We study how to convert OpenStreetMap data to road networks for downstream applications. OpenStreetMap data has different formats. Extensible Markup Language (XML) is one of them. OSM data consist of nodes, ways, and relations. We process OSM XML data to extract the information of nodes and ways to obtain the map of streets of the Memphis area. We can use this map for different downstream applications.
Motivation: Visualization of data is a crucial step to understanding and deriving hypotheses from clinical data. However, for clinicians, visualization often comes with great effort due to the lack of technical knowledge about data handling and visualization. The application offers an easy-to-use solution with an intuitive design that enables various kinds of plotting functions. The aim was to provide an intuitive solution with a low entrance barrier for clinical users. Little to no onboarding is required before creating plots, while the complexity of questions can grow up to specific corner cases. To allow for an easy start and testing with SCAview, we incorporated a synthetic cohort dataset based on real data of rare neurological movement disorders: the most common autosomal-dominantly inherited spinocerebellar ataxias (SCAs) type 1, 2, 3, and 6 (SCA1, 2, 3 and 6). Methods: We created a Django-based backend application that serves the data to a React-based frontend that uses Plotly for plotting. A synthetic cohort was created to deploy a version of SCAview without violating any data protection guidelines. Here, we added normal distributed noise to the data and therefore prevent re-identification while keeping distributions and general correlations. Results: This work presents SCAview, an user-friendly, interactive web-based service that enables data visualization in a clickable interface allowing intuitive graphical handling that aims to enable data visualization in a clickable interface. The service is deployed and can be tested with a synthetic cohort created based on a large, longitudinal dataset from observational studies in the most common SCAs.
Dimension reduction and data visualization aim to project a high-dimensional dataset to a low-dimensional space while capturing the intrinsic structures in the data. It is an indispensable part of modern data science, and many dimensional reduction and visualization algorithms have been developed. However, different algorithms have their own strengths and weaknesses, making it critically important to evaluate their relative performance for a given dataset, and to leverage and combine their individual strengths. In this paper, we propose an efficient spectral method for assessing and combining multiple visualizations of a given dataset produced by diverse algorithms. The proposed method provides a quantitative measure -- the visualization eigenscore -- of the relative performance of the visualizations for preserving the structure around each data point. Then it leverages the eigenscores to obtain a consensus visualization, which has much improved { quality over the individual visualizations in capturing the underlying true data structure.} Our approach is flexible and works as a wrapper around any visualizations. We analyze multiple simulated and real-world datasets from diverse applications to demonstrate the effectiveness of the eigenscores for evaluating visualizations and the superiority of the proposed consensus visualization. Furthermore, we establish rigorous theoretical justification of our method based on a general statistical framework, yielding fundamental principles behind the empirical success of consensus visualization along with practical guidance.
Pharmaceutical researchers are continually searching for techniques to improve both drug development processes and patient outcomes. An area of recent interest is the potential for machine learning (ML) applications within pharmacology. One such application not yet given close study is the unsupervised clustering of plasma concentration-time curves, hereafter, pharmacokinetic (PK) curves. In this paper, we present our findings on how to cluster PK curves by their similarity. Specifically, we find clustering to be effective at identifying similar-shaped PK curves and informative for understanding patterns within each cluster of PK curves. Because PK curves are time series data objects, our approach utilizes the extensive body of research related to the clustering of time series data as a starting point. As such, we examine many dissimilarity measures between time series data objects to find those most suitable for PK curves. We identify Euclidean distance as generally most appropriate for clustering PK curves, and we further show that dynamic time warping, Fr\'{e}chet, and structure-based measures of dissimilarity like correlation may produce unexpected results. As an illustration, we apply these methods in a case study with 250 PK curves used in a previous pharmacogenomic study. Our case study finds that an unsupervised ML clustering with Euclidean distance, without any subject genetic information, is able to independently validate the same conclusions as the reference pharmacogenomic results. To our knowledge, this is the first such demonstration. Further, the case study demonstrates how the clustering of PK curves may generate insights that could be difficult to perceive solely with population level summary statistics of PK metrics.
Recently, Transformer is much popular and plays an important role in the fields of Machine Learning (ML), Natural Language Processing (NLP), and Computer Vision (CV), etc. In this paper, based on the Vision Transformer (ViT) model, a new dimensionality reduction (DR) model is proposed, named Transformer-DR. From data visualization, image reconstruction and face recognition, the representation ability of Transformer-DR after dimensionality reduction is studied, and it is compared with some representative DR methods to understand the difference between Transformer-DR and existing DR methods. The experimental results show that Transformer-DR is an effective dimensionality reduction method.
Recommender systems have become an essential tool for providers and users of online services and goods, especially with the increased use of the Internet to access information and purchase products and services. This work proposes a novel recommendation method based on complex networks generated by a similarity-popularity model to predict ones. We first construct a model of a network having users and items as nodes from observed ratings and then use it to predict unseen ratings. The prospect of producing accurate rating predictions using a similarity-popularity model with hidden metric spaces and dot-product similarity is explored. The proposed approach is implemented and experimentally compared against baseline and state-of-the-art recommendation methods on 21 datasets from various domains. The experimental results demonstrate that the proposed method produces accurate predictions and outperforms existing methods. We also show that the proposed approach produces superior results in low dimensions, proving its effectiveness for data visualization and exploration.
Volume data is found in many important scientific and engineering applications. Rendering this data for visualization at high quality and interactive rates for demanding applications such as virtual reality is still not easily achievable even using professional-grade hardware. We introduce FoVolNet -- a method to significantly increase the performance of volume data visualization. We develop a cost-effective foveated rendering pipeline that sparsely samples a volume around a focal point and reconstructs the full-frame using a deep neural network. Foveated rendering is a technique that prioritizes rendering computations around the user's focal point. This approach leverages properties of the human visual system, thereby saving computational resources when rendering data in the periphery of the user's field of vision. Our reconstruction network combines direct and kernel prediction methods to produce fast, stable, and perceptually convincing output. With a slim design and the use of quantization, our method outperforms state-of-the-art neural reconstruction techniques in both end-to-end frame times and visual quality. We conduct extensive evaluations of the system's rendering performance, inference speed, and perceptual properties, and we provide comparisons to competing neural image reconstruction techniques. Our test results show that FoVolNet consistently achieves significant time saving over conventional rendering while preserving perceptual quality.
Graph embedding methods aim at finding useful graph representations by mapping nodes to a low-dimensional vector space. It is a task with important downstream applications, such as link prediction, graph reconstruction, data visualization, node classification, and language modeling. In recent years, the field of graph embedding has witnessed a shift from linear algebraic approaches towards local, gradient-based optimization methods combined with random walks and deep neural networks to tackle the problem of embedding large graphs. However, despite this improvement in the optimization tools, graph embedding methods are still generically designed in a way that is oblivious to the particularities of real-life networks. Indeed, there has been significant progress in understanding and modeling complex real-life networks in recent years. However, the obtained results have had a minor influence on the development of graph embedding algorithms. This paper aims to remedy this by designing a graph embedding method that takes advantage of recent valuable insights from the field of network science. More precisely, we present a novel graph embedding approach based on the popularity-similarity and local attraction paradigms. We evaluate the performance of the proposed approach on the link prediction task on a large number of real-life networks. We show, using extensive experimental analysis, that the proposed method outperforms state-of-the-art graph embedding algorithms. We also demonstrate its robustness to data scarcity and the choice of embedding dimensionality.
Time series are measured and analyzed across the sciences. One method of quantifying the structure of time series is by calculating a set of summary statistics or `features', and then representing a time series in terms of its properties as a feature vector. The resulting feature space is interpretable and informative, and enables conventional statistical learning approaches, including clustering, regression, and classification, to be applied to time-series datasets. Many open-source software packages for computing sets of time-series features exist across multiple programming languages, including catch22 (22 features: Matlab, R, Python, Julia), feasts (42 features: R), tsfeatures (63 features: R), Kats (40 features: Python), tsfresh (779 features: Python), and TSFEL (390 features: Python). However, there are several issues: (i) a singular access point to these packages is not currently available; (ii) to access all feature sets, users must be fluent in multiple languages; and (iii) these feature-extraction packages lack extensive accompanying methodological pipelines for performing feature-based time-series analysis, such as applications to time-series classification. Here we introduce a solution to these issues in an R software package called theft: Tools for Handling Extraction of Features from Time series. theft is a unified and extendable framework for computing features from the six open-source time-series feature sets listed above. It also includes a suite of functions for processing and interpreting the performance of extracted features, including extensive data-visualization templates, low-dimensional projections, and time-series classification operations. With an increasing volume and complexity of time-series datasets in the sciences and industry, theft provides a standardized framework for comprehensively quantifying and interpreting informative structure in time series.
Deep learning based latent representations have been widely used for numerous scientific visualization applications such as isosurface similarity analysis, volume rendering, flow field synthesis, and data reduction, just to name a few. However, existing latent representations are mostly generated from raw data in an unsupervised manner, which makes it difficult to incorporate domain interest to control the size of the latent representations and the quality of the reconstructed data. In this paper, we present a novel importance-driven latent representation to facilitate domain-interest-guided scientific data visualization and analysis. We utilize spatial importance maps to represent various scientific interests and take them as the input to a feature transformation network to guide latent generation. We further reduced the latent size by a lossless entropy encoding algorithm trained together with the autoencoder, improving the storage and memory efficiency. We qualitatively and quantitatively evaluate the effectiveness and efficiency of latent representations generated by our method with data from multiple scientific visualization applications.
This paper presents 3D-RadViz, a visualization method for high dimensional data using a three dimensional radial visualization technique. The proposed technique extends the capabilities of the classical two dimensional radial visualization (RadViz) in order to reduce overlapping data points. For evaluation purposes, the paper applies the proposed 3D-RadViz alongside with t-SNE and a recently published 3-dimensional radial visualization technique to the same real-world datasets from the UCI machine learning repository. The contribution of the work is an interactive, deterministic, and high-performance library, implemented in Python, that can be utilized to realize better high dimensional data visualization using the proposed 3D-RadViz technique. The paper also suggests some directions for future enhancements to the proposed visualization approach.
Dimensionality reduction techniques aim at representing high-dimensional data in low-dimensional spaces to extract hidden and useful information or facilitate visual understanding and interpretation of the data. However, few of them take into consideration the potential cluster information contained implicitly in the high-dimensional data. In this paper, we propose LaptSNE, a new graph-layout nonlinear dimensionality reduction method based on t-SNE, one of the best techniques for visualizing high-dimensional data as 2D scatter plots. Specifically, LaptSNE leverages the eigenvalue information of the graph Laplacian to shrink the potential clusters in the low-dimensional embedding when learning to preserve the local and global structure from high-dimensional space to low-dimensional space. It is nontrivial to solve the proposed model because the eigenvalues of normalized symmetric Laplacian are functions of the decision variable. We provide a majorization-minimization algorithm with convergence guarantee to solve the optimization problem of LaptSNE and show how to calculate the gradient analytically, which may be of broad interest when considering optimization with Laplacian-composited objective. We evaluate our method by a formal comparison with state-of-the-art methods on seven benchmark datasets, both visually and via established quantitative measurements. The results demonstrate the superiority of our method over baselines such as t-SNE and UMAP. We also provide out-of-sample extension, large-scale extension and mini-batch extension for our LaptSNE to facilitate dimensionality reduction in various scenarios.
Data visualization captions help readers understand the purpose of a visualization and are crucial for individuals with visual impairments. The prevalence of poor figure captions and the successful application of deep learning approaches to image captioning motivate the use of similar techniques for automated figure captioning. However, research in this field has been stunted by the lack of suitable datasets. We introduce LineCap, a novel figure captioning dataset of 3,528 figures, and we provide insights from curating this dataset and using end-to-end deep learning models for automated figure captioning.
This work develops a smart mat for monitoring body positions. We use Velostat as a force sensor resistance (FSR) to construct a sensor matrix over the mat to receive the pressure distribution of the patient's body, and then upload the processed distribution information to the PC for data visualization through Arduino. Data visualization on the PC side is compiled through Python language to realize the functions of patient body pressure distribution monitoring, long-term pressure alarm and posture prediction. The purpose of this work is to relieve the work stress on medical staff caused by pressure injuries during the treatment and care of patients during the pandemic. This paper includes the literature review on similar previous works and combines the test results to design the structure and circuit of the smart mat.
The utilization of artificial intelligence (AI) applications has experienced tremendous growth in recent years, bringing forth numerous benefits and conveniences. However, this expansion has also provoked ethical concerns, such as privacy breaches, algorithmic discrimination, security and reliability issues, transparency, and other unintended consequences. To determine whether a global consensus exists regarding the ethical principles that should govern AI applications and to contribute to the formation of future regulations, this paper conducts a meta-analysis of 200 governance policies and ethical guidelines for AI usage published by public bodies, academic institutions, private companies, and civil society organizations worldwide. We identified at least 17 resonating principles prevalent in the policies and guidelines of our dataset, released as an open-source database and tool. We present the limitations of performing a global scale analysis study paired with a critical analysis of our findings, presenting areas of consensus that should be incorporated into future regulatory efforts. All components tied to this work can be found in https://nkluge-correa.github.io/worldwide_AI-ethics/
Visual analytics is arguably the most important step in getting acquainted with your data. This is especially the case for time series, as this data type is hard to describe and cannot be fully understood when using for example summary statistics. To realize effective time series visualization, four requirements have to be met; a tool should be (1) interactive, (2) scalable to millions of data points, (3) integrable in conventional data science environments, and (4) highly configurable. We observe that open source Python visualization toolkits empower data scientists in most visual analytics tasks, but lack the combination of scalability and interactivity to realize effective time series visualization. As a means to facilitate these requirements, we created Plotly-Resampler, an open source Python library. Plotly-Resampler is an add-on for Plotly's Python bindings, enhancing line chart scalability on top of an interactive toolkit by aggregating the underlying data depending on the current graph view. Plotly-Resampler is built to be snappy, as the reactivity of a tool qualitatively affects how analysts visually explore and analyze data. A benchmark task highlights how our toolkit scales better than alternatives in terms of number of samples and time series. Additionally, Plotly-Resampler's flexible data aggregation functionality paves the path towards researching novel aggregation techniques. Plotly-Resampler's integrability, together with its configurability, convenience, and high scalability, allows to effectively analyze high-frequency data in your day-to-day Python environment.
Soil moisture (SM) is referred to as a finite amount of water molecules within the pore spaces and it is a crucial parameter of Hydro-Meteorological processes. The behaviour of soil moisture water changes spatially and temporally in response to topography, soil characteristics, and climate[1]. Soil moisture is overseen by various hydro-meteorological factors that vary vertically with depth, laterally across terrestrial shapes, and temporarily in feedback to the climate. The precise monitoring and quantification of high-resolution surface and subsurface soil moisture observations are very important [13]. This paper highlights the outcomes of the fieldwork carried out at IITM, Pune, wherein we have developed a soil moisture and temperature measurement system using Raspberry Pi and the Internet of things (IoT). The development is classified into three stages, the first stage includes the assembly of the sensor with the microprocessor. The deployment of the low-cost system, data generation, and communication through a wireless sensor network is part of the second stage. Finally, the third stage includes real-time data visualization using a mobile application and data server for analysing soil moisture and temperature. The soil moisture profile obtained through the sensor deployed is highly correlated (r=.9) with in-situ gravimetric observations, having a root mean square error (RMSE) of about 3.1%. Similarly, the temperature observations are well-matched with the in-situ standard temperature observation. Here we present the preliminary results and compare the accuracy with the state-of-the-art sensors.
Dimensionality reduction is a popular preprocessing and a widely used tool in data mining. Transparency, which is usually achieved by means of explanations, is nowadays a widely accepted and crucial requirement of machine learning based systems like classifiers and recommender systems. However, transparency of dimensionality reduction and other data mining tools have not been considered in much depth yet, still it is crucial to understand their behavior -- in particular practitioners might want to understand why a specific sample got mapped to a specific location. In order to (locally) understand the behavior of a given dimensionality reduction method, we introduce the abstract concept of contrasting explanations for dimensionality reduction, and apply a realization of this concept to the specific application of explaining two dimensional data visualization.
Developing Machine Learning (ML) algorithms for heterogeneous/mixed data is a longstanding problem. Many ML algorithms are not applicable to mixed data, which include numeric and non-numeric data, text, graphs and so on to generate interpretable models. Another longstanding problem is developing algorithms for lossless visualization of multidimensional mixed data. The further progress in ML heavily depends on success interpretable ML algorithms for mixed data and lossless interpretable visualization of multidimensional data. The later allows developing interpretable ML models using visual knowledge discovery by end-users, who can bring valuable domain knowledge which is absent in the training data. The challenges for mixed data include: (1) generating numeric coding schemes for non-numeric attributes for numeric ML algorithms to provide accurate and interpretable ML models, (2) generating methods for lossless visualization of n-D non-numeric data and visual rule discovery in these visualizations. This paper presents a classification of mixed data types, analyzes their importance for ML and present the developed experimental toolkit to deal with mixed data. It combines the Data Types Editor, VisCanvas data visualization and rule discovery system which is available on GitHub.
Contrastive learning, especially self-supervised contrastive learning (SSCL), has achieved great success in extracting powerful features from unlabeled data. In this work, we contribute to the theoretical understanding of SSCL and uncover its connection to the classic data visualization method, stochastic neighbor embedding (SNE), whose goal is to preserve pairwise distances. From the perspective of preserving neighboring information, SSCL can be viewed as a special case of SNE with the input space pairwise similarities specified by data augmentation. The established correspondence facilitates deeper theoretical understanding of learned features of SSCL, as well as methodological guidelines for practical improvement. Specifically, through the lens of SNE, we provide novel analysis on domain-agnostic augmentations, implicit bias and robustness of learned features. To illustrate the practical advantage, we demonstrate that the modifications from SNE to $t$-SNE can also be adopted in the SSCL setting, achieving significant improvement in both in-distribution and out-of-distribution generalization.