Multi-Integration of Labels across Categories for Component Identification (MILCCI)

Many fields collect large-scale temporal data through repeated measurements (trials), where each trial is labeled with a set of metadata variables spanning several categories. For example, a trial in a neuroscience study may be linked to a value from category (a): task difficulty, and category (b): animal choice. A critical challenge in time-series analysis is to understand how these labels are encoded within the multi-trial observations, and disentangle the distinct effect of each label entry across categories. Here, we present MILCCI, a novel data-driven method that i) identifies the interpretable components underlying the data, ii) captures cross-trial variability, and iii) integrates label information to understand each category's representation within the data. MILCCI extends a sparse per-trial decomposition that leverages label similarities within each category to enable subtle, label-driven cross-trial adjustments in component compositions and to distinguish the contribution of each category. MILCCI also learns each component's corresponding temporal trace, which evolves over time within each trial and varies flexibly across trials. We demonstrate MILCCI's performance through both synthetic and real-world examples, including voting patterns, online page view trends, and neuronal recordings.

AntigenLM: Structure-Aware DNA Language Modeling for Influenza

Language models have advanced sequence analysis, yet DNA foundation models often lag behind task-specific methods for unclear reasons. We present AntigenLM, a generative DNA language model pretrained on influenza genomes with intact, aligned functional units. This structure-aware pretraining enables AntigenLM to capture evolutionary constraints and generalize across tasks. Fine-tuned on time-series hemagglutinin (HA) and neuraminidase (NA) sequences, AntigenLM accurately forecasts future antigenic variants across regions and subtypes, including those unseen during training, outperforming phylogenetic and evolution-based models. It also achieves near-perfect subtype classification. Ablation studies show that disrupting genomic structure through fragmentation or shuffling severely degrades performance, revealing the importance of preserving functional-unit integrity in DNA language modeling. AntigenLM thus provides both a powerful framework for antigen evolution prediction and a general principle for building biologically grounded DNA foundation models.

LEFT: Learnable Fusion of Tri-view Tokens for Unsupervised Time Series Anomaly Detection

As a fundamental data mining task, unsupervised time series anomaly detection (TSAD) aims to build a model for identifying abnormal timestamps without assuming the availability of annotations. A key challenge in unsupervised TSAD is that many anomalies are too subtle to exhibit detectable deviation in any single view (e.g., time domain), and instead manifest as inconsistencies across multiple views like time, frequency, and a mixture of resolutions. However, most cross-view methods rely on feature or score fusion and do not enforce analysis-synthesis consistency, meaning the frequency branch is not required to reconstruct the time signal through an inverse transform, and vice versa. In this paper, we present Learnable Fusion of Tri-view Tokens (LEFT), a unified unsupervised TSAD framework that models anomalies as inconsistencies across complementary representations. LEFT learns feature tokens from three views of the same input time series: frequency-domain tokens that embed periodicity information, time-domain tokens that capture local dynamics, and multi-scale tokens that learns abnormal patterns at varying time series granularities. By learning a set of adaptive Nyquist-constrained spectral filters, the original time series is rescaled into multiple resolutions and then encoded, allowing these multi-scale tokens to complement the extracted frequency- and time-domain information. When generating the fused representation, we introduce a novel objective that reconstructs fine-grained targets from coarser multi-scale structure, and put forward an innovative time-frequency cycle consistency constraint to explicitly regularize cross-view agreement. Experiments on real-world benchmarks show that LEFT yields the best detection accuracy against SOTA baselines, while achieving a 5x reduction on FLOPs and 8x speed-up for training.

Statistical benchmarking of transformer models in low signal-to-noise time-series forecasting

We study the performance of transformer architectures for multivariate time-series forecasting in low-data regimes consisting of only a few years of daily observations. Using synthetically generated processes with known temporal and cross-sectional dependency structures and varying signal-to-noise ratios, we conduct bootstrapped experiments that enable direct evaluation via out-of-sample correlations with the optimal ground-truth predictor. We show that two-way attention transformers, which alternate between temporal and cross-sectional self-attention, can outperform standard baselines-Lasso, boosting methods, and fully connected multilayer perceptrons-across a wide range of settings, including low signal-to-noise regimes. We further introduce a dynamic sparsification procedure for attention matrices applied during training, and demonstrate that it becomes significantly effective in noisy environments, where the correlation between the target variable and the optimal predictor is on the order of a few percent. Analysis of the learned attention patterns reveals interpretable structure and suggests connections to sparsity-inducing regularization in classical regression, providing insight into why these models generalize effectively under noise.

Visual Reasoning over Time Series via Multi-Agent System

Time series analysis underpins many real-world applications, yet existing time-series-specific methods and pretrained large-model-based approaches remain limited in integrating intuitive visual reasoning and generalizing across tasks with adaptive tool usage. To address these limitations, we propose MAS4TS, a tool-driven multi-agent system for general time series tasks, built upon an Analyzer-Reasoner-Executor paradigm that integrates agent communication, visual reasoning, and latent reconstruction within a unified framework. MAS4TS first performs visual reasoning over time series plots with structured priors using a Vision-Language Model to extract temporal structures, and subsequently reconstructs predictive trajectories in latent space. Three specialized agents coordinate via shared memory and gated communication, while a router selects task-specific tool chains for execution. Extensive experiments on multiple benchmarks demonstrate that MAS4TS achieves state-of-the-art performance across a wide range of time series tasks, while exhibiting strong generalization and efficient inference.

Moving Beyond Functional Connectivity: Time-Series Modeling for fMRI-Based Brain Disorder Classification

Functional magnetic resonance imaging (fMRI) enables non-invasive brain disorder classification by capturing blood-oxygen-level-dependent (BOLD) signals. However, most existing methods rely on functional connectivity (FC) via Pearson correlation, which reduces 4D BOLD signals to static 2D matrices, discarding temporal dynamics and capturing only linear inter-regional relationships. In this work, we benchmark state-of-the-art temporal models (e.g., time-series models such as PatchTST, TimesNet, and TimeMixer) on raw BOLD signals across five public datasets. Results show these models consistently outperform traditional FC-based approaches, highlighting the value of directly modeling temporal information such as cycle-like oscillatory fluctuations and drift-like slow baseline trends. Building on this insight, we propose DeCI, a simple yet effective framework that integrates two key principles: (i) Cycle and Drift Decomposition to disentangle cycle and drift within each ROI (Region of Interest); and (ii) Channel-Independence to model each ROI separately, improving robustness and reducing overfitting. Extensive experiments demonstrate that DeCI achieves superior classification accuracy and generalization compared to both FC-based and temporal baselines. Our findings advocate for a shift toward end-to-end temporal modeling in fMRI analysis to better capture complex brain dynamics. The code is available at https://github.com/Levi-Ackman/DeCI.

TSAQA: Time Series Analysis Question And Answering Benchmark

Time series data are integral to critical applications across domains such as finance, healthcare, transportation, and environmental science. While recent work has begun to explore multi-task time series question answering (QA), current benchmarks remain limited to forecasting and anomaly detection tasks. We introduce TSAQA, a novel unified benchmark designed to broaden task coverage and evaluate diverse temporal analysis capabilities. TSAQA integrates six diverse tasks under a single framework ranging from conventional analysis, including anomaly detection and classification, to advanced analysis, such as characterization, comparison, data transformation, and temporal relationship analysis. Spanning 210k samples across 13 domains, the dataset employs diverse formats, including true-or-false (TF), multiple-choice (MC), and a novel puzzling (PZ), to comprehensively assess time series analysis. Zero-shot evaluation demonstrates that these tasks are challenging for current Large Language Models (LLMs): the best-performing commercial LLM, Gemini-2.5-Flash, achieves an average score of only 65.08. Although instruction tuning boosts open-source performance: the best-performing open-source model, LLaMA-3.1-8B, shows significant room for improvement, highlighting the complexity of temporal analysis for LLMs.

Sample Complexity of Causal Identification with Temporal Heterogeneity

Recovering a unique causal graph from observational data is an ill-posed problem because multiple generating mechanisms can lead to the same observational distribution. This problem becomes solvable only by exploiting specific structural or distributional assumptions. While recent work has separately utilized time-series dynamics or multi-environment heterogeneity to constrain this problem, we integrate both as complementary sources of heterogeneity. This integration yields unified necessary identifiability conditions and enables a rigorous analysis of the statistical limits of recovery under thin versus heavy-tailed noise. In particular, temporal structure is shown to effectively substitute for missing environmental diversity, possibly achieving identifiability even under insufficient heterogeneity. Extending this analysis to heavy-tailed (Student's t) distributions, we demonstrate that while geometric identifiability conditions remain invariant, the sample complexity diverges significantly from the Gaussian baseline. Explicit information-theoretic bounds quantify this cost of robustness, establishing the fundamental limits of covariance-based causal graph recovery methods in realistic non-stationary systems. This work shifts the focus from whether causal structure is identifiable to whether it is statistically recoverable in practice.

Spatio-Temporal Transformers for Long-Term NDVI Forecasting

Long-term satellite image time series (SITS) analysis in heterogeneous landscapes faces significant challenges, particularly in Mediterranean regions where complex spatial patterns, seasonal variations, and multi-decade environmental changes interact across different scales. This paper presents the Spatio-Temporal Transformer for Long Term Forecasting (STT-LTF ), an extended framework that advances beyond purely temporal analysis to integrate spatial context modeling with temporal sequence prediction. STT-LTF processes multi-scale spatial patches alongside temporal sequences (up to 20 years) through a unified transformer architecture, capturing both local neighborhood relationships and regional climate influences. The framework employs comprehensive self-supervised learning with spatial masking, temporal masking, and horizon sampling strategies, enabling robust model training from 40 years of unlabeled Landsat imagery. Unlike autoregressive approaches, STT-LTF directly predicts arbitrary future time points without error accumulation, incorporating spatial patch embeddings, cyclical temporal encoding, and geographic coordinates to learn complex dependencies across heterogeneous Mediterranean ecosystems. Experimental evaluation on Landsat data (1984-2024) demonstrates that STT-LTF achieves a Mean Absolute Error (MAE) of 0.0328 and R^2 of 0.8412 for next-year predictions, outperforming traditional statistical methods, CNN-based approaches, LSTM networks, and standard transformers. The framework's ability to handle irregular temporal sampling and variable prediction horizons makes it particularly suitable for analysis of heterogeneous landscapes experiencing rapid ecological transitions.

Benchmarking Anomaly Detection Across Heterogeneous Cloud Telemetry Datasets

Anomaly detection is important for keeping cloud systems reliable and stable. Deep learning has improved time-series anomaly detection, but most models are evaluated on one dataset at a time. This raises questions about whether these models can handle different types of telemetry, especially in large-scale and high-dimensional environments. In this study, we evaluate four deep learning models, GRU, TCN, Transformer, and TSMixer. We also include Isolation Forest as a classical baseline. The models are tested across four telemetry datasets: the Numenta Anomaly Benchmark, Microsoft Cloud Monitoring dataset, Exathlon dataset, and IBM Console dataset. These datasets differ in structure, dimensionality, and labelling strategy. They include univariate time series, synthetic multivariate workloads, and real-world production telemetry with over 100,000 features. We use a unified training and evaluation pipeline across all datasets. The evaluation includes NAB-style metrics to capture early detection behaviour for datasets where anomalies persist over contiguous time intervals. This enables window-based scoring in settings where anomalies occur over contiguous time intervals, even when labels are recorded at the point level. The unified setup enables consistent analysis of model behaviour under shared scoring and calibration assumptions. Our results demonstrate that anomaly detection performance in cloud systems is governed not only by model architecture, but critically by calibration stability and feature-space geometry. By releasing our preprocessing pipelines, benchmark configuration, and evaluation artifacts, we aim to support reproducible and deployment-aware evaluation of anomaly detection systems for cloud environments.