Time-Series Classification

Transfer learning is an effective technique for addressing data scarcity in deep learning for time series classification, but its success depends on the selection of source datasets. Conventional transferability estimation methods are often computationally expensive, as they require fully pre-training a model on each potential source dataset to assess its suitability. This paper introduces a novel, training-free source selection method named Shapelet Matching. Our approach first identifies discriminative shapelets from the target and potential source datasets. Then, Shapelet Matching quantifies dataset similarity by comparing the extracted sets of shapelets. To mitigate the risk of negative transfer from selecting an unsuitable single source, we introduce a multi-source transfer learning method. We select several source datasets based on their shapelet-based similarity scores, combine them into a single multi-source dataset, and use this aggregated dataset for pre-training. The model is then fine-tuned on the target task. We evaluated our method on 128 datasets from the UCR Archive using both temporal CNN and Transformer architectures. The empirical results demonstrate that our multi-source pre-training reduces the risk of negative transfer on average. Shapelet Matching achieves the strongest performance for the CNN backbone and remains competitive for patch-based Transformer architectures, while avoiding the cost of pre-training a separate model for every candidate source.

Time series data is very common in many real-world applications and in numerous domains, with increasing interest for automated information extraction using machine learning. One of these subfields is time series clustering, which consists in identifying clusters among a set of time series in an unsupervised fashion. Most time series clustering algorithms suffer from the same balancing act: they trade clustering performance for faster runtimes or vice versa. We present a novel time series clustering algorithm that we call CLUES-WEASEL, which stands for CLustering with the UnsupervisEd Second version of Word ExtrAction for time SEries cLassification. CLUES-WEASEL extracts features using the unsupervised version of the transformation step of WEASEL 2.0, which is a time series classification algorithm, then reduces these features using principal component analysis, and finally performs clustering with the $k$-means algorithm using these reduced extracted features. Through extensive experiments, we prove that CLUES-WEASEL is significantly better than any other existing time series clustering algorithm while being (much) faster than any state-of-the-art one. We also show that the architecture of CLUES-WEASEL can work well with other time series feature extraction algorithms. Our findings highlight the relevance of CLUES-WEASEL for time series clustering.

In this paper, we propose a class-wise dimension (channel) selection framework for Multivariate Time Series Classification (MTSC). Rather than applying a single global dimension selection process, the proposed approach independently identifies informative dimensions for each class. A dedicated learning process is subsequently performed for each class, followed by a fusion stage for final prediction. The objective is to improve the generation of discriminative feature representations while reducing the influence of noisy or non-informative dimensions. The proposed framework is evaluated using MiniRocket, a random kernel-based baseline method. Experimental results indicate that class-wise dimension selection improves the quality of extracted representations and can enhance classification performance, particularly in high-dimensional settings. These findings suggest that incorporating class-specific information into the training process represents a promising direction for MTSC, improving robustness through consistent gains across heterogeneous datasets, and interpretability through the explicit identification of class-relevant dimensions.

Imbalanced time series classification is often addressed by changing the training distribution, objective, logits, or final threshold. These interventions address important biases, yet leave a representation-level question unmeasured: after minority support is reduced, does a learned feature space remain locally reliable around minority regions? We identify a training-local geometry failure: under imbalance, minority cases can lie in sparse, rest-dominated, or mixed feature-space neighborhoods, even when the representation retains useful global class structure. To diagnose and repair this failure, we propose Local Reference Geometry (LRG), a lightweight post-hoc feature augmentation module applied between a fixed feature extractor and the classifier head. Using training features only, LRG measures local exposure and class-mixture risk, then augments each fixed feature with a standardized signed displacement from nearby training geometry and an LDA-projected residual summary. On controlled UCR/Bake Off Redux imbalance benchmarks, paired raw-versus-LRG comparisons show gains for learned, pretrained, and fixed representations, including when LRG is combined with training-level interventions and post-encoder classifier corrections. Ablations show that the gain comes from the signed local residual appended to the original feature, rather than from generic prototype distances, affinity features, scalar statistics, or VLAD-style codes. Further analyses support the proposed local-geometry failure hypothesis: minority neighborhoods become increasingly rest-exposed under imbalance, training-local risk identifies error-prone regions, and LRG gains concentrate in those high-risk regions.

Dynamic Time Warping (DTW)-based Nearest-Neighbor (NN) classifiers are effective for time-series classification but are vulnerable to mislabeled training samples and require numerous DTW computations during inference. We propose DTW-based Granular Ball Computing (DTW-GBC), which organizes temporally similar training samples into granular balls and performs classification at the granule level. We further develop two granular-ball construction strategies for DTW-GBC. Experiments on four benchmark datasets with symmetric label noise show that the two DTW-GBC variants generally mitigate the performance degradation caused by label noise while requiring substantially fewer comparisons than DTW-based 1-NN during inference. These findings suggest that DTW-GBC provides a favorable balance between classification robustness and inference efficiency.

Healthcare data, such as Intensive Care Unit (ICU) records, comprise heterogeneous multivariate time series sampled at irregular intervals with pervasive missingness. However, clinical applications demand predictive models that are both accurate and interpretable. We present our Graph Attention-based Relational Learning for Intensive Care (GARLIC) model, a novel neural network architecture that imputes missing data through a learnable exponential-decay encoder, captures inter-sensor dependencies via time-lagged summary graphs, and fuses global patterns with cross-dimensional sequential attention. All attention weights and graph edges are learned end-to-end to serve as built-in observation-, signal-, and edge-level explanations. To reconcile auxiliary reconstruction and primary classification objectives, we developed an alternating decoupled optimization scheme that stabilizes training. On three ICU benchmarks (PhysioNet 2012 & 2019, MIMIC-III), GARLIC sets the new state of the art in outcome prediction, significantly improving AUROC and AUPRC over best-performing baselines at comparable computational cost. Ablation studies confirm the contribution of each module, and feature-removal trials validate the fidelity of importance attribution through a monotonic performance drop (full > top 50% > random 50% > bottom 50%). Real-time case studies demonstrate actionable risk warnings with transparent explanations, marking a significant advance toward accurate, explainable deep learning for irregularly sampled ICU time series data. Moreover, we demonstrated \proposed{}'s superiority in data imputation and classification on various time-series datasets beyond the ICU domain, showing its generalizability and applicability to broader tasks.

Unsupervised time-series domain adaptation (DA) addresses the challenge of transferring a classifier from a labeled source domain to an unlabeled target domain under distribution shifts induced by different users, sensors, devices, acquisition conditions, or temporal dynamics. Existing methods typically mitigate this shift by aligning marginal feature distributions through adversarial training, optimal transport, or moment-based discrepancies. In this paper, we propose Class-Conditional Path Distribution Alignment (CPDA), a non-adversarial discrepancy-based framework that aligns source and target class-conditional latent path distributions rather than only global feature marginals. CPDA introduces a composite signature-spectral kernel that jointly captures pooled semantic features, temporal path structure, frequency-domain information, and low-rank path-signature dynamics, while using source labels and target soft pseudo-labels to perform class-preserving alignment. We further provide a theoretical analysis showing that CPDA defines a valid kernel discrepancy, admits existing moment-matching methods as restricted cases, and yields a class-conditional target-risk bound. Extensive experiments with CNN, ResNet18, and TCN backbones on 13 different time-series DA benchmarks demonstrate the effectiveness of CPDA against 30 discrepancy, adversarial, and pseudo-labeling baselines.

Multivariate Time Series Classification (MTSC) demands models that can effectively capture complex temporal patterns across multiple scales while remaining computationally efficient. However, existing approaches generally struggle to reconcile fine-grained representation learning, especially under class imbalance and real-world constraints. In this paper, we present FreSH, a Frequency-Segmented Hierarchical Multi-Expert Framework designed to address these challenges. FreSH introduces a new perspective for MTSC by enabling adaptive, multi-scale analysis of temporal signals, allowing different aspects of the data to be modeled in a complementary and coordinated manner. By combining localized specialization with holistic context modeling, FreSH achieves strong representational capacity without incurring excessive computational overhead. An adaptive fusion strategy further enhances flexibility, enabling the model to dynamically emphasize the most informative components of the input. In addition, we incorporate a more robust optimization objective that improves learning stability across varying sample difficulties and class distributions. Extensive evaluations on 30 UEA benchmark datasets and real-world vibration data demonstrate that FreSH consistently outperforms state-of-the-art methods in classification accuracy, while substantially reducing model size and efficiency.

Inspired by recent evidence that transformer architectures benefit from Self-PreTraining (SPT) on long-context benchmarks, we investigate whether similar gains extend to multimodal, multivariate, and even simple univariate medical time series. Our objective is to assess the impact of SPT on the performance and scalability of transformer-based models across diverse medical applications, particularly under limited data conditions. We evaluate transformer architectures on three representative medical time-series tasks: rehabilitation robotics (Camargo dataset), stress detection (Non-EEG Stress), and Parkinson's disease detection (Gait Parkinson's Disease). Models are trained either from scratch or through SPT using four masking-based objectives designed to promote temporal and cross-modal representation learning, and we systematically vary model depth to examine how capacity interacts with pre-training benefits. Across datasets and configurations, SPT consistently improves classification accuracy by 0-6 percentage points depending on masking strategy, dataset and architecture, with gains observed not only in multivariate settings but also when models are restricted to simple univariate inputs. The improvements increase for deeper models that can better exploit the enriched temporal representations learned during pre-training. These findings indicate that SPT is a simple and general strategy that enhances transformer performance on medical time-series tasks without requiring task-specific architectural changes, supporting its potential to improve robustness and accuracy in data-limited clinical settings.

Oscillatory signals, such as vibration, carry class-discriminative information in specific frequency bands; perturbing them in raw feature space for counterfactual analysis easily destroys their temporal structure and produces physically implausible results. In this work, we introduce IMFACT (IMF-based counterfACTuals), a model-agnostic framework for generating plausible counterfactual explanations for time series classifiers that operates in the decomposition space of Empirical Mode Decomposition. An input signal is split into Intrinsic Mode Functions (IMFs), and selected IMFs are progressively substituted with those of a Nearest Unlike Neighbour (NUN) until the classifier flips to the target class. We evaluate six IMF-selection strategies and a multi-NUN cycling extension on two UCR benchmarks (FaultDetectionA, FruitFlies). The variance-based strategy with three NUNs outperforms two prominent baseline techniques on reliability and plausibility metrics, while cycling across three NUNs yields the best proximity across both datasets.

Time series data are ubiquitous in practical applications, where classification (TSC) and extrinsic regression (TSER) have emerged as essential tasks for obtaining value from temporal sequences. While the literature has seen significant progress through feature-based and deep learning models, existing methods often focus either on the quality of feature extraction or on the intrinsic predictive power of complex architectures applied to raw data. This division creates a gap between the control offered by feature engineering and the automated performance of end-to-end models. This paper proposes TS2TabPFN, a framework that bridges this gap by integrating explicit feature extraction with TabPFN 2.5, a cutting-edge foundation model for tabular data, to leverage its predictive capabilities. Our extensive experimental evaluation demonstrates that TS2TabPFN significantly outperforms state-of-the-art models in TSER tasks with statistical significance, providing a robust and efficient alternative for TSC and surpassing most of the currently best-performing algorithms. These results suggest that combining foundation models with structured features overcomes single-paradigm limitations, establishing a new time series state-of-the-art.

In recent years, numerous open-source software libraries have been developed for computing sets of features from univariate time series. The type and number of features vary across these feature sets, which have been constructed with varying disciplinary perspectives on quantifying structure in time-series data. To date, the relative strengths and weaknesses of these feature sets on time-series classification problems remains largely unexplored. Here we aimed to understand the relative performance of six open-source feature sets and three baseline feature sets (based on distributional and/or basic spectral structure) across 124 univariate time-series classification problems using a normalization-based approach to problem-level benchmarking that better indexes the relative strengths and weaknesses of different algorithms compared to prior rank-based approaches. Despite their dramatic differences in size, composition, and computation time, we found that feature sets performed relatively similarly overall (85.3% of pairwise comparisons resulted in ties), with the largest feature set, tsfresh, exhibiting the strongest overall performance (29.03% wins across all pairwise comparisons against other feature sets). We also highlighted specific problems on which the specific composition of a given feature set gave it a substantial performance advantage or disadvantage, and problems where simple baselines comprised of Fourier coefficients and quantiles were sufficient to achieve strong performance. Our results demonstrate the need to consider problem-level performance when benchmarking time-series feature sets, and highlight the importance of feature make-up in driving relative classification performance.

In Non-Intrusive Load Monitoring (NILM), adaptive segmentation of electricity consumption time series is critical for appliance recognition. However, prevailing methods face challenges including heuristic parameter tuning, boundary sensitivity, and metric saturation. This paper proposes BayesSeg, a unified framework integrating time-series segmentation, multidimensional evaluation, and automatic parameter optimization. The segmentation layer employs a dual steady-state criterion based on the tail value and mean of preceding subsequences, combined with a sequential extraction and complement-set parsing strategy, to achieve precise unsupervised partitioning of steady-state and transition-state segments. The evaluation layer maps segmentation results to binary state sequences and formulates a composite metric integrating an event-level F1 score (event_F1) with Normalized Mutual Information (NMI). The event_F1 quantifies switching-event precision and recall via tolerance matching, while NMI captures global structural consistency, jointly overcoming the boundary sensitivity and limited discriminability of point-wise metrics. In the optimization layer, the composite score serves as the objective function for Bayesian optimization, which constructs a TPE surrogate model for efficient global parameter-space exploration. Experiments on the SustDataED2 dataset demonstrate that Bayesian optimization requires only ~100 objective evaluations to locate a parameter region within 0.35% deviation of the exhaustive grid-search optimum. The framework achieves a weighted composite score of 0.7149 and an event_F1 of 0.9340 while reducing optimization latency from ~5300 seconds to under 1 second, a speedup exceeding 5700x. BayesSeg automates segmentation configuration and provides a scalable, efficient solution for time-series analysis in NILM and related domains.

Wearable sensors continuously capture fine-grained multivariate time-series data, providing opportunities to model behavioural patterns associated with health outcomes. However, existing deep learning methods prioritise predictive accuracy over interpretability, limiting their application in health research. In this study, we present HealthCAT, a flexible framework that integrates an Encoder-only Transformer with an Attentive Class Activation Token (AttentiveCAT) to generate class-specific, time-step-level interpretations. These interpretations can be mapped back onto behavioural cycles that are relevant to the domain (e.g., time-of-day), supporting individual-level analysis of wearable sensor data. We evaluated HealthCAT using two real-world wearable sensor datasets (306 participants in total). HealthCAT outperformed deep learning baselines by up to 17% in F1-score and 12% in accuracy on both datasets ($p<0.05$). In masking experiments, the time steps identified by HealthCAT carried significantly more predictive value than random selection across all masking conditions ($p<0.05$), indicating that the identified time steps are predictively informative. By coupling predictive performance with validated time-step-level interpretability, HealthCAT moves wearable sensor analysis beyond aggregated metrics towards temporal patterns that support health monitoring, behavioural pattern analysis, and intervention design in health research. The significance of this work is that it enables accurate prediction of health indicators from wearable sensor data while providing insights into when and how physical activity patterns occur, rather than relying solely on aggregated summary measures.

Understanding disease trajectories from longitudinal clinical data remains challenging due to complex temporal dynamics and heterogeneous patient cohorts. Here, we present a contrastive representation learning framework that models multivariate disease trajectories as temporal graphs and learns representations using contrastive graph neural networks. Nodes represent patient observations over time, while edges capture temporal continuity and structural similarity between trajectories. Structure-aware random walks guide contrastive learning to generate embeddings that preserve temporal context and trajectory topology. The resulting representations enable robust clustering of patients with similar disease progression patterns and reveal latent structure in longitudinal data.

Accurate yield forecasting at the individual-plant level is critical for precision agriculture and supply-chain planning, yet public datasets capturing both visual growth dynamics and per-plant measurement labels are scarce. In this paper, we introduce a novel, annotated image time-series dataset of 691 sweet pepper plants monitored over two growing seasons, comprising 4837 images with per-plant fruit counts categorized by maturity. We propose a multimodal deep learning framework that fuses high-dimensional image features, extracted using the DinoV3 encoder, with numerical count measurements. Our architecture utilizes a Long Short-Term Memory (LSTM) network to model temporal dependencies and handles irregular sampling intervals common in greenhouse monitoring. Through quantitative experiments, we demonstrate that this multimodal approach reduces RMSE over a persistence baseline by 33% and 38% in the 2022 and 2023 seasons, respectively, with a further 1.2% average gain over a measurement-only model. Furthermore, we employ Deep Ensembles and Gaussian Negative Log-Likelihood (NLL) to provide calibrated uncertainty estimates, with an Uncertainty Calibration Error (UCE) ranging from 0.39 to 0.89 depending on the cross-season evaluation direction, offering a principled confidence signal for real-world agricultural decision-making. We release the dataset and code to support reproducible research and to accelerate development of data-driven yield forecasting methods for horticultural crops.

Time series classification is central to domains like medical signal analysis, industrial monitoring, and sensor-based activity recognition, where class information manifests as localized shapes, specific frequencies, temporal shifts, or complex cross-channel interactions. Random convolutional transforms efficiently map these sequences to fixed-dimensional tabular features but are traditionally paired with simple linear classifiers. We investigate whether a pretrained tabular foundation model can more effectively harness these rich representations. We propose MASHT, a pipeline that marries MultiRocket and Hydra features with the power of in-context tabular foundation models. By leveraging a pretrained tabular foundation model, our approach completely bypasses task-specific model training, requiring only feature extraction and direct inference. Extensive experiments demonstrate that MASHT matches state-of-the-art time series classification baselines on univariate tasks, achieving a lower average rank than HIVE-COTE 2.0. On multivariate datasets, MASHT remains highly competitive with the strongest reference methods.

Explainable AI (XAI) for time series has seen significant algorithmic growth, but its utility in providing measurable performance gains for downstream tasks remains under-explored. This paper bridges this gap by introducing drXAI, a novel methodology that repurposes XAI attribution methods for effective data reduction in Time Series Classification (TSC). The core challenge in modern TSC is scalability; state-of-the-art models, such as Transformers, exhibit quadratic complexity relative to sequence length and linear complexity relative to the number of channels. This renders them computationally prohibitive for massive datasets. drXAI addresses this by using a fast, GPU-accelerated classifier (Hydra) to generate local attributions. We aggregate these into global feature importance scores and employ an automated elbow-cut heuristic to select the most salient features without requiring manual thresholds. We evaluate our approach on both synthetic and real-world univariate and multivariate datasets. On synthetic benchmarks, drXAI successfully recovers ground-truth features where traditional baselines fail. On real-world data, drXAI achieves between 80% and 90% data reduction while maintaining classification accuracy comparable to models trained on the full dataset. Most importantly, we show that drXAI allows resource-intensive models like ConvTran to scale to datasets that were previously inaccessible due to memory constraints. Our results show the benefits of using XAI not just for interpretability, but as a robust tool for feature selection and scalability in time series analysis. All our code and data are openly available.

Clinical time series are central to patient monitoring, risk assessment, and clinical decision support. However, they are often sparse, irregularly sampled, and asynchronous, making it difficult for models to identify the temporal evidence required for clinical Question Answering (QA). Existing benchmarks primarily focus on regularly sampled time-series QA or medical QA over static data, and therefore rarely assess whether models can faithfully ground their answers in irregular temporal observations. To fill this gap, we introduce CLIR-Bench, a benchmark for irregular clinical time series QA constructed from de-identified ICU records through a principled four-stage pipeline. CLIR-Bench contains 6,600 QA instances spanning 11 clinical variables, organized into four capability dimensions and 11 tasks. Each question is linked to explicit temporal evidence and task-specific answer derivation rules, enabling evaluation of both answer accuracy and evidence use. Experiments show that existing generalist models struggle to retrieve and reason over sparse clinical evidence, highlighting the need for stronger irregular time-series reasoning methods. Our code and data are available at https://huggingface.co/datasets/winall/CLIR-Bench.

Time series classification (TSC) is dominated by a two-stage paradigm: train a feature encoder -- either from scratch on the target dataset or via pretraining on large corpora -- and then fit a task-specific classifier on top. While effective, this decoupling optimizes representation learning independently of the classification objective, requires per-dataset training, and prevents the model from exploiting label information during inference. We introduce TimEE, a 4.5M-parameter foundation model for end-to-end TSC via in-context learning. Given a labeled support set and a query time series, TimEE directly outputs a predicted class distribution in a single forward pass with no per-dataset training required. Following the prior-data fitted network (PFN) framework, TimEE is meta-trained exclusively on synthetic TSC tasks, where each task contains time series with distinct class identities arising from structured distributional shifts in the generative process. Despite seeing no real time series during pre-training, TimEE ranks first in ROC AUC (and third on accuracy) on the UCR benchmark among all compared methods, which include both foundation models and supervised deep learning baselines. To our knowledge, TimEE is the first purely synthetic-pretrained model to reach state-of-the-art performance on the UCR benchmark. These results establish end-to-end ICL with synthetic priors as a compelling, largely unexplored direction for TSC, with scaling, prior design, and richer generation mechanisms as natural avenues for improvement. Code is publicly available at http://github.com/automl/timee.

In many realistic scenarios, large volumes of time series data are generated with limited or expensive annotations. This limitation makes supervised learning methods difficult to apply and leads to the use of unsupervised approaches capable of discovering meaningful structures directly from raw data. Clustering therefore plays a crucial role in organizing time series into groups that share similar temporal patterns, enabling exploratory analysis and downstream tasks without requiring manual labeling. However, existing deep clustering methods often struggle to capture long-range temporal dependencies or rely on architectures with high computational cost. This paper introduces FMMVCC, a Mamba-based deep clustering framework for time series that leverages state space sequence modeling to efficiently learn temporal representations with linear complexity. Additionally, it utilizes multi-view self-supervised learning with temporal masking and augmentations. Experimental evaluation in 15 benchmark datasets proves that FMMVCC consistently outperforms state-of-the-art baselines, achieving the best overall performance in 29 of 60 total metric evaluations and the highest average rank in all tested scenarios.

Deep learning has achieved remarkable success in various domains including time series analysis, computer vision and natural language processing. However, high computational and memory demands of state-of-the-art architectures pose challenges for deployment in resource-limited environments. Knowledge Distillation (KD) addresses this by transferring knowledge from a large teacher model to a smaller, more efficient student model while maintaining competitive performance. In this work, we investigate the effectiveness of KD for Time Series Classification (TSC) across three architectures: the classical Fully Convolutional Network (FCN), the convolutional Inception model and the transformer-based ConvTran model. We evaluate our approach on UCR Archive, the largest benchmark repository of time series datasets, by modifying architectural components such as convolutional filters, Inception modules and attention heads across the three architectures. Our results consistently show that KD most effectively benefits student models of intermediate complexity across all three architectures, with the distilled FCN student reducing parameters by a factor of 38, the distilled Inception student achieving nearly the same performance as the teacher with 42% fewer parameters and the distilled ConvTran student with 2 attention heads showing the most significant improvement through distillation. To encourage further research and reproducibility, we provide our implementation at https://github.com/MSD-IRIMAS/KD-4-TSC.

Rendering time series as chart images for CNN-based classification has become increasingly common in time-series classification (TSC). However, it remains unclear whether models learn underlying temporal patterns or rely on encoding-specific visual cues introduced by chart design. We present VEIL: a systematic study examining how chart encodings influence learned representations through complementary analyses of similarity, transferability, and attribution. Attention-guided training appears to mitigate this effect when encoding sensitivity is consistently identified across diagnostics, but provides limited or negative benefit when such signals are absent. These findings position VEIL within the broader question of how machines perceive visualizations -- extending graphical perception from human readers to vision models -- and show that visualization design choices shape learned representations in ways that warrant treating chart-based TSC as a representation and measurement problem rather than a simple modeling decision.

Clinical time series prediction in intensive care units remains challenging due to heterogeneous physiological variables and informative missingness. The presence or absence of a measurement can reflect clinical decisions and patient severity, and thus missingness can serve as a predictive signal rather than a simple data artifact. This work presents CISM, a Channel-Independent Spectrogram framework with a Missingness stream for clinical multivariate time series prediction. CISM converts each clinical variable into a variable-wise time-frequency spectrogram, preserves variable identity through variable-aligned encoding, and aligns an explicit missingness stream with the spectrogram representation. Experiments on an in-hospital mortality task derived from MIMIC-IV show that CISM achieves the highest mean AUROC (0.7225), AUPRC (0.3308), and F1 (0.3808) among the compared time series, missingness-aware, vision, and time-frequency baselines. Ablation studies further show that observation patterns provide a meaningful informative signal. Pixel-level mask injection improves performance over plain spectrogram inputs and recovers much of this predictive value. The aligned missingness stream contributes a further, complementary gain in both AUROC and AUPRC. These results highlight the importance of modeling observation patterns as structured signals in clinical time series prediction.

Time series are central to modern data mining applications, from industrial telemetry and server metrics to finance and physiology, yet time-series self-supervised learning often depends on view and augmentation choices that encode domain-specific invariances. We study how an SSL recipe behaves when its method-specific configuration is reused unchanged after the pretraining signal family changes, framing this as a fixed-recipe stress test rather than a comparison against optimally tuned methods. We introduce Latent Euclidean Next-Embedding Prediction Architecture (LeNEPA), a no-augmentation next-latent-token objective with a causal backbone. LeNEPA replaces the stop-gradient/EMA stabilization used by vanilla NEPA with SIGReg-based isotropy regularization and computes the predictive loss in a lightweight projected space that is discarded for evaluation. We compare LeNEPA with an ECG-tuned JEPA recipe under a fixed-horizon frozen-probe protocol on PTB-XL and Diag, a synthetic diagnostic corpus generated with Aionoscope. Both methods are retrained independently on each dataset while keeping their method-specific recipes unchanged. In this protocol, the ECG-tuned JEPA recipe is strong in-domain on PTB-XL but weaker when reused unchanged on Diag, whereas LeNEPA preserves useful frozen-probe gains on both datasets. Learning curves suggest faster early representation acquisition: LeNEPA reaches 80% of its final AUROC/AUPRC gain after 2--5k updates, compared with 5--10k updates for the faster JEPA readout. As a separate external frozen-encoder check, a CauKer-pretrained LeNEPA variant reaches 77.65% mean UCR-128 Random-Forest accuracy in a single-seed, best-checkpoint run, within 1.16 points of Mantis and within 0.24 points of MOMENT (77.89%). Overall, the results support no-augmentation latent prediction as a useful candidate recipe for low-retuning time-series SSL.

Despite the increasing sophistication of industrial AI systems, the ability to reliably detect subtle and noisy anomalies in complex time series data remains a critical yet unresolved challenge. In large-scale industrial applications, labeling time series data is often prohibitively expensive and time-consuming, making unsupervised learning a practical and widely adopted approach. However, existing unsupervised methods frequently struggle to distinguish near-normal anomalies from normal patterns and are vulnerable to noise contamination within normal samples. To address these limitations, we propose a novel framework that leverages active learning to iteratively enhance the performance of unsupervised models. Our framework's core contributions are (1) a masked time-series reconstruction feedback strategy that forces the model to learn robust temporal dependencies, and (2) a minimax learning strategy that promotes robustness by differentially treating normal and abnormal samples. This process encourages the model to better capture the dynamics of subtle and noisy patterns. The proposed framework is evaluated across 28 test cases involving four multivariate time-series datasets and seven unsupervised backbone models. Experimental results demonstrate a 12.39% improvement in AUC compared to the original models, confirming that our method can be readily integrated into existing unsupervised reconstruction-based anomaly detection systems to significantly enhance their performance.

Staff absenteeism imposes substantial operational costs in high-demand work environments such as healthcare, emergency services, meat processing, construction, and courier and delivery services, where proactive workforce planning depends on reliable individual-level absence prediction. Existing regression and classification approaches share a structural limitation; they map features observed at time t to labels at the same time t, reproducing already-realised outcomes rather than predicting future events, and discard the sequential behavioural structure inherent in individual attendance histories. We propose a Time Series Classification (TSC) framework that separates historical attendance sequences from future absence labels, enabling genuinely proactive prediction. Due to the lack of public longitudinal attendance data, we construct a reproducible simulated dataset calibrated to the UCI dataset. We analyse Binary Focal Loss (BFL) and Geometric Mean (G-Mean) loss under severe class imbalance using only the imbalance ratio $ρ$. For BFL, the initial gradient ratio is $ρα/(1-α)$, implying the balanced weight $α= 1/(1+ρ) \approx 0.023$. Experiments show that performance is governed mainly by $α$, with BFL achieving specificity 0.813 and balanced accuracy 0.888, comparable to G-Mean. Unlike BFL, G-Mean adapts automatically without parameter calibration. Among three deep learning architectures evaluated, Long Short-Term Memory (LSTM), Convolutional Neural Network (CNN), and the hybrid LSTM-Fully Convolutional Network (LSTM-FCN), the LSTM-FCN delivers strong precision and specificity. Stable performance is obtained with batch sizes >= 64 and window sizes between 40-80 days, yielding balanced accuracy of approximately 80% on held-out test data.

Accurately predicting the temporal evolution of clinical biomarkers is crucial for the early diagnosis and management of neurodegenerative diseases such as Alzheimer's disease. However, this relies on longitudinal data to capture biomarker changes over time, which is often sparse and irregular due to the high cost, labor-intensive nature, and patient burden. To address these challenges, we propose ENC-ODE, an Event-level Neurodegenerative modeling in Continuous time with neural Ordinary Differential Equations. ENC-ODE predicts future biomarker evolution by modeling clinical events through diagnosis-conditioned continuous dynamics. A target-conditioned attention mechanism weights and aggregates event-level predictions for the target time and modality without history compression. Extensive experiments on Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset demonstrate that ENC-ODE outperforms representative sequence models while offering a scalable and neuroscientifically grounded solution for clinical support. The code is available at https://github.com/JardinDelSol/enc-ode.

Effective sub-typing (also known as grouping or clustering) of patients using their electronic health record (EHR) data can greatly inform precision medicine efforts. However, subtyping temporal EHR datasets is known to be challenging due to inherent EHR issues, including complexity and irregularity. In this study, we propose a self-supervised Mamba-based model that learns effective EHR representations and enables enhanced patient subtyping. We evaluate the proposed model on public and private real-world EHR datasets to classify the data based on the available labels and subtype patients based on the representations learned from the model. Through an extensive set of experiments, we demonstrate that our model's design choices lead to better performance compared to competitive baseline models for prediction. Moreover, we evaluate several clustering techniques to demonstrate that our findings offer valuable insights into subtyping patients based on temporal records from EHR models\footnote{Our implementations are available at https://github.com/healthylaife/triplet_mamba.

Light curves describe temporal variations in the brightness of celestial objects. Learning robust representations of light curves is essential for large-scale automatic discovery in the dynamic universe, but existing time-series foundation models often struggle with the uneven sampling, complex noise, and wide range of physical timescales that characterize astronomical observations. We propose a domain-informed representation learning framework for irregular astronomical time series with Joint-Embedding predictive architecture (JEPA), combining semantics-preserving views, uncertainty-aware tokenization, and multi-view self-distillation. The encoders are trained with multi-view self-distillation using LeJEPA regularization on the LEAVES dataset and evaluated on the StarEmbed classification benchmark. On StarEmbed, our model outperforms hand-crafted features on 15 of 16 classification metrics. In few-shot linear probing, it achieves macro-F1 scores of 42.56 $\pm$ 7.21 with one sample per class and 63.58 $\pm$ 1.20 with 100 samples per class, consistently improving over hand-crafted features. Beyond variable-star classification, the learned representation supports similarity search, parameter estimation, and photometric zero-point drift detection. We further evaluate cross-domain adaptation on 12 heterogeneous irregular time-series datasets from PYRREGULAR, where the adapted variant matches or exceeds previous state-of-the-art performance on 5 datasets, compared with at most 3 wins by any single prior baseline. These results demonstrate that domain-informed multi-view self-distillation is an effective strategy for learning representations of irregular time series, while also highlighting that successful time-series representation learning requires domain-specific inductive biases rather than a universally optimal architecture.

Dynamic Time Warping (DTW) is a cornerstone for time series classification, but its reliance on Euclidean distances fails to capture latent cross-channel correlations in complex multivariate data. We propose a hybrid Quantum Dynamic Time Warping (qDTW) architecture, replacing the classical distance metric with the parameterized geometry of a quantum Hilbert space. Through structural ablation on benchmarks up to $C=8$ spatial dimensions, we establish fundamental topological rules for quantum sequence alignment. We introduce a Unified Pre-Embedding Adjoint Ansatz that decouples trainable entanglement from classical data, eliminating the severe phase-scrambling and information bottlenecks inherent to traditional measurements. We demonstrate this decoupled architecture allows untrained quantum kernels to act as highly expressive baselines, while parameterized training effectively untangles deeply overlapping hyper-dimensional data. Furthermore, we identify a strict spatial-temporal expressivity tradeoff: temporal depth (data re-uploading) is necessary for dimensionally restricted univariate circuits, but applying it to wide multi-qubit registers triggers chaotic frequency-spectrum explosions and representation collapse. By navigating these topological hazards, our multivariate quantum architecture outperforms classical baselines, setting a new standard for integrating parameterized quantum circuits with dynamic programming

Time series classification involves learning a mapping from a continuous, temporally ordered sequence of real-valued observations to a discrete response variable, like class labels. This task is fundamental in domains, including health monitoring, where the temporal structure of data is critical for accurate prediction. Dynamic Time Warping (DTW) is a standard technique for measuring similarity between sequences varying in time or speed. However, DTW is restricted to discrete point matching. To move beyond pairwise alignment, we propose a theoretical framework that learns mappings between real-valued functions. These mappings approximate the flow associated with the characteristic curves of a linear transport equation with a space-dependent velocity field, providing a diffeomorphic transformation between two time series. Using the method of characteristics, we transform this partial differential equation into ordinary differential equations (ODEs) modeling system dynamics. The objective function used to learn these ODEs derives from the fundamental theorem of calculus. To enable flexible, expressive representations of the velocity field, we utilize reproducing kernel Hilbert spaces and optimal control methods. Our method, Diffeomorphic Time Warping (DiffTW), provides a theoretically grounded dissimilarity measure. Using a 1-nearest neighbor classifier, DiffTW outperforms DTW on 60 of 86 datasets.

Supervised learning demands large quantities of labeled data, a bottleneck that is expensive and reliant on domain-specific expertise. Self-supervised learning, particularly contrastive learning, has emerged as a compelling alternative, enabling rich representation learning directly from unlabeled data. Yet its success hinges critically on the design of positive and negative sample pairs. Existing approaches for time series rely on hand-crafted augmentations and masking heuristics that embed strong domain assumptions, often limiting generalization across diverse temporal patterns and potentially introducing spurious correlations. In this work, we challenge this paradigm by demonstrating that explicitly encoding temporal shift invariance through a simple, deterministic view construction is sufficient to learn strong representations for time series classification. By exploiting temporal structure, our method, Shift Invariant Feature Training (ShiFT), achieves state-of-the-art performance on six diverse real-world time series benchmark datasets, as well as the UCR and UEA archives, while reducing training time. Beyond empirical performance, we present a systematic analysis of contrastive learning dynamics in time series settings, examining the effects of batch size and the number of negatives on downstream performance. Our findings provide practical insights for designing efficient contrastive learning frameworks for time series representation learning. The source code is publicly available at https://github.com/sfi-norwai/ShiFT.

We introduce RocketPFN, a training-free pipeline for time series classification that combines random convolutional feature extraction (Rocket) with in-context classification via a pretrained tabular foundation model (TabPFN v2.5). On 92 UCR datasets (30-resample protocol), RocketPFN matches HC2, the strongest published method on the archive, in mean accuracy (both 0.900, Wilcoxon p=0.50), with no training on the target data and a median inference time of 30 seconds per fold. It also significantly outperforms every individual classifier in the HC2 ensemble. On UEA (20 datasets) the difference is likewise not statistically significant. A separate comparison concerns TSC foundation models: when paired with the same downstream classifier, MOMENT, Mantis, and MantisV2 are all significantly outperformed by RocketPFN using fewer extracted features and no learned parameters (p<0.001 in each case). This holds even when the encoders were pretrained on corpora that include the UCR training samples. We propose this two-stage pipeline as a reference point for evaluating zero-shot TSC foundation models.

A Prior-data fitted Network learns the posterior predictive induced by its training prior; bringing this paradigm to multivariate time-series classification therefore calls for a synthetic generator that produces complete labelled datasets with temporal structure. We introduce a causal prior that synthesizes each dataset from a randomly sampled DAG over typed nodes across two modalities (tabular attributes and time series), natively producing multivariate, multi-class TSC datasets with cross-modal causal structure across channels, timesteps and labels, a regime not addressed by existing synthetic priors. To validate the prior, we finetune TabPFN v2.5 with minimal adaptations and evaluate on 75 UCR/UEA datasets within TabPFN's operating regime. Finetuning on our generator significantly outperforms both the unmodified upstream model and a tabular-only ablation of the same prior (Wilcoxon signed-rank $p=3.0\times 10^{-8}$ on ROC-AUC), isolating the contribution of the cross-modal temporal structure.

Medical time series (MedTS) signals such as electroencephalography (EEG) and electrocardiography (ECG) support many clinical applications. However, substantial subject-level heterogeneity often induces subject-level distribution shift, causing a fixed parameter set to generalize poorly to unseen individuals. Compared with domain adaptation methods that often depend on extra adaptation components or target-batch statistics, Test-Time Training (TTT) provides a more practical solution for sequential clinical data by enabling online adaptation from unlabeled test samples. However, many representative TTT methods require iterative inner-loop optimization, increasing test-time overhead. In this paper, we propose MedTS-TTT, a test-time training framework for medical time series modeling. MedTS-TTT is built upon Closed-Loop Self-Alignment Test-Time Training (CLSA-TTT) and a Gated Convolutional Backbone (GCB). CLSA-TTT constructs a token-level self-supervised target and performs a single-step fast-weight update for intra-layer closed-loop alignment, enabling rapid sample-wise adaptation without iterative inner-loop optimization. GCB combines CLSA-TTT-based fast adaptation and token-level fusion with a gated convolutional branch to balance local dynamic modeling and information-flow control. On 4 public datasets (2 EEG and 2 ECG) with subject-independent splits, MedTS-TTT achieves 11 top-1 rankings out of 12 evaluations across 9 baselines and 3 metrics. The code is publicly available at https://github.com/mingzhi-c/MedTS-TTT.

Modeling long-sequence medical time series data, such as electrocardiograms (ECG), poses significant challenges due to high sampling rates, multichannel signal complexity, inherent noise, and limited labeled data. While recent self-supervised learning (SSL) methods, based on various encoder architectures such as convolutional neural networks, have been proposed to learn representations from unlabeled data, they often fall short in capturing long-range dependencies and noise-invariant features. Structured state space models (S4) excel at long-sequence modeling, but existing S4 architectures fail to capture the unique characteristics of multichannel physiological waveforms. In this work, we propose SL-S4Wave, a self-supervised learning framework that combines contrastive learning with a tailored encoder built on structured state space models. The encoder incorporates multi-layer global convolution using multiscale subkernels, enabling the capture of both fine-grained local patterns and long-range temporal dependencies in noisy, high-resolution multichannel waveforms. Extensive experiments on real-world datasets demonstrate that SL-S4Wave (1) consistently outperforms state-of-the-art supervised and self-supervised baselines in a challenging arrhythmia detection task, (2) achieves high performance with significantly fewer labeled examples, showcasing strong label efficiency, and (3) maintains robust performance on long waveform segments, highlighting its capacity to model complex temporal dynamics in long sequences that most existing approaches fail to efficiently model, and (4) transfers effectively to unseen arrhythmia types, underscoring its robust cross-domain generalization. We additionally evaluate SL-S4Wave on multiple EEG tasks, achieving superior performance over strong baselines, demonstrating generalizability of our approach beyond cardiac waveforms.

Laboratory tests in electronic health records are collected irregularly, and the absence of a test order can be as informative as the measurement itself. Such missingness reflects clinicians' decisions and patient physiology, making it important to model it directly rather than treat it as a preprocessing artifact. Here we present a diffusion-based approach for generating clinical time series that jointly models laboratory values and their observation patterns using the public Data Analytics Challenge on Missing Data Imputation (DACMI) benchmark derived from MIMIC-III. To preserve realistic sampling, we align chart times into 4-hour intervals and segment admissions into 7-day windows, producing trajectories that pair each lab value with a corresponding observation indicator. Standard transformations and normalization are applied to stabilize training. Our method extends the TimeDiff framework to learn continuous lab values and discrete missingness patterns through complementary diffusion objectives. Experiments show that the generated data closely match real patient trajectories across individual lab distributions and joint value-missingness embeddings, demonstrating that diffusion models can capture clinically meaningful dependencies between patient physiology and clinicians' testing behavior under MNAR-like (missing-not-at-random) missingness. These preliminary results indicate that our model can serve as an initial component toward developing clinical foundation models. By producing synthetic priors that preserve key physiology-missingness relationships, this work motivates the subsequent training of Prior-Data Fitted Networks capable of leveraging informative missingness, which we will investigate in the extended work.

Training deep neural networks for clinical time-series analysis is computationally demanding, yet many healthcare settings lack the resources required for repeated model development and deployment. This challenge is particularly evident in electrocardiogram classification, where large datasets and long training schedules make efficiency practically important. Progressive Data Dropout reduces training cost by excluding samples from gradient updates once they are learned, but it relies on model confidence and may retain samples that are difficult due to noise or ambiguity rather than useful signal. In this work, we introduce ERTS, an explainability-based reliability training signal for efficient ECG classification. ERTS uses explanation quality during training to distinguish between informative and unreliable uncertainty. Building on progressive data selection, we compute Grad-CAM attention maps for candidate samples and derive a focus score that measures whether model predictions are supported by coherent and localised patterns. Samples with low focus are filtered out, while those with meaningful attention are prioritised for gradient updates. We evaluate ERTS across three ECG datasets and multiple backbone architectures, showing consistent improvements in macro-F1 alongside reduced effective training cost. These results suggest that explanation quality can serve as a practical signal for improving both efficiency and reliability in clinical time-series learning. Code will be released.

Time-series clustering remains challenging due to the inherent trade-off between clustering effectiveness and computational efficiency. Similarity-based methods often suffer from quadratic complexity caused by pairwise distance computations, while deep learning-based approaches typically rely on costly iterative training and a large number of trainable parameters. In this paper, we propose MSRGC-Net, an efficient time-series clustering framework that integrates multiscale reservoir computing, granular-ball-based anchoring graph construction, and consensus learning. MSRGC-Net adopts a training-free reservoir computing paradigm to extract multiscale temporal representations from raw time series without backpropagation, significantly reducing computational overhead. To capture the intrinsic structure of the resulting representations, granular-ball computing is employed to adaptively model data distributions via density-consistent regions, yielding compact and robust anchor graph representations. Furthermore, a consensus-based anchoring graph optimization strategy is introduced to effectively align multiscale reservoir representations and integrate complementary information across temporal scales. Extensive experiments on widely used univariate and multivariate benchmark datasets demonstrate that MSRGC-Net consistently outperforms state-of-the-art methods in clustering performance while maintaining superior computational efficiency.

Clinical early warning systems built on electronic health records, in which clinical observations are recorded as irregularly sampled medical time series (ISMTS), must deliver both calibrated risk scores for patient triage and interpretable rationales that clinicians can verify. Large Language Models (LLMs) have been explored for this task, yet they collapse graded clinical risk into overconfident binary predictions. This risk polarization undermines both calibration and cross-patient comparability. To address this, we propose TRIAGE, a framework that trains an LLM to generate dialectical reasoning over competing clinical outcomes by eliciting outcome-specific rationales. This dialectical formulation mitigates risk polarization, enabling a single LLM to yield continuous risk scores grounded in explicit clinical reasoning. Evaluated on three ISMTS benchmarks, TRIAGE achieves an average AUPRC improvement of 3.3% and reduces calibration error by 81% compared to the competitive baselines. An LLM-as-a-judge assessment further shows that our rationales surpass post-hoc explanations from the baseline by 20% in clinical reasoning quality. The source code is available at https://github.com/HyeongWon-Jang/TRIAGE .

In healthcare, multimodal time series tasks often operate on incomplete observations in practice, for example when ECG segments are lost because electrodes detach or an entire respiratory channel is unavailable during overnight monitoring. Such missingness typically appears in two structurally distinct patterns: within-modality missing, where values are absent within an otherwise observed modality, and modality-level missing, where an entire modality is unavailable. Existing methods typically represent unobserved data implicitly through masks or missing embeddings, without learning instance-specific missing information, and most are designed for only one missingness pattern. A natural approach is to explicitly estimate the missing data; however, existing imputation methods treat missingness uniformly despite their different structural priors, and the imputation process is often isolated from downstream tasks, preventing downstream tasks from guiding imputation toward more informative representations. To address these limitations, we present PAMF, a multimodal time-series framework that explicitly handles different missingness patterns while coupling imputation with downstream prediction through prior-aware flow matching and weight sharing. Specifically, the method initializes the flow-matching source state with type-specific priors to distinguish two missing types. It further connects imputation and classification through architecturally matched encoders with weight sharing, transferring task-relevant representations into the imputation process. Experiments on multiple multimodal healthcare time-series benchmarks show that the proposed method achieves the strongest overall downstream performance across diverse datasets and missing settings compared with existing baselines.

Multivariate time series classification (MTSC) is pivotal in high-stakes domains, such as clinical diagnosis and industrial fault detection, where safe deployment necessitates transparent decision-making. However, isolating the temporal segments that drive model predictions is challenging because discriminative signals in real-world time series are typically sparse, heterogeneous, and heavily obscured by background noise. This paper, therefore, proposes AnchorMoE, an interpretable-by-construction classification framework. Built upon a Mixture-of-Experts (MoE) architecture, AnchorMoE encodes multi-view representations of local patches and routes them to specialized experts, ensuring that the final prediction is formulated as an exact additive decomposition over the input segments, facilitating ante-hoc transparency rather than relying on post-hoc estimations. To maintain the reliability of this decomposition under sparse signal distributions, we introduce a geometric orthogonality constraint that penalizes representational redundancy, compelling distinct experts to specialize in heterogeneous predictive patterns. Furthermore, an uncertainty-aware reliability gate is designed to dynamically calibrate the contribution of each segment, effectively suppressing residual background noise. Extensive experiments on real-world and synthetic benchmarks demonstrate that AnchorMoE achieves highly competitive classification performance while faithfully grounding its decisions in the raw time series.

Many systems used in real-world environments require adding new categories and incorporating new information without forgetting what was previously learnt by the classification model. This is known as class-incremental continual learning, and in the case of multivariate time-series, is further complicated by the temporal structure of the data. In this paper, we present a novel approach for performing class incremental continual learning for the classification of multivariate time series data based upon the construction of a dual-stream feature extraction pipeline (using both deep temporal embedding features generated via a pre-trained frozen foundation model and application of statistical features). Evaluated on five benchmark datasets, the proposed system achieves competitive average accuracy across all datasets while maintaining low forgetting rates across all experimental configurations.

Out-of-distribution (OOD) detection for time-series data remains comparatively underexplored compared to vision and language, with a limited principled understanding of how supervised time-series representations can be leveraged for reliable detection under distributional shifts. This work formulates time-series OOD detection as representation learning with hyperspherical embeddings, where class-conditional structure is induced by a von Mises-Fisher (vMF) likelihood-based objective on the unit sphere. The learned representation combines time- and frequency-domain views of the input signal via domain-specific encoders, integrating them into a joint embedding space for OOD detection. Detection uses distance-based scores over the learned embeddings, including k-nearest neighbors (k-NN) and Mahalanobis scores. We evaluate the approach at scale on the complete UCR and UEA time-series archives under a cross-dataset protocol. Empirical results show consistent improvements under both k-NN and Mahalanobis scoring over strong contrastive learning and post-hoc baselines in the same setting. Code is available at https://github.com/tiiuae/hypertf-time-series-ood.

High-dimensional biomedical data, such as cell-by-gene matrices, are increasingly generated temporally. However, Manifold Learning algorithms, like t-SNE and UMAP, cannot incorporate time-ordering in their layouts, obfuscating the dynamics of cell types or other classes. As a solution, we present IRIS, a new Manifold Learning algorithm that structures layouts both chronologically and by manifold topology. IRIS can visualize a wide range of dynamic biomedical data, including scRNA-seq, comparative metagenomics, and literature.

We present a unified experiment, analysis, and benchmark study of multivariate time-series (MTS) anomaly detection. Ten family-representative detectors -- spanning statistical, reconstruction, association, frequency, and generic-transformer families -- are evaluated on five datasets (SMD, MSL, SMAP, PSM, and MSDS) under effectiveness, efficiency, robustness, and cross-dataset generalisation. All methods share the same windowing, scoring, hardware, and metric protocols. Effectiveness, ablation, and robustness use three random seeds; cross-dataset transfer uses seed~0 because each extra seed requires $250$ source-target evaluations. The benchmark yields three method-independent findings: no single-bias baseline dominates; absolute perturbation VUS-ROC is more informative than retention ratios; and MSDS behaves as an event-dense deployment workload rather than a sparse point-anomaly benchmark. Under this protocol we also introduce \ours{}, an adaptive detector family combining a NOTEARS-constrained directed channel-graph view with optional patch-attention and temporal-association views. \ours{} achieves the best macro-average VUS-ROC ($0.675$, $+5.1$~pt over the second-best LSTM-AE), ranks first overall, and reaches the top-3 on all five datasets. Its wins on MSL and MSDS are narrow, while its average and robustness gains are larger: under the same three-seed robustness protocol for every method, it obtains the strongest absolute VUS-ROC across noise, channel dropout, and time-shift perturbations. We release the MSDS preprocessing protocol, configurations, scripts, and seed-level metric dumps.

Clinical time-series learning is routinely constrained by small, heterogeneous cohorts and protocol drift, while its downstream use spans both classification (e.g., pathology diagnosis) and regression (e.g., temporal forecasting). These constraints make foundation-model pretraining appealing, but raises an important question of which inductive biases should the pretraining objective impose so that representations transfer across task types and subjects. We study this question in pathological gait analysis for spinal cord injury (SCI) via PathoFM, an encoder-centric transformer pretrained on multivariate gait windows with three complementary objectives: Local Completion (reconstruct contiguous masked spans to enforce local structure), Temporal Continuity (predict a masked mid-horizon continuation from an observed prefix to enforce smoothness and causal consistency), and Unsupervised In-Context Dynamics (support-query reconstruction conditioned on subject exemplar windows via attention). Empirically comparing objective families (grouping/contrastive, dynamics-based, and generative reconstruction), we find that dynamics-centric mixtures produce the most balanced transfer: grouping objectives favor discriminative margins but can degrade magnitude fidelity needed for continuous targets, whereas reconstruction-only objectives preserve waveform structure but may underperform on classification. Overall, combining local reconstruction with temporal continuity, and adding in-context conditioning when exemplar access is realistic, yields robust subject-generalizing representations.

Time series anomaly detection (TSAD) has long been a hot research topic in data mining due to its various applications. Recent studies challenge the effectiveness of popular deep learning methods for TSAD, suggesting their failure in detecting subtle and prolonged anomalies. Outlier Exposure (OE) and Masked Autoencoder (MAE) emerge as two promising paradigms (classification and reconstruction) for solving the above problems. However, OE-based methods are constrained by poor generalization, while MAE-based methods are limited by masking misalignment issues. To address these limitations, this paper proposes a novel framework, CoAD, which unifies the two paradigms to leverage their complementary strengths while mitigating their respective weaknesses. In this framework, the classification module generates probability-informed soft masks for the reconstruction module, which in turn alleviates the generalization problem of the classification module. This cooperative design enables CoAD to effectively detect subtle and complex anomalies that are often overlooked by existing methods. Additionally, the classification module is carefully designed to resolve issues related to improper classification granularity and the neglect of frequency information. Extensive experiments on high-quality benchmark datasets, conducted under rigorous evaluation protocols, demonstrate that CoAD significantly outperforms both state-of-the-art deep learning and traditional data mining methods, highlighting the potential of deep learning in TSAD. Moreover, CoAD is lightweight and substantially faster than existing SOTA methods, demonstrating its practical value for large-scale, real-time applications.

Medical time series are central to healthcare, enabling continuous monitoring and supporting timely clinical decisions. Despite recent progress, existing methods struggle to jointly model local-global dynamics and handle nonstationarities like baseline drift, while often failing to capture latent channel interactions. To address these challenges, we propose MedMamba, an end-to-end architecture that integrates state space models with domain-specific inductive biases. Specifically, MedMamba first employs multi-scale convolutional embeddings to capture discriminative local morphology. Second, to mitigate nonstationarity, we introduce a tri-branch differential state space encoder that processes raw, temporal-difference, and frequency-domain views, fusing them to emphasize informative patterns while suppressing drift. Furthermore, to uncover latent channel correlations, we design a spatial graph Mamba module that learns a directed dependency structure regularized toward sparsity and acyclicity, which obviates the need for predefined graphs. Extensive experiments on five real-world datasets demonstrate that MedMamba achieves state-of-the-art performance while maintaining linear computational complexity, and ablation studies validate each component's contribution.Code is available at https://github.com/zhangda1018/MedMamba.

Time Series Foundation Models (TSFMs) have become a new component of the state-of-the-art in general time series forecasting. However, adapting them to specialized classification tasks remains constrained by two interconnected challenges: the quadratic cost of standard attention mechanisms and the inability to disentangle the structural components underlying time series variability. This technical report introduces ChronoVAE-HOPE, a next-generation TSFM that reconciles massive generalization with structured latent representation for time series classification. The core of the proposal is a Variational Autoencoder (VAE) framework built upon the HOPE Block, which replaces quadratic attention with a dual-memory system: Titans modules for dynamic short-term retention and a Continuum Memory System (CMS) for the abstraction of long-term historical context. A key architectural novelty is the disentangled latent space, which factorizes representations into independent trend and seasonal components via dedicated encoder heads and separate decoder pathways. ChronoVAE-HOPE undergoes self-supervised pre-training on the Monash archive, combining a Masked Time Series Modeling (MTSM) auxiliary objective with a disentangled VAE reconstruction loss. The pre-trained encoder is subsequently frozen and used to generate fixed-length embeddings for downstream classification on the UCR benchmark datasets. Empirical results demonstrate strong performance across diverse temporal domains, particularly in settings characterized by strict causal structure. ChronoVAE-HOPE establishes a robust and interpretable framework for the adaptation of foundation models to time series classification through structured generative representations.

Time Series Classification (TSC) is a long-standing research problem that has gained increasing attention in recent years with the rapid growth of large-scale temporal data. Despite substantial progress enabled by deep learning, designing TSC models that are both accurate and interpretable remains a challenging task. Many existing approaches adopt a direct feature-to-label classification paradigm, by collapsing high-dimensional temporal embeddings into class logits via a single linear projection (often after global pooling), the paradigm conflates feature extraction and decision logic into an inseparable mapping. To address these limitations, we propose PDFTime, a prototype-guided framework that reformulates time series classification as a multi-stage decision process. Instead of direct feature-to-label mapping, PDFTime leverages learned prototypes to approximate class-conditional feature distributions in the latent space, enabling progressive discrimination through classification sub-tasks of varying granularity. To our knowledge, PDFTime is the first framework to reformulate time series classification as a decoupled, multi-stage similarity-based reasoning process, breaking the long-standing paradigm of direct, black-box feature-to-label mapping. Extensive evaluations demonstrate that PDFTime achieves state-of-the-art (SOTA) performance across UEA and UCR benchmarks. Notably, it secures the top-$1$ accuracy on 80 out of 128 datasets in the UCR archive, significantly outperforming recent strong baselines in both consistency and generalization.

Multivariate time series (MTS) classification is foundational to pervasive computing and financial analysis, yet existing multi-scale paradigms are often constrained by suboptimal representation fidelity. We identify two critical bottlenecks: temporal non-causality in standard encoders that induces temporal confounding in non-stationary dynamics, and the absence of explicit channel saliency mechanisms that allows noise to contaminate the latent space. To address these challenges, we propose the Causal Attention and Spatio-temporal Encoder Network (CASE-NET), an architecture designed for structural manifold pre-conditioning. CASE-NET synergizes a Causal Temporal Encoder, which enforces physical arrow-of-time constraints via masked self-attention and causal convolutions, with an Adaptive Channel Recalibration module functioning as an information bottleneck to suppress detrimental noise. Comprehensive evaluations across six heterogeneous domains demonstrate that CASE-NET establishes new state-of-the-art benchmarks on four tasks, achieving a peak accuracy of 98.6% on the AWR dataset and superior robustness in non-stationary regimes.

Discovering shapelets -- i.e., discriminative temporal patterns within time series -- has been widely studied to address the inherent complexity of time-series classification (TSC) and to make model decision-making processes more transparent. However, existing methods primarily focus on population-level shapelets optimized across the entire dataset, which leads to two fundamental limitations: (i) population-level patterns often misalign with instance-specific features, resulting in suboptimal performance and potentially misleading interpretations, and (ii) most methods treat shapelets as independent entities, overlooking important temporal dependencies and interactions among multiple patterns. To address these limitations, we propose INSHAPE, an interpretable TSC framework that discovers variable-length, discriminative temporal patterns specific to each time series. INSHAPE identifies these patterns as non-overlapping segments and models their temporal dependencies, thereby providing clear instance-level interpretations while achieving strong predictive performance. Furthermore, INSHAPE bridges local and global interpretability through a bottom-up approach, aggregating instance-level shapelets into prototypical (population-level) shapelets. Extensive experiments on 128 UCR and 30 UEA benchmark datasets show that INSHAPE consistently outperforms state-of-the-art shapelet-based methods while providing more intuitive and interpretable insights.

Numerical time-series models can effectively process irregular electronic health record (EHR) trajectories, but they do not naturally expose the measurements and temporal patterns supporting each risk estimate as readable evidence. Existing text-based interfaces improve readability, but typically rely on either raw serialization, which is lengthy and redundant, or patient-level free-form summaries, which are difficult to trace to source measurements and time windows. To bridge this gap, we introduce TreeText-CTS (Clinical Time-Series), which converts irregular EHR trajectories into human-readable, compact, source-traceable tree-path evidence units without patient-level summarization or inference-time autoregressive decoding. TreeText-CTS routes multi-scale window summaries through frozen XGBoost models and verbalizes activated tree paths as deterministic, source-traceable evidence units composed of threshold conditions. An evidence selector assembles an informative subset of these units, which a language-model encoder then integrates for prediction. Across PhysioNet 2012 mortality, MIMIC-III mortality, and PhysioNet 2019 sepsis-onset forecasting, TreeText-CTS achieves the best AUROC and AUPRC among evaluated text-based EHR time-series interfaces, improving AUPRC by 6.0 to 9.7 absolute percentage points over the strongest prior text-based interface while remaining competitive with numerical time-series models. Ablations show that tree-path evidence construction, evidence selection, and language-model composition each contribute to performance. Because every span passed to the language-model encoder is constructed from activated tree-path threshold conditions, TreeText-CTS makes the evidence supplied to the final predictor inspectable and source-traceable.

The rapid adoption of deep learning has increasingly led to data-driven models replacing classical model-based algorithms, even in domains governed by well-understood physical laws. While data-driven models, such as long short-term memory (LSTM) networks, have become a popular choice for time-series analysis, their performance relative to model-based approaches in structured environments is rarely evaluated objectively. This paper presents a performance evaluation framework comparing an LSTM classifier against a model-based expectation maximization (EM) classifier for binary time-series classification. The evaluation is conducted on two scalar linear Gaussian state space models differing only in their noise statistics, where the Kalman filter likelihood ratio test with true parameters serves as a reference for the best achievable classification performance.Through Monte Carlo simulations, the classifiers are evaluated across three axes: task difficulty, controlled by the separation in process or measurement noise between the two models; sequence length; and training dataset size. The results show that the EM classifier, which exploits the known model structure, performs strongly when the data conform to the assumed model class. The LSTM classifier requires a larger separation in noise statistics to achieve reliable classification, and its performance saturates below the reference classifier when the models differ only in measurement noise, regardless of sequence length or training dataset size.

Time series classification (TSC) of biological signals has progressed from handcrafted, modality-specific approaches to deep architectures capable of representing the diverse waveform structures of underlying physiological processes (i.e., morphology). This review introduces a unified morphology--modality framework that connects waveform structure to a methodological design, revealing how spikes, bursts, oscillations, slow drift, and hierarchical rhythms inform model design. By analyzing electroencephalography, electromyography, electrocardiography, photoplethysmography, and ocular modalities (electrooculography, pupillometry, eye-tracking), the review demonstrates how morphology determines preprocessing and modeling strategies. Integrating evidence across these biological signals, the framework reveals that morphology, not model class, most strongly determines performance and interpretability. This provides insight into why deep models succeed when their inductive biases align with underlying waveform dynamics. This review also identifies future work including morphological data augmentation and evaluation metrics to improve generalization. Together, these insights position morphology-aware modeling as a unifying principle for developing generalizable, interpretable, and physiologically meaningful TSC models across biological signals.

Timeseries regression models often struggle to leverage large volumes of labeled multimodal data, particularly when the data are irregularly sampled or contain missing values. This is common in domains like healthcare and predictive maintenance, where data are collected from unreliable sources, and labeling requires expert knowledge or costly equipments. Transformer-based large language models have proven effective on structured data such as text through self-supervised learning (SSL) and generative pretraining (GPT) frameworks. However, such models lack the flexibility to efficiently process irregularly sampled multimodal timeseries data. In this paper, we introduce ITGPT, an attention-based architecture designed for handling multimodal, irregularly sampled timeseries by allowing training with both SSL losses and GPT-like objectives. We evaluate its performance on a healthcare task with the TIHM dataset, and a predictive maintenance task with the CompX dataset. Our results demonstrate that ITGPT achieves state-of-the-art performance without requiring resampling, feature fusion or explicit data imputation. Furthermore, when labels are scarce, ITGPT effectively leverages unlabeled data through SSL and GPT training, outperforming the purely supervised approach. This represents an important step towards efficiently using large and unstructured timeseries datasets for practical inference tasks.

State Space Models (SSMs) are inherently recurrent along the sequence dimension, yet depth-recurrence - reusing the same block repeatedly across layers, as recently applied in looped transformers - has not been explored in this model family. We show that a looped SSM with $k$ parameters iterated $L$ times consistently closely matches or outperforms a standard SSM with $k \cdot L$ independent parameters across four architectures (LRU, S5, LinOSS, LrcSSM) and six time series classification benchmarks, despite operating within a strictly smaller hypothesis space, as we formally establish. Since the larger model contains the looped model as a special case, this dominance cannot be explained by expressivity and instead points to parameter sharing across depth as a beneficial inductive bias that simplifies optimization. These results demonstrate that depth-recurrence is orthogonal to sequence-recurrence and independently beneficial. We further show that input reshaping is an equally neglected design axis: concatenating timesteps for low-dimensional inputs, or flattening and rechunking the joint feature-time dimension for high-dimensional ones, yields accuracy gains of 1-6% across all models, confirmed over 5 random seeds. Both techniques provide standalone improvements that compound when combined, suggesting that depth and input reshaping are two independent and underexplored design axes for SSMs on time series.

Reconstructing precise clinical timelines is essential for modeling patient trajectories and forecasting risk in complex, heterogeneous conditions like sepsis. While unstructured clinical narratives offer semantically rich and contextually complete descriptions of a patient's course, they often lack temporal precision and contain ambiguous event timing. Conversely, structured electronic health record (EHR) data provides precise temporal anchors but misses a substantial portion of clinically meaningful events. We introduce a retrieval-augmented multimodal alignment framework that bridges this gap to improve the temporal precision of absolute clinical timelines extracted from text. Our approach formulates timeline reconstruction as a graph-based multistep process: it first extracts central anchor events from narratives to build an initial temporal scaffold, places non-central events relative to this backbone, and then calibrates the timeline using retrieved structured EHR rows as external temporal evidence. Evaluated using instruction-tuned large language models on the i2m4 benchmark spanning MIMIC-III and MIMIC-IV, our multimodal pipeline consistently improves absolute timestamp accuracy (AULTC) and improves temporal concordance across nearly all evaluated models over unimodal text-only reconstruction, without compromising event match rates. Furthermore, our empirical gap analysis reveals that 34.8% of text-derived events are entirely absent from tabular records, demonstrating that aligning these modalities can produce a more temporally faithful and clinically informative reconstruction of patient trajectories than either source alone.