Irregular Time-Series Modeling

Real-world spatio-temporal forecasting must handle irregular time points, spatially sparse observations, and the need for uncertainty quantification. This setting is often further compounded by nonlocal interactions (long-range spatial coupling). Modeling continuous-space, continuous-time nonlocal dynamics naturally leads to infinite-dimensional integro-differential equations (IDEs), making principled Bayesian inference intractable. We propose the NonLocal Bayesian Spatio-Temporal model (NLBST), a hierarchical Bayesian framework for continuous spatio-temporal fields that learns explicit nonlocal coupling while retaining tractable inference. NLBST represents the latent field via a coordinate-based spatial basis expansion and models the coefficient process with a continuous-time ODE whose learnable linear operator corresponds to a Galerkin reduction of a nonlocal IDE; a Neural ODE residual captures additional nonlinear dynamics. A linear-Gaussian observation model enables Kalman-style sequential updates under missing and irregular observations, while the spatial basis representation enables inductive prediction at unmeasured locations without retraining. Global parameters are learned via variational inference, and uncertainty is handled through a Bayesian hierarchy. Experiments on synthetic and real-world datasets demonstrate strong forecasting and spatial generalization with well-calibrated uncertainty, yielding substantial gains over baselines in strongly nonlocal and partially observed regimes.

Time series prototype learning is fundamentally challenged by observational ambiguity. Discrete architectures fail to resolve this, as they lack the capacity to decouple stochastic noise from continuous dynamics. Furthermore, rigid closed-set assumptions fail to capture unseen diversity. To address these limitations, we propose a hierarchical ordinary differential equation clustering network, which utilizes neural ordinary differential equation to model latent state evolution as a continuous integral curve. This formulation enforces temporal continuity to effectively disentangle smooth feature trends from stochastic noise, while our adaptive hierarchical mechanism autonomously determines the appropriate number of prototypes without rigid prior constraints. Validated on the early link failure detection task with irregularly sampled time series, the proposed method effectively extracts underlying physical prototypes, thereby enabling robust failure detection. Our code is available at https://github.com/NJ-LNN/Hierarchical-ODE.

The Differential Time-Varying Effect Model (DTVEM) of Jacobson et al. (2019) is a popular tool for finding the best time lag in intensive longitudinal data, but it assumes everyone shares the same lag structure. The original authors named fixing this as future work, and it clashes with the premise of modern clinical research, which is that people differ. We present DTVEM-RE, an extension that lets each person have their own lag coefficients, with two versions of the confirmatory step: a discrete-time hierarchical Bayesian VAR in Stan, which pools across people and gives calibrated uncertainty, and a continuous-time per-person Ornstein-Uhlenbeck model in ctsem, which handles unevenly spaced beeps directly. We report four results. A simulation shows the Bayesian version recovers the between-person spread tau_a with bias below 0.01 and coverage of 90 to 93 percent. On the Fisher et al. (2017) EMA dataset (N=40), person-specific lag-1 effects vary by an order of magnitude across three mood items, the Bayesian and GAMM estimates agree closely (r=0.87 to 0.92), and DTVEM-RE gives the best one-step-ahead prediction among four discrete-time methods. A multi-lag version shows all nine tau_k values have credible intervals excluding zero, and the lag where people differ most changes across items, something lag-1-only methods like mlVAR cannot detect. Finally, the two versions agree almost exactly on person-specific lag-1 estimates (r >= 0.995), differing only as shrinkage predicts. DTVEM-RE is, to our knowledge, the first person-specific implementation of DTVEM-style lag detection, and it contains standard DTVEM as a special case.

Accurate estimation of long-term care transition probabilities is central to disability insurance pricing, reserving, and solvency assessment. Classical actuarial multi-state models commonly rely on Markov, semi-Markov, or proportional-hazard specifications, which provide a direct connection to cohort projection but may be restrictive for irregular longitudinal health data with nonlinear aging patterns and heterogeneous covariate histories. This paper develops a well-calibrated estimator of multi-state transition probabilities for irregular longitudinal health data. The model learns from individual health history, incorporates the time elapsed between observations, and conditions transition probabilities on demographic and socioeconomic attributes. It produces a valid probability distribution over the next observed health state, with four possible states: healthy, mild disability, severe disability, and death. Individual probabilities are aggregated by age group and origin state to form transition matrices compatible with actuarial cohort projection. Using longitudinal data from the Health and Retirement Study, we compare the proposed estimator with logistic regression, gradient-boosted trees, a recurrent neural network, and a last-state persistence benchmark. The evaluation considers probabilistic accuracy, endpoint discrimination and calibration for severe disability and death, risk concentration, and transition matrix error after aggregation. The proposed estimator improves severe disability discrimination relative to logistic regression and gradient-boosted tree benchmarks, maintains strong calibration, and yields the lowest transition matrix error among the evaluated models in the held-out test analysis. Results show that a structured machine learning estimator can support long-term care transition modeling when judged by calibration and projection fidelity, beyond discrimination.

Real-world time series are often highly incomplete and irregular due to sensor dormancy, transmission delays, and event-driven sampling, making reliable forecasting fundamentally challenging. Existing methods have evolved from impute-then-forecast pipelines to continuous-time models such as Neural ODEs and continuous-time graph networks. While these approaches improve the modeling of historical irregularity, they still rely on an implicit oracle assumption at inference time: the timestamps of future valid observations are presumed to be known in advance. This assumption limits practical relevance, since in many real systems the more fundamental question is not only what the future value will be, but also whether a valid observation will occur at all. In this paper, we propose Timeflies, a unified framework that reformulates forecasting as a joint problem of future observability inference and value estimation. To explicitly model the interaction between observation dynamics and state evolution, Timeflies adopts an observation stream and a value stream, coupled through three dedicated modules for reliability-aware embedding, observation-guided dependency modeling, and joint prediction. We further construct Shadow, a benchmark that combines natural missingness from public datasets with real-world industrial data, and introduce the Observation-Value Joint Entropy (OVJE) metric to comprehensively evaluate this coupled predictability. Extensive experiments show that Timeflies consistently outperforms existing methods, highlighting the importance of explicitly modeling future observability in time series forecasting with missing values. Code and dataset are available in https://github.com/ant-intl/Timeflies.

Multivariate time-series data often exhibit complex temporal dependencies, irregular sampling, and heterogeneous dynamics across multiple time scales, making accurate sequence modeling particularly challenging. Traditional recurrent neural networks (RNNs), such as Long Short-Term Memory (LSTM) networks, operate in discrete time and may struggle to effectively capture continuous and irregular temporal behaviors. Liquid Neural Networks (LNNs) address some of these limitations through continuous-time dynamics, but standard LNN architectures typically rely on a single dynamical system, limiting their ability to model heterogeneous temporal patterns. To address these challenges, we propose a Multi-Rate Mixture-of-Experts (MR-MoE) framework built on top of Liquid Neural Networks. In the proposed architecture, multiple LNN-based experts operate at distinct time scales, enabling the model to explicitly separate fast-changing dynamics from slow-evolving temporal trends. A gating network further enables adaptive expert specialization based on input conditions. In addition, we incorporate both feature-level and temporal attention mechanisms to improve robustness, interpretability, and long-range dependency modeling. Feature-level attention suppresses noisy or irrelevant variables, while temporal attention selectively focuses on informative historical states. We evaluate the proposed framework on a complex multivariate time-series prediction task and compare it against strong baselines, including LSTM, monolithic LNN, and standard MoE models. Experimental results demonstrate that the proposed MR-MoE framework consistently achieves improved AUROC and AUPRC performance while maintaining favorable computational efficiency. These results highlight the effectiveness of combining continuous-time dynamics, multi-scale expert decomposition, and adaptive attention mechanisms for time-series modeling.

Understanding and forecasting lake dynamics is critical for monitoring water quality and ecosystem health across lakes and reservoirs. While machine learning methods have been recently applied to ecological time-series data, existing works assume regular sampling in time and depth, and struggle to generalize across lakes with heterogeneous variables, depths, and observation patterns. To address these limitations, we introduce \textsc{LakeFM}, a foundation model for aquatic systems, pre-trained on large-scale ecological datasets comprising both simulated and observed lakes. Through extensive empirical evaluation, we show that \textsc{LakeFM} learns meaningful representations spanning broader lake-level characteristics, and achieves competitive or often superior-forecasting performance compared to existing time-series foundation and non-foundation models, while producing physically plausible predictions consistent with real-world lake dynamics.

Alzheimer's disease (AD) progression is highly heterogeneous and is typically observed through sparse and irregular longitudinal data, posing challenges for prediction and personalised monitoring. Existing machine learning approaches have improved AD prediction using multimodal data, yet often focus on static classification or cohort-level risk estimation, providing limited support for subject-specific modelling and uncertainty-aware reasoning. To address these limitations, we present a personalised digital twin framework for AD prediction and scenario-based analysis using multimodal longitudinal data. The proposed approach integrates complementary modelling strategies to capture clinical transitions and temporal dependencies across visits. Using data from the Alzheimer's Disease Neuroimaging Initiative (ADNI), including cognitive assessments, clinical variables, and MRI-derived phenotypes, the framework predicts cognitive status and diagnostic categories while quantifying predictive uncertainty and enabling patient-specific what-if trajectory analysis. Evaluation on leak-free subject-level splits demonstrates strong performance in score forecasting and diagnosis classification. In this sparse and irregular ADNI setting, transition-based modelling of adjacent visits achieved higher predictive accuracy than the sequence-based branch, suggesting that local transition modelling may be more data-efficient. While sequence models remain valuable for uncertainty-aware trajectory forecasting, local transition modelling offers a more data-efficient and robust predictive strategy. These findings highlight the importance of aligning temporal modelling strategies with clinical data structure and suggest that transition-based digital twin formulations may provide a practical and interpretable approach for personalised disease forecasting in neurodegenerative disorders.

Clinical early warning systems built on irregularly sampled medical time series (ISMTS) from electronic health records must deliver continuous risk scores for patient triage as well as interpretable rationales that clinicians can verify. Large language models (LLMs) are uniquely positioned for both, deriving risk from their output probabilities and rationales from their medical knowledge. However, we find that conventional LLM reasoning collapses graded risk into overconfident predictions and thereby undermines the cross-patient comparability on which triage depends. We refer to this failure mode as risk polarization and identify two underlying behaviors: early commitment to a single outcome, and one-sided reasoning that focuses only on the evidence for that outcome. To address this, we propose TRIAGE, a framework that trains an LLM to reason dialectically over competing clinical outcomes by eliciting outcome-specific rationales. This dialectical formulation mitigates risk polarization, enabling a single LLM to jointly provide explicit clinical rationales and risk scores comparable across patients. Across five ISMTS benchmarks, TRIAGE improves mean AUPRC by 17.0% and reduces mean calibration error by 82.8% relative to the competitive LLM-based baseline, while surpassing the strongest ISMTS baseline by 3.5% in mean AUPRC.

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.

Foundation models mark a profound paradigm shift in time series modeling, with task-specific models being superseded by general-purpose zero-shot models. Yet, current approaches primarily focus on forecasting, while real-world time series are often irregularly and partially observed, requiring models that can jointly forecast, impute missing values, and handle degraded sampling conditions. To address these challenges, we introduce TS-ICL, a novel probabilistic In-Context Learning encoder--regressor Transformer that unifies forecasting and imputation. TS-ICL formulates time series tasks as timestamp-aligned regression and naturally incorporates covariates by training on synthetic dependency structures generated from a novel causal data prior. Empirically, TS-ICL achieves a new state-of-the-art in imputation, while remaining competitive with leading forecasting foundation models across both univariate and covariate-aware benchmarks. It shows particularly strong performance in forecasting with partially observed look-back windows.

Multivariate time series forecasting plays a critical role in real-world applications, including weather prediction, stock analysis, and health monitoring. Due to the diversity of data sources, time series exhibit diverse temporal dynamics, often accompanied by various irregularities such as missing values and non-uniform sampling frequencies. Such irregularities lead to complex and asynchronous temporal dependencies across channels. Thus, a single model with a fixed patching scheme often fails to adapt well to diverse multivariate time series, hindering accurate forecasting. In this paper, we propose TiWeaver, a unified framework designed to handle temporal dynamics and fine-grained inter-channel dependencies adaptively. Specifically, we introduce a Graph-Guided Adaptive Tokenizer (G$^2$AT) that divides time series into high contextually coherent patches by jointly considering temporal density and representation consistency. In addition, we propose a Fine-grained Asynchronous Dependency Extractor (FADE), which is designed to model fine-grained asynchronous inter-channel dependencies while incorporating long-term historical dependencies. We evaluate TiWeaver on 12 real-world time series datasets, where it achieves state-of-the-art performance, outperforming existing methods up to 25%. These results demonstrate its robustness and effectiveness across diverse domains and data characteristics.

Accurate Remaining Useful Life prediction is critical for industrial predictive maintenance. However, real-world deployment is challenging due to the irregular nature of sensor observations, characterized by asynchronous sampling, burst missingness, and temporal jitter. Compounding this issue, purely data-driven models often generate physically implausible degradation trajectories that violate the irreversible nature of damage accumulation. To address this, we propose PC-MambaSDE, a unified continuous-time framework for robust RUL prediction under irregular observations. Specifically, we design a Mask-Aware Continuous Mamba Encoder that explicitly leverages observation masks to extract context-rich control signals. Furthermore, we introduce a Physics-Guided Latent SDE with parametrically rectified hybrid drift, superimposing a global physical bias to enforce monotonic degradation even amid severe observation gaps. Additionally, we formulate RUL prediction as a boundary value problem via a Terminal Degradation Penalty, which decouples a Health Index dimension and applies a penalty loss to guide trajectories toward the failure state. Theoretically, we prove that our variational objective is mathematically equivalent to minimizing the KL divergence via Girsanov's theorem, and we guarantee the global asymptotic stability of the learned dynamics through Lyapunov analysis. To enable rigorous evaluation, we develop a Hybrid Irregularity Generation Scheme that simulates realistic industrial imperfections. Extensive experiments on public benchmarks demonstrate that PC-MambaSDE significantly outperforms state-of-the-art methods, particularly under extreme observation scarcity, validating the efficacy of embedding physical priors into continuous-time latent dynamics.

Continuous glucose monitoring (CGM) provides a dense view of daily metabolic physiology, yet existing generic time-series and CGM-specific foundation models often encode glucose traces as entangled single-stream sequences, leaving the distinct temporal structure of glycemic dynamics only implicitly modeled. We present GlucoFM, a lightweight CGM foundation model that aligns irregular recordings to a 24-hour chronological grid, preserves observation masks, and decomposes glucose dynamics into slow physiological state and transient event streams, capturing low-frequency glycemic baselines and short-term deviations that may reflect acute physiological responses or sensor artifacts. GlucoFM is pretrained on 109,066 hours of unlabeled CGM recordings from 477 subjects with two complementary objectives: masked contextual latent prediction over fused daily representations and temporal dynamics prediction over state and event streams. Across four diverse cohorts and seven clinical prediction tasks, GlucoFM achieves the strongest subject-disjoint linear-probing performance among evaluated baselines, improving average PR-AUC by 4.1 points over the best CGM-specific foundation model. Its gains are most pronounced on core metabolic outcomes, leading PR-AUC on all diabetes-risk and $β$-cell dysfunction tasks and on 3 of 4 insulin-resistance tasks. GlucoFM also achieves the best overall cross-dataset transfer performance and strong few-shot adaptation among evaluated methods, and consistent gains when aggregating multiple days for subject-level prediction, highlighting physiology-aware decomposition as an effective inductive bias for transferable CGM representation learning.

Continuous-time models are a natural choice for irregular and asynchronous data. A central design choice is how to embed discrete observations into continuous time. Interpolation- and imputation-based embeddings reconstruct a continuous observation path, making the model sensitive to the choice of reconstruction. We show that this reconstruction step is unnecessary; under mild conditions, compact-set universality on the model input space transfers to the data space whenever the embedding from data to input is continuous and injective. Guided by this result, and building on the rectilinear control path for Neural Controlled Differential Equations (NCDEs), we introduce a continuous and injective embedding for Log-NCDEs, a universal class of continuous-time models. Our approach records observations as increments and composes them over arbitrary query intervals to directly form log-signatures. This provides interval-level summaries without first interpolating the observed variables, while supporting online computation. Experiments on synthetic controlled dynamics and real-world time-series datasets show that the representation is accurate, efficient, and robust to irregular, asynchronous, and sparse observations.

Irregular multivariate time series forecasting is critical in many real-world applications, where time series are irregularly sampled and exhibit dynamically evolving missingness patterns. Although existing methods perform well in offline settings, they often suffer from significant performance degradation when deployed online due to dynamic shifts in data distribution. Maintaining forecasting capability in such dynamic scenarios typically necessitates online adaptation techniques. Since irregular sampling fundamentally undermines temporal continuity and periodicity, we cannot leverage these widely studied characteristics from regular MTS for online learning. To this end, we study the problem of online IMTS forecasting and propose Under-Cali, an uncertainty-driven dual-expert calibration framework consisting of three core components: an uncertainty estimator, a dual-expert calibration module, and an adaptive routing module. We design an uncertainty estimator that serves as the core control signal to jointly manage inference and adaptation processes. In our framework, the uncertainty estimator first assesses uncertainty for each incoming batch. The adaptive routing module then directs samples with high uncertainty to the unreliable expert for calibration, while low uncertainty samples remain with the reliable expert. Subsequently, the system updates the reliable expert and the uncertainty estimator using well-calibrated reliable samples, and updates the unreliable expert with challenging samples, enabling stable and efficient online learning. Under-Cali keeps the source forecasting model frozen and performs adaptation only through a lightweight, model-agnostic calibration module, enabling efficient adaptation. Extensive experiments on IMTS benchmarks demonstrate consistent improvements with low computational cost. Our code is available at https://github.com/HaonanWen/Under-Cali.

Irregular Multivariate Time Series (IMTS) are common in practice, yet their irregular sampling complicates effective modeling. Existing approaches typically either (i) design specialized architectures that limit the reuse of proven Multivariate Time Series (MTS) models, or (ii) map IMTS onto regular temporal grids through interpolation, which may distort temporal dynamics by introducing artificial values. To address these limitations, we propose a new input-embedding-based approach. We identify that the key bottleneck lies not in the backbone architecture, but in conventional embedding layers that assume uniform sampling. In this work, we introduce QuITE (Query-Based Irregular Time Series Embedding), a simple yet effective plug-and-play embedding module for IMTS. QuITE employs learnable query tokens to aggregate irregular observations through a single self-attention layer, directly producing backbone-compatible latent representations without artificial value generation or architectural modification. Extensive experiments on real-world benchmarks show that QuITE consistently improves MTS models, yielding average relative gains of up to $54.7\%$ in forecasting and $15.8\%$ in classification across diverse datasets and backbone architectures. Code is available at: https://github.com/Meaningfull9502/QuITE.

Astrophysical observations from Earth are subject to weather, environmental, and scientific constraints that lead to sparse, irregular light curves. On the eve of the Vera C. Rubin Observatory Legacy Survey of Space and Time, its dataset offers unprecedented opportunities for transient science. Yet a key challenge remains its cadence, sparse and irregular across six bands, limiting inference. Interpolation helps mitigate this, with Gaussian Processes the standard, but they struggle with cross-band correlations, require a priori kernel specification, and must be fit to each light curve individually, hence scaling poorly. Here, we introduce the neural process family for light curve reconstruction, combining the probabilistic framework of Gaussian Processes with the scalability of deep learning. By meta-learning on diverse simulated transients, Attentive Neural Processes shift the bulk of computation to training, enabling rapid, amortized inference with a class-agnostic model. Evaluated on realistic Rubin cadences across 15 transient classes, we show that even an unoptimized, out-of-the-box Attentive Neural Process consistently outperforms all benchmarks -- a suite of Gaussian Processes and neural networks -- on every tested metric, spanning regression quality, astrophysical feature recovery, and probabilistic calibration. Our model interpolates all bands simultaneously in microseconds, over four orders of magnitude faster than the next-best neural benchmark and five faster than Gaussian Processes, demonstrating the potential of neural processes for the nightly Rubin alert stream. Attentive Neural Processes avoid the overconfidence of standard neural networks and the underconfidence of Gaussian Processes, delivering sharp, well-calibrated uncertainties. This work establishes the neural process family as a scalable, probabilistic foundation for real-time transient science in the Rubin era.

Extending discrete-time causal Prior-data Fitted Networks for time series to continuous time invites writing the mechanism as a stochastic differential equation (SDE) -- but if the SDE is integrated \emph{once per observation gap}, the trajectory law depends on when it is observed, and the prior remains a discrete-time Markov model in SDE clothing. We propose a precise continuity criterion -- trajectory-law invariance to the observation schedule -- together with a three-tier taxonomy (discrete; naive observation-grid integration; fine-grid integration with decoupled observation) and a construction realising the top tier on a random DAG with OU or small-MLP nonlinear drifts, irregular observation schedules, and hard / soft / time-varying interventions. A $2 \times 2$ encoder $\times$ integrator ablation, run independently on a linear and a nonlinear prior, finds fine-grid integration beats naive on 8/8 cells (sign-consistency $p < 1/256$) with the gap growing as the eval grid refines; the encoder axis is null with fine integration but time-aware-leading with naive. We release the prior and a preliminary zero-shot protocol on pharmacokinetic and physical-system data.

We introduce CopFITi, a copula model for probabilistic forecasting of irregular multivariate time series (IMTS). Our model combines the expressivity of normalizing flows for univariate marginals with the consistency and flexibility of a Gaussian Mixture Copula for the joint dependency structure. Our experiments show that copula-based approaches, which decouple the marginals from the joint, yield better marginal models than architectures that directly fit the full joint. With CopFITi, we propose the first IMTS copula that is marginalization-consistent by construction and establish a new state of the art in joint IMTS density modeling.

Effective diabetes management requires continuous monitoring of glycemic levels. Clinically, glycemic control is assessed using metrics such as Time in Range (TIR), Time Below Range (TBR), and Time Above Range (TAR), typically derived from continuous glucose monitoring (CGM). However, many patients rely on self-monitoring of blood glucose (SMBG) due to the high cost and limited accessibility of CGM. Unlike CGM, SMBG provides sparse and irregular measurements, making accurate estimation of these metrics challenging. Conventional supervised learning approaches struggle under such sparsity, leading to poor generalization and unstable performance. To address this, we propose PACD-Net, a self-supervised contrastive knowledge distillation framework for estimating glycemic control from SMBG. Pseudo-SMBG samples with richer temporal coverage are used as teacher signals to guide learning from sparse observations. In addition, multi-view contrastive learning enforces representation consistency across diverse sampling patterns. The model adopts a hybrid Swin Transformer-CNN backbone to capture temporal dependencies in sparse SMBG sequences. Experimental results demonstrate that PACD-Net consistently outperforms existing methods in estimating TAR, TIR, and TBR from real-world SMBG data, achieving improved accuracy as well as enhanced stability and generalization under extremely sparse observation settings. The proposed framework provides a practical tool for clinical SMBG interpretation and offers a generalizable approach for learning from sparse and irregularly sampled sensor data in broader applications.

Irregular multivariate time series impose a trade-off for long-horizon forecasting: discrete methods can distort temporal structure via re-gridding, while continuous-time models often require sequential solvers prone to drift. To bridge this gap, we present Latent Laplace Diffusion (LLapDiff), a generative framework that models the target as a low-dimensional latent trajectory, enabling horizon-wide generation without step-by-step integration over physical time. We guide the reverse process utilizing a stable modal parameterization motivated by stochastic port-Hamiltonian dynamics, and parameterize its mean evolution in the Laplace domain via learnable complex-conjugate poles, enabling direct evaluation over irregular timestamps. We also link continuous dynamics to irregular observations through renewal-averaging analysis, which maps sampling gaps to effective event-domain poles and motivates a gap-aware history summarizer. Extensive experiments show that LLapDiff improves over baselines in long-horizon forecasting, and its continuous-time generative nature supports missing-value imputation by querying the same model at historical timestamps. Code is available at https://github.com/pixelhero98/LLapDiffusion.

Numerical time-series models effectively process irregular electronic health record (EHR) trajectories, but do not expose which temporal patterns support each prediction as readable evidence. Existing text-based interfaces either serialize observations, preserving source traceability but offering limited clinical interpretation, or generate patient-level summaries that improve readability but can obscure links to source measurements. We introduce STEP-CTS (Source-Traceable Evidence for Prediction from Clinical Time-Series), which learns to select source-traceable text evidence for a language-model predictor. Multi-scale window statistics of each trajectory are verbalized as sets of deterministic threshold predicates, each set linked to its source window (e.g., "[5-7 h]: last temperature at least 38C"). An offline LLM, run once per unique predicate set without access to patient records, the prediction task, or outcome labels, attaches clinical concepts such as "fever" to their supporting predicates and abstains when none applies. Each predicate set, together with its concepts, forms an evidence unit. A learned Evidence Selector selects a fixed-size subset of the evidence units, which a pretrained clinical language-model encoder reads to make the prediction, with no patient-level text generation. Across three ICU benchmarks, STEP-CTS outperforms evaluated text-based baselines, improving AUPRC over the strongest by 5.1, 3.7, and 11.7 percentage points on P2012, MIMIC-III, and P2019, respectively, and is competitive with dedicated numerical time-series models. Ablations show that clinical concepts and learned evidence selection each contribute to predictive performance. In a blinded clinician study, the selected evidence is rated as traceable as deterministic serialization, near the ceiling of the scale, and above generated summaries on clinical interpretation.

Microsimulation models used by ministries of finance and central banks rely on parametric processes for lifetime earnings that capture only first and second moments of the conditional distribution and miss long-range nonlinear structure. We propose SAGA, a decoder-only transformer for irregular tabular panel sequences, paired with a split conformal calibration wrapper that delivers individual-level prediction intervals with finite-sample marginal coverage guarantees. Trained on the longitudinal Swedish LISA register over 1990 to 2022, comprising 2,143,817 individuals and 61,284,903 person-years, the model forecasts annual labor earnings at horizons of one to thirty years and aggregates them by Monte Carlo into present-discounted lifetime earnings distributions. Against the canonical Guvenen, Karahan, Ozkan, and Song parametric process and tabular and recurrent baselines, SAGA reduces continuous ranked probability score by 31.9 percent at the ten-year horizon and mean absolute error by 37.7 percent at the twenty-year horizon. Conformal intervals achieve nominal coverage to within 0.4 percentage points marginally and within 2.4 percentage points on the worst-case demographic subgroup. The reconstructed lifetime earnings Gini coefficient is 0.327 against the partially observed truth of 0.341 and the GKOS estimate of 0.378. Model weights, calibration tables, and a synthetic equivalent dataset are released for replication outside the protected SCB MONA environment.

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.

Irregularly sampled multivariate event streams remain a difficult modality for generative modeling: tokenization-based approaches break down when inter-event intervals vary by orders of magnitude. We (i) propose \textbf{SurF}, a generative model that uses the Time Rescaling Theorem (TRT) as a learnable bijection between event sequences and i.i.d.\ unit-rate exponential noise, enabling a single model to be trained across heterogeneous event-stream datasets; (ii) three efficient parameterizations of the cumulative intensity that scale to long sequences; and (iii) a Transformer-based encoder for multi-dataset pretraining. On six real-world benchmarks, SurF achieves the best reported time RMSE on Earthquake, Retweet, and Taobao, and is within trial-level noise of the strongest specialist on the remaining three. Under a strict leave-one-out protocol, the held-out checkpoint beats every classical and neural-autoregressive baseline on $5/6$ datasets and beats every baseline on Amazon and Earthquake, an initial step toward foundation models over asynchronous event streams (Code is available at https://github.com/MrRezaeiUofT/SurF).

Multimodal irregular time series (MITS) consist of asynchronous and irregularly sampled observations from heterogeneous numerical and textual channels. In healthcare, for example, patients' electronic health records (EHR) include irregular lab measurements and clinical notes. The irregular timing and channel patterns of observations carry predictive signal alongside the numerical values and textual content. LLMs are natural candidates for processing such heterogeneous data, given their extensive pretrained knowledge spanning textual and numerical domains. We introduce MILM (Multimodal Irregular time series Language Model), which represents MITS as time-ordered triplets in Extensible Markup Language (XML) format and fine-tunes an LLM through a two-stage strategy for MITS classification. The first stage trains on value-redacted MITS to predict from sampling patterns alone, and the second stage trains on full MITS to jointly model sampling patterns and observed values. Our two-stage model (MILM-2S) and its single-stage counterpart (MILM-Direct) achieve the best and second-best average performance on multiple EHR datasets. Further value redaction evaluations confirm that sampling patterns carry predictive signal and that MILM-2S learns to exploit them. In the value pending evaluation we introduce, where some values are unavailable at prediction time, MILM-2S outperforms MILM-Direct by a larger margin compared to standard evaluation. For MILM-2S, preserving the time and channel of value-pending observations as additional sampling information further improves in-hospital mortality prediction.

Neural Flows efficiently model irregular multivariate time series by directly learning ODE solution trajectories with neural networks, bypassing step-by-step numerical solvers. Despite their efficiency, many existing approaches treat variables independently, leaving inter-variable interactions underexplored. Moreover, their one-step mapping makes interaction modeling inherently challenging, as it removes the iterative refinement of interactions during learning. To address this challenge, we propose one-step Graph-Structured Neural Flows (GSNF), which introduce two auxiliary-trajectory self-supervision strategies to strengthen interaction learning: (i) interaction-aware trajectory generation via re-initialization, which induces trajectory divergence to expose graph-induced interactions, with a theoretically derived lower bound on divergence; and (ii) reverse-time trajectory generation, which enforces forward-backward consistency to regularize graph learning, enabled by flow invertibility. Experiments on five real-world datasets show that GSNF achieves state-of-the-art classification performance with highly competitive training time and memory usage.

Clinical time-series data are difficult to model with methods designed for regular sequences because they exhibit irregular sampling, frequent missing values, and heterogeneous observation patterns across variables. Existing approaches commonly use observation masks and time-gap information, but they do not continuously capture the decaying reliability of past observations or consistently organize multi-resolution information within a coherent temporal context during aggregation. To address these limitations, we propose Reliability-aware Temporal Aggregation with Mamba (ReTAMamba), which reconstructs clinical time series as time-variable token sequences, estimates observation reliability from missingness and elapsed time, and augments interval summaries with statistical descriptors. Chronological Weaving is used to integrate short- and long-term temporal information within a coherent temporal context, and a budgeted token router is applied to constrain sequence length while preserving informative summaries. Experiments on MIMIC-IV, eICU, and PhysioNet 2012 show that ReTAMamba consistently improves AUPRC over strong baselines, with average relative gains of 7.51%, 7.80%, and 10.15%, respectively. Cohort-level and patient-level analyses on eICU further showed that the learned mean decay for more dynamic signals, such as heart rate and blood pressure, was 24.3% larger than that for relatively static signals, such as laboratory test variables. These findings suggest that effective prediction in irregular clinical time series requires modeling not only what was measured, but also when and how it was observed, including information freshness and observation timeliness.

Selective state space models (SSMs), such as Mamba, achieve strong per-token expressivity by making the time discretization step $\TildeΔ$ a learned function of the input. However, in doing so, $\TildeΔ$ no longer equals the physical time gap $Δ$ between consecutive observations, limiting the ability of these models to handle irregular time series. Continuous time SSMs, such as S5, keep $\TildeΔ\equivΔ$ and therefore handle irregular timestamps natively, but their dynamics remain linear time invariant (LTI), limiting per token expressivity. We propose \textbf{TIDES}, a selective SSM variant that reconciles selective and continuous architectures by moving input dependence off the step size and onto the diagonal state matrix. As a result, $\TildeΔ\equivΔ$ as in S5, allowing the model to handle irregular timestamps natively without sacrificing the per-token expressivity that makes selective SSMs effective. We show this on a novel \emph{Fading Flash} experimental benchmark, a compact controlled diagnostic for sequence models that jointly tests input dependence and extrapolation to out-of-distribution $Δ$ values, and isolates the distinct failure modes of current state-of-the-art architectures that TIDES avoids by construction. On large-scale benchmarks, TIDES sets the new best average rank on UEA time series classification and the Physiome ODE regression benchmark, and matches or exceeds the reference baseline model on 6 of 8 natively irregular datasets from astronomy, agriculture, neuromorphic sensing, and climate events. Code available at: https://github.com/TaylanSoydan/TIDES.