论文检索

Applications · Neuroscience, Cognitive Science

Zijian Dong, Ruilin Li, Joanna Chong, Niousha Dehestani, Yinghui Teng, Yi Lin, Zhizhou Li, Yichi Zhang, Yapei Xie, Leon Ooi 等

We present **Brain Harmony (BrainHarmonix)**, the first multimodal brain foundation model that unifies structural morphology and functional dynamics into compact 1D token representations. The model was pretrained on two of the largest neuroimaging datasets to date, encompassing 64,594 T1-weighted structural MRI 3D volumes (～ 14 million images) and 70,933 functional MRI (fMRI) time series. BrainHarmonix is grounded in two foundational neuroscience principles: *structure complements function* - structural and functional modalities offer distinct yet synergistic insights into brain organization; *function follows structure* - brain functional dynamics are shaped by cortical morphology. The modular pretraining process involves single-modality training with geometric pre-alignment followed by modality fusion through shared brain hub tokens. Notably, our dynamics encoder uniquely handles fMRI time series with heterogeneous repetition times (TRs), addressing a major limitation in existing models. BrainHarmonix is also the first to deeply compress high-dimensional neuroimaging signals into unified, continuous 1D tokens, forming a compact latent space of the human brain. BrainHarmonix achieves strong generalization across diverse downstream tasks, including neurodevelopmental and neurodegenerative disorder classification and cognition prediction - consistently outperforming previous approaches. Our models - pretrained on 8 H100 GPUs - aim to catalyze a new era of AI-driven neuroscience powered by large-scale multimodal neuroimaging.

General Machine Learning · Causality

Yuchen Ma, Dennis Frauen, Jonas Schweisthal, Stefan Feuerriegel

Estimating treatment effects is crucial for personalized decision-making in medicine, but this task faces unique challenges in clinical practice. At training time, models for estimating treatment effects are typically trained on well-structured medical datasets that contain detailed patient information. However, at inference time, predictions are often made using textual descriptions (e.g., descriptions with self-reported symptoms), which are incomplete representations of the original patient information. In this work, we make three contributions. (1) We show that the discrepancy between the data available during training time and inference time can lead to biased estimates of treatment effects. We formalize this issue as an \emph{inference time text confounding} problem, where confounders are fully observed during training time but only partially available through text at inference time. (2) To address this problem, we propose a novel framework for estimating treatment effects that explicitly accounts for inference time text confounding. Our framework leverages large language models (LLMs) together with a custom doubly robust learner to mitigate biases caused by the inference time text confounding. (3) Through a series of experiments, we demonstrate the effectiveness of our framework in real-world applications.

Applications · Time Series

Yuan Yuan, Chonghua Han, Jingtao Ding, Guozhen Zhang, Depeng Jin, Yong Li

The urban environment is characterized by complex spatio-temporal dynamics arising from diverse human activities and interactions. Effectively modeling these dynamics is essential for understanding and optimizing urban systems. In this work, we introduce UrbanDiT, a foundation model for open-world urban spatio-temporal learning that successfully scales up diffusion transformers in this field. UrbanDiT pioneers a unified model that integrates diverse data sources and types while learning universal spatio-temporal patterns across different cities and scenarios. This allows the model to unify both multi-data and multi-task learning, and effectively support a wide range of spatio-temporal applications. Its key innovation lies in the elaborated prompt learning framework, which adaptively generates both data-driven and task-specific prompts, guiding the model to deliver superior performance across various urban applications. UrbanDiT offers three advantages: 1) It unifies diverse data types, such as grid-based and graph-based data, into a sequential format; 2) With task-specific prompts, it supports a wide range of tasks, including bi-directional spatio-temporal prediction, temporal interpolation, spatial extrapolation, and spatio-temporal imputation; and 3) It generalizes effectively to open-world scenarios, with its powerful zero-shot capabilities outperforming nearly all baselines with training data. UrbanDiT sets up a new benchmark for foundation models in the urban spatio-temporal domain. Code and datasets are publicly available at \url{https://github.com/tsinghua-fib-lab/UrbanDiT}.

Applications · Time Series

Jiaming Ma, Binwu Wang, Qihe Huang, Guanjun Wang, Pengkun Wang, Zhengyang Zhou, Yang Wang

The stable periodic patterns present in the time series data serve as the foundation for long-term forecasting. However, existing models suffer from limitations such as continuous and chaotic input partitioning, as well as weak inductive biases, which restrict their ability to capture such recurring structures. In this paper, we propose MoFo, which interprets periodicity as both the correlation of period-aligned time steps and the trend of period-offset time steps. We first design period-structured patches—2D tensors generated through discrete sampling—where each row contains only period-aligned time steps, enabling direct modeling of periodic correlations. Period-offset time steps within a period are aligned in columns. To capture trends across these offset time steps, we introduce a period-aware modulator. This modulator introduces an adaptive strong inductive bias through a regulated relaxation function, encouraging the model to generate attention coefficients that align with periodic trends. This function is end-to-end trainable, enabling the model to adaptively capture the distinct periodic patterns across diverse datasets. Extensive empirical results on widely used benchmark datasets demonstrate that MoFo achieves competitive performance while maintaining high memory efficiency and fast training speed.

Deep Learning · Generative Models and Autoencoders

Zhiyi Lyu, Jianguo Huang, Yanchen Deng, Steven Hoi, Bo An

Large Language Models (LLMs) with inference-time scaling techniques show promise for code generation, yet face notable efficiency and scalability challenges. Construction-based tree-search methods suffer from rapid growth in tree size, high token consumption, and lack of anytime property. In contrast, improvement-based methods offer better performance but often struggle with uninformative reward signals and inefficient search strategies. In this work, we propose $\textbf{ReLoc}$, a unified local search framework which effectively performs step-by-step code revision. Specifically, ReLoc explores a series of local revisions through four key algorithmic components: initial code drafting, neighborhood code generation, candidate evaluation, and incumbent code updating, each of which can be instantiated with specific decision rules to realize different local search algorithms such as Hill Climbing (HC) or Genetic Algorithm (GA). Furthermore, we develop a specialized revision reward model that evaluates code quality based on revision distance to produce fine-grained preferences that guide the local search toward more promising candidates. Finally, our extensive experimental results demonstrate that our approach achieves superior performance across diverse code generation tasks, significantly outperforming both construction-based tree search as well as the state-of-the-art improvement-based code generation methods.

Applications

Chaohao Yuan, Maoji Wen, Ercan KURUOGLU, Yang Liu, Jia Li, Tingyang Xu, Deli Zhao, Hong Cheng, Yu Rong

To enhance the generalization ability of graph neural networks (GNNs) in learning and simulation physical dynamics, a series of equivariant GNNs have been developed to incorporate the symmetric inductive bias. However, the existing methods do not take into account the non-stationarity nature of physical dynamics, where the joint distribution changes over time. Moreover, previous approaches for modeling non-stationary time series typically involve normalizing the data, which disrupts the symmetric assumption inherent in physical dynamics. To model the non-stationary physical dynamics while preserving the symmetric inductive bias, we introduce a Non-Stationary Equivariant Graph Neural Network (NS-EGNN) to capture the non-stationarity in physical dynamics while preserving the symmetric property of the model. Specifically, NS-EGNN employs Fourier Transform on segments of physical dynamics to extract time-varying frequency information from the trajectories. It then uses the first and second-order differences to mitigate non-stationarity, followed by pooling for future predictions. Through capturing varying frequency characteristics and alleviate the linear and quadric trend in the raw physical dynamics, NS-EGNN better models the temporal dependencies in the physical dynamics. NS-EGNN has been applied on various types of physical dynamics, including molecular, motion and protein dynamics. In various scenario, NS-EGNN consistently surpasses the performance of existing state-of-the-art algorithms, underscoring its effectiveness. The implementation of NS-EGNN is available at https://github.com/MaojiWEN/NS-EGNN.

Applications · Neuroscience, Cognitive Science

Yifan WANG, Hongfeng Ai, ruiqi li, Maowei Jiang, Quangao Liu, Jiahua Dong, ruiyuan kang, Alan Liang, Zihang Wang, ruikai liu 等

Medical time-series data play a vital role in disease diagnosis but suffer from limited labeled samples and single-center bias, which hinder model generalization and lead to overfitting. To address these challenges, we propose DAAC (Discrepancy-Aware Adaptive Contrastive learning), a learnable multi-view contrastive framework that integrates external normal samples and enhances feature learning through adaptive contrastive strategies. DAAC consists of two key modules: (1) a Discrepancy Estimator, built upon a GAN-enhanced encoder-decoder architecture, captures the distribution of normal data and computes reconstruction errors as indicators of abnormality. These discrepancy features augment the target dataset to mitigate overfitting. (2) an Adaptive Contrastive Learner uses multi-head attention to extract discriminative representations by contrasting embeddings across multiple views and data granularities (subject, trial, epoch, and temporal levels), eliminating the need for handcrafted positive-negative sample pairs. Extensive experiments on three clinical datasets—covering Alzheimer’s disease, Parkinson’s disease, and myocardial infarction—demonstrate that DAAC significantly outperforms existing methods, even when only 10\% of labeled data is available, showing strong generalization and diagnostic performance. Our code is available at https://github.com/CUHKSZ-MED-BioE/DAAC.

Applications · Language, Speech and Dialog

Fengwei Teng, Quan Shi, Zhaoyang Yu, Jiayi Zhang, Yuyu Luo, Chenglin Wu, Zhijiang Guo

Large Language Models (LLMs) achieve superior performance through training-time scaling, and test-time scaling further enhances their capabilities by conducting effective reasoning during inference. However, as the scale of reasoning increases, existing test-time scaling methods suffer from accumulated historical information, which not only wastes computational resources but also interferes with effective reasoning. To address this issue, we observe that complex reasoning can be achieved by solving a series of independent and self-contained subquestions. These subquestions are essentially \textit{atomic questions}, exhibiting the memoryless property similar to Markov processes. Based on this observation, we propose Atom of Thoughts (\our), where each state transition consists of decomposing the current question into a dependency-based directed acyclic graph and contracting its subquestions, forming a simplified question that maintains answer equivalence with the original problem. This answer preservation enables the iterative \textit{decomposition-contraction} process to naturally form a meaningful Markov reasoning process. Furthermore, these atomic states can be seamlessly integrated into existing test-time scaling methods, enabling \our to serve as a plug-in enhancement for improving reasoning capabilities.

General Machine Learning · Everything Else

Ting Liang, Xiaoliang Wu, Junyu Huang, Jianxin Wang, Qilong Feng

Clustering is a fundamental problem that has been extensively studied over past few decades, with most research focusing on point-based clustering such as $k$-means, $k$-median, and $k$-center. However, numerous real-world applications, such as motion analysis, computer vision, and missing data analysis, require clustering over structured data, including lines, time series and affine subspaces (flats), where traditional point-based clustering algorithms often fall short. In this paper, we study the $k$-means of lines problem, where the input is a set $L$ of lines in $\mathbb{R}^d$, and the goal is to find $k$ centers $C$ in $\mathbb{R}^d$ such that the sum of squared distances from each line in $L$ to its nearest center in $C$ is minimized. The local search algorithm is a well-established strategy for point-based $k$-means clustering, known for its efficiency and provable approximation guarantees. However, extending local search algorithm to the $k$-means of lines problem is nontrivial, as the capture relation used in point-based clustering does not generalize to the line setting. This is because that the point-to-line distance function lack the triangle inequality property that supports geometric analysis in point-based clustering. Moreover, since lines extend infinitely in space, it is difficult to identify effective swap points that can significantly reduce the clustering cost. To overcome above obstacles, we introduce a *proportional capture relation* that links optimal and current centers based the assignment proportions of lines, enabling a refined analysis that bypasses the triangle inequality barrier. We also introduce a *CrossLine* structure, which provides a principled discretization of the geometric space around line pairs, and ensures coverage of high-quality swap points essential for local search, thereby enabling effective execution of the local search process. Consequently, based on the proposed components, we develop the first single-swap local search algorithm for the $k$-means of lines problem, achieving a $(500+\varepsilon)$-approximation in polynomial time for low-dimensional Euclidean space.

Applications · Time Series

Yisong Fu, Zezhi Shao, Chengqing Yu, Yujie Li, Zhulin An, Qi Wang, Yongjun Xu, Fei Wang

Benefiting from high capacity for capturing complex temporal patterns, deep learning (DL) has significantly advanced time series forecasting (TSF). However, deep models tend to suffer from severe overfitting due to the inherent vulnerability of time series to noise and anomalies. The prevailing DL paradigm uniformly optimizes all timesteps through the MSE loss and learns those uncertain and anomalous timesteps without difference, ultimately resulting in overfitting. To address this, we propose a novel selective learning strategy for deep TSF. Specifically, selective learning screens a subset of the whole timesteps to calculate the MSE loss in optimization, guiding the model to focus on generalizable timesteps while disregarding non-generalizable ones. Our framework introduces a dual-mask mechanism to target timesteps: (1) an uncertainty mask leveraging residual entropy to filter uncertain timesteps, and (2) an anomaly mask employing residual lower bound estimation to exclude anomalous timesteps. Extensive experiments across eight real-world datasets demonstrate that selective learning can significantly improve the predictive performance for typical state-of-the-art deep models, including 37.4% MSE reduction for Informer, 8.4% for TimesNet, and 6.5% for iTransformer.

Applications · Time Series

Xingjian Wu, Xiangfei Qiu, Hanyin Cheng, Zhengyu Li, Jilin Hu, Chenjuan Guo, Bin Yang

Time Series Forecasting has made significant progress with the help of Patching technique, which partitions time series into multiple patches to effectively retain contextual semantic information into a representation space beneficial for modeling long-term dependencies. However, conventional patching partitions a time series into adjacent patches, which causes a fixed representation space, thus resulting in insufficiently expressful representations. In this paper, we pioneer the exploration of constructing a selective representation space to flexibly include the most informative patches for forecasting. Specifically, we propose the Selective Representation Space (SRS) module, which utilizes the learnable Selective Patching and Dynamic Reassembly techniques to adaptively select and shuffle the patches from the contextual time series, aiming at fully exploiting the information of contextual time series to enhance the forecasting performance of patch-based models. To demonstrate the effectiveness of SRS module, we propose a simple yet effective SRSNet consisting of SRS and an MLP head, which achieves state-of-the-art performance on real-world datasets from multiple domains. Furthermore, as a novel plugin-and-play module, SRS can also enhance the performance of existing patch-based models. The resources are available at https://github.com/decisionintelligence/SRSNet.

Yuxuan Yang, Dalin Zhang, Yuxuan Liang, Hua Lu, Gang Chen, Huan Li

Time Series Forecasting (TSF) is a crucial task in various domains, yet existing TSF models rely heavily on high-quality data and insufficiently exploit all available data. This paper explores a novel self-supervised approach to re-label time series datasets by inherently constructing candidate datasets. During the optimization of a simple reconstruction network, intermediates are used as pseudo labels in a self-supervised paradigm, improving generalization for any predictor. We introduce the Self-Correction with Adaptive Mask (SCAM), which discards overfitted components and selectively replaces them with pseudo labels generated from reconstructions. Additionally, we incorporate Spectral Norm Regularization (SNR) to further suppress overfitting from a loss landscape perspective. Our experiments on eleven real-world datasets demonstrate that SCAM consistently improves the performance of various backbone models. This work offers a new perspective on constructing datasets and enhancing the generalization of TSF models through self-supervised learning. The code is available at https://github.com/SuDIS-ZJU/SCAM.

Applications · Health

Eunbyeol Cho, Jiyoun Kim, Minjae Lee, Sungjin Park, Edward Choi

Electronic Health Records (EHR) are time-series relational databases that record patient interactions and medical events over time, serving as a critical resource for healthcare research and applications. However, privacy concerns and regulatory restrictions limit the sharing and utilization of such sensitive data, necessitating the generation of synthetic EHR datasets. Unlike previous EHR synthesis methods—which typically generate medical records consisting of expert-chosen features (e.g., a few vital signs, structured codes only)—we introduce RawMed, the first framework to synthesize multi-table, time-series EHR data that closely resembles raw EHRs. Using text-based representation and compression techniques, RawMed captures complex structures and temporal dynamics with minimal lossy preprocessing. We also propose a new evaluation framework for multi-table time-series synthetic EHRs, assessing distributional similarity, inter-table relationships, temporal dynamics, and privacy. Validated on two open-source EHR datasets, RawMed outperforms baseline models in fidelity and utility. The code is available at [https://github.com/eunbyeol-cho/RawMed](https://github.com/eunbyeol-cho/RawMed)

Applications · Time Series

Jiaming Ma, Binwu Wang, Guanjun Wang, Kuo Yang, Zhengyang Zhou, Pengkun Wang, Xu Wang, Yang Wang

The effectiveness of Spatiotemporal Graph Neural Networks (STGNNs) critically hinges on the quality of the underlying graph topology. While end-to-end adaptive graph learning methods have demonstrated promising results in capturing latent spatiotemporal dependencies, they often suffer from high computational complexity and limited expressive capacity. In this paper, we propose MAGE for efficient spatiotemporal forecasting. We first conduct a theoretical analysis demonstrating that the ReLU activation function employed in existing methods amplifies edge-level noise during graph topology learning, thereby compromising the fidelity of the learned graph structures. To enhance model expressiveness, we introduce a sparse yet balanced mixture-of-experts strategy, where each expert perceives the unique underlying graph through kernel-based functions and operates with linear complexity relative to the number of nodes. The sparsity mechanism ensures that each node interacts exclusively with compatible experts, while the balancing mechanism promotes uniform activation across all experts, enabling diverse and adaptive graph representations. Furthermore, we theoretically establish that a single graph convolution using the learned graph in MAGE is mathematically equivalent to multiple convolutional steps under conventional graphs. We evaluate MAGE against advanced baselines on multiple real-world spatiotemporal datasets. MAGE achieves competitive performance while maintaining strong computational efficiency.

Applications · Time Series

Donghao Luo, Xue Wang

In this paper, we pioneer the idea of implicit decomposition. And based on this idea, we propose a powerful decomposition-based enhancement framework, namely DecompNet. Our method converts the time series decomposition into an implicit process, where it can give a time series model the decomposition-related knowledge during inference, even though this model does not actually decompose the input time series. Thus, our DecompNet can enable a model to inherit the performance promotion brought by time series decomposition but will not introduce any additional inference costs, successfully enhancing the model performance while enjoying better efficiency. Experimentally, our DecompNet exhibits promising enhancement capability and compelling framework generality. Especially, it can also enhance the performance of the latest and state-of-the-art models, greatly pushing the performance limit of time series forecasting. Through comprehensive comparisons, DecompNet also shows excellent performance and efficiency superiority, making the decomposition-based enhancement framework surpass the well-recognized normalization-based frameworks for the first time. Code is available at this repository: https://github.com/luodhhh/DecompNet.

Applications · Health

Xiang Lan, Feng Wu, Kai He, Qinghao Zhao, Shenda Hong, Mengling Feng

While recent multimodal large language models (MLLMs) have advanced automated ECG interpretation, they still face two key limitations: (1) insufficient multimodal synergy between ECG time series and ECG images, and (2) limited explainability in linking diagnoses to granular waveform evidence. We introduce GEM, the first MLLM unifying ECG time series, 12-lead ECG images and text for grounded and clinician-aligned ECG interpretation. GEM enables feature-grounded analysis, evidence-driven reasoning, and a clinician-like diagnostic process through three core innovations: a dual-encoder framework extracting complementary time series and image features, cross-modal alignment for effective multimodal understanding, and knowledge-guided instruction data generation for generating high-granularity grounding data (ECG-Grounding) linking diagnoses to measurable parameters ($e.g.$, QRS/PR Intervals). Additionally, we propose the Grounded ECG Understanding task, a clinically motivated benchmark designed to comprehensively assess the MLLM's capability in grounded ECG understanding. Experimental results on both existing and our proposed benchmarks show GEM significantly improves predictive performance (CSN $7.4\%$ $\uparrow$), explainability ($22.7\%$ $\uparrow$), and grounding ($25.3\%$ $\uparrow$), making it a promising approach for real-world clinical applications. Codes, model, and data are available at https://github.com/lanxiang1017/GEM.

Applications · Time Series

ChengAo Shen, Wenchao Yu, Ziming Zhao, Dongjin Song, Wei Cheng, Haifeng Chen, Jingchao Ni

Time series, typically represented as numerical sequences, can also be transformed into images and texts, offering multi-modal views (MMVs) of the same underlying signal. These MMVs can reveal complementary patterns and enable the use of powerful pre-trained large models, such as large vision models (LVMs), for long-term time series forecasting (LTSF). However, as we identified in this work, the state-of-the-art (SOTA) LVM-based forecaster poses an inductive bias towards "forecasting periods". To harness this bias, we propose DMMV, a novel decomposition-based multi-modal view framework that leverages trend-seasonal decomposition and a novel backcast-residual based adaptive decomposition to integrate MMVs for LTSF. Comparative evaluations against 14 SOTA models across diverse datasets show that DMMV outperforms single-view and existing multi-modal baselines, achieving the best mean squared error (MSE) on 6 out of 8 benchmark datasets. The code for this paper is available at: https://github.com/D2I-Group/dmmv.

Applications · Time Series

Yushan Jiang, Wenchao Yu, Geon Lee, Dongjin Song, Kijung Shin, Wei Cheng, Yanchi Liu, Haifeng Chen

Time series analysis provides essential insights for real-world system dynamics and informs downstream decision-making, yet most existing methods often overlook the rich contextual signals present in auxiliary modalities. To bridge this gap, we introduce TimeXL, a multi-modal prediction framework that integrates a prototype-based time series encoder with three collaborating Large Language Models (LLMs) to deliver more accurate predictions and interpretable explanations. First, a multi-modal prototype-based encoder processes both time series and textual inputs to generate preliminary forecasts alongside case-based rationales. These outputs then feed into a prediction LLM, which refines the forecasts by reasoning over the encoder's predictions and explanations. Next, a reflection LLM compares the predicted values against the ground truth, identifying textual inconsistencies or noise. Guided by this feedback, a refinement LLM iteratively enhances text quality and triggers encoder retraining. This closed-loop workflow---prediction, critique (reflect), and refinement---continuously boosts the framework's performance and interpretability. Empirical evaluations on four real-world datasets demonstrate that TimeXL achieves up to 8.9\% improvement in AUC and produces human-centric, multi-modal explanations, highlighting the power of LLM-driven reasoning for time series prediction.

Applications · Time Series

Sai Shankar Narasimhan, Shubhankar Agarwal, Litu Rout, Sanjay Shakkottai, Sandeep Chinchali

Generating realistic time series samples is crucial for stress-testing models and protecting user privacy by using synthetic data. In engineering and safety-critical applications, these samples must meet certain hard constraints that are domain-specific or naturally imposed by physics or nature. Consider, for example, generating electricity demand patterns with constraints on peak demand times. This can be used to stress-test the functioning of power grids during adverse weather conditions. Existing approaches for generating constrained time series are either not scalable or degrade sample quality. To address these challenges, we introduce Constrained Posterior Sampling (CPS), a diffusion-based sampling algorithm that aims to project the posterior mean estimate into the constraint set after each denoising update. Notably, CPS scales to a large number of constraints ($\sim100$) without requiring additional training. We provide theoretical justifications highlighting the impact of our projection step on sampling. Empirically, CPS outperforms state-of-the-art methods in sample quality and similarity to real time series by around 70\% and 22\%, respectively, on real-world stocks, traffic, and air quality datasets.

Applications · Time Series

Qingyi Pan, Yicheng Li

Real-world time series analysis, such as healthcare, autonomous driving, and solar energy, faces unique challenges arising from the scarcity of labeled data, highlighting the need for effective semi-supervised learning methods. While the Virtual Adversarial Training (VAT) method has shown promising performance in leveraging unlabeled data for smoother predictive distributions, straightforward extensions of VAT often fall short on time series tasks as they neglect the temporal structure of the data in the adversarial perturbation. In this paper, we propose the framework of functional Virtual Adversarial Training (f-VAT) that can incorporate the functional structure of the data into perturbations. By theoretically establishing a duality between the perturbation norm and the functional model sensitivity, we propose to use an appropriate Sobolev ($H^{-s}$) norm to generate structured functional adversarial perturbations for semi-supervised time series classification. Our proposed f-VAT method outperforms recent methods and achieves superior performance in extensive semi-supervised time series classification tasks (e.g., up to $ \approx 9$ % performance improvement). We also provide additional visualization studies to offer further insights into the superiority of f-VAT.