Sophisticated visualization tools are essential for the presentation and exploration of human neuroimaging data. While two-dimensional orthogonal views of neuroimaging data are conventionally used to display activity and statistical analysis, three-dimensional (3D) representation is useful for showing the spatial distribution of a functional network, as well as its temporal evolution. For these purposes, there is currently no open-source, 3D neuroimaging tool that can simultaneously visualize desired combinations of MRI, CT, EEG, MEG, fMRI, PET, and intracranial EEG (i.e., ECoG, depth electrodes, and DBS). Here we present the Multi-Modal Visualization Tool (MMVT), which is designed for researchers to interact with their neuroimaging functional and anatomical data through simultaneous visualization of these existing imaging modalities. MMVT contains two separate modules: The first includes complete stand-alone pre-processing pipelines, from raw data to statistical maps. The second module is an add-on to the open-source, 3D-rendering program Blender. It is an interactive graphical interface that enables users to simultaneously visualize multi-modality functional and statistical data on the cortex and in subcortical surfaces as well as the activity of invasive electrodes. This tool also enables highly accurate 3D visualization of neuroanatomy, including the location of invasive electrodes relative to brain structures. Each of the modules and module features can be integrated, separate from the tool, into existing data pipelines. MMVT leverages open-source software to build a comprehensive tool for data visualization and exploration This gives the tool a distinct advantage in both clinical and research domains as each has highly specialized visual and processing needs.
To empower users of wearable medical devices, it is important to enable methods that facilitate reflection on previous care to improve future outcomes. In this work, we conducted a two-phase user-study involving patients, caregivers, and clinicians to understand gaps in current approaches that support reflection and user needs for new solutions. Our results show that users desire to have specific summarization metrics, solutions that minimize cognitive effort, and solutions that enable data integration to support meaningful reflection on diabetes management. In addition, we developed and evaluated a visualization called PixelGrid that presents key metrics in a matrix-based plot. Majority of users (84%) found the matrix-based approach to be useful for identifying salient patterns related to certain times and days in blood glucose data. Through our evaluation we identified that users desire data visualization solutions with complementary textual descriptors, concise and flexible presentation, contextually-fitting content, and informative and actionable insights. Directions for future research on tools that automate pattern discovery, detect abnormalities, and provide recommendations to improve care were also identified.
A central challenge in data visualization is to understand which data samples are required to generate an image of a data set in which the relevant information is encoded. In this work, we make a first step towards answering the question of whether an artificial neural network can predict where to sample the data with higher or lower density, by learning of correspondences between the data, the sampling patterns and the generated images. We introduce a novel neural rendering pipeline, which is trained end-to-end to generate a sparse adaptive sampling structure from a given low-resolution input image, and reconstructs a high-resolution image from the sparse set of samples. For the first time, to the best of our knowledge, we demonstrate that the selection of structures that are relevant for the final visual representation can be jointly learned together with the reconstruction of this representation from these structures. Therefore, we introduce differentiable sampling and reconstruction stages, which can leverage back-propagation based on supervised losses solely on the final image. We shed light on the adaptive sampling patterns generated by the network pipeline and analyze its use for volume visualization including isosurface and direct volume rendering.
Large observational clinical datasets become increasingly available for mining associations between various disease traits and administered therapy. These datasets can be considered as representations of the landscape of all possible disease conditions, in which a concrete pathology develops through a number of stereotypical routes, characterized by `points of no return' and `final states' (such as lethal or recovery states). Extracting this information directly from the data remains challenging, especially in the case of synchronic (with a short-term follow up) observations. Here we suggest a semi-supervised methodology for the analysis of large clinical datasets, characterized by mixed data types and missing values, through modeling the geometrical data structure as a bouquet of bifurcating clinical trajectories. The methodology is based on application of elastic principal graphs which can address simultaneously the tasks of dimensionality reduction, data visualization, clustering, feature selection and quantifying the geodesic distances (pseudotime) in partially ordered sequences of observations. The methodology allows positioning a patient on a particular clinical trajectory (pathological scenario) and characterizing the degree of progression along it with a qualitative estimate of the uncertainty of the prognosis. Overall, our pseudo-time quantification-based approach gives a possibility to apply the methods developed for dynamical disease phenotyping and illness trajectory analysis (diachronic data analysis) to synchronic observational data. We developed a tool $ClinTrajan$ for clinical trajectory analysis implemented in Python programming language. We test the methodology in two large publicly available datasets: myocardial infarction complications and readmission of diabetic patients data.
The COVID-19 outbreak has dramatically changed travel behavior in affected cities. The C2SMART research team has been investigating the impact of COVID-19 on mobility and sociability. New York City (NYC) and Seattle, two of the cities most affected by COVID-19 in the U.S. were included in our initial study. An all-in-one dashboard with data mining and cloud computing capabilities was developed for interactive data analytics and visualization to facilitate the understanding of the impact of the outbreak and corresponding policies such as social distancing on transportation systems. This platform is updated regularly and continues to evolve with the addition of new data, impact metrics, and visualizations to assist public and decision-makers to make informed decisions. This paper presents the architecture of the COVID related mobility data dashboard and preliminary mobility and sociability metrics for NYC and Seattle.
Originally, tangles were invented as an abstract tool in mathematical graph theory to prove the famous graph minor theorem. In this paper, we showcase the practical potential of tangles in machine learning applications. Given a collection of cuts of any dataset, tangles aggregate these cuts to point in the direction of a dense structure. As a result, a cluster is softly characterized by a set of consistent pointers. This highly flexible approach can solve clustering problems in various setups, ranging from questionnaires over community detection in graphs to clustering points in metric spaces. The output of our proposed framework is hierarchical and induces the notion of a soft dendrogram, which can help explore the cluster structure of a dataset. The computational complexity of aggregating the cuts is linear in the number of data points. Thus the bottleneck of the tangle approach is to generate the cuts, for which simple and fast algorithms form a sufficient basis. In our paper we construct the algorithmic framework for clustering with tangles, prove theoretical guarantees in various settings, and provide extensive simulations and use cases. Python code is available on github.
Ubiquitous linear Gaussian exploratory tools such as principle component analysis (PCA) and factor analysis (FA) remain widely used as tools for: exploratory analysis, pre-processing, data visualization and related tasks. However, due to their rigid assumptions including crowding of high dimensional data, they have been replaced in many settings by more flexible and still interpretable latent feature models. The Feature allocation is usually modelled using discrete latent variables assumed to follow either parametric Beta-Bernoulli distribution or Bayesian nonparametric prior. In this work we propose a simple and tractable parametric feature allocation model which can address key limitations of current latent feature decomposition techniques. The new framework allows for explicit control over the number of features used to express each point and enables a more flexible set of allocation distributions including feature allocations with different sparsity levels. This approach is used to derive a novel adaptive Factor analysis (aFA), as well as, an adaptive probabilistic principle component analysis (aPPCA) capable of flexible structure discovery and dimensionality reduction in a wide case of scenarios. We derive both standard Gibbs sampler, as well as, an expectation-maximization inference algorithms that converge orders of magnitude faster to a reasonable point estimate solution. The utility of the proposed aPPCA model is demonstrated for standard PCA tasks such as feature learning, data visualization and data whitening. We show that aPPCA and aFA can infer interpretable high level features both when applied on raw MNIST and when applied for interpreting autoencoder features. We also demonstrate an application of the aPPCA to more robust blind source separation for functional magnetic resonance imaging (fMRI).
Dimensionality reduction is often used as an initial step in data exploration, either as preprocessing for classification or regression or for visualization. Most dimensionality reduction techniques to date are unsupervised; they do not take class labels into account (e.g., PCA, MDS, t-SNE, Isomap). Such methods require large amounts of data and are often sensitive to noise that may obfuscate important patterns in the data. Various attempts at supervised dimensionality reduction methods that take into account auxiliary annotations (e.g., class labels) have been successfully implemented with goals of increased classification accuracy or improved data visualization. Many of these supervised techniques incorporate labels in the loss function in the form of similarity or dissimilarity matrices, thereby creating over-emphasized separation between class clusters, which does not realistically represent the local and global relationships in the data. In addition, these approaches are often sensitive to parameter tuning, which may be difficult to configure without an explicit quantitative notion of visual superiority. In this paper, we describe a novel supervised visualization technique based on random forest proximities and diffusion-based dimensionality reduction. We show, both qualitatively and quantitatively, the advantages of our approach in retaining local and global structures in data, while emphasizing important variables in the low-dimensional embedding. Importantly, our approach is robust to noise and parameter tuning, thus making it simple to use while producing reliable visualizations for data exploration.
Topological Data Analysis (TDA) provides novel approaches that allow us to analyze the geometrical shapes and topological structures of a dataset. As one important application, TDA can be used for data visualization and dimension reduction. We follow the framework of circular coordinate representation, which allows us to perform dimension reduction and visualization for high-dimensional datasets on a torus using persistent cohomology. In this paper, we propose a method to adapt the circular coordinate framework to take into account the roughness of circular coordinates in change-point and high-dimensional applications. We use a generalized penalty function instead of an $L_{2}$ penalty in the traditional circular coordinate algorithm. We provide simulation experiments and real data analysis to support our claim that circular coordinates with generalized penalty will detect the change in high-dimensional datasets under different sampling schemes while preserving the topological structures.
With the spread and development of new epidemics, it is of great reference value to identify the changing trends of epidemics in public emotions. We designed and implemented the COVID-19 public opinion monitoring system based on time series thermal new word mining. A new word structure discovery scheme based on the timing explosion of network topics and a Chinese sentiment analysis method for the COVID-19 public opinion environment is proposed. Establish a "Scrapy-Redis-Bloomfilter" distributed crawler framework to collect data. The system can judge the positive and negative emotions of the reviewer based on the comments, and can also reflect the depth of the seven emotions such as Hopeful, Happy, and Depressed. Finally, we improved the sentiment discriminant model of this system and compared the sentiment discriminant error of COVID-19 related comments with the Jiagu deep learning model. The results show that our model has better generalization ability and smaller discriminant error. We designed a large data visualization screen, which can clearly show the trend of public emotions, the proportion of various emotion categories, keywords, hot topics, etc., and fully and intuitively reflect the development of public opinion.
The Coronavirus pandemic has created complex challenges and adverse circumstances. This research discovers public sentiment amidst problematic socioeconomic consequences of the lockdown, and explores ensuing four potential sentiment associated scenarios. The severity and brutality of COVID-19 have led to the development of extreme feelings, and emotional and mental healthcare challenges. This research identifies emotional consequences - the presence of extreme fear, confusion and volatile sentiments, mixed along with trust and anticipation. It is necessary to gauge dominant public sentiment trends for effective decisions and policies. This study analyzes public sentiment using Twitter Data, time-aligned to COVID-19, to identify dominant sentiment trends associated with the push to 'reopen' the economy. Present research uses textual analytics methodologies to analyze public sentiment support for two potential divergent scenarios - an early opening and a delayed opening, and consequences of each. Present research concludes on the basis of exploratory textual analytics and textual data visualization, that Tweets data from American Twitter users shows more trust sentiment support, than fear, for reopening the US economy. With additional validation, this could present a valuable time sensitive opportunity for state governments, the federal government, corporations and societal leaders to guide the nation into a successful new normal future.
Autoencoders are techniques for data representation learning based on artificial neural networks. Differently to other feature learning methods which may be focused on finding specific transformations of the feature space, they can be adapted to fulfill many purposes, such as data visualization, denoising, anomaly detection and semantic hashing. This work presents these applications and provides details on how autoencoders can perform them, including code samples making use of an R package with an easy-to-use interface for autoencoder design and training, \texttt{ruta}. Along the way, the explanations on how each learning task has been achieved are provided with the aim to help the reader design their own autoencoders for these or other objectives.
This paper proposes a faceted information exploration model that supports coarse-grained and fine-grained focusing of geographic maps by offering a graphical representation of data attributes within interactive widgets. The proposed approach enables (i) a multi-category projection of long-lasting geographic maps, based on the proposal of efficient facets for data exploration in sparse and noisy datasets, and (ii) an interactive representation of the search context based on widgets that support data visualization, faceted exploration, category-based information hiding and transparency of results at the same time. The integration of our model with a semantic representation of geographical knowledge supports the exploration of information retrieved from heterogeneous data sources, such as Public Open Data and OpenStreetMap. We evaluated our model with users in the OnToMap collaborative Web GIS. The experimental results show that, when working on geographic maps populated with multiple data categories, it outperforms simple category-based map projection and traditional faceted search tools, such as checkboxes, in both user performance and experience.
Crowd simulation is a central topic in several fields including graphics. To achieve high-fidelity simulations, data has been increasingly relied upon for analysis and simulation guidance. However, the information in real-world data is often noisy, mixed and unstructured, making it difficult for effective analysis, therefore has not been fully utilized. With the fast-growing volume of crowd data, such a bottleneck needs to be addressed. In this paper, we propose a new framework which comprehensively tackles this problem. It centers at an unsupervised method for analysis. The method takes as input raw and noisy data with highly mixed multi-dimensional (space, time and dynamics) information, and automatically structure it by learning the correlations among these dimensions. The dimensions together with their correlations fully describe the scene semantics which consists of recurring activity patterns in a scene, manifested as space flows with temporal and dynamics profiles. The effectiveness and robustness of the analysis have been tested on datasets with great variations in volume, duration, environment and crowd dynamics. Based on the analysis, new methods for data visualization, simulation evaluation and simulation guidance are also proposed. Together, our framework establishes a highly automated pipeline from raw data to crowd analysis, comparison and simulation guidance. Extensive experiments and evaluations have been conducted to show the flexibility, versatility and intuitiveness of our framework.
Here, we propose an unsupervised fuzzy rule-based dimensionality reduction method primarily for data visualization. It considers the following important issues relevant to dimensionality reduction-based data visualization: (i) preservation of neighborhood relationships, (ii) handling data on a non-linear manifold, (iii) the capability of predicting projections for new test data points, (iv) interpretability of the system, and (v) the ability to reject test points if required. For this, we use a first-order Takagi-Sugeno type model. We generate rule antecedents using clusters in the input data. In this context, we also propose a new variant of the Geodesic c-means clustering algorithm. We estimate the rule parameters by minimizing an error function that preserves the inter-point geodesic distances (distances over the manifold) as Euclidean distances on the projected space. We apply the proposed method on three synthetic and three real-world data sets and visually compare the results with four other standard data visualization methods. The obtained results show that the proposed method behaves desirably and performs better than or comparable to the methods compared with. The proposed method is found to be robust to the initial conditions. The predictability of the proposed method for test points is validated by experiments. We also assess the ability of our method to reject output points when it should. Then, we extend this concept to provide a general framework for learning an unsupervised fuzzy model for data projection with different objective functions. To the best of our knowledge, this is the first attempt to manifold learning using unsupervised fuzzy modeling.
Based on a combined data set of 4000 high resolution facial scans, we introduce a non-linear morphable face model, capable of producing multifarious face geometry of pore-level resolution, coupled with material attributes for use in physically-based rendering. We aim to maximize the variety of face identities, while increasing the robustness of correspondence between unique components, including middle-frequency geometry, albedo maps, specular intensity maps and high-frequency displacement details. Our deep learning based generative model learns to correlate albedo and geometry, which ensures the anatomical correctness of the generated assets. We demonstrate potential use of our generative model for novel identity generation, model fitting, interpolation, animation, high fidelity data visualization, and low-to-high resolution data domain transferring. We hope the release of this generative model will encourage further cooperation between all graphics, vision, and data focused professionals while demonstrating the cumulative value of every individual's complete biometric profile.
The objective of this study is to predict suicidal and non-suicidal deaths from DNA methylation data using a modern machine learning algorithm. We used support vector machines to classify existing secondary data consisting of normalized values of methylated DNA probe intensities from tissues of two cortical brain regions to distinguish suicide cases from control cases. Before classification, we employed Principal component analysis (PCA) and t-distributed Stochastic Neighbor Embedding (t-SNE) to reduce the dimension of the data. In comparison to PCA, the modern data visualization method t-SNE performs better in dimensionality reduction. t-SNE accounts for the possible non-linear patterns in low-dimensional data. We applied four-fold cross-validation in which the resulting output from t-SNE was used as training data for the Support Vector Machine (SVM). Despite the use of cross-validation, the nominally perfect prediction of suicidal deaths for BA11 data suggests possible over-fitting of the model. The study also may have suffered from 'spectrum bias' since the individuals were only studied from two extreme scenarios. This research constitutes a baseline study for classifying suicidal and non-suicidal deaths from DNA methylation data. Future studies with larger sample size, while possibly incorporating methylation data from living individuals, may reduce the bias and improve the accuracy of the results.
Similarity learning has gained a lot of attention from researches in recent years and tons of successful approaches have been recently proposed. However, the majority of the state-of-the-art similarity learning methods consider only a binary similarity. In this paper we introduce a new loss function called Continuous Histogram Loss (CHL) which generalizes recently proposed Histogram loss to multiple-valued similarities, i.e. allowing the acceptable values of similarity to be continuously distributed within some range. The novel loss function is computed by aggregating pairwise distances and similarities into 2D histograms in a differentiable manner and then computing the probability of condition that pairwise distances will not decrease as the similarities increase. The novel loss is capable of solving a wider range of tasks including similarity learning, representation learning and data visualization.
Visualizing high-dimensional data is an essential task in Data Science and Machine Learning. The Centroid-Encoder (CE) method is similar to the autoencoder but incorporates label information to keep objects of a class close together in the reduced visualization space. CE exploits nonlinearity and labels to encode high variance in low dimensions while capturing the global structure of the data. We present a detailed analysis of the method using a wide variety of data sets and compare it with other supervised dimension reduction techniques, including NCA, nonlinear NCA, t-distributed NCA, t-distributed MCML, supervised UMAP, supervised PCA, Colored Maximum Variance Unfolding, supervised Isomap, Parametric Embedding, supervised Neighbor Retrieval Visualizer, and Multiple Relational Embedding. We empirically show that centroid-encoder outperforms most of these techniques. We also show that when the data variance is spread across multiple modalities, centroid-encoder extracts a significant amount of information from the data in low dimensional space. This key feature establishes its value to use it as a tool for data visualization.
This paper describes the development of a system that enables real time data visualization via a webapp regarding sound intensity using multiple node devices connected through internet. The prototypes were realized using ATmega328 (Arduino Nano) and ESP8266 hardware modules, NodeMCU Arduino wrapper library, Google maps and firebase API along with JavaScript webapp. System architecture is such that multiple node devices will be installed in different locations of the target area. On each node device, an Arduino Nano interfaced with a Sound Sensor measures the ambient sound intensity and ESP8266 Wi-Fi module transmits the data to a database via web API. On the webapp, it plots all the real-time data from the devices over Google maps according to the locations of the node devices. The logged data that is collected can then be used to carry out researches regarding sound pollution in targeted areas.