Uncertainty in Federated Granger Causality: From Origins to Systemic Consequences

Granger Causality (GC) provides a rigorous framework for learning causal structures from time-series data. Recent federated variants of GC have targeted distributed infrastructure applications (e.g., smart grids) with distributed clients that generate high-dimensional data bound by data-sovereignty constraints. However, Federated GC algorithms only yield deterministic point estimates of causality and neglect uncertainty. This paper establishes the first methodology for rigorously quantifying uncertainty and its propagation within federated GC frameworks. We systematically classify sources of uncertainty, explicitly differentiating aleatoric (data noise) from epistemic (model variability) effects. We derive closed-form recursions that model the evolution of uncertainty through client-server interactions and identify four novel cross-covariance components that couple data uncertainties with model parameter uncertainties across the federated architecture. We also define rigorous convergence conditions for these uncertainty recursions and obtain explicit steady-state variances for both server and client model parameters. Our convergence analysis demonstrates that steady-state variances depend exclusively on client data statistics, thus eliminating dependence on initial epistemic priors and enhancing robustness. Empirical evaluations on synthetic benchmarks and real-world industrial datasets demonstrate that explicitly characterizing uncertainty significantly improves the reliability and interpretability of federated causal inference.

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.

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.

AIRS-Bench: a Suite of Tasks for Frontier AI Research Science Agents

LLM agents hold significant promise for advancing scientific research. To accelerate this progress, we introduce AIRS-Bench (the AI Research Science Benchmark), a suite of 20 tasks sourced from state-of-the-art machine learning papers. These tasks span diverse domains, including language modeling, mathematics, bioinformatics, and time series forecasting. AIRS-Bench tasks assess agentic capabilities over the full research lifecycle -- including idea generation, experiment analysis and iterative refinement -- without providing baseline code. The AIRS-Bench task format is versatile, enabling easy integration of new tasks and rigorous comparison across different agentic frameworks. We establish baselines using frontier models paired with both sequential and parallel scaffolds. Our results show that agents exceed human SOTA in four tasks but fail to match it in sixteen others. Even when agents surpass human benchmarks, they do not reach the theoretical performance ceiling for the underlying tasks. These findings indicate that AIRS-Bench is far from saturated and offers substantial room for improvement. We open-source the AIRS-Bench task definitions and evaluation code to catalyze further development in autonomous scientific research.

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.

Tighnari v2: Mitigating Label Noise and Distribution Shift in Multimodal Plant Distribution Prediction via Mixture of Experts and Weakly Supervised Learning

Large-scale, cross-species plant distribution prediction plays a crucial role in biodiversity conservation, yet modeling efforts in this area still face significant challenges due to the sparsity and bias of observational data. Presence-Absence (PA) data provide accurate and noise-free labels, but are costly to obtain and limited in quantity; Presence-Only (PO) data, by contrast, offer broad spatial coverage and rich spatiotemporal distribution, but suffer from severe label noise in negative samples. To address these real-world constraints, this paper proposes a multimodal fusion framework that fully leverages the strengths of both PA and PO data. We introduce an innovative pseudo-label aggregation strategy for PO data based on the geographic coverage of satellite imagery, enabling geographic alignment between the label space and remote sensing feature space. In terms of model architecture, we adopt Swin Transformer Base as the backbone for satellite imagery, utilize the TabM network for tabular feature extraction, retain the Temporal Swin Transformer for time-series modeling, and employ a stackable serial tri-modal cross-attention mechanism to optimize the fusion of heterogeneous modalities. Furthermore, empirical analysis reveals significant geographic distribution shifts between PA training and test samples, and models trained by directly mixing PO and PA data tend to experience performance degradation due to label noise in PO data. To address this, we draw on the mixture-of-experts paradigm: test samples are partitioned according to their spatial proximity to PA samples, and different models trained on distinct datasets are used for inference and post-processing within each partition. Experiments on the GeoLifeCLEF 2025 dataset demonstrate that our approach achieves superior predictive performance in scenarios with limited PA coverage and pronounced distribution shifts.

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.

Deep Modeling and Interpretation for Bladder Cancer Classification

Deep models based on vision transformer (ViT) and convolutional neural network (CNN) have demonstrated remarkable performance on natural datasets. However, these models may not be similar in medical imaging, where abnormal regions cover only a small portion of the image. This challenge motivates this study to investigate the latest deep models for bladder cancer classification tasks. We propose the following to evaluate these deep models: 1) standard classification using 13 models (four CNNs and eight transormer-based models), 2) calibration analysis to examine if these models are well calibrated for bladder cancer classification, and 3) we use GradCAM++ to evaluate the interpretability of these models for clinical diagnosis. We simulate $\sim 300$ experiments on a publicly multicenter bladder cancer dataset, and the experimental results demonstrate that the ConvNext series indicate limited generalization ability to classify bladder cancer images (e.g., $\sim 60\%$ accuracy). In addition, ViTs show better calibration effects compared to ConvNext and swin transformer series. We also involve test time augmentation to improve the models interpretability. Finally, no model provides a one-size-fits-all solution for a feasible interpretable model. ConvNext series are suitable for in-distribution samples, while ViT and its variants are suitable for interpreting out-of-distribution samples.

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.

Time-to-Event Transformer to Capture Timing Attention of Events in EHR Time Series

Automatically discovering personalized sequential events from large-scale time-series data is crucial for enabling precision medicine in clinical research, yet it remains a formidable challenge even for contemporary AI models. For example, while transformers capture rich associations, they are mostly agnostic to event timing and ordering, thereby bypassing potential causal reasoning. Intuitively, we need a method capable of evaluating the "degree of alignment" among patient-specific trajectories and identifying their shared patterns, i.e., the significant events in a consistent sequence. This necessitates treating timing as a true \emph{computable} dimension, allowing models to assign ``relative timestamps'' to candidate events beyond their observed physical times. In this work, we introduce LITT, a novel Timing-Transformer architecture that enables temporary alignment of sequential events on a virtual ``relative timeline'', thereby enabling \emph{event-timing-focused attention} and personalized interpretations of clinical trajectories. Its interpretability and effectiveness are validated on real-world longitudinal EHR data from 3,276 breast cancer patients to predict the onset timing of cardiotoxicity-induced heart disease. Furthermore, LITT outperforms both the benchmark and state-of-the-art survival analysis methods on public datasets, positioning it as a significant step forward for precision medicine in clinical AI.