High-dimensional Data Analysis Research Articles

Maternal Exposure to Trace Elements, Toxic Metals, and Longitudinal Changes in Infancy Anthropometry and Growth Trajectories: A Prospective Cohort Study.

Exploration of stage-specific effects of maternal exposure to trace elements and toxic metals on infancy continuous growth and trajectories is critical for early-life health management. Within a Chinese prospective cohort in 2014-2015, a total of 919 mother-infant pairs were included, and the urinary levels of 17 elements including vanadium (V), chromium (Cr), manganese, iron, cobalt, nickel, copper, zinc, arsenic, molybdenum, palladium, cadmium, tin, gold, mercury, thallium, and lead in early (mean: 11.9 weeks), and late pregnancy (mean: 32.4 weeks) were assessed. Standardized anthropometric assessments of infants were conducted at 1, 3, 6, 8, and 12 months of age. A three-step longitudinal and high-dimensional data analysis procedure was carried out to estimate the impacts of exposome on dynamic growth. Early-pregnancy exposures to V and Cr were positively associated with repeated measurements of length-for-age z-scores (LAZ). Six trajectories were identified based on LAZ. Maternal single exposure to V and Cr as well as mixed exposure to trace elements in early pregnancy were associated with raised odds for the high-stable group. Our results suggested positive associations between maternal trace element exposome and infancy dynamic growth. V and Cr were the key elements and the early pregnancy might be the critical window.

Exploitation of surrogate variables in random forests for unbiased analysis of mutual impact and importance of features.

Random forest is a popular machine learning approach for the analysis of high-dimensional data because it is flexible and provides variable importance measures for the selection of relevant features. However, the complex relationships between the features are usually not considered for the selection and thus also neglected for the characterization of the analysed samples. Here we propose two novel approaches that focus on the mutual impact of features in random forests. Mutual forest impact (MFI) is a relation parameter that evaluates the mutual association of the features to the outcome and, hence, goes beyond the analysis of correlation coefficients. Mutual impurity reduction (MIR) is an importance measure that combines this relation parameter with the importance of the individual features. MIR and MFI are implemented together with testing procedures that generate P-values for the selection of related and important features. Applications to one experimental and various simulated datasets and the comparison to other methods for feature selection and relation analysis show that MFI and MIR are very promising to shed light on the complex relationships between features and outcome. In addition, they are not affected by common biases, e.g. that features with many possible splits or high minor allele frequencies are preferred. The approaches are implemented in Version 0.3.3 of the R package RFSurrogates that is available at github.com/AGSeifert/RFSurrogates and the data are available at doi.org/10.25592/uhhfdm.12620.

Fast optimization methods for high-dimensional row-sparse multivariate quantile linear regression

Sparse quantile regression is a useful tool for variable selection, robust estimation and heteroscedasticity treatment in high-dimensional data analysis. Due to the non-smooth of quantile loss, the computation is heavier than the least square models. In the literature, there are various numerical methods for linear quantile regression, such as ADMM developed in Gu et al. [Technometrics. 2017;60(3):319–331]. However, the computation of multivariate quantile regression has not yet been fully resolved, especially when the dimension is high. Motivated by this, we will focus on the design of fast numerical algorithms for row-sparse multivariate quantile regression model. By virtue of proximal operator and Majorize–Minimization, four smoothed algorithms are designed. For all the obtained algorithms, we analyse their convergence and the parameter selection. We conduct plenty of simulations and four real data sets analysis. Finally, we conclude that the smoothed method is faster than the non-smooth method, especially when the number of predictors is large.

High-Dimensional Feature Selection Based on Improved Binary Ant Colony Optimization Combined with Hybrid Rice Optimization Algorithm

In the realm of high-dimensional data analysis, numerous fields stand to benefit from its applications, including the biological and medical sectors that are crucial for computer-aided disease diagnosis and prediction systems. However, the presence of a significant number of redundant or irrelevant features can adversely affect system accuracy and real-time diagnosis efficiency. To mitigate this issue, this paper proposes two innovative wrapper feature selection (FS) methods that integrate the ant colony optimization (ACO) algorithm and hybrid rice optimization (HRO). HRO is a recently developed metaheuristic that mimics the breeding process of the three-line hybrid rice, which is yet to be thoroughly explored in the context of solving high-dimensional FS problems. In the first hybridization, ACO is embedded as an evolutionary operator within HRO and updated alternately with it. In the second form of hybridization, two subpopulations evolve independently, sharing the local search results to assist individual updating. In the initial stage preceding hybridization, a problem-oriented heuristic factor assignment strategy based on the importance of the knee point feature is introduced to enhance the global search capability of ACO in identifying the smallest and most representative features. The performance of the proposed algorithms is evaluated on fourteen high-dimensional biomedical datasets and compared with other recently advanced FS methods. Experimental results suggest that the proposed methods are efficient and computationally robust, exhibiting superior performance compared to the other algorithms involved in this study.

Analysis of high-dimensional metabolomics data with complex temporal dynamics using RM-ASCA.

The intricate dependency structure of biological "omics" data, particularly those originating from longitudinal intervention studies with frequently sampled repeated measurements renders the analysis of such data challenging. The high-dimensionality, inter-relatedness of multiple outcomes, and heterogeneity in the studied systems all add to the difficulty in deriving meaningful information. In addition, the subtle differences in dynamics often deemed meaningful in nutritional intervention studies can be particularly challenging to quantify. In this work we demonstrate the use of quantitative longitudinal models within the repeated-measures ANOVA simultaneous component analysis+ (RM-ASCA+) framework to capture the dynamics in frequently sampled longitudinal data with multivariate outcomes. We illustrate the use of linear mixed models with polynomial and spline basis expansion of the time variable within RM-ASCA+ in order to quantify non-linear dynamics in a simulation study as well as in a metabolomics data set. We show that the proposed approach presents a convenient and interpretable way to systematically quantify and summarize multivariate outcomes in longitudinal studies while accounting for proper within subject dependency structures.

Unsupervised classification applications in enhancing lithological mapping and geological understanding: a case study from Northern Ireland

Pattern classification algorithms can help us to recognize and predict patterns in large and complex multivariate datasets. Self-organizing maps (SOMs), which use competitive learning, are unsupervised classification tools that are considered to be very useful in pattern classification and recognition. This technique is based on the principles of vector quantification of similarities and clustering in a high-dimensional space and the method can handle the analysis and visualization of high-dimensional data. This tool is ideal for analysing a complex combination of categorical and continuous spatial variables, with particular applications to geological features. We used SOMs to predict geological features based on airborne geophysical data acquired through the Tellus Project in Northern Ireland. The SOMs were applied through 20 experiments (iterations), incorporating radiometric data in combination with geological features, including elevation, slope angle, terrain ruggedness and geochronology. The SOMs were able to differentiate contrasting bedrock geology, such as acidic v. mafic igneous rocks, although data clustering over intermediate rocks was less clear. The presence of a thick cover of glacial deposits in most of the study area presented a challenge for data clustering, particularly over the intermediate igneous and sedimentary bedrock types. Supplementary material: Twenty iterations were carried out during this research. Only six are included in the article. The rest of the iterations are available at https://doi.org/10.6084/m9.figshare.c.6603098

Hedging Covid-19 risk with ESG disclosure

Covid-19 has led to major changes worldwide and has had a significant impact on market risk. We characterize this uncertainty as innovations extracted from the Covid Risk Index on the Wall Street Journal through a textual analysis of high-dimensional data. We hedge the risk with mimicking portfolios constructed using the ESG (environmental, social, and governance) disclosure score as a measure of firm-level exposure to Covid-19 risk. The hedge portfolios perform well both in and out of sample. We also test the role of ESG in hedging and discover that during the Covid-19 pandemic firms with greater ESG disclosure generate higher returns as well as experience lower downside risk. The further analysis suggests that the portfolio returns can be explained by Covid risk shock and investment inflow, and the hedge effect mainly comes from the social part of ESG.

Prediction approaches for partly missing multi‐omics covariate data: A literature review and an empirical comparison study

AbstractAs the availability of omics data has increased in the last few years, more multi‐omics data have been generated, that is, high‐dimensional molecular data consisting of several types such as genomic, transcriptomic, or proteomic data, all obtained from the same patients. Such data lend themselves to being used as covariates in automatic outcome prediction because each omics type may contribute unique information, possibly improving predictions compared to using only one omics data type. Frequently, however, in the training data and the data to which automatic prediction rules should be applied, the test data, the different omics data types are not available for all patients. We refer to this type of data as block‐wise missing multi‐omics data. First, we provide a literature review on existing prediction methods applicable to such data. Subsequently, using a collection of 13 publicly available multi‐omics data sets, we compare the predictive performances of several of these approaches for different block‐wise missingness patterns. Finally, we discuss the results of this empirical comparison study and draw some tentative conclusions.This article is categorized under: Applications of Computational Statistics > Genomics/Proteomics/Genetics Applications of Computational Statistics > Health and Medical Data/Informatics Statistical and Graphical Methods of Data Analysis > Analysis of High Dimensional Data

Statistical analysis of high-dimensional biomedical data: a gentle introduction to analytical goals, common approaches and challenges

BackgroundIn high-dimensional data (HDD) settings, the number of variables associated with each observation is very large. Prominent examples of HDD in biomedical research include omics data with a large number of variables such as many measurements across the genome, proteome, or metabolome, as well as electronic health records data that have large numbers of variables recorded for each patient. The statistical analysis of such data requires knowledge and experience, sometimes of complex methods adapted to the respective research questions.MethodsAdvances in statistical methodology and machine learning methods offer new opportunities for innovative analyses of HDD, but at the same time require a deeper understanding of some fundamental statistical concepts. Topic group TG9 “High-dimensional data” of the STRATOS (STRengthening Analytical Thinking for Observational Studies) initiative provides guidance for the analysis of observational studies, addressing particular statistical challenges and opportunities for the analysis of studies involving HDD. In this overview, we discuss key aspects of HDD analysis to provide a gentle introduction for non-statisticians and for classically trained statisticians with little experience specific to HDD.ResultsThe paper is organized with respect to subtopics that are most relevant for the analysis of HDD, in particular initial data analysis, exploratory data analysis, multiple testing, and prediction. For each subtopic, main analytical goals in HDD settings are outlined. For each of these goals, basic explanations for some commonly used analysis methods are provided. Situations are identified where traditional statistical methods cannot, or should not, be used in the HDD setting, or where adequate analytic tools are still lacking. Many key references are provided.ConclusionsThis review aims to provide a solid statistical foundation for researchers, including statisticians and non-statisticians, who are new to research with HDD or simply want to better evaluate and understand the results of HDD analyses.

Post-pubertal developmental trajectories of laryngeal shape and size in humans

Laryngeal morphotypes have been hypothesized related to both phonation and to laryngeal pathologies. Morphotypes have not been validated or demonstrated quantitatively and sources of shape and size variation are incompletely understood but are critical for the explanation of behavioral changes (e.g., changes of physical properties of a voice) and for therapeutic approaches to the larynx. This is the first study to take this crucial step and results are likely to have implications for surgeons and speech language pathologists. A stratified human sample was interrogated for phenotypic variation of the vocal organ. First, computed tomography image stacks were used to generate three-dimensional reconstructions of the thyroid cartilage. Then cartilage shapes were quantified using multivariate statistical analysis of high dimensional shape data from margins and surfaces of the thyroid cartilage. The effects of sex, age, body mass index (BMI) and body height on size and shape differences were analyzed. We found that sex, age, BMI and the age–sex interaction showed significant effects on the mixed sex sample. Among males, only age showed a strong effect. The thyroid cartilage increased in overall size, and the angulation between left and right lamina decreased in older males. Age, BMI and the age–height interaction were statistically significant factors within females. The angulation between left and right lamina increased in older females and was smaller in females with greater BMI. A cluster analysis confirmed the strong age effect on larynx shape in males and a complex interaction between the age, BMI and height variables in the female sample. The investigation demonstrated that age and BMI, two risk factors in a range of clinical conditions, are associated with shape and size variation of the human larynx. The effects influence shape differently in female and male larynges. The male–female shape dichotomy is partly size-dependent but predominantly size-independent.

Application of Aligned-UMAP to longitudinal biomedical studies

High-dimensional data analysis starts with projecting the data to low dimensions to visualize and understand the underlying data structure. Several methods have been developed for dimensionality reduction, but they are limited to cross-sectional datasets. The recently proposed Aligned-UMAP, an extension of the uniform manifold approximation and projection (UMAP) algorithm, can visualize high-dimensional longitudinal datasets. We demonstrated its utility for researchers to identify exciting patterns and trajectories within enormous datasets in biological sciences. We found that the algorithm parameters also play a crucial role and must be tuned carefully to utilize the algorithm's potential fully. We also discussed key points to remember and directions for future extensions of Aligned-UMAP. Further, we made our code open source to enhance the reproducibility and applicability of our work. We believe our benchmarking study becomes more important as more and more high-dimensional longitudinal data in biomedical research become available.

CosTaL: an accurate and scalable graph-based clustering algorithm for high-dimensional single-cell data analysis.

With the aim of analyzing large-sized multidimensional single-cell datasets, we are describing a method for Cosine-based Tanimoto similarity-refined graph for community detection using Leiden's algorithm (CosTaL). As a graph-based clustering method, CosTaL transforms the cells with high-dimensional features into a weighted k-nearest-neighbor (kNN) graph. The cells are represented by the vertices of the graph, while an edge between two vertices in the graph represents the close relatedness between the two cells. Specifically, CosTaL builds an exact kNN graph using cosine similarity and uses the Tanimoto coefficient as the refining strategy to re-weight the edges in order to improve the effectiveness of clustering. We demonstrate that CosTaL generally achieves equivalent or higher effectiveness scores on seven benchmark cytometry datasets and six single-cell RNA-sequencing datasets using six different evaluation metrics, compared with other state-of-the-art graph-based clustering methods, including PhenoGraph, Scanpy and PARC. As indicated by the combined evaluation metrics, Costal has high efficiency with small datasets and acceptable scalability for large datasets, which is beneficial for large-scale analysis.

Map-in-Parallel-Coordinates Plot (MPCP): Field Trial Studies of High-Dimensional Geographical Data Analysis

As the world has become increasingly digitalized in recent years, high-dimensional data with geographical location coordinate attributes, mainly referring to latitude and longitude, have been accumulated and spread to many disciplines. It is challenging to analyze such data. The map-in-parallel-coordinates plot (MPCP) is an incorporate visual analysis method that can express, filter, and highlight high-dimensional geographical data to facilitate data exploration and comprehension. In this paper, the MPCP underwent a series of field trial studies to verify its applicability, adaptability, and high efficacy in the real-world. The results of the evaluation were positive, which provides reasonable proof and new insights into the benefits of using MPCP to visually analyze high-dimensional geographical datasets.

PyInfinityFlow: optimized imputation and analysis of high-dimensional flow cytometry data for millions of cells.

While conventional flow cytometry is limited to dozens of markers, new experimental and computational strategies, such as Infinity Flow, allow for the generation and imputation of hundreds of cell surface protein markers in millions of cells. Here, we describe an end-to-end analysis workflow for Infinity Flow data in Python. pyInfinityFlow enables the efficient analysis of millions of cells, without down-sampling, through direct integration with well-established Python packages for single-cell genomics analysis. pyInfinityFlow accurately identifies both common and extremely rare cell populations which are challenging to define from single-cell genomics studies alone. We demonstrate that this workflow can nominate novel markers to design new flow cytometry gating strategies for predicted cell populations. pyInfinityFlow can be extended to diverse cell discovery analyses with flexibility to adapt to diverse Infinity Flow experimental designs. pyInfinityFlow is freely available in GitHub (https://github.com/KyleFerchen/pyInfinityFlow) and on PyPI (https://pypi.org/project/pyInfinityFlow/). Package documentation with tutorials on a test dataset is available by Read the Docs (pyinfinityflow.readthedocs.io). The scripts and data for reproducing the results are available at https://github.com/KyleFerchen/pyInfinityFlow/tree/main/analysis_scripts, along with the raw flow cytometry input data.

A unified strategy to rebalance multifactorial designs with unequal group sizes: application to analysis of variance multiblock orthogonal partial least squares

BackgroundAdequately handling unbalanced groups remains one of the major challenges for the analysis of multivariate data collected from multifactorial experimental designs. While partial least squares-based methods, such as analysis of variance multiblock orthogonal partial least squares (AMOPLS), can offer better discrimination between factor levels, they can be more heavily affected by this issue, and unbalanced designs of experiments may lead to a substantial confusion of the effects. Even state-of-the-art analysis of variance (ANOVA) decomposition methodologies using general linear models (GLM) lack the ability to efficiently disentangle these sources of variation when combined with AMOPLS. ResultsA versatile solution developed as an extension of a prior rebalancing strategy is proposed for the first decomposition step based on ANOVA. This approach has the advantage of yielding an unbiased estimation of the parameters and retaining the within-group variation in the rebalanced design, while preserving the orthogonality of effect matrices, even in presence of unequal group sizes. This property is of utmost importance for model interpretation because it avoids mixing sources of variation related to the different effects in the design. A real case study involving metabolomic data from in vitro toxicological experiments was used to demonstrate the potential of this strategy to handle unequal group sizes using a supervised approach. Primary 3D rat neural cell cultures were exposed to trimethyltin following a multifactorial design of experiments involving three fixed effect factors. Significance and NoveltyThe rebalancing strategy was demonstrated as a novel and potent solution to handle unbalanced experimental designs by offering unbiased parameter estimators and orthogonal submatrices, thus avoiding confusion of the effects and facilitating model interpretation. Moreover, it can be combined with any multivariate method used for the analysis of high-dimensional data collected from multifactorial designs.

Penguins Go Parallel: A Grammar of Graphics Framework for Generalized Parallel Coordinate Plots

Parallel Coordinate Plots (PCP) are a valuable tool for exploratory data analysis of high-dimensional numerical data. The use of PCPs is limited when working with categorical variables or a mix of categorical and continuous variables. In this article, we propose Generalized Parallel Coordinate Plots (GPCP) to extend the ability of PCPs from just numeric variables to dealing seamlessly with a mix of categorical and numeric variables in a single plot. In this process we find that existing solutions for categorical values only, such as hammock plots or parsets become edge cases in the new framework. By focusing on individual observations rather than a marginal frequency we gain additional flexibility. The resulting approach is implemented in the R package ggpcp. Supplementary materials for this article are available online.

Functional Proteomic Profiling Analysis in Four Major Types of Gastrointestinal Cancers.

Gastrointestinal (GI) cancer accounts for one in four cancer cases and one in three cancer-related deaths globally. A deeper understanding of cancer development mechanisms can be applied to cancer medicine. Comprehensive sequencing applications have revealed the genomic landscapes of the common types of human cancer, and proteomics technology has identified protein targets and signalling pathways related to cancer growth and progression. This study aimed to explore the functional proteomic profiles of four major types of GI tract cancer based on The Cancer Proteome Atlas (TCPA). We provided an overview of functional proteomic heterogeneity by performing several approaches, including principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), t-stochastic neighbour embedding (t-SNE) analysis, and hierarchical clustering analysis in oesophageal carcinoma (ESCA), stomach adenocarcinoma (STAD), colon adenocarcinoma (COAD), and rectum adenocarcinoma (READ) tumours, to gain a system-wide understanding of the four types of GI cancer. The feature selection approach, mutual information feature selection (MIFS) method, was conducted to screen candidate protein signature subsets to better distinguish different cancer types. The potential clinical implications of candidate proteins in terms of tumour progression and prognosis were also evaluated based on TCPA and The Cancer Genome Atlas (TCGA) databases. The results suggested that functional proteomic profiling can identify different patterns among the four types of GI cancers and provide candidate proteins for clinical diagnosis and prognosis evaluation. We also highlighted the application of feature selection approaches in high-dimensional biological data analysis. Overall, this study could improve the understanding of the complexity of cancer phenotypes and genotypes and thus be applied to cancer medicine.

3D-MSNet: a point cloud-based deep learning model for untargeted feature detection and quantification in profile LC-HRMS data.

Liquid chromatography coupled with high-resolution mass spectrometry is widely used in composition profiling in untargeted metabolomics research. While retaining complete sample information, mass spectrometry (MS) data naturally have the characteristics of high dimensionality, high complexity, and huge data volume. In mainstream quantification methods, none of the existing methods can perform direct 3D analysis on lossless profile MS signals. All software simplify calculations by dimensionality reduction or lossy grid transformation, ignoring the full 3D signal distribution of MS data and resulting in inaccurate feature detection and quantification. On the basis that the neural network is effective for high-dimensional data analysis and can discover implicit features from large amounts of complex data, in this work, we propose 3D-MSNet, a novel deep learning-based model for untargeted feature extraction. 3D-MSNet performs direct feature detection on 3D MS point clouds as an instance segmentation task. After training on a self-annotated 3D feature dataset, we compared our model with nine popular software (MS-DIAL, MZmine 2, XCMS Online, MarkerView, Compound Discoverer, MaxQuant, Dinosaur, DeepIso, PointIso) on two metabolomics and one proteomics public benchmark datasets. Our 3D-MSNet model outperformed other software with significant improvement in feature detection and quantification accuracy on all evaluation datasets. Furthermore, 3D-MSNet has high feature extraction robustness and can be widely applied to profile MS data acquired with various high-resolution mass spectrometers with various resolutions. 3D-MSNet is an open-source model and is freely available at https://github.com/CSi-Studio/3D-MSNet under a permissive license. Benchmark datasets, training dataset, evaluation methods, and results are available at https://doi.org/10.5281/zenodo.6582912.

HSCFC: High-dimensional streaming data clustering algorithm based on feedback control system

At present, few studies have considered the clustering analysis of high-dimensional data collected by many sensors in a real-time streaming environment. Existing clustering analysis algorithms for high-dimensional data are primarily based on batch processing models, and most of them cannot meet the requirements of incremental high-dimensional data streams, which are extremely common in practical applications. To address the aforementioned problems, this paper focuses on the study of high-dimensional data clustering based on stream processing, and proposes a high-dimensional data stream clustering algorithm based on a feedback control system, which comprises three stages: window principal component analysis, feedback stream clustering, and feedback controller. The classic exponentially weighted attenuation function is used in the window principal component analysis to avoid concept drift in the data stream, and incremental feature extraction executes through the sliding window to improve the iterative efficiency of the data in the window. To minimize the errors caused by variability in projection angles during dimensionality reduction, a feedback stream clustering stage is designed with alternating iterations of window clustering and cluster aggregation. Aiming at the problems caused by manually adjusting the hyperparameters used in high-dimensional data stream clustering, a feedback controller is developed to adjust the hyperparameters in the two other stages by analyzing the clustering results in real time and using a discriminant score to adopt corresponding feedback strategies. The experimental comparisons between the proposed and the traditional algorithms on multiple datasets demonstrate the effectiveness of the former.

Springer: An R package for bi-level variable selection of high-dimensional longitudinal data.

In high-dimensional data analysis, the bi-level (or the sparse group) variable selection can simultaneously conduct penalization on the group level and within groups, which has been developed for continuous, binary, and survival responses in the literature. Zhou et al. (2022) (PMID: 35766061) has further extended it under the longitudinal response by proposing a quadratic inference function-based penalization method in gene-environment interaction studies. This study introduces "springer," an R package implementing the bi-level variable selection within the QIF framework developed in Zhou et al. (2022). In addition, R package "springer" has also implemented the generalized estimating equation-based sparse group penalization method. Alternative methods focusing only on the group level or individual level have also been provided by the package. In this study, we have systematically introduced the longitudinal penalization methods implemented in the "springer" package. We demonstrate the usage of the core and supporting functions, which is followed by the numerical examples and discussions. R package "springer" is available at https://cran.r-project.org/package=springer.