论文检索

Applications · Neuroscience, Cognitive Science

Changze Lv, Yansen Wang, Dongqi Han, Yifei Shen, Xiaoqing Zheng, Xuanjing Huang, Dongsheng Li

Spiking neural networks (SNNs) are bio-inspired networks that mimic how neurons in the brain communicate through discrete spikes, which have great potential in various tasks due to their energy efficiency and temporal processing capabilities. SNNs with self-attention mechanisms (spiking Transformers) have recently shown great advancements in various tasks, and inspired by traditional Transformers, several studies have demonstrated that spiking absolute positional encoding can help capture sequential relationships for input data, enhancing the capabilities of spiking Transformers for tasks such as sequential modeling and image classification. However, how to incorporate relative positional information into SNNs remains a challenge. In this paper, we introduce several strategies to approximate relative positional encoding (RPE) in spiking Transformers while preserving the binary nature of spikes. Firstly, we formally prove that encoding relative distances with Gray Code ensures that the binary representations of positional indices maintain a constant Hamming distance whenever their decimal values differ by a power of two, and we propose **Gray-PE** based on this property. In addition, we propose another RPE method called **Log-PE**, which combines the logarithmic form of the relative distance matrix directly into the spiking attention map. Furthermore, we extend our RPE methods to a two-dimensional form, making them suitable for processing image patches. We evaluate our RPE methods on various tasks, including time series forecasting, text classification, and patch-based image classification, and the experimental results demonstrate a satisfying performance gain by incorporating our RPE methods across many architectures. Our results provide fresh perspectives on designing spiking Transformers to advance their sequential modeling capability, thereby expanding their applicability across various domains. Our code is available at https://github.com/microsoft/SeqSNN.

Deep Learning · Generative Models and Autoencoders

Nadhir Hassen, Zhen Zhang, Johan Verjans

Probabilistic time series forecasting, essential in domains like healthcare and neuroscience, requires models capable of capturing uncertainty and intricate temporal dependencies. While deep learning has advanced forecasting, generating calibrated probability distributions over continuous future values remains challenging. We introduce Temporal Generative Flow Networks (Temporal GFNs), adapting Generative Flow Networks (GFNs) – a powerful framework for generating compositional objects – to this sequential prediction task. GFNs learn policies to construct objects (eg. forecast trajectories) step-by-step, sampling final objects proportionally to a reward signal. However, applying GFNs directly to continuous time series necessitates addressing their inherently discrete action spaces and ensuring differentiability. Our framework tackles this by representing time series segments as states and sequentially generating future values via quantized actions chosen by a forward policy. We introduce two key innovations: (1) An adaptive, curriculum-based quantization strategy that dynamically adjusts the number of discretization bins based on reward improvement and policy entropy, balancing precision and exploration throughout training. (2) A straight-through estimator mechanism enabling the forward policy to output both discrete (hard) samples for trajectory construction and continuous (soft) samples for stable gradient propagation. Training utilizes a trajectory balance loss objective, ensuring flow consistency, augmented by an entropy regularizer. We provide rigorous theoretical bounds on the quantization error's impact and the adaptive factor's range. We demonstrate how Temporal GFNs offer a principled way to leverage the structured generation capabilities of GFNs for probabilistic forecasting in continuous domains.

Applications · Neuroscience, Cognitive Science

Wentao Lu, Dong Nie, Pengcheng Xue, Zheng Cui, Piji Li, Daoqiang Zhang, Xuyun Wen

Decoding natural language text from non-invasive brain signals, such as functional magnetic resonance imaging (fMRI), remains a central challenge in brain-computer interface research. While recent advances in large language models (LLMs) have enabled open-vocabulary fMRI-to-text decoding, existing frameworks typically process the entire fMRI sequence in a single step, leading to performance degradation when handling long input sequences due to memory overload and semantic drift. To address this limitation, we propose a brain-inspired sequential fMRI-to-text decoding framework that mimics the human cognitive strategy of segmented and inductive language processing. Specifically, we divide long fMRI time series into consecutive segments aligned with optimal language comprehension length. Each segment is decoded incrementally, followed by a wrap-up mechanism that summarizes the semantic content and incorporates it as prior knowledge into subsequent decoding steps. This sequence-wise approach alleviates memory burden and ensures semantic continuity across segments. In addition, we introduce a text-guided masking strategy integrated with a masked autoencoder (MAE) framework for fMRI representation learning. This method leverages attention distributions over key semantic tokens to selectively mask the corresponding fMRI time points, and employs MAE to guide the model toward focusing on neural activity at semantically salient moments, thereby enhancing the capability of fMRI embeddings to represent textual information. Experimental results on the two datasets demonstrate that our method significantly outperforms state-of-the-art approaches, with performance gains increasing as decoding length grows.

Probabilistic Methods · Gaussian Processes

Wenlong Chen, Naoki Kiyohara, Harrison Zhu, Jacob Curran-Sebastian, Samir Bhatt, Yingzhen Li

We propose a novel online Gaussian process (GP) model that is capable of capturing long-term memory in sequential data in an online learning setting. Our model, Online HiPPO Sparse Variational Gaussian Process (OHSVGP), leverages the HiPPO (High-order Polynomial Projection Operators) framework, which is popularized in the RNN domain due to its long-range memory modeling capabilities. We interpret the HiPPO time-varying orthogonal projections as inducing variables with time-dependent orthogonal polynomial basis functions, which allows the SVGP inducing points to memorize the process history. We show that the HiPPO framework fits naturally into the interdomain GP framework and demonstrate that the kernel matrices can also be updated online in a recurrence form based on the ODE evolution of HiPPO. We evaluate OHSVGP with online prediction for 1D time series, continual learning in discriminative GP model for data with multidimensional inputs, and deep generative modeling with sparse Gaussian process variational autoencoder, showing that it outperforms existing online GP methods in terms of predictive performance, long-term memory preservation, and computational efficiency.

General Machine Learning · Everything Else

Matthew Tamayo-Rios, Alexander Schell, Rima Alaifari

The signature kernel is a recent state-of-the-art tool for analyzing high-dimensional sequential data, valued for its theoretical guarantees and strong empirical performance. In this paper, we present a novel method for efficiently computing the signature kernel of long, high-dimensional time series via adaptively truncated recursive local power series expansions. Building on the characterization of the signature kernel as the solution of a Goursat PDE, our approach employs tilewise Neumann‐series expansions to derive rapidly converging power series approximations of the signature kernel that are locally defined on subdomains and propagated iteratively across the entire domain of the Goursat solution by exploiting the geometry of the time series. Algorithmically, this involves solving a system of interdependent Goursat PDEs via adaptively truncated local power series expansions and recursive propagation of boundary conditions along a directed graph in a topological ordering. This method strikes an effective balance between computational cost and accuracy, achieving substantial performance improvements over state-of-the-art approaches for computing the signature kernel. It offers (a) adjustable and superior accuracy, even for time series with very high roughness; (b) drastically reduced memory requirements; and (c) scalability to efficiently handle very long time series (e.g., with up to one million data points or more) on a single GPU. As demonstrated in our benchmarks, these advantages make our method particularly well-suited for rough-path-assisted machine learning, financial modeling, and signal processing applications involving very long and highly volatile sequential data.

Applications · Time Series

Barak Bringoltz, Elisha Halperin, Ran Feraru, Evgeny Blaichman, Amit Berman

Over the last decade, ransomware detection has become a central topic in cybersecurity research. Due to ransomware's direct interaction with storage devices, analyzing I/O streams has become an effective detection method and represents a vital area of focus for research. A major challenge in this field is the lack of publicly accessible data featuring individual command labeling. To address this problem, we introduce the Command LEvel Annotated Ransomware (CLEAR) dataset, a large-scale collection of storage devices' stream data. The dataset comprises 1,045 TiB of I/O traffic data, featuring malicious traffic from 137 ransomware variants. It offers two orders of magnitude more I/O traffic data and one order of magnitude more ransomware variants than any other publicly accessible dataset. Importantly, it is the only dataset that individually labels each I/O command as either ransomware or benign activity. This labeling enables the use of advanced sequential models, which we show to outperform existing state-of-the-art models by up to 82% in data loss prevention. Additionally, this allows us to create new tasks, such as data recovery, by selectively reverting only the commands recognized as ransomware while preserving benign activity. The CLEAR dataset also includes supplementary auxiliary features derived from the data, which we demonstrate to improve performance through feature ablation studies. Lastly, a critical aspect of any ransomware detection model is its robustness to new, unseen ransomware variants, as new strains constantly emerge. Therefore, we propose a benchmark based on our dataset to evaluate performance against unknown ransomware samples and illustrate its application across different models.

Applications · Time Series

Hossein Babaei, Mel White, Sina Alemohammad, Richard Baraniuk

State-Space Models (SSMs) have proven to be powerful tools for online function approximation and for modeling long-range dependencies in sequential data. While recent methods such as HiPPO have demonstrated strong performance using a few polynomial bases, they remain limited by their reliance on closed-form solutions for specific, well-behaved bases. The SaFARi framework generalizes this approach, enabling the construction of SSMs from arbitrary frames, including non-orthogonal and redundant ones, thus allowing an infinite diversity of possible "species'' within the SSM family. In this paper, we introduce WaLRUS (Wavelets for Long-range Representation Using SSMs), a new species of SaFARi built from Daubechies wavelet frames. We instantiate two variants, scaled-Walrus and translated-Walrus, and show that their multiresolution and localized nature offers significant advantages in representing non-smooth and transient signals. We compare Walrus to HiPPO-based models and demonstrate improved accuracy, better numerical properties, and more efficient implementations for online function approximation tasks.

Applications · Climate

Haobo Li, Eunseo Jung, Zixin CHEN, Zhaowei Wang, Yueya WANG, Huamin Qu, Alexis Lau

Multimodal time series forecasting is foundational in various fields, such as utilizing satellite imagery and numerical data for predicting typhoons in climate science. However, existing multimodal approaches primarily focus on utilizing text data to help time series forecasting, leaving the visual data in existing time series datasets underexplored. Furthermore, it is challenging for models to effectively capture the physical information embedded in visual data, such as satellite imagery's temporal and geospatial context, which extends beyond images themselves. To address this gap, we propose physics-informed positional encoding (PIPE), a lightweight method that embeds physical information into vision language models (VLMs). PIPE introduces two key innovations: (1) a physics-informed positional indexing scheme for mapping physics to positional IDs, and (2) a variant-frequency positional encoding mechanism for encoding frequency information of physical variables and sequential order of tokens within the embedding space. By preserving both the physical information and sequential order information, PIPE significantly improves multimodal alignment and forecasting accuracy. Through the experiments on the most representative and the largest open-sourced satellite image dataset, PIPE achieves state-of-the-art performance in both deep learning forecasting and climate domain methods, demonstrating superiority across benchmarks, including a 12\% improvement in typhoon intensity forecasting over prior works.

Probabilistic Methods · Bayesian Models and Methods

Junxi Xiao, Qinliang Su, Zexin Yuan

Mean-field variational inference (VI), despite its scalability, is limited by the independence assumption, making it unsuitable for scenarios with correlated data instances. Existing structured VI methods either focus on correlations among latent dimensions which lack scalability for modeling instance-level correlations, or are restricted to simple first-order dependencies, limiting their expressiveness. In this paper, we propose High-order Tree-structured Variational Inference (HoT-VI), that explicitly models $k$-order instance-level correlations among latent variables. By expressing the global posterior through overlapping $k$-dimensional local marginals, our method enables efficient parameterized sampling via a sequential procedure. To ensure the validity of these marginals, we introduce a conditional correlation parameterization method that guarantees positive definiteness of their correlation matrices. We further extend our method with a tree-structured backbone to capture more flexible dependency patterns. Extensive experiments on time-series and graph-structured datasets demonstrate that modeling higher-order correlations leads to significantly improved posterior approximations and better performance across various downstream tasks.

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}.

Theory · Learning Theory

Wei Shi, Yuan Cao

Transformers have proven highly effective across various applications, especially in handling sequential data such as natural languages and time series. However, transformer models often lack clear interpretability, and the success of transformers has not been well understood in theory. In this paper, we study the capability and interpretability of transformers in learning a family of classic statistical models, namely random walks on circles. We theoretically demonstrate that, after training with gradient descent, a one-layer transformer model can achieve optimal accuracy in predicting random walks. Importantly, our analysis reveals that the trained model is interpretable: the trained softmax attention serves as a token selector, focusing on the direct parent state; subsequently, the value matrix executes a one-step probability transition to predict the location of the next state based on this parent state. We also show that certain edge cases not covered by our theory are indeed failure cases, demonstrating that our theoretical conditions are tight. By investigating these success and failure cases, it is revealed that gradient descent with small initialization may fail or struggle to converge to a good solution in certain simple tasks even beyond random walks. Experiments are conducted to support our theoretical findings.

Theory · Everything Else

Mario Morawski, Anaïs Després, Remi Rehm

Sequential data—ranging from financial time series to natural language—has driven the growing adoption of autoregressive models. However, these algorithms rely on the presence of underlying patterns in the data, and their identification often depends heavily on human expertise. Misinterpreting these patterns can lead to model misspecification, resulting in increased generalization error and degraded performance. The recently proposed $\texttt{evolving pattern (EvoRate)}$ metric addresses this by using the mutual information between the next data point and its past to guide regression order estimation and feature selection. Building on this idea, we introduce a general framework based on predictive information—the mutual information between the past and the future, $\mathbf{I}(X_{\text{past}}; X_{\text{future}})$. This quantity naturally defines an information-theoretic learning curve, which quantifies the amount of predictive information available as the observation window grows. Using this formalism, we show that the presence or absence of temporal patterns fundamentally constrains the learnability of sequential models: even an optimal predictor cannot outperform the intrinsic information limit imposed by the data. We validate our framework through experiments on synthetic data, demonstrating its ability to assess model adequacy, quantify the inherent complexity of a dataset, and reveal interpretable structure in sequential data.

Zijian Li, Minghao Fu, Junxian Huang, Yifan Shen, Ruichu Cai, Yuewen Sun, Guangyi Chen, Kun Zhang

Modeling hierarchical latent dynamics behind time series data is critical for capturing temporal dependencies across multiple levels of abstraction in real-world tasks. However, existing temporal causal representation learning methods fail to capture such dynamics, as they fail to recover the joint distribution of hierarchical latent variables from \textit{single-timestep observed variables}. Interestingly, we find that the joint distribution of hierarchical latent variables can be uniquely determined using three conditionally independent observations. Building on this insight, we propose a Causally Hierarchical Latent Dynamic (CHiLD) identification framework. Our approach first employs temporal contextual observed variables to identify the joint distribution of multi-layer latent variables. Sequentially, we exploit the natural sparsity of the hierarchical structure among latent variables to identify latent variables within each layer. Guided by the theoretical results, we develop a time series generative model grounded in variational inference. This model incorporates a contextual encoder to reconstruct multi-layer latent variables and normalize flow-based hierarchical prior networks to impose the independent noise condition of hierarchical latent dynamics. Empirical evaluations on both synthetic and real-world datasets validate our theoretical claims and demonstrate the effectiveness of CHiLD in modeling hierarchical latent dynamics.

General Machine Learning · Representation Learning

Tal Barami, Nimrod Berman, Ilan Naiman, Amos H Hason, Rotem Ezra, Omri Azencot

Learning disentangled representations in sequential data is a key goal in deep learning, with broad applications in vision, audio, and time series. While real-world data involves multiple interacting semantic factors over time, prior work has mostly focused on simpler two-factor static and dynamic settings, primarily because such settings make data collection easier, thereby overlooking the inherently multi-factor nature of real-world data. We introduce the first standardized benchmark for evaluating multi-factor sequential disentanglement across six diverse datasets spanning video, audio, and time series. Our benchmark includes modular tools for dataset integration, model development, and evaluation metrics tailored to multi-factor analysis. We additionally propose a post-hoc Latent Exploration Stage to automatically align latent dimensions with semantic factors, and introduce a Koopman-inspired model that achieves state-of-the-art results. Moreover, we show that Vision-Language Models can automate dataset annotation and serve as zero-shot disentanglement evaluators, removing the need for manual labels and human intervention. Together, these contributions provide a robust and scalable foundation for advancing multi-factor sequential disentanglement. Our code is available on GitHub, and the datasets and trained models are available on Hugging Face.

Applications · Time Series

Jianyang Qin, Chaoyang Li, Jinhao Cui, Lingzhi Wang, Zhao Liu, Qing Liao

Recent studies reveal that Large Language Models (LLMs) exhibit strong sequential reasoning capabilities, allowing them to replace specialized time-series models and serve as foundation models for complex time-series analysis. To activate the capabilities of LLMs for time-series tasks, numerous studies have attempted to bridge the gap between time series and linguistics by aligning textual representations with time-series patterns. However, it is a non-trivial endeavor to losslessly capture the infinite time-domain variability using natural language, leading to suboptimal alignment performance. Beyond representation, contextual differences, where semantics in time series are conveyed by consecutive points, unlike in text by individual tokens, are often overlooked by existing methods. To address these, we propose S$^2$TS-LLM, a simple yet effective framework to repurpose LLMs for universal time series analysis through the following two main paradigms: (i) a spectral symbolization paradigm transforms time series into frequency-domain representations characterized by a fixed number of components and prominent amplitudes, which enables a limited set of symbols to effectively abstract key frequency features; (ii) a contextual segmentation paradigm partitions the sequence into blocks based on temporal patterns and reassigns positional encodings accordingly, thereby mitigating the structural mismatch between time series and natural language. Together, these paradigms bootstrap the LLMs' perception of temporal patterns and structures, effectively bridging time series and linguistics. Extensive experiments show that S$^2$TS-LLM can serve as a powerful time series analyzer, outperforming state-of-the-art methods across time series tasks.

Tingfeng Hui, Zhenyu Zhang, Shuohuan Wang, Weiran Xu, Yu Sun, Hua Wu

Large language models (LLMs) with one or more fine-tuning phases have become necessary to unlock various capabilities, enabling LLMs to follow natural language instructions and align with human preferences. However, it carries the risk of catastrophic forgetting during sequential training, the parametric knowledge or the ability learned in previous stages may be overwhelmed by incoming training data. This paper finds that LLMs can restore some original knowledge by regularly resetting partial parameters. Inspired by this, we introduce Half Fine-Tuning (HFT) for LLMs, as a substitute for full fine-tuning (FFT), to mitigate the forgetting issues, where half of the parameters are selected to learn new tasks. In contrast, the other half are frozen to retain previous knowledge. We provide a feasibility analysis from the optimization perspective and interpret the parameter selection operation as a regularization term. HFT could be seamlessly integrated into existing fine-tuning frameworks without changing the model architecture. Extensive experiments and analysis on supervised fine-tuning, direct preference optimization, and continual learning consistently demonstrate the effectiveness, robustness, and efficiency of HFT. Compared with FFT, HFT not only significantly alleviates the forgetting problem, but also achieves the best performance in a series of downstream benchmarks, with an approximately 30% reduction in training time.

Shuai Niu, Jing Ma, Hongzhan Lin, Liang Bai, Zhihua Wang, Yida Xu, Yunya Song, Xian Yang

Interpretation is critical for disease diagnosis, but existing models struggle to balance predictive accuracy with human-understandable rationales. While large language models (LLMs) offer strong reasoning abilities, their clinical use is limited by high computational costs and restricted multimodal reasoning ability. Small language models (SLMs) are efficient but lack advanced reasoning for integrating multimodal medical data. In addition, both LLMs and SLMs lack domain knowledge for trustworthy reasoning. Therefore, we propose ClinRaGen, enhancing SLMs by leveraging LLM-derived reasoning ability via rationale distillation and domain knowledge injection for trustworthy multimodal rationale generation. Key innovations include a sequential rationale distillation framework that equips SLMs with LLM-comparable multimodal reasoning abilities, and a knowledge-augmented attention mechanism that jointly unifies multimodal representation from time series and textual data in the same encoding space, enabling it to be naturally interpreted by SLMs while incorporating domain knowledge for reliable rationale generation. Experiments on real-world medical datasets show that ClinRaGen achieves state-of-the-art performance in disease diagnosis and rationale generation, demonstrating the effectiveness of combining LLM-driven reasoning with knowledge augmentation for improved interpretability.

Zhiyuan Zeng, Qinyuan Cheng, Zhangyue Yin, Yunhua Zhou, Xipeng Qiu

The advent of test-time scaling in large language models (LLMs), exemplified by OpenAI’s o1 series, has advanced reasoning capabilities by scaling computational resource allocation during inference. While successors like QwQ, Deepseek-R1 (R1) and LIMO replicate these advancements, whether these models truly possess test-time scaling capabilities remains underexplored. This study found that longer CoTs of these o1-like models do not consistently enhance accuracy; in fact, correct solutions are often shorter than incorrect ones for the same questions. Further investigation shows this phenomenon is closely related to models’ self-revision capabilities - longer CoTs contain more self-revisions, which often lead to performance degradation. We then compare sequential and parallel scaling strategies on QwQ, R1 and LIMO, finding that parallel scaling achieves better coverage and scalability. Based on these insights, we propose “Shortest Majority Vote”, a method that combines parallel scaling strategies with CoT length characteristics, significantly improving models’ test-time scalability compared to conventional majority voting approaches.

Md Nayem Uddin, Amir Saeidi, Divij Handa, Agastya Seth, Tran Cao Son, Eduardo Blanco, Steven Corman, Chitta Baral

This paper introduces UnSeenTimeQA, a novel data contamination-free time-sensitive question-answering (TSQA) benchmark. It differs from existing TSQA benchmarks by avoiding web-searchable queries grounded in the real world. We present a series of time-sensitive event scenarios based on synthetically generated facts. It requires large language models (LLMs) to engage in genuine temporal reasoning without depending on the factual knowledge acquired during the pre-training phase. Our data generation framework enables on-demand generation of new samples, mitigating the risk of data leakage. We designed three types of time-sensitive questions to test LLMs’ temporal reasoning abilities over sequential and parallel event occurrences. Our evaluation of five LLMs on synthetic fact-based TSQA reveals mixed results: while they perform well on simpler subsets, their overall performance remains inferior as compared to real world fact-based TSQA. Error analysis indicates that LLMs face difficulties in reasoning over long-range event dependencies and parallel events.

Deep Learning · Sequential Models, Time series

Ming-Yi Hong, Yen-Jung Hsu, Miao-Chen Chiang, Che Lin

Sequential recommendation in e-commerce utilizes users' anonymous browsing histories to personalize product suggestions without relying on private information. Existing item ID-based methods and multimodal models often overlook the temporal alignment of modalities like textual descriptions, visual content, and prices in user browsing sequences. To address this limitation, this paper proposes the Multimodal Time-aligned Shared Token Recommender (MTSTRec), a transformer-based framework with a single time-aligned shared token per product for efficient cross-modality fusion. MTSTRec preserves the distinct contributions of each modality while aligning them temporally to better capture user preferences. Extensive experiments demonstrate that MTSTRec achieves state-of-the-art performance across multiple sequential recommendation benchmarks, significantly improving upon existing multimodal fusion. Our code is available at https://github.com/idssplab/MTSTRec.