A Novel Recurrent Neural Network Framework for Prediction and Treatment of Oncogenic Mutation Progression

Despite significant medical advancements, cancer remains the second leading cause of death, with over 600,000 deaths per year in the US. One emerging field, pathway analysis, is promising but still relies on manually derived wet lab data, which is time-consuming to acquire. This work proposes an efficient, effective end-to-end framework for Artificial Intelligence (AI) based pathway analysis that predicts both cancer severity and mutation progression, thus recommending possible treatments. The proposed technique involves a novel combination of time-series machine learning models and pathway analysis. First, mutation sequences were isolated from The Cancer Genome Atlas (TCGA) Database. Then, a novel preprocessing algorithm was used to filter key mutations by mutation frequency. This data was fed into a Recurrent Neural Network (RNN) that predicted cancer severity. Then, the model probabilistically used the RNN predictions, information from the preprocessing algorithm, and multiple drug-target databases to predict future mutations and recommend possible treatments. This framework achieved robust results and Receiver Operating Characteristic (ROC) curves (a key statistical metric) with accuracies greater than 60%, similar to existing cancer diagnostics. In addition, preprocessing played an instrumental role in isolating important mutations, demonstrating that each cancer stage studied may contain on the order of a few-hundred key driver mutations, consistent with current research. Heatmaps based on predicted gene frequency were also generated, highlighting key mutations in each cancer. Overall, this work is the first to propose an efficient, cost-effective end-to-end framework for projecting cancer progression and providing possible treatments without relying on expensive, time-consuming wet lab work.

TimeCluster with PCA is Equivalent to Subspace Identification of Linear Dynamical Systems

TimeCluster is a visual analytics technique for discovering structure in long multivariate time series by projecting overlapping windows of data into a low-dimensional space. We show that, when Principal Component Analysis (PCA) is chosen as the dimensionality reduction technique, this procedure is mathematically equivalent to classical linear subspace identification (block-Hankel matrix plus Singular Vector Decomposition (SVD)). In both approaches, the same low-dimensional linear subspace is extracted from the time series data. We first review the TimeCluster method and the theory of subspace system identification. Then we show that forming the sliding-window matrix of a time series yields a Hankel matrix, so applying PCA (via SVD) to this matrix recovers the same principal directions as subspace identification. Thus the cluster coordinates from TimeCluster coincide with the subspace identification methods. We present experiments on synthetic and real dynamical signals confirming that the two embeddings coincide. Finally, we explore and discuss future opportunities enabled by this equivalence, including forecasting from the identified state space, streaming/online extensions, incorporating and visualising external inputs and robust techniques for displaying underlying trends in corrupted data.

Prediction and Causality of functional MRI and synthetic signal using a Zero-Shot Time-Series Foundation Model

Time-series forecasting and causal discovery are central in neuroscience, as predicting brain activity and identifying causal relationships between neural populations and circuits can shed light on the mechanisms underlying cognition and disease. With the rise of foundation models, an open question is how they compare to traditional methods for brain signal forecasting and causality analysis, and whether they can be applied in a zero-shot setting. In this work, we evaluate a foundation model against classical methods for inferring directional interactions from spontaneous brain activity measured with functional magnetic resonance imaging (fMRI) in humans. Traditional approaches often rely on Wiener-Granger causality. We tested the forecasting ability of the foundation model in both zero-shot and fine-tuned settings, and assessed causality by comparing Granger-like estimates from the model with standard Granger causality. We validated the approach using synthetic time series generated from ground-truth causal models, including logistic map coupling and Ornstein-Uhlenbeck processes. The foundation model achieved competitive zero-shot forecasting fMRI time series (mean absolute percentage error of 0.55 in controls and 0.27 in patients). Although standard Granger causality did not show clear quantitative differences between models, the foundation model provided a more precise detection of causal interactions. Overall, these findings suggest that foundation models offer versatility, strong zero-shot performance, and potential utility for forecasting and causal discovery in time-series data.

FoundationalECGNet: A Lightweight Foundational Model for ECG-based Multitask Cardiac Analysis

Cardiovascular diseases (CVDs) remain a leading cause of mortality worldwide, underscoring the importance of accurate and scalable diagnostic systems. Electrocardiogram (ECG) analysis is central to detecting cardiac abnormalities, yet challenges such as noise, class imbalance, and dataset heterogeneity limit current methods. To address these issues, we propose FoundationalECGNet, a foundational framework for automated ECG classification. The model integrates a dual-stage denoising by Morlet and Daubechies wavelets transformation, Convolutional Block Attention Module (CBAM), Graph Attention Networks (GAT), and Time Series Transformers (TST) to jointly capture spatial and temporal dependencies in multi-channel ECG signals. FoundationalECGNet first distinguishes between Normal and Abnormal ECG signals, and then classifies the Abnormal signals into one of five cardiac conditions: Arrhythmias, Conduction Disorders, Myocardial Infarction, QT Abnormalities, or Hypertrophy. Across multiple datasets, the model achieves a 99% F1-score for Normal vs. Abnormal classification and shows state-of-the-art performance in multi-class disease detection, including a 99% F1-score for Conduction Disorders and Hypertrophy, as well as a 98.9% F1-score for Arrhythmias. Additionally, the model provides risk level estimations to facilitate clinical decision-making. In conclusion, FoundationalECGNet represents a scalable, interpretable, and generalizable solution for automated ECG analysis, with the potential to improve diagnostic precision and patient outcomes in healthcare settings. We'll share the code after acceptance.

MAESTRO: Multi-modal Adaptive Ensemble for Spectro-Temporal Robust Optimization

Timely and robust influenza incidence forecasting is critical for public health decision-making. To address this, we present MAESTRO, a Multi-modal Adaptive Ensemble for Spectro-Temporal Robust Optimization. MAESTRO achieves robustness by adaptively fusing multi-modal inputs-including surveillance, web search trends, and meteorological data-and leveraging a comprehensive spectro-temporal architecture. The model first decomposes time series into seasonal and trend components. These are then processed through a hybrid feature enhancement pipeline combining Transformer-based encoders, a Mamba state-space model for long-range dependencies, multi-scale temporal convolutions, and a frequency-domain analysis module. A cross-channel attention mechanism further integrates information across the different data modalities. Finally, a temporal projection head performs sequence-to-sequence forecasting, with an optional estimator to quantify prediction uncertainty. Evaluated on over 11 years of Hong Kong influenza data (excluding the COVID-19 period), MAESTRO shows strong competitive performance, demonstrating a superior model fit and relative accuracy, achieving a state-of-the-art R-square of 0.956. Extensive ablations confirm the significant contributions of both multi-modal fusion and the spectro-temporal components. Our modular and reproducible pipeline is made publicly available to facilitate deployment and extension to other regions and pathogens.Our publicly available pipeline presents a powerful, unified framework, demonstrating the critical synergy of advanced spectro-temporal modeling and multi-modal data fusion for robust epidemiological forecasting.

VARMA-Enhanced Transformer for Time Series Forecasting

Transformer-based models have significantly advanced time series forecasting. Recent work, like the Cross-Attention-only Time Series transformer (CATS), shows that removing self-attention can make the model more accurate and efficient. However, these streamlined architectures may overlook the fine-grained, local temporal dependencies effectively captured by classical statistical models like Vector AutoRegressive Moving Average model (VARMA). To address this gap, we propose VARMAformer, a novel architecture that synergizes the efficiency of a cross-attention-only framework with the principles of classical time series analysis. Our model introduces two key innovations: (1) a dedicated VARMA-inspired Feature Extractor (VFE) that explicitly models autoregressive (AR) and moving-average (MA) patterns at the patch level, and (2) a VARMA-Enhanced Attention (VE-atten) mechanism that employs a temporal gate to make queries more context-aware. By fusing these classical insights into a modern backbone, VARMAformer captures both global, long-range dependencies and local, statistical structures. Through extensive experiments on widely-used benchmark datasets, we demonstrate that our model consistently outperforms existing state-of-the-art methods. Our work validates the significant benefit of integrating classical statistical insights into modern deep learning frameworks for time series forecasting.

BEDTime: A Unified Benchmark for Automatically Describing Time Series

Many recent studies have proposed general-purpose foundation models designed for a variety of time series analysis tasks. While several established datasets already exist for evaluating these models, previous works frequently introduce their models in conjunction with new datasets, limiting opportunities for direct, independent comparisons and obscuring insights into the relative strengths of different methods. Additionally, prior evaluations often cover numerous tasks simultaneously, assessing a broad range of model abilities without clearly pinpointing which capabilities contribute to overall performance. To address these gaps, we formalize and evaluate 3 tasks that test a model's ability to describe time series using generic natural language: (1) recognition (True/False question-answering), (2) differentiation (multiple choice question-answering), and (3) generation (open-ended natural language description). We then unify 4 recent datasets to enable head-to-head model comparisons on each task. Experimentally, in evaluating 13 state-of-the-art language, vision--language, and time series--language models, we find that (1) popular language-only methods largely underperform, indicating a need for time series-specific architectures, (2) VLMs are quite successful, as expected, identifying the value of vision models for these tasks and (3) pretrained multimodal time series--language models successfully outperform LLMs, but still have significant room for improvement. We also find that all approaches exhibit clear fragility in a range of robustness tests. Overall, our benchmark provides a standardized evaluation on a task necessary for time series reasoning systems.

Safe Gap-based Planning in Dynamic Settings

This chapter extends the family of perception-informed gap-based local planners to dynamic environments. Existing perception-informed local planners that operate in dynamic environments often rely on emergent or empirical robustness for collision avoidance as opposed to performing formal analysis of dynamic obstacles. This proposed planner, dynamic gap, explicitly addresses dynamic obstacles through several steps in the planning pipeline. First, polar regions of free space known as gaps are tracked and their dynamics are estimated in order to understand how the local environment evolves over time. Then, at planning time, gaps are propagated into the future through novel gap propagation algorithms to understand what regions are feasible for passage. Lastly, pursuit guidance theory is leveraged to generate local trajectories that are provably collision-free under ideal conditions. Additionally, obstacle-centric ungap processing is performed in situations where no gaps exist to robustify the overall planning framework. A set of gap-based planners are benchmarked against a series of classical and learned motion planners in dynamic environments, and dynamic gap is shown to outperform all other baselines in all environments. Furthermore, dynamic gap is deployed on a TurtleBot2 platform in several real-world experiments to validate collision avoidance behaviors.

Temporal social network modeling of mobile connectivity data with graph neural networks

Graph neural networks (GNNs) have emerged as a state-of-the-art data-driven tool for modeling connectivity data of graph-structured complex networks and integrating information of their nodes and edges in space and time. However, as of yet, the analysis of social networks using the time series of people's mobile connectivity data has not been extensively investigated. In the present study, we investigate four snapshot - based temporal GNNs in predicting the phone call and SMS activity between users of a mobile communication network. In addition, we develop a simple non - GNN baseline model using recently proposed EdgeBank method. Our analysis shows that the ROLAND temporal GNN outperforms the baseline model in most cases, whereas the other three GNNs perform on average worse than the baseline. The results show that GNN based approaches hold promise in the analysis of temporal social networks through mobile connectivity data. However, due to the relatively small performance margin between ROLAND and the baseline model, further research is required on specialized GNN architectures for temporal social network analysis.

Orientability of Causal Relations in Time Series using Summary Causal Graphs and Faithful Distributions

Understanding causal relations between temporal variables is a central challenge in time series analysis, particularly when the full causal structure is unknown. Even when the full causal structure cannot be fully specified, experts often succeed in providing a high-level abstraction of the causal graph, known as a summary causal graph, which captures the main causal relations between different time series while abstracting away micro-level details. In this work, we present conditions that guarantee the orientability of micro-level edges between temporal variables given the background knowledge encoded in a summary causal graph and assuming having access to a faithful and causally sufficient distribution with respect to the true unknown graph. Our results provide theoretical guarantees for edge orientation at the micro-level, even in the presence of cycles or bidirected edges at the macro-level. These findings offer practical guidance for leveraging SCGs to inform causal discovery in complex temporal systems and highlight the value of incorporating expert knowledge to improve causal inference from observational time series data.