Tingsong Xiao

Wenchong He, Zhe Jiang, Tingsong Xiao et al.

Transformers are widely used deep learning architectures. Existing transformers are mostly designed for sequences (texts or time series), images or videos, and graphs. This paper proposes a novel transformer model for massive (up to a million) point samples in continuous space. Such data are ubiquitous in environment sciences (e.g., sensor observations), numerical simulations (e.g., particle-laden flow, astrophysics), and location-based services (e.g., POIs and trajectories). However, designing a transformer for massive spatial points is non-trivial due to several challenges, including implicit long-range and multi-scale dependency on irregular points in continuous space, a non-uniform point distribution, the potential high computational costs of calculating all-pair attention across massive points, and the risks of over-confident predictions due to varying point density. To address these challenges, we propose a new hierarchical spatial transformer model, which includes multi-resolution representation learning within a quad-tree hierarchy and efficient spatial attention via coarse approximation. We also design an uncertainty quantification branch to estimate prediction confidence related to input feature noise and point sparsity. We provide a theoretical analysis of computational time complexity and memory costs. Extensive experiments on both real-world and synthetic datasets show that our method outperforms multiple baselines in prediction accuracy and our model can scale up to one million points on one NVIDIA A100 GPU. The code is available at \url{https://github.com/spatialdatasciencegroup/HST}.

Zikai Zhang, Suman Rath, Jiahao Xu et al.

The Smart Grid (SG) is a critical energy infrastructure that collects real-time electricity usage data to forecast future energy demands using information and communication technologies (ICT). Due to growing concerns about data security and privacy in SGs, federated learning (FL) has emerged as a promising training framework. FL offers a balance between privacy, efficiency, and accuracy in SGs by enabling collaborative model training without sharing private data from IoT devices. In this survey, we thoroughly review recent advancements in designing FL-based SG systems across three stages: generation, transmission and distribution, and consumption. Additionally, we explore potential vulnerabilities that may arise when implementing FL in these stages. Furthermore, we discuss the gap between state-of-the-art (SOTA) FL research and its practical applications in SGs, and we propose future research directions. Unlike traditional surveys addressing security issues in centralized machine learning methods for SG systems, this survey is the first to specifically examine the applications and security concerns unique to FL-based SG systems. We also introduce FedGridShield, an open-source framework featuring implementations of SOTA attack and defense methods. Our aim is to inspire further research into applications and improvements in the robustness of FL-based SG systems.

Wenchong He, Zhe Jiang, Tingsong Xiao et al.

Deep neural networks (DNNs) have achieved tremendous success in computer vision, natural language processing, and scientific and engineering domains. However, DNNs can make unexpected, incorrect, yet overconfident predictions, leading to serious consequences in high-stakes applications such as autonomous driving, medical diagnosis, and disaster response. Uncertainty quantification (UQ) estimates the confidence of DNN predictions in addition to their accuracy. In recent years, many UQ methods have been developed for DNNs. It is valuable to systematically categorize these methods and compare their strengths and limitations. Existing surveys mostly categorize UQ methodologies by neural network architecture or Bayesian formulation, while overlooking the uncertainty sources each method addresses, making it difficult to select an appropriate approach in practice. To fill this gap, this paper presents a taxonomy of UQ methods for DNNs based on uncertainty sources (e.g., data versus model uncertainty). We summarize the advantages and disadvantages of each category, and illustrate how UQ can be applied to machine learning problems (e.g., active learning, out-of-distribution robustness, and deep reinforcement learning). We also identify future research directions, including UQ for large language models (LLMs), AI-driven scientific simulations, and deep neural networks with structured outputs.

Zibo Liu, Zhe Jiang, Zelin Xu et al.

Traffic forecasting uses recent measurements by sensors installed at chosen locations to forecast the future road traffic. Existing work either assumes all locations are equipped with sensors or focuses on short-term forecast. This paper studies partial sensing forecast of long-term traffic, assuming sensors are available only at some locations. The problem is challenging due to the unknown data distribution at unsensed locations, the intricate spatio-temporal correlation in long-term forecasting, as well as noise to traffic patterns. We propose a Spatio-temporal Long-term Partial sensing Forecast model (SLPF) for traffic prediction, with several novel contributions, including a rank-based embedding technique to reduce the impact of noise in data, a spatial transfer matrix to overcome the spatial distribution shift from sensed locations to unsensed locations, and a multi-step training process that utilizes all available data to successively refine the model parameters for better accuracy. Extensive experiments on several real-world traffic datasets demonstrate its superior performance. Our source code is at https://github.com/zbliu98/SLPF

Zelin Xu, Yupu Zhang, Saugat Adhikari et al.

Benchmarking spatial reasoning in multimodal large language models (MLLMs) has attracted growing interest in computer vision due to its importance for embodied AI and other agentic systems that require precise interaction with the physical world. However, spatial reasoning on Earth imagery has lagged behind, as it uniquely involves grounding objects in georeferenced images and quantitatively reasoning about distances, directions, and topological relations using both visual cues and vector geometry coordinates (e.g., 2D bounding boxes, polylines, and polygons). Existing benchmarks for Earth imagery primarily focus on 2D spatial grounding, image captioning, and coarse spatial relations (e.g., simple directional or proximity cues). They lack support for quantitative direction and distance reasoning, systematic topological relations, and complex object geometries beyond bounding boxes. To fill this gap, we propose \textbf{EarthSpatialBench}, a comprehensive benchmark for evaluating spatial reasoning in MLLMs on Earth imagery. The benchmark contains over 325K question-answer pairs spanning: (1) qualitative and quantitative reasoning about spatial distance and direction; (2) systematic topological relations; (3) single-object queries, object-pair queries, and compositional aggregate group queries; and (4) object references expressed via textual descriptions, visual overlays, and explicit geometry coordinates, including 2D bounding boxes, polylines, and polygons. We conducted extensive experiments on both open-source and proprietary models to identify limitations in the spatial reasoning of MLLMs.

Zelin Xu, Tingsong Xiao, Wenchong He et al.

Deep learning for Earth imagery plays an increasingly important role in geoscience applications such as agriculture, ecology, and natural disaster management. Still, progress is often hindered by the limited training labels. Given Earth imagery with limited training labels, a base deep neural network model, and a spatial knowledge base with label constraints, our problem is to infer the full labels while training the neural network. The problem is challenging due to the sparse and noisy input labels, spatial uncertainty within the label inference process, and high computational costs associated with a large number of sample locations. Existing works on neuro-symbolic models focus on integrating symbolic logic into neural networks (e.g., loss function, model architecture, and training label augmentation), but these methods do not fully address the challenges of spatial data (e.g., spatial uncertainty, the trade-off between spatial granularity and computational costs). To bridge this gap, we propose a novel Spatial Knowledge-Infused Hierarchical Learning (SKI-HL) framework that iteratively infers sample labels within a multi-resolution hierarchy. Our framework consists of a module to selectively infer labels in different resolutions based on spatial uncertainty and a module to train neural network parameters with uncertainty-aware multi-instance learning. Extensive experiments on real-world flood mapping datasets show that the proposed model outperforms several baseline methods. The code is available at \url{https://github.com/ZelinXu2000/SKI-HL}.

Tingsong Xiao, Zelin Xu, Wenchong He et al.

Adverse clinical events related to unsafe care are among the top ten causes of death in the U.S. Accurate modeling and prediction of clinical events from electronic health records (EHRs) play a crucial role in patient safety enhancement. An example is modeling de facto care pathways that characterize common step-by-step plans for treatment or care. However, clinical event data pose several unique challenges, including the irregularity of time intervals between consecutive events, the existence of cycles, periodicity, multi-scale event interactions, and the high computational costs associated with long event sequences. Existing neural temporal point processes (TPPs) methods do not effectively capture the multi-scale nature of event interactions, which is common in many real-world clinical applications. To address these issues, we propose the cross-temporal-scale transformer (XTSFormer), specifically designed for irregularly timed event data. Our model consists of two vital components: a novel Feature-based Cycle-aware Time Positional Encoding (FCPE) that adeptly captures the cyclical nature of time, and a hierarchical multi-scale temporal attention mechanism, where different temporal scales are determined by a bottom-up clustering approach. Extensive experiments on several real-world EHR datasets show that our XTSFormer outperforms multiple baseline methods. The code is available at https://github.com/spatialdatasciencegroup/XTSFormer.

Jing Su, Chufeng Jiang, Xin Jin et al. · cmu

This systematic literature review comprehensively examines the application of Large Language Models (LLMs) in forecasting and anomaly detection, highlighting the current state of research, inherent challenges, and prospective future directions. LLMs have demonstrated significant potential in parsing and analyzing extensive datasets to identify patterns, predict future events, and detect anomalous behavior across various domains. However, this review identifies several critical challenges that impede their broader adoption and effectiveness, including the reliance on vast historical datasets, issues with generalizability across different contexts, the phenomenon of model hallucinations, limitations within the models' knowledge boundaries, and the substantial computational resources required. Through detailed analysis, this review discusses potential solutions and strategies to overcome these obstacles, such as integrating multimodal data, advancements in learning methodologies, and emphasizing model explainability and computational efficiency. Moreover, this review outlines critical trends that are likely to shape the evolution of LLMs in these fields, including the push toward real-time processing, the importance of sustainable modeling practices, and the value of interdisciplinary collaboration. Conclusively, this review underscores the transformative impact LLMs could have on forecasting and anomaly detection while emphasizing the need for continuous innovation, ethical considerations, and practical solutions to realize their full potential.

Qingyang Wu, Ying Xu, Tingsong Xiao et al.

Large Language Models (LLMs) have emerged as potent tools for advancing the United Nations' Sustainable Development Goals (SDGs). However, the attitudinal disparities between LLMs and humans towards these goals can pose significant challenges. This study conducts a comprehensive review and analysis of the existing literature on the attitudes of LLMs towards the 17 SDGs, emphasizing the comparison between their attitudes and support for each goal and those of humans. We examine the potential disparities, primarily focusing on aspects such as understanding and emotions, cultural and regional differences, task objective variations, and factors considered in the decision-making process. These disparities arise from the underrepresentation and imbalance in LLM training data, historical biases, quality issues, lack of contextual understanding, and skewed ethical values reflected. The study also investigates the risks and harms that may arise from neglecting the attitudes of LLMs towards the SDGs, including the exacerbation of social inequalities, racial discrimination, environmental destruction, and resource wastage. To address these challenges, we propose strategies and recommendations to guide and regulate the application of LLMs, ensuring their alignment with the principles and goals of the SDGs, and therefore creating a more just, inclusive, and sustainable future.

Yupu Zhang, Zelin Xu, Tingsong Xiao et al.

Predicting the binding affinity of protein-ligand complexes plays a vital role in drug discovery. Unfortunately, progress has been hindered by the lack of large-scale and high-quality binding affinity labels. The widely used PDBbind dataset has fewer than 20K labeled complexes. Self-supervised learning, especially graph contrastive learning (GCL), provides a unique opportunity to break the barrier by pre-training graph neural network models based on vast unlabeled complexes and fine-tuning the models on much fewer labeled complexes. However, the problem faces unique challenges, including a lack of a comprehensive unlabeled dataset with well-defined positive/negative complex pairs and the need to design GCL algorithms that incorporate the unique characteristics of such data. To fill the gap, we propose DecoyDB, a large-scale, structure-aware dataset specifically designed for self-supervised GCL on protein-ligand complexes. DecoyDB consists of high-resolution ground truth complexes (less than 2.5 Angstrom) and diverse decoy structures with computationally generated binding poses that range from realistic to suboptimal (negative pairs). Each decoy is annotated with a Root Mean Squared Deviation (RMSD) from the native pose. We further design a customized GCL framework to pre-train graph neural networks based on DecoyDB and fine-tune the models with labels from PDBbind. Extensive experiments confirm that models pre-trained with DecoyDB achieve superior accuracy, label efficiency, and generalizability.

Zibo Liu, Zhe Jiang, Zelin Xu et al.

Spatio-Temporal Multivariate time series Forecast (STMF) uses the time series of $n$ spatially distributed variables in a period of recent past to forecast their values in a period of near future. It has important applications in spatio-temporal sensing forecast such as road traffic prediction and air pollution prediction. Recent papers have addressed a practical problem of missing variables in the model input, which arises in the sensing applications where the number $m$ of sensors is far less than the number $n$ of locations to be monitored, due to budget constraints. We observe that the state of the art assumes that the $m$ variables (i.e., locations with sensors) in the model input are pre-determined and the important problem of how to choose the $m$ variables in the input has never been studied. This paper fills the gap by studying a new problem of STMF with chosen variables, which optimally selects $m$-out-of-$n$ variables for the model input in order to maximize the forecast accuracy. We propose a unified framework that jointly performs variable selection and model optimization for both forecast accuracy and model efficiency. It consists of three novel technical components: (1) masked variable-parameter pruning, which progressively prunes less informative variables and attention parameters through quantile-based masking; (2) prioritized variable-parameter replay, which replays low-loss past samples to preserve learned knowledge for model stability; (3) dynamic extrapolation mechanism, which propagates information from variables selected for the input to all other variables via learnable spatial embeddings and adjacency information. Experiments on five real-world datasets show that our work significantly outperforms the state-of-the-art baselines in both accuracy and efficiency, demonstrating the effectiveness of joint variable selection and model optimization.

Tingsong Xiao, Yao An Lee, Zelin Xu et al.

Disease progression modeling aims to characterize and predict how a patient's disease complications worsen over time based on longitudinal electronic health records (EHRs). Accurate modeling of disease progression, such as type 2 diabetes, can enhance patient sub-phenotyping and inform effective and timely interventions. However, the problem is challenging due to the need to learn continuous-time dynamics of progression patterns based on irregular-time event samples and patient heterogeneity (\eg different progression rates and pathways). Existing mechanistic and data-driven methods either lack adaptability to learn from real-world data or fail to capture complex continuous-time dynamics on progression trajectories. To address these limitations, we propose Temporally Detailed Hypergraph Neural Ordinary Differential Equation (TD-HNODE), which represents disease progression on clinically recognized trajectories as a temporally detailed hypergraph and learns the continuous-time progression dynamics via a neural ODE framework. TD-HNODE contains a learnable TD-Hypergraph Laplacian that captures the interdependency of disease complication markers within both intra- and inter-progression trajectories. Experiments on two real-world clinical datasets demonstrate that TD-HNODE outperforms multiple baselines in modeling the progression of type 2 diabetes and related cardiovascular diseases.

Zelin Xu, Jie Ren, Yupu Zhang et al.

Nearly 900 million people live in low-lying coastal zones around the world and bear the brunt of impacts from more frequent and severe hurricanes and storm surges. Oceanographers simulate ocean current circulation along the coasts to develop early warning systems that save lives and prevent loss and damage to property from coastal hazards. Traditionally, such simulations are conducted using coastal ocean circulation models such as the Regional Ocean Modeling System (ROMS), which usually runs on an HPC cluster with multiple CPU cores. However, the process is time-consuming and energy expensive. While coarse-grained ROMS simulations offer faster alternatives, they sacrifice detail and accuracy, particularly in complex coastal environments. Recent advances in deep learning and GPU architecture have enabled the development of faster AI (neural network) surrogates. This paper introduces an AI surrogate based on a 4D Swin Transformer to simulate coastal tidal wave propagation in an estuary for both hindcast and forecast (up to 12 days). Our approach not only accelerates simulations but also incorporates a physics-based constraint to detect and correct inaccurate results, ensuring reliability while minimizing manual intervention. We develop a fully GPU-accelerated workflow, optimizing the model training and inference pipeline on NVIDIA DGX-2 A100 GPUs. Our experiments demonstrate that our AI surrogate reduces the time cost of 12-day forecasting of traditional ROMS simulations from 9,908 seconds (on 512 CPU cores) to 22 seconds (on one A100 GPU), achieving over 450$\times$ speedup while maintaining high-quality simulation results. This work contributes to oceanographic modeling by offering a fast, accurate, and physically consistent alternative to traditional simulation models, particularly for real-time forecasting in rapid disaster response.