A Review of Graph Neural Networks in Epidemic Modeling

Since the onset of the COVID-19 pandemic, there has been a growing interest in studying epidemiological models. Traditional mechanistic models mathematically describe the transmission mechanisms of infectious diseases. However, they often fall short when confronted with the growing challenges of today. Consequently, Graph Neural Networks (GNNs) have emerged as a progressively popular tool in epidemic research. In this paper, we endeavor to furnish a comprehensive review of GNNs in epidemic tasks and highlight potential future directions. To accomplish this objective, we introduce hierarchical taxonomies for both epidemic tasks and methodologies, offering a trajectory of development within this domain. For epidemic tasks, we establish a taxonomy akin to those typically employed within the epidemic domain. For methodology, we categorize existing work into \textit{Neural Models} and \textit{Hybrid Models}. Following this, we perform an exhaustive and systematic examination of the methodologies, encompassing both the tasks and their technical details. Furthermore, we discuss the limitations of existing methods from diverse perspectives and systematically propose future research directions. This survey aims to bridge literature gaps and promote the progression of this promising field. We hope that it will facilitate synergies between the communities of GNNs and epidemiology, and contribute to their collective progress.

LSTPrompt: Large Language Models as Zero-Shot Time Series Forecasters by Long-Short-Term Prompting

Time-series forecasting (TSF) finds broad applications in real-world scenarios. Prompting off-the-shelf Large Language Models (LLMs) demonstrates strong zero-shot TSF capabilities while preserving computational efficiency. However, existing prompting methods oversimplify TSF as language next-token predictions, overlooking its dynamic nature and lack of integration with state-of-the-art prompt strategies such as Chain-of-Thought. Thus, we propose LSTPrompt, a novel approach for prompting LLMs in zero-shot TSF tasks. LSTPrompt decomposes TSF into short-term and long-term forecasting sub-tasks, tailoring prompts to each. LSTPrompt guides LLMs to regularly reassess forecasting mechanisms to enhance adaptability. Extensive evaluations demonstrate consistently better performance of LSTPrompt than existing prompting methods, and competitive results compared to foundation TSF models.

A Comprehensive Survey on Graph Reduction: Sparsification, Coarsening, and Condensation

Many real-world datasets can be naturally represented as graphs, spanning a wide range of domains. However, the increasing complexity and size of graph datasets present significant challenges for analysis and computation. In response, graph reduction techniques have gained prominence for simplifying large graphs while preserving essential properties. In this survey, we aim to provide a comprehensive understanding of graph reduction methods, including graph sparsification, graph coarsening, and graph condensation. Specifically, we establish a unified definition for these methods and introduce a hierarchical taxonomy to categorize the challenges they address. Our survey then systematically reviews the technical details of these methods and emphasizes their practical applications across diverse scenarios. Furthermore, we outline critical research directions to ensure the continued effectiveness of graph reduction techniques, as well as provide a comprehensive paper list at https://github.com/ChandlerBang/awesome-graph-reduction. We hope this survey will bridge literature gaps and propel the advancement of this promising field.

Large Pre-trained time series models for cross-domain Time series analysis tasks

Large pre-trained models have been instrumental in significant advancements in domains like language and vision making model training for individual downstream tasks more efficient as well as provide superior performance. However, tackling time-series analysis tasks usually involves designing and training a separate model from scratch leveraging training data and domain expertise specific to the task. We tackle a significant challenge for pre-training a general time-series model from multiple heterogeneous time-series dataset: providing semantically useful inputs to models for modeling time series of different dynamics from different domains. We observe that partitioning time-series into segments as inputs to sequential models produces semantically better inputs and propose a novel model LPTM that automatically identifies optimal dataset-specific segmentation strategy leveraging self-supervised learning loss during pre-training. LPTM provides performance similar to or better than domain-specific state-of-art model and is significantly more data and compute efficient taking up to 40% less data as well as 50% less training time to achieve state-of-art performance in a wide range of time-series analysis tasks from multiple disparate domain.

PEMS: Pre-trained Epidemic Time-series Models

Providing accurate and reliable predictions about the future of an epidemic is an important problem for enabling informed public health decisions. Recent works have shown that leveraging data-driven solutions that utilize advances in deep learning methods to learn from past data of an epidemic often outperform traditional mechanistic models. However, in many cases, the past data is sparse and may not sufficiently capture the underlying dynamics. While there exists a large amount of data from past epidemics, leveraging prior knowledge from time-series data of other diseases is a non-trivial challenge. Motivated by the success of pre-trained models in language and vision tasks, we tackle the problem of pre-training epidemic time-series models to learn from multiple datasets from different diseases and epidemics. We introduce Pre-trained Epidemic Time-Series Models (PEMS) that learn from diverse time-series datasets of a variety of diseases by formulating pre-training as a set of self-supervised learning (SSL) tasks. We tackle various important challenges specific to pre-training for epidemic time-series such as dealing with heterogeneous dynamics and efficiently capturing useful patterns from multiple epidemic datasets by carefully designing the SSL tasks to learn important priors about the epidemic dynamics that can be leveraged for fine-tuning to multiple downstream tasks. The resultant PEM outperforms previous state-of-the-art methods in various downstream time-series tasks across datasets of varying seasonal patterns, geography, and mechanism of contagion including the novel Covid-19 pandemic unseen in pre-trained data with better efficiency using smaller fraction of datasets.

When Rigidity Hurts: Soft Consistency Regularization for Probabilistic Hierarchical Time Series Forecasting

Probabilistic hierarchical time-series forecasting is an important variant of time-series forecasting, where the goal is to model and forecast multivariate time-series that have underlying hierarchical relations. Most methods focus on point predictions and do not provide well-calibrated probabilistic forecasts distributions. Recent state-of-art probabilistic forecasting methods also impose hierarchical relations on point predictions and samples of distribution which does not account for coherency of forecast distributions. Previous works also silently assume that datasets are always consistent with given hierarchical relations and do not adapt to real-world datasets that show deviation from this assumption. We close both these gap and propose PROFHiT, which is a fully probabilistic hierarchical forecasting model that jointly models forecast distribution of entire hierarchy. PROFHiT uses a flexible probabilistic Bayesian approach and introduces a novel Distributional Coherency regularization to learn from hierarchical relations for entire forecast distribution that enables robust and calibrated forecasts as well as adapt to datasets of varying hierarchical consistency. On evaluating PROFHiT over wide range of datasets, we observed 41-88% better performance in accuracy and significantly better calibration. Due to modeling the coherency over full distribution, we observed that PROFHiT can robustly provide reliable forecasts even if up to 10% of input time-series data is missing where other methods' performance severely degrade by over 70%.

Performative Time-Series Forecasting

Time-series forecasting is a critical challenge in various domains and has witnessed substantial progress in recent years. Many real-life scenarios, such as public health, economics, and social applications, involve feedback loops where predictions can influence the predicted outcome, subsequently altering the target variable's distribution. This phenomenon, known as performativity, introduces the potential for 'self-negating' or 'self-fulfilling' predictions. Despite extensive studies in classification problems across domains, performativity remains largely unexplored in the context of time-series forecasting from a machine-learning perspective. In this paper, we formalize performative time-series forecasting (PeTS), addressing the challenge of accurate predictions when performativity-induced distribution shifts are possible. We propose a novel approach, Feature Performative-Shifting (FPS), which leverages the concept of delayed response to anticipate distribution shifts and subsequently predicts targets accordingly. We provide theoretical insights suggesting that FPS can potentially lead to reduced generalization error. We conduct comprehensive experiments using multiple time-series models on COVID-19 and traffic forecasting tasks. The results demonstrate that FPS consistently outperforms conventional time-series forecasting methods, highlighting its efficacy in handling performativity-induced challenges.

DF2: Distribution-Free Decision-Focused Learning

Decision-focused learning (DFL) has recently emerged as a powerful approach for predict-then-optimize problems by customizing a predictive model to a downstream optimization task. However, existing end-to-end DFL methods are hindered by three significant bottlenecks: model mismatch error, sample average approximation error, and gradient approximation error. Model mismatch error stems from the misalignment between the model's parameterized predictive distribution and the true probability distribution. Sample average approximation error arises when using finite samples to approximate the expected optimization objective. Gradient approximation error occurs as DFL relies on the KKT condition for exact gradient computation, while most methods approximate the gradient for backpropagation in non-convex objectives. In this paper, we present DF2 -- the first \textit{distribution-free} decision-focused learning method explicitly designed to address these three bottlenecks. Rather than depending on a task-specific forecaster that requires precise model assumptions, our method directly learns the expected optimization function during training. To efficiently learn the function in a data-driven manner, we devise an attention-based model architecture inspired by the distribution-based parameterization of the expected objective. Our method is, to the best of our knowledge, the first to address all three bottlenecks within a single model. We evaluate DF2 on a synthetic problem, a wind power bidding problem, and a non-convex vaccine distribution problem, demonstrating the effectiveness of DF2.

PINNsFormer: A Transformer-Based Framework For Physics-Informed Neural Networks

Physics-Informed Neural Networks (PINNs) have emerged as a promising deep learning framework for approximating numerical solutions for partial differential equations (PDEs). While conventional PINNs and most related studies adopt fully-connected multilayer perceptrons (MLP) as the backbone structure, they have neglected the temporal relations in PDEs and failed to approximate the true solution. In this paper, we propose a novel Transformer-based framework, namely PINNsFormer, that accurately approximates PDEs' solutions by capturing the temporal dependencies with multi-head attention mechanisms in Transformer-based models. Instead of approximating point predictions, PINNsFormer adapts input vectors to pseudo sequences and point-wise PINNs loss to a sequential PINNs loss. In addition, PINNsFormer is equipped with a novel activation function, namely Wavelet, which anticipates the Fourier decomposition through deep neural networks. We empirically demonstrate PINNsFormer's ability to capture the PDE solutions for various scenarios, in which conventional PINNs have failed to learn. We also show that PINNsFormer achieves superior approximation accuracy on such problems than conventional PINNs with non-sensitive hyperparameters, in trade of marginal computational and memory costs, with extensive experiments.