This work introduces the LLM Online Spatial-temporal Reconstruction (LLM-OSR) framework, which integrates Graph Signal Processing (GSP) and Large Language Models (LLMs) for online spatial-temporal signal reconstruction. The LLM-OSR utilizes a GSP-based spatial-temporal signal handler to enhance graph signals and employs LLMs to predict missing values based on spatiotemporal patterns. The performance of LLM-OSR is evaluated on traffic and meteorological datasets under varying Gaussian noise levels. Experimental results demonstrate that utilizing GPT-4-o mini within the LLM-OSR is accurate and robust under Gaussian noise conditions. The limitations are discussed along with future research insights, emphasizing the potential of combining GSP techniques with LLMs for solving spatiotemporal prediction tasks.
Freezing of gait (FOG) is a debilitating symptom of Parkinson's disease that impairs mobility and safety by increasing the risk of falls. An effective FOG detection system must be accurate, real-time, and deployable in free-living environments to enable timely interventions. However, existing detection methods face challenges due to (1) intra- and inter-patient variability, (2) subject-specific training, (3) using multiple sensors in FOG dominant locations (e.g., ankles) leading to high failure points, (4) centralized, non-adaptive learning frameworks that sacrifice patient privacy and prevent collaborative model refinement across populations and disease progression, and (5) most systems are tested in controlled settings, limiting their real-world applicability for continuous in-home monitoring. Addressing these gaps, we present FOGSense, a real-world deployable FOG detection system designed for uncontrolled, free-living conditions using only a single sensor. FOGSense uses Gramian Angular Field (GAF) transformations and privacy-preserving federated deep learning to capture temporal and spatial gait patterns missed by traditional methods with a low false positive rate. We evaluated our system using a public Parkinson's dataset collected in a free-living environment. FOGSense improves accuracy by 10.4% over a single-axis accelerometer, reduces failure points compared to multi-sensor systems, and demonstrates robustness to missing values. The federated architecture allows personalized model adaptation and efficient smartphone synchronization during off-peak hours, making it effective for long-term monitoring as symptoms evolve. Overall, FOGSense achieved a 22.2% improvement in F1-score and a 74.53% reduction in false positive rate compared to state-of-the-art methods, along with enhanced sensitivity for FOG episode detection.
Inherently interpretable machine learning (IML) models provide valuable insights for clinical decision-making but face challenges when features have missing values. Classical solutions like imputation or excluding incomplete records are often unsuitable in applications where values are missing at test time. In this work, we conducted a survey with 71 clinicians from 29 trauma centers across France, including 20 complete responses to study the interaction between medical professionals and IML applied to data with missing values. This provided valuable insights into how missing data is interpreted in clinical machine learning. We used the prediction of hemorrhagic shock as a concrete example to gauge the willingness and readiness of the participants to adopt IML models from three classes of methods. Our findings show that, while clinicians value interpretability and are familiar with common IML methods, classical imputation techniques often misalign with their intuition, and that models that natively handle missing values are preferred. These results emphasize the need to integrate clinical intuition into future IML models for better human-computer interaction.
We present TRACE (Transformer-based Risk Assessment for Clinical Evaluation), a novel method for clinical risk assessment based on clinical data, leveraging the self-attention mechanism for enhanced feature interaction and result interpretation. Our approach is able to handle different data modalities, including continuous, categorical and multiple-choice (checkbox) attributes. The proposed architecture features a shared representation of the clinical data obtained by integrating specialized embeddings of each data modality, enabling the detection of high-risk individuals using Transformer encoder layers. To assess the effectiveness of the proposed method, a strong baseline based on non-negative multi-layer perceptrons (MLPs) is introduced. The proposed method outperforms various baselines widely used in the domain of clinical risk assessment, while effectively handling missing values. In terms of explainability, our Transformer-based method offers easily interpretable results via attention weights, further enhancing the clinicians' decision-making process.
Discrete Choice Modelling serves as a robust framework for modelling human choice behaviour across various disciplines. Building a choice model is a semi structured research process that involves a combination of a priori assumptions, behavioural theories, and statistical methods. This complex set of decisions, coupled with diverse workflows, can lead to substantial variability in model outcomes. To better understand these dynamics, we developed the Serious Choice Modelling Game, which simulates the real world modelling process and tracks modellers' decisions in real time using a stated preference dataset. Participants were asked to develop choice models to estimate Willingness to Pay values to inform policymakers about strategies for reducing noise pollution. The game recorded actions across multiple phases, including descriptive analysis, model specification, and outcome interpretation, allowing us to analyse both individual decisions and differences in modelling approaches. While our findings reveal a strong preference for using data visualisation tools in descriptive analysis, it also identifies gaps in missing values handling before model specification. We also found significant variation in the modelling approach, even when modellers were working with the same choice dataset. Despite the availability of more complex models, simpler models such as Multinomial Logit were often preferred, suggesting that modellers tend to avoid complexity when time and resources are limited. Participants who engaged in more comprehensive data exploration and iterative model comparison tended to achieve better model fit and parsimony, which demonstrate that the methodological choices made throughout the workflow have significant implications, particularly when modelling outcomes are used for policy formulation.
We propose a novel approach to effectively detect cloned identities of social-sensor cloud service providers (i.e. social media users) in the face of incomplete non-privacy-sensitive profile data. Named ICD-IPD, the proposed approach first extracts account pairs with similar usernames or screen names from a given set of user accounts collected from a social media. It then learns a multi-view representation associated with a given account and extracts two categories of features for every single account. These two categories of features include profile and Weighted Generalised Canonical Correlation Analysis (WGCCA)-based features that may potentially contain missing values. To counter the impact of such missing values, a missing value imputer will next impute the missing values of the aforementioned profile and WGCCA-based features. After that, the proposed approach further extracts two categories of augmented features for each account pair identified previously, namely, 1) similarity and 2) differences-based features. Finally, these features are concatenated and fed into a Light Gradient Boosting Machine classifier to detect identity cloning. We evaluated and compared the proposed approach against the existing state-of-the-art identity cloning approaches and other machine or deep learning models atop a real-world dataset. The experimental results show that the proposed approach outperforms the state-of-the-art approaches and models in terms of Precision, Recall and F1-score.
Pedestrian trajectory prediction is crucial for several applications such as robotics and self-driving vehicles. Significant progress has been made in the past decade thanks to the availability of pedestrian trajectory datasets, which enable trajectory prediction methods to learn from pedestrians' past movements and predict future trajectories. However, these datasets and methods typically assume that the observed trajectory sequence is complete, ignoring real-world issues such as sensor failure, occlusion, and limited fields of view that can result in missing values in observed trajectories. To address this challenge, we present TrajImpute, a pedestrian trajectory prediction dataset that simulates missing coordinates in the observed trajectory, enhancing real-world applicability. TrajImpute maintains a uniform distribution of missing data within the observed trajectories. In this work, we comprehensively examine several imputation methods to reconstruct the missing coordinates and benchmark them for imputing pedestrian trajectories. Furthermore, we provide a thorough analysis of recent trajectory prediction methods and evaluate the performance of these models on the imputed trajectories. Our experimental evaluation of the imputation and trajectory prediction methods offers several valuable insights. Our dataset provides a foundational resource for future research on imputation-aware pedestrian trajectory prediction, potentially accelerating the deployment of these methods in real-world applications. Publicly accessible links to the datasets and code files are available at https://github.com/Pranav-chib/TrajImpute.
Data increasingly take the form of a multi-way array, or tensor, in several biomedical domains. Such tensors are often incompletely observed. For example, we are motivated by longitudinal microbiome studies in which several timepoints are missing for several subjects. There is a growing literature on missing data imputation for tensors. However, existing methods give a point estimate for missing values without capturing uncertainty. We propose a multiple imputation approach for tensors in a flexible Bayesian framework, that yields realistic simulated values for missing entries and can propagate uncertainty through subsequent analyses. Our model uses efficient and widely applicable conjugate priors for a CANDECOMP/PARAFAC (CP) factorization, with a separable residual covariance structure. This approach is shown to perform well with respect to both imputation accuracy and uncertainty calibration, for scenarios in which either single entries or entire fibers of the tensor are missing. For two microbiome applications, it is shown to accurately capture uncertainty in the full microbiome profile at missing timepoints and used to infer trends in species diversity for the population. Documented R code to perform our multiple imputation approach is available at https://github.com/lockEF/MultiwayImputation .
Aggregated relative search frequencies offer a unique composite signal reflecting people's habits, concerns, interests, intents, and general information needs, which are not found in other readily available datasets. Temporal search trends have been successfully used in time series modeling across a variety of domains such as infectious diseases, unemployment rates, and retail sales. However, most existing applications require curating specialized datasets of individual keywords, queries, or query clusters, and the search data need to be temporally aligned with the outcome variable of interest. We propose a novel approach for generating an aggregated and anonymized representation of search interest as foundation features at the community level for geospatial modeling. We benchmark these features using spatial datasets across multiple domains. In zip codes with a population greater than 3000 that cover over 95% of the contiguous US population, our models for predicting missing values in a 20% set of holdout counties achieve an average $R^2$ score of 0.74 across 21 health variables, and 0.80 across 6 demographic and environmental variables. Our results demonstrate that these search features can be used for spatial predictions without strict temporal alignment, and that the resulting models outperform spatial interpolation and state of the art methods using satellite imagery features.
Traditional decision trees are limited by axis-orthogonal splits, which can perform poorly when true decision boundaries are oblique. While oblique decision tree methods address this limitation, they often face high computational costs, difficulties with multi-class classification, and a lack of effective feature selection. In this paper, we introduce LDATree and FoLDTree, two novel frameworks that integrate Uncorrelated Linear Discriminant Analysis (ULDA) and Forward ULDA into a decision tree structure. These methods enable efficient oblique splits, handle missing values, support feature selection, and provide both class labels and probabilities as model outputs. Through evaluations on simulated and real-world datasets, LDATree and FoLDTree consistently outperform axis-orthogonal and other oblique decision tree methods, achieving accuracy levels comparable to the random forest. The results highlight the potential of these frameworks as robust alternatives to traditional single-tree methods.
Developing a foundation model for time series forecasting across diverse domains has attracted significant attention in recent years. Existing works typically assume regularly sampled, well-structured data, limiting their applicability to more generalized scenarios where time series often contain missing values, unequal sequence lengths, and irregular time intervals between measurements. To cover diverse domains and handle variable regularities, we propose FlexTSF, a universal time series forecasting model that possesses better generalization and natively support both regular and irregular time series. FlexTSF produces forecasts in an autoregressive manner and incorporates three novel designs: VT-Norm, a normalization strategy to ablate data domain barriers, IVP Patcher, a patching module to learn representations from flexibly structured time series, and LED attention, an attention mechanism to seamlessly integrate these two and propagate forecasts with awareness of domain and time information. Experiments on 12 datasets show that FlexTSF outperforms state-of-the-art forecasting models respectively designed for regular and irregular time series. Furthermore, after self-supervised pre-training, FlexTSF shows exceptional performance in both zero-shot and few-show settings for time series forecasting.
Causal discovery in real-world systems, such as biological networks, is often complicated by feedback loops and incomplete data. Standard algorithms, which assume acyclic structures or fully observed data, struggle with these challenges. To address this gap, we propose MissNODAG, a differentiable framework for learning both the underlying cyclic causal graph and the missingness mechanism from partially observed data, including data missing not at random. Our framework integrates an additive noise model with an expectation-maximization procedure, alternating between imputing missing values and optimizing the observed data likelihood, to uncover both the cyclic structures and the missingness mechanism. We demonstrate the effectiveness of MissNODAG through synthetic experiments and an application to real-world gene perturbation data.
In this paper, we propose a novel framework that leverages large language models (LLMs) for predicting missing values in time-varying graph signals by exploiting spatial and temporal smoothness. We leverage the power of LLM to achieve a message-passing scheme. For each missing node, its neighbors and previous estimates are fed into and processed by LLM to infer the missing observations. Tested on the task of the online prediction of wind-speed graph signals, our model outperforms online graph filtering algorithms in terms of accuracy, demonstrating the potential of LLMs in effectively addressing partially observed signals in graphs.
We provide a framework for efficiently estimating impulse response functions with Local Projections (LPs). Our approach offers a Bayesian treatment for LPs with Instrumental Variables, accommodating multiple shocks and instruments per shock, accounts for autocorrelation in multi-step forecasts by jointly modeling all LPs as a seemingly unrelated system of equations, defines a flexible yet parsimonious joint prior for impulse responses based on a Gaussian Process, allows for joint inference about the entire vector of impulse responses, and uses all available data across horizons by imputing missing values.
The reliance on data-driven decision-making across sectors highlights the critical need for high-quality data; despite advancements, data quality issues persist, significantly impacting business strategies and scientific research. Current data quality methods fail to leverage the semantic richness embedded in words inside attribute labels (or column names/headers in tables) across diverse datasets and domains, leaving a crucial gap in comprehensive data quality evaluation. This research addresses this gap by introducing an innovative methodology centered around Attribute-Based Semantic Type Detection and Data Quality Assessment. By leveraging semantic information within attribute labels, combined with rule-based analysis and comprehensive Formats and Abbreviations dictionaries, our approach introduces a practical semantic type classification system comprising approximately 23 types, including numerical non-negative, categorical, ID, names, strings, geographical, temporal, and complex formats like URLs, IP addresses, email, and binary values plus several numerical bounded types, such as age and percentage. A comparative analysis with Sherlock, a state-of-the-art Semantic Type Detection system, shows the advantages of our approach in terms of classification robustness and applicability to data quality assessment tasks. Our research focuses on well-known data quality issues and their corresponding data quality dimension violations, grounding our methodology in a robust academic framework. Detailed analysis of fifty distinct datasets from the UCI Machine Learning Repository showcases our method's proficiency in identifying potential data quality issues. Compared to established tools like YData Profiling, our method exhibits superior accuracy, detecting 81 missing values across 922 attributes where YData identified only one.
Data imputation addresses the challenge of imputing missing values in database instances, ensuring consistency with the overall semantics of the dataset. Although several heuristics which rely on statistical methods, and ad-hoc rules have been proposed. These do not generalise well and often lack data context. Consequently, they also lack explainability. The existing techniques also mostly focus on the relational data context making them unsuitable for wider application contexts such as in graph data. In this paper, we propose a graph data imputation approach called GIG which relies on graph differential dependencies (GDDs). GIG, learns the GDDs from a given knowledge graph, and uses these rules to train a transformer model which then predicts the value of missing data within the graph. By leveraging GDDs, GIG incoporates semantic knowledge into the data imputation process making it more reliable and explainable. Experimental results on seven real-world datasets highlight GIG's effectiveness compared to existing state-of-the-art approaches.
Deep generative models have significantly advanced medical imaging analysis by enhancing dataset size and quality. Beyond mere data augmentation, our research in this paper highlights an additional, significant capacity of deep generative models: their ability to reveal and demonstrate patterns in medical images. We employ a generative structure with hybrid conditions, combining clinical data and segmentation masks to guide the image synthesis process. Furthermore, we innovatively transformed the tabular clinical data into textual descriptions. This approach simplifies the handling of missing values and also enables us to leverage large pre-trained vision-language models that investigate the relations between independent clinical entries and comprehend general terms, such as gender and smoking status. Our approach differs from and presents a more challenging task than traditional medical report-guided synthesis due to the less visual correlation of our clinical information with the images. To overcome this, we introduce a text-visual embedding mechanism that strengthens the conditions, ensuring the network effectively utilizes the provided information. Our pipeline is generalizable to both GAN-based and diffusion models. Experiments on chest CT, particularly focusing on the smoking status, demonstrated a consistent intensity shift in the lungs which is in agreement with clinical observations, indicating the effectiveness of our method in capturing and visualizing the impact of specific attributes on medical image patterns. Our methods offer a new avenue for the early detection and precise visualization of complex clinical conditions with deep generative models. All codes are https://github.com/junzhin/DGM-VLC.
Accurate long-term predictions are the foundations for many machine learning applications and decision-making processes. Traditional time series approaches for prediction often focus on either autoregressive modeling, which relies solely on past observations of the target ``endogenous variables'', or forward modeling, which considers only current covariate drivers ``exogenous variables''. However, effectively integrating past endogenous and past exogenous with current exogenous variables remains a significant challenge. In this paper, we propose ExoTST, a novel transformer-based framework that effectively incorporates current exogenous variables alongside past context for improved time series prediction. To integrate exogenous information efficiently, ExoTST leverages the strengths of attention mechanisms and introduces a novel cross-temporal modality fusion module. This module enables the model to jointly learn from both past and current exogenous series, treating them as distinct modalities. By considering these series separately, ExoTST provides robustness and flexibility in handling data uncertainties that arise from the inherent distribution shift between historical and current exogenous variables. Extensive experiments on real-world carbon flux datasets and time series benchmarks demonstrate ExoTST's superior performance compared to state-of-the-art baselines, with improvements of up to 10\% in prediction accuracy. Moreover, ExoTST exhibits strong robustness against missing values and noise in exogenous drivers, maintaining consistent performance in real-world situations where these imperfections are common.
A key task in AutoML is to model learning curves of machine learning models jointly as a function of model hyper-parameters and training progression. While Gaussian processes (GPs) are suitable for this task, na\"ive GPs require $\mathcal{O}(n^3m^3)$ time and $\mathcal{O}(n^2 m^2)$ space for $n$ hyper-parameter configurations and $\mathcal{O}(m)$ learning curve observations per hyper-parameter. Efficient inference via Kronecker structure is typically incompatible with early-stopping due to missing learning curve values. We impose $\textit{latent Kronecker structure}$ to leverage efficient product kernels while handling missing values. In particular, we interpret the joint covariance matrix of observed values as the projection of a latent Kronecker product. Combined with iterative linear solvers and structured matrix-vector multiplication, our method only requires $\mathcal{O}(n^3 + m^3)$ time and $\mathcal{O}(n^2 + m^2)$ space. We show that our GP model can match the performance of a Transformer on a learning curve prediction task.
Many real-world applications of tabular data involve using historic events to predict properties of new ones, for example whether a credit card transaction is fraudulent or what rating a customer will assign a product on a retail platform. Existing approaches to event prediction include costly, brittle, and application-dependent techniques such as time-aware positional embeddings, learned row and field encodings, and oversampling methods for addressing class imbalance. Moreover, these approaches often assume specific use-cases, for example that we know the labels of all historic events or that we only predict a pre-specified label and not the data's features themselves. In this work, we propose a simple but flexible baseline using standard autoregressive LLM-style transformers with elementary positional embeddings and a causal language modeling objective. Our baseline outperforms existing approaches across popular datasets and can be employed for various use-cases. We demonstrate that the same model can predict labels, impute missing values, or model event sequences.