Modern methods for data visualization via dimensionality reduction, such as t-SNE, usually have performance issues that prohibit their application to large amounts of high-dimensional data. In this work, we propose NCVis -- a high-performance dimensionality reduction method built on a sound statistical basis of noise contrastive estimation. We show that NCVis outperforms state-of-the-art techniques in terms of speed while preserving the representation quality of other methods. In particular, the proposed approach successfully proceeds a large dataset of more than 1 million news headlines in several minutes and presents the underlying structure in a human-readable way. Moreover, it provides results consistent with classical methods like t-SNE on more straightforward datasets like images of hand-written digits. We believe that the broader usage of such software can significantly simplify the large-scale data analysis and lower the entry barrier to this area.
Two decades ago three pioneering papers turned the attention to complex networks and initiated a new era of research, establishing an interdisciplinary field called network science. Namely, these highly-cited seminal papers were written by Watts&Strogatz, Barab\'asi&Albert, and Girvan&Newman on small-world networks, on scale-free networks and on the community structure of complex networks, respectively. In the past 20 years - due to the multidisciplinary nature of the field - a diverse but not divided network science community has emerged. In this paper, we investigate how this community has evolved over time with respect to speed, diversity and interdisciplinary nature as seen through the growing co-authorship network of network scientists (here the notion refers to a scholar with at least one paper citing at least one of the three aforementioned milestone papers). After providing a bibliographic analysis of 31,763 network science papers, we construct the co-authorship network of 56,646 network scientists and we analyze its topology and dynamics. We shed light on the collaboration patterns of the last 20 years of network science by investigating numerous structural properties of the co-authorship network and by using enhanced data visualization techniques. We also identify the most central authors, the largest communities, investigate the spatiotemporal changes, and compare the properties of the network to scientometric indicators.
Augmented Reality has been subject to various integration efforts within industries due to its ability to enhance human machine interaction and understanding. Neural networks have achieved remarkable results in areas of computer vision, which bear great potential to assist and facilitate an enhanced Augmented Reality experience. However, most neural networks are computationally intensive and demand huge processing power thus, are not suitable for deployment on Augmented Reality devices. In this work we propose a method to deploy state of the art neural networks for real time 3D object localization on augmented reality devices. As a result, we provide a more automated method of calibrating the AR devices with mobile robotic systems. To accelerate the calibration process and enhance user experience, we focus on fast 2D detection approaches which are extracting the 3D pose of the object fast and accurately by using only 2D input. The results are implemented into an Augmented Reality application for intuitive robot control and sensor data visualization. For the 6D annotation of 2D images, we developed an annotation tool, which is, to our knowledge, the first open source tool to be available. We achieve feasible results which are generally applicable to any AR device thus making this work promising for further research in combining high demanding neural networks with Internet of Things devices.
We present ShapeVis, a scalable visualization technique for point cloud data inspired from topological data analysis. Our method captures the underlying geometric and topological structure of the data in a compressed graphical representation. Much success has been reported by the data visualization technique Mapper, that discreetly approximates the Reeb graph of a filter function on the data. However, when using standard dimensionality reduction algorithms as the filter function, Mapper suffers from considerable computational cost. This makes it difficult to scale to high-dimensional data. Our proposed technique relies on finding a subset of points called landmarks along the data manifold to construct a weighted witness-graph over it. This graph captures the structural characteristics of the point cloud, and its weights are determined using a Finite Markov Chain. We further compress this graph by applying induced maps from standard community detection algorithms. Using techniques borrowed from manifold tearing, we prune and reinstate edges in the induced graph based on their modularity to summarize the shape of data. We empirically demonstrate how our technique captures the structural characteristics of real and synthetic data sets. Further, we compare our approach with Mapper using various filter functions like t-SNE, UMAP, LargeVis and show that our algorithm scales to millions of data points while preserving the quality of data visualization.
To ensure the security of the general mass, crime prevention is one of the most higher priorities for any government. An accurate crime prediction model can help the government, law enforcement to prevent violence, detect the criminals in advance, allocate the government resources, and recognize problems causing crimes. To construct any future-oriented tools, examine and understand the crime patterns in the earliest possible time is essential. In this paper, I analyzed a real-world crime and accident dataset of Denver county, USA, from January 2014 to May 2019, which containing 478,578 incidents. This project aims to predict and highlights the trends of occurrence that will, in return, support the law enforcement agencies and government to discover the preventive measures from the prediction rates. At first, I apply several statistical analysis supported by several data visualization approaches. Then, I implement various classification algorithms such as Random Forest, Decision Tree, AdaBoost Classifier, Extra Tree Classifier, Linear Discriminant Analysis, K-Neighbors Classifiers, and 4 Ensemble Models to classify 15 different classes of crimes. The outcomes are captured using two popular test methods: train-test split, and k-fold cross-validation. Moreover, to evaluate the performance flawlessly, I also utilize precision, recall, F1-score, Mean Squared Error (MSE), ROC curve, and paired-T-test. Except for the AdaBoost classifier, most of the algorithms exhibit satisfactory accuracy. Random Forest, Decision Tree, Ensemble Model 1, 3, and 4 even produce me more than 90% accuracy. Among all the approaches, Ensemble Model 4 presented superior results for every evaluation basis. This study could be useful to raise the awareness of peoples regarding the occurrence locations and to assist security agencies to predict future outbreaks of violence in a specific area within a particular time.
Reeb spaces, as well as their discretized versions called Mappers, are common descriptors used in Topological Data Analysis, with plenty of applications in various fields of science, such as computational biology and data visualization, among others. The stability and quantification of the rate of convergence of the Mapper to the Reeb space has been studied a lot in recent works [BBMW19, CO17, CMO18, MW16], focusing on the case where a scalar-valued filter is used for the computation of Mapper. On the other hand, much less is known in the multivariate case, when the codomain of the filter is $\mathbb{R}^p$, and in the general case, when it is a general metric space $(Z, d_Z)$, instead of $\mathbb{R}$. The few results that are available in this setting [DMW17, MW16] can only handle continuous topological spaces and cannot be used as is for finite metric spaces representing data, such as point clouds and distance matrices. In this article, we introduce a slight modification of the usual Mapper construction and we give risk bounds for estimating the Reeb space using this estimator. Our approach applies in particular to the setting where the filter function used to compute Mapper is also estimated from data, such as the eigenfunctions of PCA. Our results are given with respect to the Gromov-Hausdorff distance, computed with specific filter-based pseudometrics for Mappers and Reeb spaces defined in [DMW17]. We finally provide applications of this setting in statistics and machine learning for different kinds of target filters, as well as numerical experiments that demonstrate the relevance of our approach
Non-parametric dimensionality reduction techniques, such as t-SNE and UMAP, are proficient in providing visualizations for datasets of fixed sizes. However, they cannot incrementally map and insert new data points into an already provided data visualization. We present Self-Organizing Nebulous Growths (SONG), a parametric nonlinear dimensionality reduction technique that supports incremental data visualization, i.e., incremental addition of new data while preserving the structure of the existing visualization. In addition, SONG is capable of handling new data increments, no matter whether they are similar or heterogeneous to the already observed data distribution. We test SONG on a variety of real and simulated datasets. The results show that SONG is superior to Parametric t-SNE, t-SNE and UMAP in incremental data visualization. Specifically, for heterogeneous increments, SONG improves over Parametric t-SNE by 14.98 % on the Fashion MNIST dataset and 49.73% on the MNIST dataset regarding the cluster quality measured by the Adjusted Mutual Information scores. On similar or homogeneous increments, the improvements are 8.36% and 42.26% respectively. Furthermore, even when the above datasets are presented all at once, SONG performs better or comparable to UMAP, and superior to t-SNE. We also demonstrate that the algorithmic foundations of SONG render it more tolerant to noise compared to UMAP and t-SNE, thus providing greater utility for data with high variance, high mixing of clusters, or noise.
In this short paper, a neural network that is able to form a low dimensional topological hidden representation is explained. The neural network can be trained as an autoencoder, a classifier or mix of both, and produces different low dimensional topological map for each of them. When it is trained as an autoencoder, the inherent topological structure of the data can be visualized, while when it is trained as a classifier, the topological structure is further constrained by the concept, for example the labels the data, hence the visualization is not only structural but also conceptual. The proposed neural network significantly differ from many dimensional reduction models, primarily in its ability to execute both supervised and unsupervised dimensional reduction. The neural network allows multi perspective visualization of the data, and thus giving more flexibility in data analysis. This paper is supported by preliminary but intuitive visualization experiments.
In recent years, data-driven models have enabled significant advances in medicine. Simultaneously, voice has shown potential for analysis in precision medicine as a biomarker for screening illnesses. There has been a growing trend to pursue voice data to understand neuropsychiatric diseases. In this paper, we present DigiVoice, a comprehensive feature extraction and analysis pipeline for voice data. DigiVoice supports raw .WAV files and text transcriptions in order to analyze the entire content of voice. DigiVoice supports feature extraction including acoustic, natural language, linguistic complexity, and semantic coherence features. DigiVoice also supports machine learning capabilities including data visualization, feature selection, feature transformation, and modeling. To our knowledge, DigiVoice provides the most comprehensive voice feature set for data analysis to date. With DigiVoice, we plan to accelerate research to correlate voice biomarkers with illness to enable data-driven treatment. We have worked closely with our industry partner, NeuroLex Laboratories, to make voice computing open source and accessible. DigiVoice enables researchers to leverage our technology across the domains of voice computing and precision medicine without domain-specific expertise. Our work allows any researchers to use voice as a biomarker in their past, current, or future studies.
A growing number of empirical studies suggest that negative advertising is effective in campaigning, while the mechanisms are rarely mentioned. With the scandal of Cambridge Analytica and Russian intervention behind the Brexit and the 2016 presidential election, people have become aware of the political ads on social media and have pressured congress to restrict political advertising on social media. Following the related legislation, social media companies began disclosing their political ads archive for transparency during the summer of 2018 when the midterm election campaign was just beginning. This research collects the data of the related political ads in the context of the U.S. midterm elections since August to study the overall pattern of political ads on social media and uses sets of machine learning methods to conduct sentiment analysis on these ads to classify the negative ads. A novel approach is applied that uses AI image recognition to study the image data. Through data visualization, this research shows that negative advertising is still the minority, Republican advertisers and third party organizations are more likely to engage in negative advertising than their counterparts. Based on ordinal regressions, this study finds that anger evoked information-seeking is one of the main mechanisms causing negative ads to be more engaging and effective rather than the negative bias theory. Overall, this study provides a unique understanding of political advertising on social media by applying innovative data science methods. Further studies can extend the findings, methods, and datasets in this study, and several suggestions are given for future research.
Choosing a suitable visualization for data is a difficult task. Current data visualization recommender systems exist to aid in choosing a visualization, yet suffer from issues such as low accessibility and indecisiveness. In this study, we first define a step-by-step guide on how to build a data visualization recommender system. We then use this guide to create a model for a data visualization recommender system for non-experts that aims to resolve the issues of current solutions. The result is a question-based model that uses a decision tree and a data visualization classification hierarchy in order to recommend a visualization. Furthermore, it incorporates both task-driven and data characteristics-driven perspectives, whereas existing solutions seem to either convolute these or focus on one of the two exclusively. Based on testing against existing solutions, it is shown that the new model reaches similar results while being simpler, clearer, more versatile, extendable and transparent. The presented guide can be used as a manual for anyone building a data visualization recommender system. The resulting model can be applied in the development of new data visualization software or as part of a learning tool.
This paper presents a method for building patient-based networks that we call Precision disease networks, and its uses for predicting medical outcomes. Our methodology consists of building networks, one for each patient or case, that describes the dis-ease evolution of the patient (PDN) and store the networks as a set of features in a data set of PDN's, one per observation. We cluster the PDN data and study the within and between cluster variability. In addition, we develop data visualization technics in order to display, compare and summarize the network data. Finally, we analyze a dataset of heart diseases patients from a New Jersey statewide data-base MIDAS (Myocardial Infarction Data Acquisition System, in order to show that the network data improve on the prediction of important patient outcomes such as death or cardiovascular death, when compared with the standard statistical analysis.
In this paper, we show how Quantitative Narrative Analysis and simple Natural Language Processing techniques apply to the extraction and categorization of data in a sample case study of the Diary of the former President of the Italian Republic (PoR), Giorgio Napolitano. The Diary contains a record of all his institutional meetings. This information, if properly handled, allows for an analysis of how the PoR used his so-called soft-powers to influence the Italian political system during his first mandate. In this paper, we propose a way to use simple, yet very effective, Natural Language Processing techniques - such as Regular Expressions and Named Entity Recognition - to extract information from the Diary. Then, we propose an innovative way to organize the extracted data relying on the methodological framework of Quantitative Narrative Analysis. Finally, we show how to analyze the structured data under different levels of detail using PC-ACE (Program for Computer-Assisted Coding of Events), a software developed specifically for this task and for data visualization.
Many end-user evaluations of data visualization techniques have been run during the last decades. Their results are cornerstones to build efficient visualization systems. However, designing such an evaluation is always complex and time-consuming and may end in a lack of statistical evidence and reproducibility. We believe that modern and efficient computer vision techniques, such as deep convolutional neural networks (CNNs), may help visualization researchers to build and/or adjust their evaluation hypothesis. The basis of our idea is to train machine learning models on several visualization techniques to solve a specific task. Our assumption is that it is possible to compare the efficiency of visualization techniques based on the performance of their corresponding model. As current machine learning models are not able to strictly reflect human capabilities, including their imperfections, such results should be interpreted with caution. However, we think that using machine learning-based pre-evaluation, as a pre-process of standard user evaluations, should help researchers to perform a more exhaustive study of their design space. Thus, it should improve their final user evaluation by providing it better test cases. In this paper, we present the results of two experiments we have conducted to assess how correlated the performance of users and computer vision techniques can be. That study compares two mainstream graph visualization techniques: node-link (\NL) and adjacency-matrix (\MD) diagrams. Using two well-known deep convolutional neural networks, we partially reproduced user evaluations from Ghoniem \textit{et al.} and from Okoe \textit{et al.}. These experiments showed that some user evaluation results can be reproduced automatically.
We provide a rigorous mathematical treatment to the crowding issue in data visualization when high dimensional data sets are projected down to low dimensions for visualization. By properly adjusting the capacity of high dimensional balls, our method makes right enough room to prepare for the embedding. A key component of the proposed method is an estimation of the correlation dimension at various scales which reflects the data density variation. The proposed adjustment to the capacity applies to any distance (Euclidean, geodesic, diffusion) and can potentially be used in many existing methods to mitigate the crowding during the dimension reduction. We demonstrate the effectiveness of the new method using synthetic and real datasets.
Multivariate spatial data plays an important role in computational science and engineering simulations. The potential features and hidden relationships in multivariate data can assist scientists to gain an in-depth understanding of a scientific process, verify a hypothesis and further discover a new physical or chemical law. In this paper, we present a comprehensive survey of the state-of-the-art techniques for multivariate spatial data visualization. We first introduce the basic concept and characteristics of multivariate spatial data, and describe three main tasks in multivariate data visualization: feature classification, fusion visualization, and correlation analysis. Finally, we prospect potential research topics for multivariate data visualization according to the current research.
The chemical sciences are producing an unprecedented amount of large, high-dimensional data sets containing chemical structures and associated properties. However, there are currently no algorithms to visualize such data while preserving both global and local features with a sufficient level of detail to allow for human inspection and interpretation. Here, we propose a solution to this problem with a new data visualization method, TMAP, capable of representing data sets of up to millions of data points and arbitrary high dimensionality as a two-dimensional tree (http://tmap.gdb.tools). Visualizations based on TMAP are better suited than t-SNE or UMAP for the exploration and interpretation of large data sets due to their tree-like nature, increased local and global neighborhood and structure preservation, and the transparency of the methods the algorithm is based on. We apply TMAP to the most used chemistry data sets including databases of molecules such as ChEMBL, FDB17, the Natural Products Atlas, DSSTox, as well as to the MoleculeNet benchmark collection of data sets. We also show its broad applicability with further examples from biology, particle physics, and literature.
Complex networks have attracted a great deal of research interest in the last two decades since Watts & Strogatz, Barab\'asi & Albert and Girvan & Newman published their highly-cited seminal papers on small-world networks, on scale-free networks and on the community structure of complex networks, respectively. These fundamental papers initiated a new era of research establishing an interdisciplinary field called network science. Due to the multidisciplinary nature of the field, a diverse but not divided network science community has emerged in the past 20 years. This paper honors the contributions of network science by exploring the evolution of this community as seen through the growing co-authorship network of network scientists (here the notion refers to a scholar with at least one paper citing at least one of the three aforementioned milestone papers). After investigating various characteristics of 29,528 network science papers, we construct the co-authorship network of 52,406 network scientists and we analyze its topology and dynamics. We shed light on the collaboration patterns of the last 20 years of network science by investigating numerous structural properties of the co-authorship network and by using enhanced data visualization techniques. We also identify the most central authors, the largest communities, investigate the spatiotemporal changes, and compare the properties of the network to scientometric indicators.
The self-organizing map (SOM) is an unsupervised artificial neural network that is widely used in, e.g., data mining and visualization. Supervised and semi-supervised learning methods have been proposed for the SOM. However, their teacher labels do not describe the relationship between the data and the location of nodes. This study proposes a landmark map (LAMA), which is an extension of the SOM that utilizes several landmarks, e.g., pairs of nodes and data points. LAMA is designed to obtain a user-intended nonlinear projection to achieve, e.g., the landmark-oriented data visualization. To reveal the learning properties of LAMA, the Zoo dataset from the UCI Machine Learning Repository and an artificial formant dataset were analyzed. The analysis results of the Zoo dataset indicated that LAMA could provide a new data view such as the landmark-centered data visualization. Furthermore, the artificial formant data analysis revealed that LAMA successfully provided the intended nonlinear projection associating articular movement with vertical and horizontal movement of a computer cursor. Potential applications of LAMA include data mining, recommendation systems, and human-computer interaction.
One aim of data mining is the identification of interesting structures in data. For better analytical results, the basic properties of an empirical distribution, such as skewness and eventual clipping, i.e. hard limits in value ranges, need to be assessed. Of particular interest is the question of whether the data originate from one process or contain subsets related to different states of the data producing process. Data visualization tools should deliver a clear picture of the univariate probability density distribution (PDF) for each feature. Visualization tools for PDFs typically use kernel density estimates and include both the classical histogram, as well as the modern tools like ridgeline plots, bean plots and violin plots. If density estimation parameters remain in a default setting, conventional methods pose several problems when visualizing the PDF of uniform, multimodal, skewed distributions and distributions with clipped data, For that reason, a new visualization tool called the mirrored density plot (MD plot), which is specifically designed to discover interesting structures in continuous features, is proposed. The MD plot does not require adjusting any parameters of density estimation, which is what may make the use of this plot compelling particularly to non-experts. The visualization tools in question are evaluated against statistical tests with regard to typical challenges of explorative distribution analysis. The results of the evaluation are presented using bimodal Gaussian, skewed distributions and several features with already published PDFs. In an exploratory data analysis of 12 features describing quarterly financial statements, when statistical testing poses a great difficulty, only the MD plots can identify the structure of their PDFs. In sum, the MD plot outperforms the above mentioned methods.