Visualization Of High-dimensional Data Research Articles

A self-organised partition of the high dimensional plasma parameter space for plasma disruption prediction

Abstract This paper introduces a disruption predictor constructed through a fully unsupervised two-dimensional mapping of the high-dimensional JET operational space. The primary strength of this disruption predictor lies in its inherent self-organization capability. Diverging from both supervised disruption predictors and earlier approaches suggested by the same authors, which were based on unsupervised models such as Self-Organizing or Generative Topographic Maps, this predictor eliminates the need for labeling data of disruption terminated pulses during training. In prior methods, labels were indeed required post-mapping to inform the model about the presence or absence of disruption precursors at each time instant during the disrupted discharges. In contrast, our approach in this study involves no labeling of data from disruption-terminated experiments. The Self-Organizing Map, operating without any a priori information, adeptly identifies the regions characterizing the pre-disruptive phase. Moreover, SOM discovers non-trivial relationships and captures the complicated interplay of device diagnostics on the internal plasma states from the experimental data. The provided model is highly interpretable; it allows the visualization of high-dimensional data and facilitates easy interrogation of the model to understand the reasons behind its correlations. Hence, utilizing SOMs across various devices can prove invaluable in extracting rules and identifying common patterns, thereby facilitating extrapolation to ITER of the knowledge acquired from existing tokamaks.

Efficient Visual-Aware Fashion Recommendation Using Compressed Node Features and Graph-Based Learning

In fashion e-commerce, predicting item compatibility using visual features remains a significant challenge. Current recommendation systems often struggle to incorporate high-dimensional visual data into graph-based learning models effectively. This limitation presents a substantial opportunity to enhance the precision and effectiveness of fashion recommendations. In this paper, we present the Visual-aware Graph Convolutional Network (VAGCN). This novel framework helps improve how visual features can be incorporated into graph-based learning systems for fashion item compatibility predictions. The VAGCN framework employs a deep-stacked autoencoder to convert the input image’s high-dimensional raw CNN visual features into more manageable low-dimensional representations. In addition to improving feature representation, the GCN can also reason more intelligently about predictions, which would not be possible without this compression. The GCN encoder processes nodes in the graph to capture structural and feature correlation. Following the GCN encoder, the refined embeddings are input to a multi-layer perceptron (MLP) to calculate compatibility scores. The approach extends to using neighborhood information only during the testing phase to help with training efficiency and generalizability in practical scenarios, a key characteristic of our model. By leveraging its ability to capture latent visual features and neighborhood-based learning, VAGCN thoroughly investigates item compatibility across various categories. This method significantly improves predictive accuracy, consistently outperforming existing benchmarks. These contributions tackle significant scalability and computational efficiency challenges, showcasing the potential transformation of recommendation systems through enhanced feature representation, paving the way for further innovations in the fashion domain.

AI-based derivation of atrial fibrillation phenotypes in the general and critical care populations

Atrial fibrillation (AF) is the most common heart arrhythmia worldwide and is linked to a higher risk of mortality and morbidity. To predict AF and AF-related complications, clinical risk scores are commonly employed, but their predictive accuracy is generally limited, given the inherent complexity and heterogeneity of patients with AF. By classifying different presentations of AF into coherent and manageable clinical phenotypes, the development of tailored prevention and treatment strategies can be facilitated. In this study, we propose an artificial intelligence (AI)-based methodology to derive meaningful clinical phenotypes of AF in the general and critical care populations. Our approach employs generative topographic mapping, a probabilistic machine learning method, to identify micro-clusters of patients with similar characteristics. It then identifies macro-cluster regions (clinical phenotypes) in the latent space using Ward's minimum variance method. We applied it to two large cohort databases (UK-Biobank and MIMIC-IV) representing general and critical care populations. The proposed methodology showed its ability to derive meaningful clinical phenotypes of AF. Because of its probabilistic foundations, it can enhance the robustness of patient stratification. It also produced interpretable visualisation of complex high-dimensional data, enhancing understanding of the derived phenotypes and their key characteristics. Using our methodology, we identified and characterised clinical phenotypes of AF across diverse patient populations. Our methodology is robust to noise, can uncover hidden patterns and subgroups, and can elucidate more specific patient profiles, contributing to more robust patient stratification, which could facilitate the tailoring of prevention and treatment programs specific to each phenotype. It can also be applied to other datasets to derive clinically meaningful phenotypes of other conditions. This study was funded by the DECIPHER project (LJMU QR-PSF) and the EU project TARGET (10113624).

Contrastive subspace distribution learning for novel category discovery in high-dimensional visual data

Discovering novel visual categories, particularly in recognition tasks, is a prominent area of research in artificial intelligence. Visual data, such as images and videos, is inherently high-dimensional and they often exhibit low-dimensional subspace structures, making the task of uncovering novel low-dimensional subspace structures a substantial challenge. To address this challenge, we develop a novel subspace discovery method, consisting of four steps. First, we introduce a base-expressive network (BENet) designed to learn coefficients that express the relationships between samples and bases. Additionally, these coefficients are normalized as a probability distribution using the softmax function. Second, to enhance this process, we propose a Contrastive Subspace Distribution Learning (CSDL) technique, utilizing Rényi Divergence. CSDL combines self-supervised and supervised contrastive distances between the normalized coefficients, considering all samples and labeled samples, respectively. Third, the base-expressive coefficients are subsequently computed by the learned SENet, which effectively transfers subspace information from labeled samples to unlabeled ones. Finally, we employ spectral clustering on the predicted coefficients to automatically assign categories to unlabeled samples. Extensive experimental results demonstrate that our approach surpasses related methods in the realms of category discovery, unsupervised clustering, and semi-supervised (subspace) clustering.

Variations of VEGFR2 Chemical Space: Stimulator and Inhibitory Peptides.

The kinase pathway plays a crucial role in blood vessel function. Particular attention is paid to VEGFR type 2 angiogenesis and vascular morphogenesis as the tyrosine kinase pathway is preferentially activated. In silico studies were performed on several peptides that affect VEGFR2 in both stimulating and inhibitory ways. This investigation aims to examine the molecular properties of VEGFR2, a molecule primarily involved in the processes of vasculogenesis and angiogenesis. These relationships were defined by the interactions between Vascular Endothelial Growth Factor receptor 2 (VEGFR2) and the structural features of the systems. The chemical space of the inhibitory peptides and stimulators was described using topological and energetic properties. Furthermore, chimeric models of stimulating and inhibitory proteins (for VEGFR2) were computed using the protein system structures. The interaction between the chimeric proteins and VEGFR was computed. The chemical space was further characterized using complex manifolds and high-dimensional data visualization. The results show that a slightly similar chemical area is shared by VEGFR2 and stimulating and inhibitory proteins. On the other hand, the stimulator peptides and the inhibitors have distinct chemical spaces.

Application of High-Dimensional Data Visualization and Visual Communication Technology in Virtual Reality Environment

How to efficiently find what you want from massive data has become a hot topic. It is precisely because network information is developing so fast that so many data-oriented software systems and pages are used to manage so much network information. Aiming at problems such as insufficient information mining of visual communication websites in ASPNET and poor visual communication effects, a design scheme for integrating high-dimensional data into visual communication websites is proposed. Its working architecture includes high-dimensional data integration, multi-type visual integration, and visual support services. The main functions of the website include comprehensive management, charts, data sources, projects, systems, etc. We have conducted specific design and Implementation of high-dimensional information integration on the website, completed the design and Implementation of integration of high-dimensional data, integration of multiple visualization types, and integrated access to visualization-supported functions. Use a deep web crawler to search the visual site. It uses a search-based approach to filter URLs and crawl valuable web pages. Practice has proved that the intelligent distribution network management page implemented by the solution proposed in this article has good performance. The system shows good performance in visualization implementation and the ability to discover information. The system achieved sound and visual communication effects.

Manifold learning-based UMAP method for geochemical anomaly identification

Geochemical data are usually high-dimensional data that could contain dozens of elements. Geochemical distribution patterns and anomalies related to mineralization and lithological features are always hidden in these high-dimensional data, which cannot be directly observed from the data. To solve this problem, a manifold learning-based uniform manifold approximation and projection (UMAP) method, was introduced to recognize mineralization-related geochemical anomalies from high-dimensional geochemical data in this study. The UMAP method is a nonlinear dimensionality reduction method, which is suitable for dimensionality reduction and visualization of high-dimensional data. A case study was conducted to demonstrate the advantages of the UMAP method for identifying ion-adsorbed rare-earth-element (REE) mineralization-related anomalies from high-dimensional data in the Nanling region, China. Factor analysis was used to determine ion-adsorbed REE mineralization-related element combination that consists of 10 elements. High-dimensional geochemical data were reduced to two dimensions based on the UMAP method. The results indicated that the UMAP method can effectively characterize the spatial distributions of ion-adsorbed REE mineralization-related anomalies by dimensionality reduction analysis and visualization analysis of high-dimensional geochemical data in the study area. To illustrate the superiority of the UMAP method, a comparative study was conducted between the UMAP and other three manifold learning methods, namely locally linear embedding (LLE), isometric feature mapping (Isomap) and t-distributed stochastic neighbor embedding (t-SNE). The performance of the four manifold learning methods was evaluated by receiver operating characteristic (ROC) curve and prediction-area (P-A) plot, showing that the performance of the UMAP method is superior to that of the LLE, Isomap and t-SNE methods in terms of recognizing ion-adsorbed REE mineralization-related anomalies and the spatial distributions of the REE-bearing geological bodies in the Nanling belt.

Visualization strategies to aid interpretation of high-dimensional genotoxicity data.

This article describes a range of high-dimensional data visualization strategies that we have explored for their ability to complement machine learning algorithm predictions derived from MultiFlow® assay results. For this exercise, we focused on seven biomarker responses resulting from the exposure of TK6 cells to each of 126 diverse chemicals over a range of concentrations. Obviously, challenges associated with visualizing seven biomarker responses were further complicated whenever there was a desire to represent the entire 126 chemical data set as opposed to results from a single chemical. Scatter plots, spider plots, parallel coordinate plots, hierarchical clustering, principal component analysis, toxicological prioritization index, multidimensional scaling, t-distributed stochastic neighbor embedding, and uniform manifold approximation and projection are each considered in turn. Our report provides a comparative analysis of these techniques. In an era where multiplexed assays and machine learning algorithms are becoming the norm, stakeholders should find some of these visualization strategies useful for efficiently and effectively interpreting their high-dimensional data.

Exploring local interpretability in dimensionality reduction: Analysis and use cases

Dimensionality reduction is a crucial area in artificial intelligence that enables the visualization and analysis of high-dimensional data. The main use of dimensionality reduction is to lower the dimensional complexity of data, improving the performance of machine learning models. Non-linear dimensionality reduction approaches, which provide higher quality representations than linear ones, lack interpretability, prohibiting their application in tasks requiring interpretability. This paper presents LXDR (Local eXplanation of Dimensionality Reduction), a local, model-agnostic technique that can be applied to any DR technique. LXDR trains linear models around a neighborhood of a specific instance and provides local interpretations using a variety of neighborhood generation techniques. Variations of the proposed technique are also introduced. The effectiveness of LXDR’s interpretations is evaluated by quantitative and qualitative experiments, as well as demonstrations of its practical implementation in diverse use cases. The experiments emphasize the importance of interpretability in dimensionality reduction and how LXDR reinforces it.

The Application and Exploration of Data Visualization Technology in Artistic Expression and Exhibition

Embarking on the transformation of virtual art museums, the confluence of data visualization technology and deep learning emerges as a catalyst for redefining artistic expression. Driven by the desire to change traditional approaches, this work utilizes a sophisticated deep learning model, the self-attention-based cycle-consistent generative adversarial network (SA-CCGAN), for transformative purposes. The objective of proposed Modernizing Virtual Art: The Collaboration of Data Visualization Technology and Self-Attention-Based Cycle-Consistent Generative Adversarial Network for Artistic Expression (MVA: DVT & SA-CCGAN) is to elevate artistic expression and exhibition practices within the virtual space, marking a paradigm shift in traditional approaches. SA-CCGAN, renowned for its ability to generate realistic and coherent artistic representations, serves as the cornerstone of this transformative endeavor. The workflow intricately incorporates SA-CCGAN into the virtual art museum context, enhancing stylized outcomes and capturing global geometric features. This yields a computationally efficient representation of high-dimensional visual data, revolutionizing digital art presentation. The fusion of data visualization technology, creativity, and meticulous design not only signals innovation but also has the potential to redefine the virtual art landscape, fostering accessibility, engagement, and a deeper cultural exchange in digital art exploration.

A review of common methods used in the analysis of human microbiome sequencing data

The past two decades have seen a rapid rise in the development and use of sequencing technologies. The advent of high-throughput sequencing (HTS) has allowed scientists sequence the genomic content of entire microbial communities rapidly and affordably. Methods for data management, visualization, and analysis of this microbiome sequencing data are now widespread in open and closed source software tools. In this review, we identify common analysis methods used in microbiome sequencing studies, including methods for normalisation of abundance table data, visualization of high-dimensional microbiome data and the analysis of longitudinal microbiome sequencing data. In particular we find that a very small proportion of metagenomic studies made use of compositional data analysis methods and none that made use of compositional methods for longitudinal microbiome data.

Accelerating Hyperbolic t-SNE.

The need to understand the structure of hierarchical or high-dimensional data is present in a variety of fields. Hyperbolic spaces have proven to be an important tool for embedding computations and analysis tasks as their non-linear nature lends itself well to tree or graph data. Subsequently, they have also been used in the visualization of high-dimensional data, where they exhibit increased embedding performance. However, none of the existing dimensionality reduction methods for embedding into hyperbolic spaces scale well with the size of the input data. That is because the embeddings are computed via iterative optimization schemes and the computation cost of every iteration is quadratic in the size of the input. Furthermore, due to the non-linear nature of hyperbolic spaces, euclidean acceleration structures cannot directly be translated to the hyperbolic setting. This article introduces the first acceleration structure for hyperbolic embeddings, building upon a polar quadtree. We compare our approach with existing methods and demonstrate that it computes embeddings of similar quality in significantly less time. Implementation and scripts for the experiments can be found at https://graphics.tudelft.nl/accelerating-hyperbolic-tsne.

ClockRay: A Wrist-Rotation Based Technique for Occluded-Target Selection in Virtual Reality.

Target selection is one of essential operation made available by interaction techniques in virtual reality (VR) environments. However, effectively positioning or selecting occluded objects is under-investigated in VR, especially in the context of high-density or a high-dimensional data visualization with VR. In this paper, we propose ClockRay, an occluded-object selection technique that can maximize the intrinsic human wrist rotation skills through the integration of emerging ray selection techniques in VR environments. We describe the design space of the ClockRay technique and then evaluate its performance in a series of user studies. Drawing on the experimental results, we discuss the benefits of ClockRay compared to two popular ray selection techniques - RayCursor and RayCasting. Our findings can inform the design of VR-based interactive visualization systems for high-density data.

Research on energy spectrum anomaly detection method for state control radiation environmental monitoring based on LOF algorithm

The state-controlled radiation environment automatic monitoring stations are important facilities for monitoring the quality and trends of the radiation environment. However, the analysis and utilization of monitoring data from these stations have limitations. To address this issue, this paper proposes an approach that utilizes the high-dimensional data visualization method based on t-SNE and PCA-BIRCH algorithm's spectrum clustering model to classify historical spectrum data. Subsequently, a local outlier factor-based environmental spectrum abnormal fluctuation detection model is established to enhance discrimination of non-environmental factors causing spectrum anomalies. Results indicate significant differences in spectrum aggregation under different meteorological conditions. The clustering algorithm effectively separates clear and rainy weather spectra based on spectral features, with minimal time consumption and reduced interference from mixed spectrum data. By utilizing local density features, we establish an anomaly detection model, assigning an abnormal score to each spectrum. Comparative analysis demonstrates improved discriminability of the anomaly detection model for unclassified datasets. Our algorithm accurately identifies spectrum fluctuations caused by non-environmental factors amidst complex backgrounds, offering valuable technical support for environmental quality assurance and nuclear emergency decision-making.

Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics.

Optimizing and benchmarking data reduction methods for dynamic or spatial visualization and interpretation (DSVI) face challenges due to many factors, including data complexity, lack of ground truth, time-dependent metrics, dimensionality bias and different visual mappings of the same data. Current studies often focus on independent static visualization or interpretability metrics that require ground truth. To overcome this limitation, we propose the MIBCOVIS framework, a comprehensive and interpretable benchmarking and computational approach. MIBCOVIS enhances the visualization and interpretability of high-dimensional data without relying on ground truth by integrating five robust metrics, including a novel time-ordered Markov-based structural metric, into a semi-supervised hierarchical Bayesian model. The framework assesses method accuracy and considers interaction effects among metric features. We apply MIBCOVIS using linear and nonlinear dimensionality reduction methods to evaluate optimal DSVI for four distinct dynamic and spatial biological processes captured by three single-cell data modalities: CyTOF, scRNA-seq and CODEX. These data vary in complexity based on feature dimensionality, unknown cell types and dynamic or spatial differences. Unlike traditional single-summary score approaches, MIBCOVIS compares accuracy distributions across methods. Our findings underscore the joint evaluation of visualization and interpretability, rather than relying on separate metrics. We reveal that prioritizing average performance can obscure method feature performance. Additionally, we explore the impact of data complexity on visualization and interpretability. Specifically, we provide optimal parameters and features and recommend methods, like the optimized variational contractive autoencoder, for targeted DSVI for various data complexities. MIBCOVIS shows promise for evaluating dynamic single-cell atlases and spatiotemporal data reduction models.

Laplacian-based Cluster-Contractive t-SNE for High-Dimensional Data Visualization

Dimensionality reduction techniques aim at representing high-dimensional data in low-dimensional spaces to extract hidden and useful information or facilitate visual understanding and interpretation of the data. However, few of them take into consideration the potential cluster information contained implicitly in the high-dimensional data. In this article, we propose Lap tSNE, a new graph-layout nonlinear dimensionality reduction method based on t-SNE, one of the best techniques for visualizing high-dimensional data as 2D scatter plots. Specifically, Lap tSNE leverages the eigenvalue information of the graph Laplacian to shrink the potential clusters in the low-dimensional embedding when learning to preserve the local and global structure from high-dimensional space to low-dimensional space. It is nontrivial to solve the proposed model because the eigenvalues of normalized symmetric Laplacian are functions of the decision variable. We provide a majorization-minimization algorithm with convergence guarantee to solve the optimization problem of Lap tSNE and show how to calculate the gradient analytically, which may be of broad interest when considering optimization with Laplacian-composited objective. We evaluate our method by a formal comparison with state-of-the-art methods on seven benchmark datasets, both visually and via established quantitative measurements. The results demonstrate the superiority of our method over baselines such as t-SNE and UMAP. We also provide out-of-sample extension, large-scale extension, and mini-batch extension for our Lap tSNE to facilitate dimensionality reduction in various scenarios.

CRUSTY: a versatile web platform for the rapid analysis and visualization of high-dimensional flow cytometry data

Flow cytometry (FCM) can investigate dozens of parameters from millions of cells and hundreds of specimens in a short time and at a reasonable cost, but the amount of data that is generated is considerable. Computational approaches are useful to identify novel subpopulations and molecular biomarkers, but generally require deep expertize in bioinformatics and the use of different platforms. To overcome these limitations, we introduce CRUSTY, an interactive, user-friendly webtool incorporating the most popular algorithms for FCM data analysis, and capable of visualizing graphical and tabular results and automatically generating publication-quality figures within minutes. CRUSTY also hosts an interactive interface for the exploration of results in real time. Thus, CRUSTY enables a large number of users to mine complex datasets and reduce the time required for data exploration and interpretation. CRUSTY is accessible at https://crusty.humanitas.it/.

Implementation of the Self Organizing Maps (SOM) Method for Grouping Provinces in Indonesia Based on the Earthquake Disaster Impact

Indonesia is a country prone to earthquakes. This is because the territory of Indonesia is located between the confluence of three tectonic plates (the Eurasian plate, the Indo-Australian plate, and the Pacific Ocean plate) and is also in the Ring of Fire. The number of earthquakes in Indonesia varies in each province due to the different characteristics of the location of the plates of each province in Indonesia. Earthquake disasters have a very detrimental impact on society, such as causing casualties, damaged houses or damage to public facilities. Therefore it is important to grouping the impact of earthquakes in Indonesia as a disaster mitigation effort in order to find out the characteristics of each province in each cluster. The grouping method used is Kohonen Self Organizing Maps (SOM). SOM is a high-dimensional data visualization technique in the form of a low-dimensional map. The results 3 clusters with the characteristics of each cluster. Cluster 1 consisting of 24 provinces has the characteristics of the highest number of earthquake incidents, the number of missing victims, the number of victims suffering and the number of damaged houses. Cluster 2 consisting of 7 provinces does not show any prominent characteristics of the cluster. Cluster 3 consists of 3 provinces with very prominent characteristics, namely the number of victims killed, the number of injured victims, the number of displaced victims, the number of damaged educational facilities, the number of damaged health facilities and the number of damaged worship facilities the most of the other clusters.

A Preprocessing Manifold Learning Strategy Based on t-Distributed Stochastic Neighbor Embedding.

In machine learning and data analysis, dimensionality reduction and high-dimensional data visualization can be accomplished by manifold learning using a t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm. We significantly improve this manifold learning scheme by introducing a preprocessing strategy for the t-SNE algorithm. In our preprocessing, we exploit Laplacian eigenmaps to reduce the high-dimensional data first, which can aggregate each data cluster and reduce the Kullback-Leibler divergence (KLD) remarkably. Moreover, the k-nearest-neighbor (KNN) algorithm is also involved in our preprocessing to enhance the visualization performance and reduce the computation and space complexity. We compare the performance of our strategy with that of the standard t-SNE on the MNIST dataset. The experiment results show that our strategy exhibits a stronger ability to separate different clusters as well as keep data of the same kind much closer to each other. Moreover, the KLD can be reduced by about 30% at the cost of increasing the complexity in terms of runtime by only 1-2%.

Low-Rank tensor completion based on nonconvex regularization

In this paper, we consider the low-rank tensor completion which aims to exactly recover incomplete high-dimensional visual data. Existing studies utilize widely tensor nuclear norm minimization (TNNM), a convex relaxation to tensor-rank minimization (TRM), to solve tensor completion tasks. Nevertheless, TNNM ignores the difference between different tensor singular values induced by the tensor singular value decompositions (t-SVD) and then the obtained solution may be suboptimal. In this paper, we propose a nonconvex minimization approach to solve the tensor completion problem more effectively by adopting a nonconvex regularization to further approximate the tensor-rank. Moreover, alternating direction method of multipliers (ADMM) and iteratively reweighted nuclear norm (IRNN) are adopted to solve the constructed nonconvex models efficiently, and the convergence can also be guaranteed. Finally, we present that the proposed nonconvex optimization methods are suitable for solving other TRM problems induced by any invertible linear transform, such as subspace clustering based on low-rank representation. Extensive experiments on real images and videos validate the superiority of our approach over the state-of-the-art algorithms.