A significant challenge in time-series (TS) modeling is the presence of missing values in real-world TS datasets. Traditional two-stage frameworks, involving imputation followed by modeling, suffer from two key drawbacks: (1) the propagation of imputation errors into subsequent TS modeling, (2) the trade-offs between imputation efficacy and imputation complexity. While one-stage approaches attempt to address these limitations, they often struggle with scalability or fully leveraging partially observed features. To this end, we propose a novel imputation-free approach for handling missing values in time series termed Missing Feature-aware Time Series Modeling (MissTSM) with two main innovations. First, we develop a novel embedding scheme that treats every combination of time-step and feature (or channel) as a distinct token. Second, we introduce a novel Missing Feature-Aware Attention (MFAA) Layer to learn latent representations at every time-step based on partially observed features. We evaluate the effectiveness of MissTSM in handling missing values over multiple benchmark datasets.
Modern data acquisition based on high-throughput technology is often facing the problem of missing data. Algorithms commonly used in the analysis of such large-scale data often depend on a complete set. Missing value imputation offers a solution to this problem. However, the majority of available imputation methods are restricted to one type of variable only: continuous or categorical. For mixed-type data the different types are usually handled separately. Therefore, these methods ignore possible relations between variable types. We propose a nonparametric method which can cope with different types of variables simultaneously. We compare several state of the art methods for the imputation of missing values. We propose and evaluate an iterative imputation method (missForest) based on a random forest. By averaging over many unpruned classification or regression trees random forest intrinsically constitutes a multiple imputation scheme. Using the built-in out-of-bag error estimates of random forest we are able to estimate the imputation error without the need of a test set. Evaluation is performed on multiple data sets coming from a diverse selection of biological fields with artificially introduced missing values ranging from 10% to 30%. We show that missForest can successfully handle missing values, particularly in data sets including different types of variables. In our comparative study missForest outperforms other methods of imputation especially in data settings where complex interactions and nonlinear relations are suspected. The out-of-bag imputation error estimates of missForest prove to be adequate in all settings. Additionally, missForest exhibits attractive computational efficiency and can cope with high-dimensional data.
Forecasting Irregular Multivariate Time Series (IMTS) has recently emerged as a distinct research field, necessitating specialized models to address its unique challenges. While most forecasting literature assumes regularly spaced observations without missing values, many real-world datasets - particularly in healthcare, climate research, and biomechanics - violate these assumptions. Time Series (TS)-mixer models have achieved remarkable success in regular multivariate time series forecasting. However, they remain unexplored for IMTS due to their requirement for complete and evenly spaced observations. To bridge this gap, we introduce IMTS-Mixer, a novel forecasting architecture designed specifically for IMTS. Our approach retains the core principles of TS mixer models while introducing innovative methods to transform IMTS into fixed-size matrix representations, enabling their seamless integration with mixer modules. We evaluate IMTS-Mixer on a benchmark of four real-world datasets from various domains. Our results demonstrate that IMTS-Mixer establishes a new state-of-the-art in forecasting accuracy while also improving computational efficiency.
This study explores a novel approach to enhance the performance of Large Language Models (LLMs) through the optimization of input data within prompts. While previous research has primarily focused on refining instruction components and augmenting input data with in-context examples, our work investigates the potential benefits of optimizing the input data itself. We introduce a two-pronged strategy for input data optimization: content engineering and structural reformulation. Content engineering involves imputing missing values, removing irrelevant attributes, and enriching profiles by generating additional information inferred from existing attributes. Subsequent to content engineering, structural reformulation is applied to optimize the presentation of the modified content to LLMs, given their sensitivity to input format. Our findings suggest that these optimizations can significantly improve the performance of LLMs in various tasks, offering a promising avenue for future research in prompt engineering. The source code is available at https://anonymous.4open.science/r/ADO-6BC5/
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular perspective reveals distinct cell states, population heterogeneity, and the underpinnings of disease pathogenesis that bulk approaches may obscure. However, SCP demands exceptional sensitivity, precise cell handling, and robust data processing to overcome the inherent challenges of analyzing picogram-level protein samples without amplification. Recent innovations in sample preparation, separations, data acquisition strategies, and specialized mass spectrometry instrumentation have substantially improved proteome coverage and throughput. Approaches that integrate complementary omics, streamline multi-step sample processing, and automate workflows through microfluidics and specialized platforms promise to further push SCP boundaries. Advances in computational methods, especially for data normalization and imputation, address the pervasive issue of missing values, enabling more reliable downstream biological interpretations. Despite these strides, higher throughput, reproducibility, and consensus best practices remain pressing needs in the field. This mini review summarizes the latest progress in SCP technology and software solutions, highlighting how closer integration of analytical, computational, and experimental strategies will facilitate deeper and broader coverage of single-cell proteomes.
Recent advancements in neural image codecs (NICs) are of significant compression performance, but limited attention has been paid to their error resilience. These resulting NICs tend to be sensitive to packet losses, which are prevalent in real-time communications. In this paper, we investigate how to elevate the resilience ability of NICs to combat packet losses. We propose ResiComp, a pioneering neural image compression framework with feature-domain packet loss concealment (PLC). Motivated by the inherent consistency between generation and compression, we advocate merging the tasks of entropy modeling and PLC into a unified framework focused on latent space context modeling. To this end, we take inspiration from the impressive generative capabilities of large language models (LLMs), particularly the recent advances of masked visual token modeling (MVTM). During training, we integrate MVTM to mirror the effects of packet loss, enabling a dual-functional Transformer to restore the masked latents by predicting their missing values and conditional probability mass functions. Our ResiComp jointly optimizes compression efficiency and loss resilience. Moreover, ResiComp provides flexible coding modes, allowing for explicitly adjusting the efficiency-resilience trade-off in response to varying Internet or wireless network conditions. Extensive experiments demonstrate that ResiComp can significantly enhance the NIC's resilience against packet losses, while exhibits a worthy trade-off between compression efficiency and packet loss resilience.
State-of-the-art methods for forecasting irregularly sampled time series with missing values predominantly rely on just four datasets and a few small toy examples for evaluation. While ordinary differential equations (ODE) are the prevalent models in science and engineering, a baseline model that forecasts a constant value outperforms ODE-based models from the last five years on three of these existing datasets. This unintuitive finding hampers further research on ODE-based models, a more plausible model family. In this paper, we develop a methodology to generate irregularly sampled multivariate time series (IMTS) datasets from ordinary differential equations and to select challenging instances via rejection sampling. Using this methodology, we create Physiome-ODE, a large and sophisticated benchmark of IMTS datasets consisting of 50 individual datasets, derived from real-world ordinary differential equations from research in biology. Physiome-ODE is the first benchmark for IMTS forecasting that we are aware of and an order of magnitude larger than the current evaluation setting of four datasets. Using our benchmark Physiome-ODE, we show qualitatively completely different results than those derived from the current four datasets: on Physiome-ODE ODE-based models can play to their strength and our benchmark can differentiate in a meaningful way between different IMTS forecasting models. This way, we expect to give a new impulse to research on ODE-based time series modeling.
We present an Adversarially Pre-trained Transformer (APT) that is able to perform zero-shot meta-learning on tabular prediction tasks without pre-training on any real-world dataset, extending on the recent development of Prior-Data Fitted Networks (PFNs) and TabPFN. Specifically, APT is pre-trained with adversarial synthetic data agents, who continue to shift their underlying data generating distribution and deliberately challenge the model with different synthetic datasets. In addition, we propose a mixture block architecture that is able to handle classification tasks with arbitrary number of classes, addressing the class size limitation -- a crucial weakness of prior deep tabular zero-shot learners. In experiments, we show that our framework matches state-of-the-art performance on small classification tasks without filtering on dataset characteristics such as number of classes and number of missing values, while maintaining an average runtime under one second. On common benchmark dataset suites in both classification and regression, we show that adversarial pre-training was able to enhance TabPFN's performance. In our analysis, we demonstrate that the adversarial synthetic data agents were able to generate a more diverse collection of data compared to the ordinary random generator in TabPFN. In addition, we demonstrate that our mixture block neural design has improved generalizability and greatly accelerated pre-training.
Multi-view clustering (MvC) utilizes information from multiple views to uncover the underlying structures of data. Despite significant advancements in MvC, mitigating the impact of missing samples in specific views on the integration of knowledge from different views remains a critical challenge. This paper proposes a novel Mask-informed Deep Contrastive Incomplete Multi-view Clustering (Mask-IMvC) method, which elegantly identifies a view-common representation for clustering. Specifically, we introduce a mask-informed fusion network that aggregates incomplete multi-view information while considering the observation status of samples across various views as a mask, thereby reducing the adverse effects of missing values. Additionally, we design a prior knowledge-assisted contrastive learning loss that boosts the representation capability of the aggregated view-common representation by injecting neighborhood information of samples from different views. Finally, extensive experiments are conducted to demonstrate the superiority of the proposed Mask-IMvC method over state-of-the-art approaches across multiple MvC datasets, both in complete and incomplete scenarios.
The rapid advancement of high-throughput sequencing and other assay technologies has resulted in the generation of large and complex multi-omics datasets, offering unprecedented opportunities for advancing precision medicine strategies. However, multi-omics data integration presents significant challenges due to the high dimensionality, heterogeneity, experimental gaps, and frequency of missing values across data types. Computational methods have been developed to address these issues, employing statistical and machine learning approaches to uncover complex biological patterns and provide deeper insights into our understanding of disease mechanisms. Here, we comprehensively review state-of-the-art multi-omics data integration methods with a focus on deep generative models, particularly variational autoencoders (VAEs) that have been widely used for data imputation and augmentation, joint embedding creation, and batch effect correction. We explore the technical aspects of loss functions and regularisation techniques including adversarial training, disentanglement and contrastive learning. Moreover, we discuss recent advancements in foundation models and the integration of emerging data modalities, while describing the current limitations and outlining future directions for enhancing multi-modal methodologies in biomedical research.
Rainfall prediction remains a persistent challenge due to the highly nonlinear and complex nature of meteorological data. Existing approaches lack systematic utilization of grid search for optimal hyperparameter tuning, relying instead on heuristic or manual selection, frequently resulting in sub-optimal results. Additionally, these methods rarely incorporate newly constructed meteorological features such as differences between temperature and humidity to capture critical weather dynamics. Furthermore, there is a lack of systematic evaluation of ensemble learning techniques and limited exploration of diverse advanced models introduced in the past one or two years. To address these limitations, we propose a robust ensemble learning grid search-tuned framework (RAINER) for rainfall prediction. RAINER incorporates a comprehensive feature engineering pipeline, including outlier removal, imputation of missing values, feature reconstruction, and dimensionality reduction via Principal Component Analysis (PCA). The framework integrates novel meteorological features to capture dynamic weather patterns and systematically evaluates non-learning mathematical-based methods and a variety of machine learning models, from weak classifiers to advanced neural networks such as Kolmogorov-Arnold Networks (KAN). By leveraging grid search for hyperparameter tuning and ensemble voting techniques, RAINER achieves promising results within real-world datasets.
Human activity recognition (HAR) ideally relies on data from wearable or environment-instrumented sensors sampled at regular intervals, enabling standard neural network models optimized for consistent time-series data as input. However, real-world sensor data often exhibits irregular sampling due to, for example, hardware constraints, power-saving measures, or communication delays, posing challenges for deployed static HAR models. This study assesses the impact of sampling irregularities on HAR by simulating irregular data through two methods: introducing slight inconsistencies in sampling intervals (timestamp variations) to mimic sensor jitter, and randomly removing data points (random dropout) to simulate missing values due to packet loss or sensor failure. We evaluate both discrete-time neural networks and continuous-time neural networks, which are designed to handle continuous-time data, on three public datasets. We demonstrate that timestamp variations do not significantly affect the performance of discrete-time neural networks, and the continuous-time neural network is also ineffective in addressing the challenges posed by irregular sampling, possibly due to limitations in modeling complex temporal patterns with missing data. Our findings underscore the necessity for new models or approaches that can robustly handle sampling irregularity in time-series data, like the reading in human activity recognition, paving the way for future research in this domain.
Missing feature values are a significant hurdle for downstream machine-learning tasks such as classification. However, imputation methods for classification might be time-consuming for high-dimensional data, and offer few theoretical guarantees on the preservation of the data distribution and imputation quality, especially for not-missing-at-random mechanisms. First, we propose an imputation approach named F3I based on the iterative improvement of a K-nearest neighbor imputation, where neighbor-specific weights are learned through the optimization of a novel concave, differentiable objective function related to the preservation of the data distribution on non-missing values. F3I can then be chained to and jointly trained with any classifier architecture. Second, we provide a theoretical analysis of imputation quality and data distribution preservation by F3I for several types of missing mechanisms. Finally, we demonstrate the superior performance of F3I on several imputation and classification tasks, with applications to drug repurposing and handwritten-digit recognition data.
The covariance matrix is a foundation in numerous statistical and machine-learning applications such as Principle Component Analysis, Correlation Heatmap, etc. However, missing values within datasets present a formidable obstacle to accurately estimating this matrix. While imputation methods offer one avenue for addressing this challenge, they often entail a trade-off between computational efficiency and estimation accuracy. Consequently, attention has shifted towards direct parameter estimation, given its precision and reduced computational burden. In this paper, we propose Direct Parameter Estimation for Randomly Missing Data with Categorical Features (DPERC), an efficient approach for direct parameter estimation tailored to mixed data that contains missing values within continuous features. Our method is motivated by leveraging information from categorical features, which can significantly enhance covariance matrix estimation for continuous features. Our approach effectively harnesses the information embedded within mixed data structures. Through comprehensive evaluations of diverse datasets, we demonstrate the competitive performance of DPERC compared to various contemporary techniques. In addition, we also show by experiments that DPERC is a valuable tool for visualizing the correlation heatmap.
Missing values of varying patterns and rates in real-world tabular data pose a significant challenge in developing reliable data-driven models. The most commonly used statistical and machine learning methods for missing value imputation may be ineffective when the missing rate is high and not random. This paper explores row and column attention in tabular data as between-feature and between-sample attention in a novel framework to reconstruct missing values. The proposed method uses CutMix data augmentation within a contrastive learning framework to improve the uncertainty of missing value estimation. The performance and generalizability of trained imputation models are evaluated in set-aside test data folds with missing values. The proposed framework is compared with 11 state-of-the-art statistical, machine learning, and deep imputation methods using 12 diverse tabular data sets. The average performance rank of our proposed method demonstrates its superiority over the state-of-the-art methods for missing rates between 10% and 90% and three missing value types, especially when the missing values are not random. The quality of the imputed data using our proposed method is compared in a downstream patient classification task using real-world electronic health records. This paper highlights the heterogeneity of tabular data sets to recommend imputation methods based on missing value types and data characteristics.
Quality-of-service (QoS) data exhibit dynamic temporal patterns that are crucial for accurately predicting missing values. These patterns arise from the evolving interactions between users and services, making it essential to capture the temporal dynamics inherent in such data for improved prediction performance. As the size and complexity of QoS datasets increase, existing models struggle to provide accurate predictions, highlighting the need for more flexible and dynamic methods to better capture the underlying patterns in large-scale QoS data. To address this issue, we introduce a neural network-based tensor factorization approach tailored for learning spatiotemporal representations of high-dimensional and incomplete (HDI) tensors, namely the Multi-head Self-attending Neural Tucker Factorization (MSNTucF). The model is elaborately designed for modeling intricate nonlinear spatiotemporal feature interaction patterns hidden in real world data with a two-fold idea. It first employs a neural network structure to generalize the traditional framework of Tucker factorization and then proposes to leverage a multi-head self-attending module to enforce nonlinear latent interaction learning. In empirical studies on two dynamic QoS datasets from real applications, the proposed MSNTucF model demonstrates superior performance compared to state-of-the-art benchmark models in estimating missing observations. This highlights its ability to learn non-linear spatiotemporal representations of HDI tensors.
Machine learning (ML) has the potential to revolutionize various domains, but its adoption is often hindered by the disconnect between the needs of domain experts and translating these needs into robust and valid ML tools. Despite recent advances in LLM-based co-pilots to democratize ML for non-technical domain experts, these systems remain predominantly focused on model-centric aspects while overlooking critical data-centric challenges. This limitation is problematic in complex real-world settings where raw data often contains complex issues, such as missing values, label noise, and domain-specific nuances requiring tailored handling. To address this we introduce CliMB-DC, a human-guided, data-centric framework for LLM co-pilots that combines advanced data-centric tools with LLM-driven reasoning to enable robust, context-aware data processing. At its core, CliMB-DC introduces a novel, multi-agent reasoning system that combines a strategic coordinator for dynamic planning and adaptation with a specialized worker agent for precise execution. Domain expertise is then systematically incorporated to guide the reasoning process using a human-in-the-loop approach. To guide development, we formalize a taxonomy of key data-centric challenges that co-pilots must address. Thereafter, to address the dimensions of the taxonomy, we integrate state-of-the-art data-centric tools into an extensible, open-source architecture, facilitating the addition of new tools from the research community. Empirically, using real-world healthcare datasets we demonstrate CliMB-DC's ability to transform uncurated datasets into ML-ready formats, significantly outperforming existing co-pilot baselines for handling data-centric challenges. CliMB-DC promises to empower domain experts from diverse domains -- healthcare, finance, social sciences and more -- to actively participate in driving real-world impact using ML.
Recommender systems have become a cornerstone of personalized user experiences, yet their development typically involves significant manual intervention, including dataset-specific feature engineering, hyperparameter tuning, and configuration. To this end, we introduce a novel paradigm: Dataset-Agnostic Recommender Systems (DAReS) that aims to enable a single codebase to autonomously adapt to various datasets without the need for fine-tuning, for a given recommender system task. Central to this approach is the Dataset Description Language (DsDL), a structured format that provides metadata about the dataset's features and labels, and allow the system to understand dataset's characteristics, allowing it to autonomously manage processes like feature selection, missing values imputation, noise removal, and hyperparameter optimization. By reducing the need for domain-specific expertise and manual adjustments, DAReS offers a more efficient and scalable solution for building recommender systems across diverse application domains. It addresses critical challenges in the field, such as reusability, reproducibility, and accessibility for non-expert users or entry-level researchers.
Data imputation is crucial for addressing challenges posed by missing values in multivariate time series data across various fields, such as healthcare, traffic, and economics, and has garnered significant attention. Among various methods, diffusion model-based approaches show notable performance improvements. However, existing methods often cause disharmonious boundaries between missing and known regions and overlook long-range dependencies in missing data estimation, leading to suboptimal results. To address these issues, we propose a Diffusion-based time Series Data Imputation (DSDI) framework. We develop a weight-reducing injection strategy that incorporates the predicted values of missing points with reducing weights into the reverse diffusion process to mitigate boundary inconsistencies. Further, we introduce a multi-scale S4-based U-Net, which combines hierarchical information from different levels via multi-resolution integration to capture long-term dependencies. Experimental results demonstrate that our model outperforms existing imputation methods.
Vertical Federated Learning (VFL) is a well-known FL variant that enables multiple parties to collaboratively train a model without sharing their raw data. Existing VFL approaches focus on overlapping samples among different parties, while their performance is constrained by the limited number of these samples, leaving numerous non-overlapping samples unexplored. Some previous work has explored techniques for imputing missing values in samples, but often without adequate attention to the quality of the imputed samples. To address this issue, we propose a Reliable Imputed-Sample Assisted (RISA) VFL framework to effectively exploit non-overlapping samples by selecting reliable imputed samples for training VFL models. Specifically, after imputing non-overlapping samples, we introduce evidence theory to estimate the uncertainty of imputed samples, and only samples with low uncertainty are selected. In this way, high-quality non-overlapping samples are utilized to improve VFL model. Experiments on two widely used datasets demonstrate the significant performance gains achieved by the RISA, especially with the limited overlapping samples, e.g., a 48% accuracy gain on CIFAR-10 with only 1% overlapping samples.