Visual Interaction with Dimensionality Reduction: A Structured Literature Analysis

TopoMap++: A Faster and More Space Efficient Technique to Compute Projections with Topological Guarantees

High-dimensional data, characterized by many features, can be difficult to visualize effectively. Dimensionality reduction techniques, such as PCA, UMAP, and t-SNE, address this challenge by projecting the data into a lower-dimensional space while preserving important relationships. TopoMap is another technique that excels at preserving the underlying structure of the data, leading to interpretable visualizations. In particular, TopoMap maps the high-dimensional data into a visual space, guaranteeing that the 0-dimensional persistence diagram of the Rips filtration of the visual space matches the one from the high-dimensional data. However, the original TopoMap algorithm can be slow and its layout can be too sparse for large and complex datasets. In this paper, we propose three improvements to TopoMap: 1) a more space-efficient layout, 2) a significantly faster implementation, and 3) a novel TreeMap-based representation that makes use of the topological hierarchy to aid the exploration of the projections. These advancements make TopoMap, now referred to as TopoMap++, a more powerful tool for visualizing high-dimensional data which we demonstrate through different use case scenarios.

FS/DS: A Theoretical Framework for the Dual Analysis of Feature Space and Data Space

With the surge of data-driven analysis techniques, there is a rising demand for enhancing the exploration of large high-dimensional data by enabling interactions for the joint analysis of features (i.e., dimensions). Such a dual analysis of the feature space and data space is characterized by three components, 1) a view visualizing feature summaries, 2) a view that visualizes the data records, and 3) a bidirectional linking of both plots triggered by human interaction in one of both visualizations, e.g., Linking & Brushing. Dual analysis approaches span many domains, e.g., medicine, crime analysis, and biology. The proposed solutions encapsulate various techniques, such as feature selection or statistical analysis. However, each approach establishes a new definition of dual analysis. To address this gap, we systematically reviewed published dual analysis methods to investigate and formalize the key elements, such as the techniques used to visualize the feature space and data space, as well as the interaction between both spaces. From the information elicited during our review, we propose a unified theoretical framework for dual analysis, encompassing all existing approaches extending the field. We apply our proposed formalization describing the interactions between each component and relate them to the addressed tasks. Additionally, we categorize the existing approaches using our framework and derive future research directions to advance dual analysis by including state-of-the-art visual analysis techniques to improve data exploration.

Who are the publics engaging in AI?

Given the importance of public engagement in governments' adoption of artificial intelligence systems, artificial intelligence researchers and practitioners spend little time reflecting on who those publics are. Classifying publics affects assumptions and affordances attributed to the publics' ability to contribute to policy or knowledge production. Further complicating definitions are the publics' role in artificial intelligence production and optimization. Our structured analysis of the corpus used a mixed method, where algorithmic generation of search terms allowed us to examine approximately 2500 articles and provided the foundation to conduct an extensive systematic literature review of approximately 100 documents. Results show the multiplicity of ways publics are framed, by examining and revealing the different semantic nuances, affordances, political and expertise lenses, and, finally, a lack of definitions. We conclude that categorizing publics represents an act of power, politics, and truth-seeking in artificial intelligence.

Vis-SPLIT: Interactive Hierarchical Modeling for mRNA Expression Classification

We propose an interactive visual analytics tool, Vis-SPLIT, for partitioning a population of individuals into groups with similar gene signatures. Vis-SPLIT allows users to interactively explore a dataset and exploit visual separations to build a classification model for specific cancers. The visualization components reveal gene expression and correlation to assist specific partitioning decisions, while also providing overviews for the decision model and clustered genetic signatures. We demonstrate the effectiveness of our framework through a case study and evaluate its usability with domain experts. Our results show that Vis-SPLIT can classify patients based on their genetic signatures to effectively gain insights into RNA sequencing data, as compared to an existing classification system.

Determining a Trustworthy Application for Medical Data Visualizations through a Knowledge-Based Fuzzy Expert System

Medical data, such as electronic health records, are a repository for a patient's medical records for use in the diagnosis of different diseases. Using medical data for individual patient care raises a number of concerns, including trustworthiness in data management, privacy, and patient data security. The introduction of visual analytics, a computing system that integrates analytics approaches with interactive visualizations, can potentially deal with information overload concerns in medical data. The practice of assessing the trustworthiness of visual analytics tools or applications using factors that affect medical data analysis is known as trustworthiness evaluation for medical data. It has a variety of major issues, such as a lack of important evaluation of medical data, the need to process much of medical data for diagnosis, the need to make trustworthy relationships clear, and the expectation that it will be automated. Decision-making strategies have been utilized in this evaluation process to avoid these concerns and intelligently and automatically analyze the trustworthiness of the visual analytics tool. The literature study found no hybrid decision support system for visual analytics tool trustworthiness in medical data diagnosis. Thus, this research develops a hybrid decision support system to assess and improve the trustworthiness of medical data for visual analytics tools using fuzzy decision systems. This study examined the trustworthiness of decision systems using visual analytics tools for medical data for the diagnosis of diseases. The hybrid multi-criteria decision-making-based decision support model, based on the analytic hierarchy process and sorting preferences by similarity to ideal solutions in a fuzzy environment, was employed in this study. The results were compared to highly correlated accuracy tests. In conclusion, we highlight the benefits of our proposed study, which includes performing a comparison analysis on the recommended models and some existing models in order to demonstrate the applicability of an optimal decision in real-world environments. In addition, we present a graphical interpretation of the proposed endeavor in order to demonstrate the coherence and effectiveness of our methodology. This research will also help medical experts select, evaluate, and rank the best visual analytics tools for medical data.

UnProjection: Leveraging Inverse-Projections for Visual Analytics of High-Dimensional Data

Projection techniques are often used to visualize high-dimensional data, allowing users to better understand the overall structure of multi-dimensional spaces on a 2D screen. Although many such methods exist, comparably little work has been done on generalizable methods of inverse-projection - the process of mapping the projected points, or more generally, the projection space back to the original high-dimensional space. In this article we present NNInv, a deep learning technique with the ability to approximate the inverse of any projection or mapping. NNInv learns to reconstruct high-dimensional data from any arbitrary point on a 2D projection space, giving users the ability to interact with the learned high-dimensional representation in a visual analytics system. We provide an analysis of the parameter space of NNInv, and offer guidance in selecting these parameters. We extend validation of the effectiveness of NNInv through a series of quantitative and qualitative analyses. We then demonstrate the method's utility by applying it to three visualization tasks: interactive instance interpolation, classifier agreement, and gradient visualization.

Visualization and Visual Analytics Approaches for Image and Video Datasets: A Survey

Image and video data analysis has become an increasingly important research area with applications in different domains such as security surveillance, healthcare, augmented and virtual reality, video and image editing, activity analysis and recognition, synthetic content generation, distance education, telepresence, remote sensing, sports analytics, art, non-photorealistic rendering, search engines, and social media. Recent advances in Artificial Intelligence (AI) and particularly deep learning have sparked new research challenges and led to significant advancements, especially in image and video analysis. These advancements have also resulted in significant research and development in other areas such as visualization and visual analytics, and have created new opportunities for future lines of research. In this survey paper, we present the current state of the art at the intersection of visualization and visual analytics, and image and video data analysis. We categorize the visualization papers included in our survey based on different taxonomies used in visualization and visual analytics research. We review these papers in terms of task requirements, tools, datasets, and application areas. We also discuss insights based on our survey results, trends and patterns, the current focus of visualization research, and opportunities for future research.

Incorporation of Human Knowledge into Data Embeddings to Improve Pattern Significance and Interpretability

Embedding is a common technique for analyzing multi-dimensional data. However, the embedding projection cannot always form significant and interpretable visual structures that foreshadow underlying data patterns. We propose an approach that incorporates human knowledge into data embeddings to improve pattern significance and interpretability. The core idea is (1) externalizing tacit human knowledge as explicit sample labels and (2) adding a classification loss in the embedding network to encode samples' classes. The approach pulls samples of the same class with similar data features closer in the projection, leading to more compact (significant) and class-consistent (interpretable) visual structures. We give an embedding network with a customized classification loss to implement the idea and integrate the network into a visualization system to form a workflow that supports flexible class creation and pattern exploration. Patterns found on open datasets in case studies, subjects' performance in a user study, and quantitative experiment results illustrate the general usability and effectiveness of the approach.

A Survey on ML4VIS: Applying Machine Learning Advances to Data Visualization

Inspired by the great success of machine learning (ML), researchers have applied ML techniques to visualizations to achieve a better design, development, and evaluation of visualizations. This branch of studies, known as ML4VIS, is gaining increasing research attention in recent years. To successfully adapt ML techniques for visualizations, a structured understanding of the integration of ML4VIS is needed. In this article, we systematically survey 88 ML4VIS studies, aiming to answer two motivating questions: "what visualization processes can be assisted by ML?" and "how ML techniques can be used to solve visualization problems? "This survey reveals seven main processes where the employment of ML techniques can benefit visualizations: Data Processing4VIS, Data-VIS Mapping, Insight Communication, Style Imitation, VIS Interaction, VIS Reading, and User Profiling. The seven processes are related to existing visualization theoretical models in an ML4VIS pipeline, aiming to illuminate the role of ML-assisted visualization in general visualizations. Meanwhile, the seven processes are mapped into main learning tasks in ML to align the capabilities of ML with the needs in visualization. Current practices and future opportunities of ML4VIS are discussed in the context of the ML4VIS pipeline and the ML-VIS mapping. While more studies are still needed in the area of ML4VIS, we hope this article can provide a stepping-stone for future exploration. A web-based interactive browser of this survey is available at https://ml4vis.github.io.

Visual analysis of blow molding machine multivariate time series data

Abstract

The recent development in the data analytics field provides a boost in production for modern industries. Small-sized factories intend to take full advantage of the data collected by sensors used in their machinery. The ultimate goal is to minimize cost and maximize quality, resulting in an increase in profit. In collaboration with domain experts, we implemented a data visualization tool to enable decision-makers in a plastic factory to improve their production process. The tool is an interactive dashboard with multiple coordinated views supporting the exploration from both local and global perspectives. In summary, we investigate three different aspects: methods for preprocessing multivariate time series data, clustering approaches for the already refined data, and visualization techniques that aid domain experts in gaining insights into the different stages of the production process. Here we present our ongoing results grounded in a human-centered development process. We adopt a formative evaluation approach to continuously upgrade our dashboard design that eventually meets partners' requirements and follows the best practices within the field. We also conducted a case study with a domain expert to validate the potential application of the tool in the real-life context. Finally, we assessed the usability and usefulness of the tool with a two-layer summative evaluation that showed encouraging results.

Graphical Abstract

Getting over High-Dimensionality: How Multidimensional Projection Methods Can Assist Data Science

The exploration and analysis of multidimensional data can be pretty complex tasks, requiring sophisticated tools able to transform large amounts of data bearing multiple parameters into helpful information. Multidimensional projection techniques figure as powerful tools for transforming multidimensional data into visual information according to similarity features. Integrating this class of methods into a framework devoted to data sciences can contribute to generating more expressive means of visual analytics. Although the Principal Component Analysis (PCA) is a well-known method in this context, it is not the only one, and, sometimes, its abilities and limitations are not adequately discussed or taken into consideration by users. Therefore, knowing in-depth multidimensional projection techniques, their strengths, and the possible distortions they can create is of significant importance for researchers developing knowledge-discovery systems. This research presents a comprehensive overview of current state-of-the-art multidimensional projection techniques and shows example codes in Python and R languages, all available on the internet. The survey segment discusses the different types of techniques applied to multidimensional projection tasks from their background, application processes, capabilities, and limitations, opening the internal processes of the methods and demystifying their concepts. We also illustrate two problems, from a genetic experiment (supervised) and text mining (non-supervised), presenting solutions through multidimensional projection application. Finally, we brought elements that reverberate the competitiveness of multidimensional projection techniques towards high-dimension data visualization, commonly needed in data sciences solutions.

An overview of literature on COVID-19, MERS and SARS: Using text mining and latent Dirichlet allocation

The unprecedented outbreak of COVID-19 is one of the most serious global threats to public health in this century. During this crisis, specialists in information science could play key roles to support the efforts of scientists in the health and medical community for combatting COVID-19. In this article, we demonstrate that information specialists can support health and medical community by applying text mining technique with latent Dirichlet allocation procedure to perform an overview of a mass of coronavirus literature. This overview presents the generic research themes of the coronavirus diseases: COVID-19, MERS and SARS, reveals the representative literature per main research theme and displays a network visualisation to explore the overlapping, similarity and difference among these themes. The overview can help the health and medical communities to extract useful information and interrelationships from coronavirus-related studies.

Complex model calibration through emulation, a worked example for a stochastic epidemic model

Uncertainty quantification is a formal paradigm of statistical estimation that aims to account for all uncertainties inherent in the modelling process of real-world complex systems. The methods are directly applicable to stochastic models in epidemiology, however they have thus far not been widely used in this context. In this paper, we provide a tutorial on uncertainty quantification of stochastic epidemic models, aiming to facilitate the use of the uncertainty quantification paradigm for practitioners with other complex stochastic simulators of applied systems. We provide a formal workflow including the important decisions and considerations that need to be taken, and illustrate the methods over a simple stochastic epidemic model of UK SARS-CoV-2 transmission and patient outcome. We also present new approaches to visualisation of outputs from sensitivity analyses and uncertainty quantification more generally in high input and/or output dimensions.

Leveraging deep contrastive learning for semantic interaction

The semantic interaction process seeks to elicit a user's mental model as they interact with and query visualizations during a sense-making activity. Semantic interaction enables the development of computational models that capture user intent and anticipate user actions. Deep learning is proving to be highly effective for learning complex functions and is, therefore, a compelling tool for encoding a user's mental model. In this paper, we show that deep contrastive learning significantly enhances semantic interaction in visual analytics systems. Our approach does so by allowing users to explore alternative arrangements of their data while simultaneously training a parametric algorithm to learn their evolving mental model. As an example of the efficacy of our approach, we deployed our model in Z-Explorer, a visual analytics extension to the widely used Zotero document management system. The user study demonstrates that this flexible approach effectively captures users' mental data models without explicit hyperparameter tuning or even requiring prior machine learning expertise.

Pathogeny Detection for Mild Cognitive Impairment via Weighted Evolutionary Random Forest with Brain Imaging and Genetic Data

Medical imaging technology and gene sequencing technology have long been widely used to analyze the pathogenesis and make precise diagnoses of mild cognitive impairment (MCI). However, few studies involve the fusion of radiomics data with genomics data to make full use of the complementarity between different omics to detect pathogenic factors of MCI. This paper performs multimodal fusion analysis based on functional magnetic resonance imaging (fMRI) data and single nucleotide polymorphism (SNP) data of MCI patients. In specific, first, using correlation analysis methods on sequence information of regions of interests (ROIs) and digitalized gene sequences, the fusion features of samples are constructed. Then, introducing weighted evolution strategy into ensemble learning, a novel weighted evolutionary random forest (WERF) model is built to eliminate the inefficient features. Consequently, with the help of WERF, an overall multimodal data analysis framework is established to effectively identify MCI patients and extract pathogenic factors. Based on the data of MCI patients from the ADNI database and compared with some existing popular methods, the superiority in performance of the framework is verified. Our study has great potential to be an effective tool for pathogenic factors detection of MCI.

Attribute-based Explanation of Non-Linear Embeddings of High-Dimensional Data

Embeddings of high-dimensional data are widely used to explore data, to verify analysis results, and to communicate information. Their explanation, in particular with respect to the input attributes, is often difficult. With linear projects like PCA the axes can still be annotated meaningfully. With non-linear projections this is no longer possible and alternative strategies such as attribute-based color coding are required. In this paper, we review existing augmentation techniques and discuss their limitations. We present the Non-Linear Embeddings Surveyor (NoLiES) that combines a novel augmentation strategy for projected data (rangesets) with interactive analysis in a small multiples setting. Rangesets use a set-based visualization approach for binned attribute values that enable the user to quickly observe structure and detect outliers. We detail the link between algebraic topology and rangesets and demonstrate the utility of NoLiES in case studies with various challenges (complex attribute value distribution, many attributes, many data points) and a real-world application to understand latent features of matrix completion in thermodynamics.

Measuring and Explaining the Inter-Cluster Reliability of Multidimensional Projections

We propose Steadiness and Cohesiveness, two novel metrics to measure the inter-cluster reliability of multidimensional projection (MDP), specifically how well the inter-cluster structures are preserved between the original high-dimensional space and the low-dimensional projection space. Measuring inter-cluster reliability is crucial as it directly affects how well inter-cluster tasks (e.g., identifying cluster relationships in the original space from a projected view) can be conducted; however, despite the importance of inter-cluster tasks, we found that previous metrics, such as Trustworthiness and Continuity, fail to measure inter-cluster reliability. Our metrics consider two aspects of the inter-cluster reliability: Steadiness measures the extent to which clusters in the projected space form clusters in the original space, and Cohesiveness measures the opposite. They extract random clusters with arbitrary shapes and positions in one space and evaluate how much the clusters are stretched or dispersed in the other space. Furthermore, our metrics can quantify pointwise distortions, allowing for the visualization of inter-cluster reliability in a projection, which we call a reliability map. Through quantitative experiments, we verify that our metrics precisely capture the distortions that harm inter-cluster reliability while previous metrics have difficulty capturing the distortions. A case study also demonstrates that our metrics and the reliability map 1) support users in selecting the proper projection techniques or hyperparameters and 2) prevent misinterpretation while performing inter-cluster tasks, thus allow an adequate identification of inter-cluster structure.

IRVINE: A Design Study on Analyzing Correlation Patterns of Electrical Engines

In this design study, we present IRVINE, a Visual Analytics (VA) system, which facilitates the analysis of acoustic data to detect and understand previously unknown errors in the manufacturing of electrical engines. In serial manufacturing processes, signatures from acoustic data provide valuable information on how the relationship between multiple produced engines serves to detect and understand previously unknown errors. To analyze such signatures, IRVINE leverages interactive clustering and data labeling techniques, allowing users to analyze clusters of engines with similar signatures, drill down to groups of engines, and select an engine of interest. Furthermore, IRVINE allows to assign labels to engines and clusters and annotate the cause of an error in the acoustic raw measurement of an engine. Since labels and annotations represent valuable knowledge, they are conserved in a knowledge database to be available for other stakeholders. We contribute a design study, where we developed IRVINE in four main iterations with engineers from a company in the automotive sector. To validate IRVINE, we conducted a field study with six domain experts. Our results suggest a high usability and usefulness of IRVINE as part of the improvement of a real-world manufacturing process. Specifically, with IRVINE domain experts were able to label and annotate produced electrical engines more than 30% faster.

Interactive Dimensionality Reduction for Comparative Analysis

Finding the similarities and differences between groups of datasets is a fundamental analysis task. For high-dimensional data, dimensionality reduction (DR) methods are often used to find the characteristics of each group. However, existing DR methods provide limited capability and flexibility for such comparative analysis as each method is designed only for a narrow analysis target, such as identifying factors that most differentiate groups. This paper presents an interactive DR framework where we integrate our new DR method, called ULCA (unified linear comparative analysis), with an interactive visual interface. ULCA unifies two DR schemes, discriminant analysis and contrastive learning, to support various comparative analysis tasks. To provide flexibility for comparative analysis, we develop an optimization algorithm that enables analysts to interactively refine ULCA results. Additionally, the interactive visualization interface facilitates interpretation and refinement of the ULCA results. We evaluate ULCA and the optimization algorithm to show their efficiency as well as present multiple case studies using real-world datasets to demonstrate the usefulness of this framework.

Developing and testing an automated qualitative assistant (AQUA) to support qualitative analysis

Qualitative research remains underused, in part due to the time and cost of annotating qualitative data (coding). Artificial intelligence (AI) has been suggested as a means to reduce those burdens, and has been used in exploratory studies to reduce the burden of coding. However, methods to date use AI analytical techniques that lack transparency, potentially limiting acceptance of results. We developed an automated qualitative assistant (AQUA) using a semiclassical approach, replacing Latent Semantic Indexing/Latent Dirichlet Allocation with a more transparent graph-theoretic topic extraction and clustering method. Applied to a large dataset of free-text survey responses, AQUA generated unsupervised topic categories and circle hierarchical representations of free-text responses, enabling rapid interpretation of data. When tasked with coding a subset of free-text data into user-defined qualitative categories, AQUA demonstrated intercoder reliability in several multicategory combinations with a Cohen’s kappa comparable to human coders (0.62–0.72), enabling researchers to automate coding on those categories for the entire dataset. The aim of this manuscript is to describe pertinent components of best practices of AI/machine learning (ML)-assisted qualitative methods, illustrating how primary care researchers may use AQUA to rapidly and accurately code large text datasets. The contribution of this article is providing guidance that should increase AI/ML transparency and reproducibility.

Dimensionality reduction in the context of dynamic social media data streams

In recent years social media became an important part of everyday life for many people. A big challenge of social media is, to find posts, that are interesting for the user. Many social networks like Twitter handle this problem with so-called hashtags. A user can label his own Tweet (post) with a hashtag, while other users can search for posts containing a specified hashtag. But what about finding posts which are not labeled by the creator? We provide a way of completing hashtags for unlabeled posts using classification on a novel real-world Twitter data stream. New posts will be created every second, thus this context fits perfectly for non-stationary data analysis. Our goal is to show, how labels (hashtags) of social media posts can be predicted by stream classifiers. In particular, we employ random projection (RP) as a preprocessing step in calculating streaming models. Also, we provide a novel real-world data set for streaming analysis called NSDQ with a comprehensive data description. We show that this dataset is a real challenge for state-of-the-art stream classifiers. While RP has been widely used and evaluated in stationary data analysis scenarios, non-stationary environments are not well analyzed. In this paper, we provide a use case of RP on real-world streaming data, especially on NSDQ dataset. We discuss why RP can be used in this scenario and how it can handle stream-specific situations like concept drift. We also provide experiments with RP on streaming data, using state-of-the-art stream classifiers like adaptive random forest and concept drift detectors. Additionally, we experimentally evaluate an online principal component analysis (PCA) approach in the same fashion as we do for RP. To obtain higher dimensional synthetic streams, we use random Fourier features (RFF) in an online manner which allows us, to increase the number of dimensions of low dimensional streams.

Treemap-Based Cluster Visualization and its Application to Text Data Analysis

This paper proposes Treemap-based visualization for supporting cluster analysis of multi-dimensional data. It is important to grasp data distribution in a target dataset for such tasks as machine learning and cluster analysis. When dealing with multi-dimensional data such as statistical data and document datasets, dimensionality reduction algorithms are usually applied to project original data to lower-dimensional space. However, dimensionality reduction tends to lose the characteristics of data in the original space. In particular, the border between different data groups could not be represented correctly in lower-dimensional space. To overcome this problem, the proposed visualization method applies Fuzzy c-Means to target data and visualizes the result on the basis of the highest and the second-highest membership values with Treemap. Visualizing the information about not only the closest clusters but also the second closest ones is expected to be useful for identifying objects around the border between different clusters, as well as for understanding the relationship between different clusters. A prototype interface is implemented, of which the effectiveness is investigated with a user experiment on a news articles dataset. As another kind of text data, a case study of applying it to a word embedding space is also shown.

DimLift: Interactive Hierarchical Data Exploration Through Dimensional Bundling

The identification of interesting patterns and relationships is essential to exploratory data analysis. This becomes increasingly difficult in high dimensional datasets. While dimensionality reduction techniques can be utilized to reduce the analysis space, these may unintentionally bury key dimensions within a larger grouping and obfuscate meaningful patterns. With this work we introduce DimLift, a novel visual analysis method for creating and interacting with dimensional bundles. Generated through an iterative dimensionality reduction or user-driven approach, dimensional bundles are expressive groups of dimensions that contribute similarly to the variance of a dataset. Interactive exploration and reconstruction methods via a layered parallel coordinates plot allow users to lift interesting and subtle relationships to the surface, even in complex scenarios of missing and mixed data types. We exemplify the power of this technique in an expert case study on clinical cohort data alongside two additional case examples from nutrition and ecology.

Implicit Multidimensional Projection of Local Subspaces

We propose a visualization method to understand the effect of multidimensional projection on local subspaces, using implicit function differentiation. Here, we understand the local subspace as the multidimensional local neighborhood of data points. Existing methods focus on the projection of multidimensional data points, and the neighborhood information is ignored. Our method is able to analyze the shape and directional information of the local subspace to gain more insights into the global structure of the data through the perception of local structures. Local subspaces are fitted by multidimensional ellipses that are spanned by basis vectors. An accurate and efficient vector transformation method is proposed based on analytical differentiation of multidimensional projections formulated as implicit functions. The results are visualized as glyphs and analyzed using a full set of specifically-designed interactions supported in our efficient web-based visualization tool. The usefulness of our method is demonstrated using various multi- and high-dimensional benchmark datasets. Our implicit differentiation vector transformation is evaluated through numerical comparisons; the overall method is evaluated through exploration examples and use cases.

Evaluation of Sampling Methods for Scatterplots

Given a scatterplot with tens of thousands of points or even more, a natural question is which sampling method should be used to create a small but "good" scatterplot for a better abstraction. We present the results of a user study that investigates the influence of different sampling strategies on multi-class scatterplots. The main goal of this study is to understand the capability of sampling methods in preserving the density, outliers, and overall shape of a scatterplot. To this end, we comprehensively review the literature and select seven typical sampling strategies as well as eight representative datasets. We then design four experiments to understand the performance of different strategies in maintaining: 1) region density; 2) class density; 3) outliers; and 4) overall shape in the sampling results. The results show that: 1) random sampling is preferred for preserving region density; 2) blue noise sampling and random sampling have comparable performance with the three multi-class sampling strategies in preserving class density; 3) outlier biased density based sampling, recursive subdivision based sampling, and blue noise sampling perform the best in keeping outliers; and 4) blue noise sampling outperforms the others in maintaining the overall shape of a scatterplot.

TopoMap: A 0-dimensional Homology Preserving Projection of High-Dimensional Data

Multidimensional Projection is a fundamental tool for high-dimensional data analytics and visualization. With very few exceptions, projection techniques are designed to map data from a high-dimensional space to a visual space so as to preserve some dissimilarity (similarity) measure, such as the Euclidean distance for example. In fact, although adopting distinct mathematical formulations designed to favor different aspects of the data, most multidimensional projection methods strive to preserve dissimilarity measures that encapsulate geometric properties such as distances or the proximity relation between data objects. However, geometric relations are not the only interesting property to be preserved in a projection. For instance, the analysis of particular structures such as clusters and outliers could be more reliably performed if the mapping process gives some guarantee as to topological invariants such as connected components and loops. This paper introduces TopoMap, a novel projection technique which provides topological guarantees during the mapping process. In particular, the proposed method performs the mapping from a high-dimensional space to a visual space, while preserving the 0-dimensional persistence diagram of the Rips filtration of the high-dimensional data, ensuring that the filtrations generate the same connected components when applied to the original as well as projected data. The presented case studies show that the topological guarantee provided by TopoMap not only brings confidence to the visual analytic process but also can be used to assist in the assessment of other projection methods.

A Visual Analytics Framework for Reviewing Multivariate Time-Series Data with Dimensionality Reduction

Data-driven problem solving in many real-world applications involves analysis of time-dependent multivariate data, for which dimensionality reduction (DR) methods are often used to uncover the intrinsic structure and features of the data. However, DR is usually applied to a subset of data that is either single-time-point multivariate or univariate time-series, resulting in the need to manually examine and correlate the DR results out of different data subsets. When the number of dimensions is large either in terms of the number of time points or attributes, this manual task becomes too tedious and infeasible. In this paper, we present MulTiDR, a new DR framework that enables processing of time-dependent multivariate data as a whole to provide a comprehensive overview of the data. With the framework, we employ DR in two steps. When treating the instances, time points, and attributes of the data as a 3D array, the first DR step reduces the three axes of the array to two, and the second DR step visualizes the data in a lower-dimensional space. In addition, by coupling with a contrastive learning method and interactive visualizations, our framework enhances analysts' ability to interpret DR results. We demonstrate the effectiveness of our framework with four case studies using real-world datasets.

ChemVA: Interactive Visual Analysis of Chemical Compound Similarity in Virtual Screening

In the modern drug discovery process, medicinal chemists deal with the complexity of analysis of large ensembles of candidate molecules. Computational tools, such as dimensionality reduction (DR) and classification, are commonly used to efficiently process the multidimensional space of features. These underlying calculations often hinder interpretability of results and prevent experts from assessing the impact of individual molecular features on the resulting representations. To provide a solution for scrutinizing such complex data, we introduce ChemVA, an interactive application for the visual exploration of large molecular ensembles and their features. Our tool consists of multiple coordinated views: Hexagonal view, Detail view, 3D view, Table view, and a newly proposed Difference view designed for the comparison of DR projections. These views display DR projections combined with biological activity, selected molecular features, and confidence scores for each of these projections. This conjunction of views allows the user to drill down through the dataset and to efficiently select candidate compounds. Our approach was evaluated on two case studies of finding structurally similar ligands with similar binding affinity to a target protein, as well as on an external qualitative evaluation. The results suggest that our system allows effective visual inspection and comparison of different high-dimensional molecular representations. Furthermore, ChemVA assists in the identification of candidate compounds while providing information on the certainty behind different molecular representations.

Visual Analysis of Class Separations With Locally Linear Segments

High-dimensional labeled data widely exists in many real-world applications such as classification and clustering. One main task in analyzing such datasets is to explore class separations and class boundaries derived from machine learning models. Dimension reduction techniques are commonly applied to support analysts in exploring the underlying decision boundary structures by depicting a low-dimensional representation of the data distributions from multiple classes. However, such projection-based analyses are limited due to their lack of ability to show separations in complex non-linear decision boundary structures and can suffer from heavy distortion and low interpretability. To overcome these issues of separability and interpretability, we propose a visual analysis approach that utilizes the power of explainability from linear projections to support analysts when exploring non-linear separation structures. Our approach is to extract a set of locally linear segments that approximate the original non-linear separations. Unlike traditional projection-based analysis where the data instances are mapped to a single scatterplot, our approach supports the exploration of complex class separations through multiple local projection results. We conduct case studies on two labeled datasets to demonstrate the effectiveness of our approach.

Integrating Machine Learning with Human Knowledge

Machine learning has been heavily researched and widely used in many disciplines. However, achieving high accuracy requires a large amount of data that is sometimes difficult, expensive, or impractical to obtain. Integrating human knowledge into machine learning can significantly reduce data requirement, increase reliability and robustness of machine learning, and build explainable machine learning systems. This allows leveraging the vast amount of human knowledge and capability of machine learning to achieve functions and performance not available before and will facilitate the interaction between human beings and machine learning systems, making machine learning decisions understandable to humans. This paper gives an overview of the knowledge and its representations that can be integrated into machine learning and the methodology. We cover the fundamentals, current status, and recent progress of the methods, with a focus on popular and new topics. The perspectives on future directions are also discussed.

Visual Genealogy of Deep Neural Networks

A comprehensive and comprehensible summary of existing deep neural networks (DNNs) helps practitioners understand the behaviour and evolution of DNNs, offers insights for architecture optimization, and sheds light on the working mechanisms of DNNs. However, this summary is hard to obtain because of the complexity and diversity of DNN architectures. To address this issue, we develop DNN Genealogy, an interactive visualization tool, to offer a visual summary of representative DNNs and their evolutionary relationships. DNN Genealogy enables users to learn DNNs from multiple aspects, including architecture, performance, and evolutionary relationships. Central to this tool is a systematic analysis and visualization of 66 representative DNNs based on our analysis of 140 papers. A directed acyclic graph is used to illustrate the evolutionary relationships among these DNNs and highlight the representative DNNs. A focus + context visualization is developed to orient users during their exploration. A set of network glyphs is used in the graph to facilitate the understanding and comparing of DNNs in the context of the evolution. Case studies demonstrate that DNN Genealogy provides helpful guidance in understanding, applying, and optimizing DNNs. DNN Genealogy is extensible and will continue to be updated to reflect future advances in DNNs.

t-viSNE: Interactive Assessment and Interpretation of t-SNE Projections

t-Distributed Stochastic Neighbor Embedding (t-SNE) for the visualization of multidimensional data has proven to be a popular approach, with successful applications in a wide range of domains. Despite their usefulness, t-SNE projections can be hard to interpret or even misleading, which hurts the trustworthiness of the results. Understanding the details of t-SNE itself and the reasons behind specific patterns in its output may be a daunting task, especially for non-experts in dimensionality reduction. In this article, we present t-viSNE, an interactive tool for the visual exploration of t-SNE projections that enables analysts to inspect different aspects of their accuracy and meaning, such as the effects of hyper-parameters, distance and neighborhood preservation, densities and costs of specific neighborhoods, and the correlations between dimensions and visual patterns. We propose a coherent, accessible, and well-integrated collection of different views for the visualization of t-SNE projections. The applicability and usability of t-viSNE are demonstrated through hypothetical usage scenarios with real data sets. Finally, we present the results of a user study where the tool's effectiveness was evaluated. By bringing to light information that would normally be lost after running t-SNE, we hope to support analysts in using t-SNE and making its results better understandable.

Supporting Analysis of Dimensionality Reduction Results with Contrastive Learning

Dimensionality reduction (DR) is frequently used for analyzing and visualizing high-dimensional data as it provides a good first glance of the data. However, to interpret the DR result for gaining useful insights from the data, it would take additional analysis effort such as identifying clusters and understanding their characteristics. While there are many automatic methods (e.g., density-based clustering methods) to identify clusters, effective methods for understanding a cluster's characteristics are still lacking. A cluster can be mostly characterized by its distribution of feature values. Reviewing the original feature values is not a straightforward task when the number of features is large. To address this challenge, we present a visual analytics method that effectively highlights the essential features of a cluster in a DR result. To extract the essential features, we introduce an enhanced usage of contrastive principal component analysis (cPCA). Our method, called ccPCA (contrasting clusters in PCA), can calculate each feature's relative contribution to the contrast between one cluster and other clusters. With ccPCA, we have created an interactive system including a scalable visualization of clusters' feature contributions. We demonstrate the effectiveness of our method and system with case studies using several publicly available datasets.

An Incremental Dimensionality Reduction Method for Visualizing Streaming Multidimensional Data

Dimensionality reduction (DR) methods are commonly used for analyzing and visualizing multidimensional data. However, when data is a live streaming feed, conventional DR methods cannot be directly used because of their computational complexity and inability to preserve the projected data positions at previous time points. In addition, the problem becomes even more challenging when the dynamic data records have a varying number of dimensions as often found in real-world applications. This paper presents an incremental DR solution. We enhance an existing incremental PCA method in several ways to ensure its usability for visualizing streaming multidimensional data. First, we use geometric transformation and animation methods to help preserve a viewer's mental map when visualizing the incremental results. Second, to handle data dimension variants, we use an optimization method to estimate the projected data positions, and also convey the resulting uncertainty in the visualization. We demonstrate the effectiveness of our design with two case studies using real-world datasets.

Multidimensional Projection for Visual Analytics: Linking Techniques with Distortions, Tasks, and Layout Enrichment

Visual analysis of multidimensional data requires expressive and effective ways to reduce data dimensionality to encode them visually. Multidimensional projections (MDP) figure among the most important visualization techniques in this context, transforming multidimensional data into scatter plots whose visual patterns reflect some notion of similarity in the original data. However, MDP come with distortions that make these visual patterns not trustworthy, hindering users to infer actual data characteristics. Moreover, the patterns present in the scatter plots might not be enough to allow a clear understanding of multidimensional data, motivating the development of layout enrichment methodologies to operate together with MDP. This survey attempts to cover the main aspects of MDP as a visualization and visual analytic tool. It provides detailed analysis and taxonomies as to the organization of MDP techniques according to their main properties and traits, discussing the impact of such properties for visual perception and other human factors. The survey also approaches the different types of distortions that can result from MDP mappings and it overviews existing mechanisms to quantitatively evaluate such distortions. A qualitative analysis of the impact of distortions on the different analytic tasks performed by users when exploring multidimensional data through MDP is also presented. Guidelines for choosing the best MDP for an intended task are also provided as a result of this analysis. Finally, layout enrichment schemes to debunk MDP distortions and/or reveal relevant information not directly inferable from the scatter plot are reviewed and discussed in the light of new taxonomies. We conclude the survey providing future research axes to fill discovered gaps in this domain.

Bridging Text Visualization and Mining: A Task-Driven Survey

Visual text analytics has recently emerged as one of the most prominent topics in both academic research and the commercial world. To provide an overview of the relevant techniques and analysis tasks, as well as the relationships between them, we comprehensively analyzed 263 visualization papers and 4,346 mining papers published between 1992-2017 in two fields: visualization and text mining. From the analysis, we derived around 300 concepts (visualization techniques, mining techniques, and analysis tasks) and built a taxonomy for each type of concept. The co-occurrence relationships between the concepts were also extracted. Our research can be used as a stepping-stone for other researchers to 1) understand a common set of concepts used in this research topic; 2) facilitate the exploration of the relationships between visualization techniques, mining techniques, and analysis tasks; 3) understand the current practice in developing visual text analytics tools; 4) seek potential research opportunities by narrowing the gulf between visualization and mining techniques based on the analysis tasks; and 5) analyze other interdisciplinary research areas in a similar way. We have also contributed a web-based visualization tool for analyzing and understanding research trends and opportunities in visual text analytics.

Visual Exploration of Neural Document Embedding in Information Retrieval: Semantics and Feature Selection

Neural embeddings are widely used in language modeling and feature generation with superior computational power. Particularly, neural document embedding - converting texts of variable-length to semantic vector representations - has shown to benefit widespread downstream applications, e.g., information retrieval (IR). However, the black-box nature makes it difficult to understand how the semantics are encoded and employed. We propose visual exploration of neural document embedding to gain insights into the underlying embedding space, and promote the utilization in prevalent IR applications. In this study, we take an IR application-driven view, which is further motivated by biomedical IR in healthcare decision-making, and collaborate with domain experts to design and develop a visual analytics system. This system visualizes neural document embeddings as a configurable document map and enables guidance and reasoning; facilitates to explore the neural embedding space and identify salient neural dimensions (semantic features) per task and domain interest; and supports advisable feature selection (semantic analysis) along with instant visual feedback to promote IR performance. We demonstrate the usefulness and effectiveness of this system and present inspiring findings in use cases. This work will help designers/developers of downstream applications gain insights and confidence in neural document embedding, and exploit that to achieve more favorable performance in application domains.

Enhancing Deep Learning with Visual Interactions

Deep learning has emerged as a powerful tool for feature-driven labeling of datasets. However, for it to be effective, it requires a large and finely labeled training dataset. Precisely labeling a large training dataset is expensive, time-consuming, and error prone. In this article, we present a visually driven deep-learning approach that starts with a coarsely labeled training dataset and iteratively refines the labeling through intuitive interactions that leverage the latent structures of the dataset. Our approach can be used to (a) alleviate the burden of intensive manual labeling that captures the fine nuances in a high-dimensional dataset by simple visual interactions, (b) replace a complicated (and therefore difficult to design) labeling algorithm by a simpler (but coarse) labeling algorithm supplemented by user interaction to refine the labeling, or (c) use low-dimensional features (such as the RGB colors) for coarse labeling and turn to higher-dimensional latent structures that are progressively revealed by deep learning, for fine labeling. We validate our approach through use cases on three high-dimensional datasets and a user study.

Visual analytics for collaborative human-machine confidence in human-centric active learning tasks

Active machine learning is a human-centric paradigm that leverages a small labelled dataset to build an initial weak classifier, that can then be improved over time through human-machine collaboration. As new unlabelled samples are observed, the machine can either provide a prediction, or query a human ‘oracle’ when the machine is not confident in its prediction. Of course, just as the machine may lack confidence, the same can also be true of a human ‘oracle’: humans are not all-knowing, untiring oracles. A human’s ability to provide an accurate and confident response will often vary between queries, according to the duration of the current interaction, their level of engagement with the system, and the difficulty of the labelling task. This poses an important question of how uncertainty can be expressed and accounted for in a human-machine collaboration. In short, how can we facilitate a mutually-transparent collaboration between two uncertain actors—a person and a machine—that leads to an improved outcome? In this work, we demonstrate the benefit of human-machine collaboration within the process of active learning, where limited data samples are available or where labelling costs are high. To achieve this, we developed a visual analytics tool for active learning that promotes transparency, inspection, understanding and trust, of the learning process through human-machine collaboration. Fundamental to the notion of confidence, both parties can report their level of confidence during active learning tasks using the tool, such that this can be used to inform learning. Human confidence of labels can be accounted for by the machine, the machine can query for samples based on confidence measures, and the machine can report confidence of current predictions to the human, to further the trust and transparency between the collaborative parties. In particular, we find that this can improve the robustness of the classifier when incorrect sample labels are provided, due to unconfidence or fatigue. Reported confidences can also better inform human-machine sample selection in collaborative sampling. Our experimentation compares the impact of different selection strategies for acquiring samples: machine-driven, human-driven, and collaborative selection. We demonstrate how a collaborative approach can improve trust in the model robustness, achieving high accuracy and low user correction, with only limited data sample selections.

SLIC Superpixel-Based l2,1-Norm Robust Principal Component Analysis for Hyperspectral Image Classification

Hyperspectral Images (HSIs) contain enriched information due to the presence of various bands, which have gained attention for the past few decades. However, explosive growth in HSIs’ scale and dimensions causes “Curse of dimensionality” and “Hughes phenomenon”. Dimensionality reduction has become an important means to overcome the “Curse of dimensionality”. In hyperspectral images, labeled samples are more difficult to collect because they require many labor and material resources. Semi-supervised dimensionality reduction is very important in mining high-dimensional data due to the lack of costly-labeled samples. The promotion of the supervised dimensionality reduction method to the semi-supervised method is mostly done by graph, which is a powerful tool for characterizing data relationships and manifold exploration. To take advantage of the spatial information of data, we put forward a novel graph construction method for semi-supervised learning, called SLIC Superpixel-based l2,1-norm Robust Principal Component Analysis (SURPCA_2,1), which integrates superpixel segmentation method Simple Linear Iterative Clustering (SLIC) into Low-rank Decomposition. First, the SLIC algorithm is adopted to obtain the spatial homogeneous regions of HSI. Then, the l2,1-norm RPCA is exploited in each superpixel area, which captures the global information of homogeneous regions and preserves spectral subspace segmentation of HSIs very well. Therefore, we have explored the spatial and spectral information of hyperspectral image simultaneously by combining superpixel segmentation with RPCA. Finally, a semi-supervised dimensionality reduction framework based on SURPCA_2,1 graph is used for feature extraction task. Extensive experiments on multiple HSIs showed that the proposed spectral-spatial SURPCA_2,1 is always comparable to other compared graphs with few labeled samples.

Interactive Intent Modeling for Exploratory Search

Exploratory search requires the system to assist the user in comprehending the information space and expressing evolving search intents for iterative exploration and retrieval of information. We introduce interactive intent modeling, a technique that models a user’s evolving search intents and visualizes them as keywords for interaction. The user can provide feedback on the keywords, from which the system learns and visualizes an improved intent estimate and retrieves information. We report experiments comparing variants of a system implementing interactive intent modeling to a control system. Data comprising search logs, interaction logs, essay answers, and questionnaires indicate significant improvements in task performance, information retrieval performance over the session, information comprehension performance, and user experience. The improvements in retrieval effectiveness can be attributed to the intent modeling and the effect on users’ task performance, breadth of information comprehension, and user experience are shown to be dependent on a richer visualization. Our results demonstrate the utility of combining interactive modeling of search intentions with interactive visualization of the models that can benefit both directing the exploratory search process and making sense of the information space. Our findings can help design personalized systems that support exploratory information seeking and discovery of novel information.

Multidimensional mechanics: Performance mapping of natural biological systems using permutated radar charts

Comparing the functional performance of biological systems often requires comparing multiple mechanical properties. Such analyses, however, are commonly presented using orthogonal plots that compare N ≤ 3 properties. Here, we develop a multidimensional visualization strategy using permutated radar charts (radial, multi-axis plots) to compare the relative performance distributions of mechanical systems on a single graphic across N ≥ 3 properties. Leveraging the fact that radar charts plot data in the form of closed polygonal profiles, we use shape descriptors for quantitative comparisons. We identify mechanical property-function correlations distinctive to rigid, flexible, and damage-tolerant biological materials in the form of structural ties, beams, shells, and foams. We also show that the microstructures of dentin, bone, tendon, skin, and cartilage dictate their tensile performance, exhibiting a trade-off between stiffness and extensibility. Lastly, we compare the feeding versus singing performance of Darwin’s finches to demonstrate the potential of radar charts for multidimensional comparisons beyond mechanics of materials.