Continuity and Ordinality Matter: Constraining Time Series Tokens for Effective Time Series Analysis with Large Language Models

Token-based time series large language models (TS-LLMs) have emerged as a promising direction for time series analysis and reasoning. However, prior studies largely overlook the inherent continuity and ordinality of time series tokens, which substantially limits model performance. In this paper, we argue that preserving these properties in time series token embeddings is crucial for the effectiveness of token-based TS-LLMs. To this end, we propose COM (Continuity and Ordinality Matter), a continuity- and ordinality-aware strategy that integrates geometric constraints into both the initialization and training stages. Empirical results on multiple time series analysis benchmarks demonstrate that COM consistently improves the performance of token-based TS-LLMs, achieving competitive results and strong generalizability. Code is available at https://anonymous.4open.science/r/COM .

A multi-agent system for spine MRI report generation from multi-sequence imaging

Spinal pathology is a leading cause of pain and disability worldwide. Spine MRI is central to clinical evaluation, yet its interpretation remains complex and time-consuming, requiring integration of information across multiple imaging sequences and anatomical regions. Despite recent advances in automated MRI analysis, effectively combining multi-sequence data while preserving sequence-specific diagnostic information remains an open challenge. Here we present SpineAgent, a multi-agent framework for spine MRI report generation built upon a multi-sequence foundation model trained on routine clinical data from 32,047 patients and 453,683 MRI series, comprising a total of 13,441,191 MRI slices. To accommodate diverse modalities of sequences, we first pre-train two DINOv3-based encoders separately on T1- and T2-weighted sequences. We then introduce a continual training strategy that learns a synthesizer to embed images of other sequences using the T1 and T2 encoders, producing patient-level embedding that integrates various signals across MRI sequences. Using these embeddings, SpineAgent achieves state-of-the-art performance, and demonstrates strong generalizability under cross-manufacturer and cross-cohort evaluation. Beyond classification, SpineAgent enables pathology localization by identifying findings-relevant slices and segmenting pathological regions. It also supports multimodal image-report retrieval, providing a solid foundation for scalable and explainable MRI report generation. We further integrate these validated capabilities of SpineAgent into 37 specialized agents. Finally, we incorporate their outputs as structured tokens within a Medical Report Agent trained end-to-end for report generation. Through both automated metrics and expert evaluation by five radiologists, SpineAgent achieves leading performance in spine MRI report generation.

Harnessing Generalist Agents for Contextualized Time Series

Time series are often embedded in rich contexts that are essential for holistic modeling. Moreover, real-world practitioners often require end-to-end workflows for analyzing temporal dynamics, where widely studied tasks such as forecasting are only one step in a broader solution loop. While generalist AI agents offer a promising interface for such workflows under complex contexts, they still operate primarily in textual spaces that are not fully aligned with structured temporal signals. In this work, we introduce TimeClaw, an agentic harness framework for time series that equips generalist LLM agents with the time series-native runtime support needed for contextualized temporal reasoning. TimeClaw integrates executable temporal tools for grounded and auditable analysis, experience-driven capability evolution for creating reusable analytical routines, and episodic multimodal memory for retrieving relevant reasoning traces. Together, these components unlock harnessed open-ended temporal reasoning with contextual information. Extensive evaluation on multiple benchmarks covering diverse tasks across energy, finance, weather, traffic, and other real-world domains demonstrates improved performance of TimeClaw. Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TimeClaw.

Spatiotemporal Seismic Hazard Assessment Using VQ-VAE and Seismic Statistical Features

In this paper we build upon a previous study in which we demonstrated, using XGBoost and earthquake catalogue data from Japan and Chile, that a set of 60 seismic statistical features (SSFs) had much greater predictive value than a set of 428 generic time series features from the tsfresh package. We here extend this previous work in two key ways, focusing on data from Japan as a large dataset is necessary in order to allow for the training of a deep learning (autoencoder) model. First, we move from whole-region prediction (considering, for each candidate event, the likelihood of an event M $\geq$ 5.0 anywhere in the region in the next 15 days) to localised predictions in which both the region of feature computation and the region of prediction are restricted to a circle of radius 24 km around the candidate event, and we show that performance remains excellent, similar to our previous whole-region study for the same area. Second, we here couple this proven set of SSFs, based on one-dimensional (catalogue) data, with a novel feature based on two-dimensional seismic maps, obtained by training a VQ-VAE model to reproduce such maps as output and identifying a measure of its error in doing so with a localised build-up of crustal stress. We show that while localised prediction based on SSFs can be effective alone, with test AUC values as high as those obtained in the case of Japan in our previous whole-region study, the inclusion of the new natively-spatial VQ-VAE-derived feature, top-ranked by SHAP analysis, can enhance performance and additionally appears to near-wholly replace the traditionally-computed $b$-value in terms of feature usage.

TRACE: A Temporal Conditional Estimation for Multimodal Time Series Foundation Models

Time series foundation models (TS-FMs) aim to learn generalizable temporal representations that can be adapted to a wide range of downstream tasks. In real-world multimodal settings, time series are frequently affected by temporal misalignment and partial modality missingness, where different modalities are observed at heterogeneous time scales or are partially absent. Existing approaches typically rely on naive imputation or masking strategies, which fail to account for cross-modal dependencies and often lead to misaligned or degraded representations. We propose TRACE, a conditional estimation paradigm for multimodal time series foundation model pipelines under missingness and irregular sampling, allowing incomplete target modalities to be systematically inferred from available auxiliary modalities. We evaluate TRACE on diverse multimodal benchmarks spanning healthcare and affective computing, including the MIMIC-IV clinical dataset and the CMU-MOSI and CMU-MOSEI benchmarks for multimodal sentiment analysis. Across a range of downstream prediction tasks and missing-modality settings, TRACE consistently outperforms prior multimodal fusion approaches, demonstrating improved robustness to severe modality missingness and more reliable cross-modal representations.

TGFormer: Towards Temporal Graph Transformer with Auto-Correlation Mechanism

The growing interest in Temporal Graph Neural Networks (TGNNs) stems from their ability to model complex dynamics and deliver superior performance. However, TGNNs encounter fundamental challenges in capturing long-term dependencies and identifying periodic patterns. To address these limitations, we propose TGFormer, a novel Transformer architecture specifically designed for temporal graphs. Our model redefines temporal graph learning by establishing a trajectory framework that aligns with time series analysis principles. This approach allows TGFormer to derive node representations through systematic analysis of historical interactions, enabling granular examination of node relationships across sequential timestamps. Building upon stochastic process theory, we develop an auto-correlation mechanism that systematically uncovers periodic dependencies in node interactions. This innovation empowers TGFormer to perform dependency discovery and representation aggregation at sub-interaction levels, demonstrating superior efficiency and accuracy compared to conventional attention mechanisms. Experimental validation across six public benchmarks confirms the effectiveness of our approach, with TGFormer at most achieving 9.35\% precision improvement compared to state-of-the-art approaches.

GETA: Generalized Encrypted Traffic Analysis

Traditional traffic analysis is being fundamentally challenged by the rapid adoption of encryption, tunnelling, and privacy-preserving protocols, which increasingly obscure packet payloads and limit the usefulness of Deep Packet Inspection (DPI). Although machine learning has advanced encrypted traffic analysis, existing approaches often remain tied to protocol-specific header features, depend on large labelled datasets, and degrade when deployed across heterogeneous network environments. We present GETA, a protocol-agnostic framework for encrypted traffic analysis that models network flows as multivariate time series using only traffic metadata, thereby avoiding reliance on packet payloads or header semantics. GETA combines meta-learning, embedding refinement, and self-attention to support few-shot adaptation to previously unseen domains with minimal labelled data. Across nine public datasets spanning application identification, VPN traffic classification, IoT device fingerprinting, and attack detection, GETA consistently outperforms state-of-the-art baselines. These results show that GETA offers a practical and generalisable foundation for robust traffic analysis in modern encrypted networks.

Uncertainty-DTW for Sequences and Visual Tokens

Aligning structured data is a fundamental problem in computer vision and machine learning, underlying tasks such as time series analysis, human action recognition, and visual representation learning. Existing alignment methods, including Dynamic Time Warping (DTW) and its differentiable variants, rely on deterministic similarity measures and are therefore sensitive to heterogeneous and noisy features. In this work, we introduce uncertainty-aware alignment, a probabilistic framework that models pairwise correspondences with heteroscedastic uncertainty and performs structured matching along alignment paths. Our formulation, uncertainty-DTW (uDTW), assigns each correspondence a Normal distribution and parametrizes each alignment path by a Maximum Likelihood Estimate objective consisting of (i) a precision-weighted matching term that suppresses unreliable features, and (ii) a log-variance regularization that prevents degenerate solutions. This yields a probabilistic alignment mechanism that is robust to noise and interpretable, as uncertainty directly reflects the reliability of matches. We further generalize this framework from temporal sequences to tokenized visual representations, enabling structured matching over sets of visual tokens. The learned uncertainty can be interpreted as a reverse-attention: semantically relevant regions exhibit low uncertainty and dominate the alignment, while ambiguous/noisy regions have high uncertainty. This provides a connection between alignment, attention, and uncertainty modeling. We evaluate the proposed framework across diverse domains. The results demonstrate consistent improvements over state-of-the-art methods and show that learned uncertainty correlates with semantic importance. These findings establish uncertainty-aware alignment as a general, robust, and interpretable framework for learning from structured data.

Pseudospectral Bounds for Transient Amplification in Coupled Gradient Descent

Coupled gradient descent--where the update of one parameter block depends on another--underlies bilevel optimization, two-time-scale stochastic approximation, and adversarial training. When the coupled Jacobian is block-triangular, asymptotic stability is governed by the spectral radii of the diagonal blocks, yet transient amplification before convergence can be arbitrarily large due to non-normality. We develop a sharp pseudospectral theory for such block-triangular Jacobians, proving that the Kreiss constant satisfies $K(J) \leq 2/(1-γ) + \|C\|/(4(1-γ))$ when the diagonal blocks are symmetric with spectral radii at most $γ< 1$, and we establish matching minimax lower bounds. We characterize the critical coupling threshold for spectral instability and extend the analysis to nearly self-referential systems via a Neumann-series perturbation framework. As a consequence, we obtain a finite-horizon iteration-complexity bound of $O(K(J)^2 \log(1/δ))$ for stochastic coupled descent. Framed as scaling laws for non-stationary two-time-scale optimization, our results expose a non-asymptotic, instance-dependent regime of high-dimensional learning dynamics that is invisible to spectral-radius analysis. Experiments on linear-quadratic problems, IQC-based comparisons, and neural-network training confirm the theory.

Benchmarking Inductive Biases for Multivariate Time-Series Anomaly Detection with a Robust Multi-View Channel-Graph Detector

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.