and achieves outstanding Root Mean Squared Error result while exhibiting higher robustness. Also, by F1-score and probability distribution analysis, we demonstrate that DVGNN better reflects the causal relationship and uncertainty of dynamic graphs.