Spatiotemporal learning is challenging due to the intricate interplay between spatial and temporal dependencies, the high dimensionality of the data, and scalability constraints. These challenges are further amplified in scientific domains, where data is often irregularly distributed (e.g., missing values from sensor failures) and high-volume (e.g., high-fidelity simulations), posing additional computational and modeling difficulties. In this paper, we present SCENT, a novel framework for scalable and continuity-informed spatiotemporal representation learning. SCENT unifies interpolation, reconstruction, and forecasting within a single architecture. Built on a transformer-based encoder-processor-decoder backbone, SCENT introduces learnable queries to enhance generalization and a query-wise cross-attention mechanism to effectively capture multi-scale dependencies. To ensure scalability in both data size and model complexity, we incorporate a sparse attention mechanism, enabling flexible output representations and efficient evaluation at arbitrary resolutions. We validate SCENT through extensive simulations and real-world experiments, demonstrating state-of-the-art performance across multiple challenging tasks while achieving superior scalability.
Background: The integration and analysis of multi-modal data are increasingly essential across various domains including bioinformatics. As the volume and complexity of such data grow, there is a pressing need for computational models that not only integrate diverse modalities but also leverage their complementary information to improve clustering accuracy and insights, especially when dealing with partial observations with missing data. Results: We propose Generalized Probabilistic Canonical Correlation Analysis (GPCCA), an unsupervised method for the integration and joint dimensionality reduction of multi-modal data. GPCCA addresses key challenges in multi-modal data analysis by handling missing values within the model, enabling the integration of more than two modalities, and identifying informative features while accounting for correlations within individual modalities. The model demonstrates robustness to various missing data patterns and provides low-dimensional embeddings that facilitate downstream clustering and analysis. In a range of simulation settings, GPCCA outperforms existing methods in capturing essential patterns across modalities. Additionally, we demonstrate its applicability to multi-omics data from TCGA cancer datasets and a multi-view image dataset. Conclusion: GPCCA offers a useful framework for multi-modal data integration, effectively handling missing data and providing informative low-dimensional embeddings. Its performance across cancer genomics and multi-view image data highlights its robustness and potential for broad application. To make the method accessible to the wider research community, we have released an R package, GPCCA, which is available at https://github.com/Kaversoniano/GPCCA.
This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE
Topological spaces, represented by simplicial complexes, capture richer relationships than graphs by modeling interactions not only between nodes but also among higher-order entities, such as edges or triangles. This motivates the representation of information defined in irregular domains as topological signals. By leveraging the spectral dualities of Hodge and Dirac theory, practical topological signals often concentrate in specific spectral subspaces (e.g., gradient or curl). For instance, in a foreign currency exchange network, the exchange flow signals typically satisfy the arbitrage-free condition and hence are curl-free. However, the presence of anomalies can disrupt these conditions, causing the signals to deviate from such subspaces. In this work, we formulate a hypothesis testing framework to detect whether simplicial complex signals lie in specific subspaces in a principled and tractable manner. Concretely, we propose Neyman-Pearson matched topological subspace detectors for signals defined at a single simplicial level (such as edges) or jointly across all levels of a simplicial complex. The (energy-based projection) proposed detectors handle missing values, provide closed-form performance analysis, and effectively capture the unique topological properties of the data. We demonstrate the effectiveness of the proposed topological detectors on various real-world data, including foreign currency exchange networks.
The imputation of the Multivariate time series (MTS) is particularly challenging since the MTS typically contains irregular patterns of missing values due to various factors such as instrument failures, interference from irrelevant data, and privacy regulations. Existing statistical methods and deep learning methods have shown promising results in time series imputation. In this paper, we propose a Temporal Gaussian Copula Model (TGC) for three-order MTS imputation. The key idea is to leverage the Gaussian Copula to explore the cross-variable and temporal relationships based on the latent Gaussian representation. Subsequently, we employ an Expectation-Maximization (EM) algorithm to improve robustness in managing data with varying missing rates. Comprehensive experiments were conducted on three real-world MTS datasets. The results demonstrate that our TGC substantially outperforms the state-of-the-art imputation methods. Additionally, the TGC model exhibits stronger robustness to the varying missing ratios in the test dataset. Our code is available at https://github.com/MVL-Lab/TGC-MTS.
Imputation of random or non-random missing data is a long-standing research topic and a crucial application for Intelligent Transportation Systems (ITS). However, with the advent of modern communication technologies such as Global Satellite Navigation Systems (GNSS), traffic data collection has outpaced traditional methods, introducing new challenges in random missing value imputation and increasing demands for spatiotemporal dependency modelings. To address these issues, we propose a novel spatiotemporal traffic imputation method, Multimode Nonlinear Transformed Tensor Nuclear Norm (MNT-TNN), grounded in the Transform-based Tensor Nuclear Norm (TTNN) optimization framework which exhibits efficient mathematical representations and theoretical guarantees for the recovery of random missing values. Specifically, we strictly extend the single-mode transform in TTNN to a multimode transform with nonlinear activation, effectively capturing the intrinsic multimode spatiotemporal correlations and low-rankness of the traffic tensor, represented as location $\times$ location $\times$ time. To solve the nonconvex optimization problem, we design a proximal alternating minimization (PAM) algorithm with theoretical convergence guarantees. We suggest an Augmented Transform-based Tensor Nuclear Norm Families (ATTNNs) framework to enhance the imputation results of TTNN techniques, especially at very high miss rates. Extensive experiments on real datasets demonstrate that our proposed MNT-TNN and ATTNNs can outperform the compared state-of-the-art imputation methods, completing the benchmark of random missing traffic value imputation.
tempdisagg is a modern, extensible, and production-ready Python framework for temporal disaggregation of time series data. It transforms low-frequency aggregates into consistent, high-frequency estimates using a wide array of econometric techniques-including Chow-Lin, Denton, Litterman, Fernandez, and uniform interpolation-as well as enhanced variants with automated estimation of key parameters such as the autocorrelation coefficient rho. The package introduces features beyond classical methods, including robust ensemble modeling via non-negative least squares optimization, post-estimation correction of negative values under multiple aggregation rules, and optional regression-based imputation of missing values through a dedicated Retropolarizer module. Architecturally, it follows a modular design inspired by scikit-learn, offering a clean API for validation, modeling, visualization, and result interpretation.
Over recent years it has become well accepted that user interest is not static or immutable. There are a variety of contextual factors, such as time of day, the weather or the user's mood, that influence the current interests of the user. Modelling approaches need to take these factors into account if they want to succeed at finding the most relevant content to recommend given the situation. A popular method for context-aware recommendation is to encode context attributes as extra dimensions of the classic user-item interaction matrix, effectively turning it into a tensor, followed by applying the appropriate tensor decomposition methods to learn missing values. However, unlike with matrix factorization, where all decompositions are essentially a product of matrices, there exist many more options for decomposing tensors by combining vector, matrix and tensor products. We study the most successful decomposition methods that use weighted square loss and categorize them based on their tensor structure and regularization strategy. Additionally, we further extend the pool of methods by filling in the missing combinations. In this paper we provide an overview of the properties of the different decomposition methods, such as their complexity, scalability, and modelling capacity. These benefits are then contrasted with the performances achieved in offline experiments to gain more insight into which method to choose depending on a specific situation and constraints.
We propose a novel approach to leveraging pre-trained language models (LMs) for early forecasting of academic trajectories in STEM students using high-dimensional longitudinal experiential data. This data, which captures students' study-related activities, behaviors, and psychological states, offers valuable insights for forecasting-based interventions. Key challenges in handling such data include high rates of missing values, limited dataset size due to costly data collection, and complex temporal variability across modalities. Our approach addresses these issues through a comprehensive data enrichment process, integrating strategies for managing missing values, augmenting data, and embedding task-specific instructions and contextual cues to enhance the models' capacity for learning temporal patterns. Through extensive experiments on a curated student learning dataset, we evaluate both encoder-decoder and decoder-only LMs. While our findings show that LMs effectively integrate data across modalities and exhibit resilience to missing data, they primarily rely on high-level statistical patterns rather than demonstrating a deeper understanding of temporal dynamics. Furthermore, their ability to interpret explicit temporal information remains limited. This work advances educational data science by highlighting both the potential and limitations of LMs in modeling student trajectories for early intervention based on longitudinal experiential data.
The explosion of Time Series (TS) data, driven by advancements in technology, necessitates sophisticated analytical methods. Modern management systems increasingly rely on analyzing this data, highlighting the importance of effcient processing techniques. State-of-the-art Machine Learning (ML) approaches for TS analysis and forecasting are becoming prevalent. This paper briefly describes and compiles suitable algorithms for TS regression task. We compare these algorithms against each other and the classic ARIMA method using diverse datasets: complete data, data with outliers, and data with missing values. The focus is on forecasting accuracy, particularly for long-term predictions. This research aids in selecting the most appropriate algorithm based on forecasting needs and data characteristics.
With the prevalence of sensor failures, imputation--the process of estimating missing values--has emerged as the cornerstone of time series data preparation. While numerous imputation algorithms have been developed to address these data gaps, existing libraries provide limited support. Furthermore, they often lack the ability to simulate realistic patterns of time series missing data and fail to account for the impact of imputation on subsequent downstream analysis. This paper introduces ImputeGAP, a comprehensive library for time series imputation that supports a diverse range of imputation methods and modular missing data simulation catering to datasets with varying characteristics. The library includes extensive customization options, such as automated hyperparameter tuning, benchmarking, explainability, downstream evaluation, and compatibility with popular time series frameworks.
Missing data often exists in real-world datasets, requiring significant time and effort for imputation to learn accurate machine learning (ML) models. In this paper, we demonstrate that imputing all missing values is not always necessary to achieve an accurate ML model. We introduce the concept of minimal data imputation, which ensures accurate ML models trained over the imputed dataset. Implementing minimal imputation guarantees both minimal imputation effort and optimal ML models. We propose algorithms to find exact and approximate minimal imputation for various ML models. Our extensive experiments indicate that our proposed algorithms significantly reduce the time and effort required for data imputation.
Electroencephalography-based eye tracking (EEG-ET) leverages eye movement artifacts in EEG signals as an alternative to camera-based tracking. While EEG-ET offers advantages such as robustness in low-light conditions and better integration with brain-computer interfaces, its development lags behind traditional methods, particularly in consumer-grade settings. To support research in this area, we present a dataset comprising simultaneous EEG and eye-tracking recordings from 113 participants across 116 sessions, amounting to 11 hours and 45 minutes of recordings. Data was collected using a consumer-grade EEG headset and webcam-based eye tracking, capturing eye movements under four experimental paradigms with varying complexity. The dataset enables the evaluation of EEG-ET methods across different gaze conditions and serves as a benchmark for assessing feasibility with affordable hardware. Data preprocessing includes handling of missing values and filtering to enhance usability. In addition to the dataset, code for data preprocessing and analysis is available to support reproducibility and further research.
Alzheimer's disease, a neurodegenerative disorder, is associated with neural, genetic, and proteomic factors while affecting multiple cognitive and behavioral faculties. Traditional AD prediction largely focuses on univariate disease outcomes, such as disease stages and severity. Multimodal data encode broader disease information than a single modality and may, therefore, improve disease prediction; but they often contain missing values. Recent "deeper" machine learning approaches show promise in improving prediction accuracy, yet the biological relevance of these models needs to be further charted. Integrating missing data analysis, predictive modeling, multimodal data analysis, and explainable AI, we propose OPTIMUS, a predictive, modular, and explainable machine learning framework, to unveil the many-to-many predictive pathways between multimodal input data and multivariate disease outcomes amidst missing values. OPTIMUS first applies modality-specific imputation to uncover data from each modality while optimizing overall prediction accuracy. It then maps multimodal biomarkers to multivariate outcomes using machine-learning and extracts biomarkers respectively predictive of each outcome. Finally, OPTIMUS incorporates XAI to explain the identified multimodal biomarkers. Using data from 346 cognitively normal subjects, 608 persons with mild cognitive impairment, and 251 AD patients, OPTIMUS identifies neural and transcriptomic signatures that jointly but differentially predict multivariate outcomes related to executive function, language, memory, and visuospatial function. Our work demonstrates the potential of building a predictive and biologically explainable machine-learning framework to uncover multimodal biomarkers that capture disease profiles across varying cognitive landscapes. The results improve our understanding of the complex many-to-many pathways in AD.
Identifying model parameters from observed configurations poses a fundamental challenge in data science, especially with limited data. Recently, diffusion models have emerged as a novel paradigm in generative machine learning, capable of producing new samples that closely mimic observed data. These models learn the gradient of model probabilities, bypassing the need for cumbersome calculations of partition functions across all possible configurations. We explore whether diffusion models can enhance parameter inference by augmenting small datasets. Our findings demonstrate this potential through a synthetic task involving inverse Ising inference and a real-world application of reconstructing missing values in neural activity data. This study serves as a proof-of-concept for using diffusion models for data augmentation in physics-related problems, thereby opening new avenues in data science.
Fairness of machine learning algorithms is receiving increasing attention, as such algorithms permeate the day-to-day aspects of our lives. One way in which bias can manifest in a dataset is through missing values. If data are missing, these data are often assumed to be missing completely randomly; in reality the propensity of data being missing is often tied to the demographic characteristics of individuals. There is limited research into how missing values and the handling thereof can impact the fairness of an algorithm. Most researchers either apply listwise deletion or tend to use the simpler methods of imputation (e.g. mean or mode) compared to the more advanced ones (e.g. multiple imputation); we therefore study the impact of the simpler methods on the fairness of algorithms. The starting point of the study is the mechanism of missingness, leading into how the missing data are processed and finally how this impacts fairness. Three popular datasets in the field of fairness are amputed in a simulation study. The results show that under certain scenarios the impact on fairness can be pronounced when the missingness mechanism is missing at random. Furthermore, elementary missing data handling techniques like listwise deletion and mode imputation can lead to higher fairness compared to more complex imputation methods like k-nearest neighbour imputation, albeit often at the cost of lower accuracy.
Water quality data can supply a substantial decision support for water resources utilization and pollution prevention. However, there are numerous missing values in water quality data due to inescapable factors like sensor failure, thereby leading to biased result for hydrological analysis and failing to support environmental governance decision accurately. A Latent Factorization of Tensors (LFT) with Stochastic Gradient Descent (SGD) proves to be an efficient imputation method. However, a standard SGD-based LFT model commonly surfers from the slow convergence that impairs its efficiency. To tackle this issue, this paper proposes a Fast Latent Factorization of Tensors (FLFT) model. It constructs an adjusted instance error into SGD via leveraging a nonlinear PID controller to incorporates the past, current and future information of prediction error for improving convergence rate. Comparing with state-of-art models in real world datasets, the results of experiment indicate that the FLFT model achieves a better convergence rate and higher accuracy.
Multilinear Principal Component Analysis (MPCA) is an important tool for analyzing tensor data. It performs dimension reduction similar to PCA for multivariate data. However, standard MPCA is sensitive to outliers. It is highly influenced by observations deviating from the bulk of the data, called casewise outliers, as well as by individual outlying cells in the tensors, so-called cellwise outliers. This latter type of outlier is highly likely to occur in tensor data, as tensors typically consist of many cells. This paper introduces a novel robust MPCA method that can handle both types of outliers simultaneously, and can cope with missing values as well. This method uses a single loss function to reduce the influence of both casewise and cellwise outliers. The solution that minimizes this loss function is computed using an iteratively reweighted least squares algorithm with a robust initialization. Graphical diagnostic tools are also proposed to identify the different types of outliers that have been found by the new robust MPCA method. The performance of the method and associated graphical displays is assessed through simulations and illustrated on two real datasets.
Missing values in multivariate time series data can harm machine learning performance and introduce bias. These gaps arise from sensor malfunctions, blackouts, and human error and are typically addressed by data imputation. Previous work has tackled the imputation of missing data in random, complete blackouts and forecasting scenarios. The current paper addresses a more general missing pattern, which we call "partial blackout," where a subset of features is missing for consecutive time steps. We introduce a two-stage imputation process using self-attention and diffusion processes to model feature and temporal correlations. Notably, our model effectively handles missing data during training, enhancing adaptability and ensuring reliable imputation and performance, even with incomplete datasets. Our experiments on benchmark and two real-world time series datasets demonstrate that our model outperforms the state-of-the-art in partial blackout scenarios and shows better scalability.
Hierarchical time series forecasting presents unique challenges, particularly when dealing with noisy data that may not perfectly adhere to aggregation constraints. This paper introduces a novel approach to soft coherency in hierarchical time series forecasting using neural networks. We present a network coherency regularization method, which we denote as CoRe (Coherency Regularization), a technique that trains neural networks to produce forecasts that are inherently coherent across hierarchies, without strictly enforcing aggregation constraints. Our method offers several key advantages. (1) It provides theoretical guarantees on the coherency of forecasts, even for out-of-sample data. (2) It is adaptable to scenarios where data may contain errors or missing values, making it more robust than strict coherency methods. (3) It can be easily integrated into existing neural network architectures for time series forecasting. We demonstrate the effectiveness of our approach on multiple benchmark datasets, comparing it against state-of-the-art methods in both coherent and noisy data scenarios. Additionally, our method can be used within existing generative probabilistic forecasting frameworks to generate coherent probabilistic forecasts. Our results show improved generalization and forecast accuracy, particularly in the presence of data inconsistencies. On a variety of datasets, including both strictly hierarchically coherent and noisy data, our training method has either equal or better accuracy at all levels of the hierarchy while being strictly more coherent out-of-sample than existing soft-coherency methods.