The visualization and detection of anomalies (outliers) are of crucial importance to many fields, particularly cybersecurity. Several approaches have been proposed in these fields, yet to the best of our knowledge, none of them has fulfilled both objectives, simultaneously or cooperatively, in one coherent framework. The visualization methods of these approaches were introduced for explaining the output of a detection algorithm, not for data exploration that facilitates a standalone visual detection. This is our point of departure: UN-AVOIDS, an unsupervised and nonparametric approach for both visualization (a human process) and detection (an algorithmic process) of outliers, that assigns invariant anomalous scores (normalized to $[0,1]$), rather than hard binary-decision. The main aspect of novelty of UN-AVOIDS is that it transforms data into a new space, which is introduced in this paper as neighborhood cumulative density function (NCDF), in which both visualization and detection are carried out. In this space, outliers are remarkably visually distinguishable, and therefore the anomaly scores assigned by the detection algorithm achieved a high area under the ROC curve (AUC). We assessed UN-AVOIDS on both simulated and two recently published cybersecurity datasets, and compared it to three of the most successful anomaly detection methods: LOF, IF, and FABOD. In terms of AUC, UN-AVOIDS was almost an overall winner. The article concludes by providing a preview of new theoretical and practical avenues for UN-AVOIDS. Among them is designing a visualization aided anomaly detection (VAAD), a type of software that aids analysts by providing UN-AVOIDS' detection algorithm (running in a back engine), NCDF visualization space (rendered to plots), along with other conventional methods of visualization in the original feature space, all of which are linked in one interactive environment.
Citation information in scholarly data is an important source of insight into the reception of publications and the scholarly discourse. Outcomes of citation analyses and the applicability of citation based machine learning approaches heavily depend on the completeness of such data. One particular shortcoming of scholarly data nowadays is that non-English publications are often not included in data sets, or that language metadata is not available. Because of this, citations between publications of differing languages (cross-lingual citations) have only been studied to a very limited degree. In this paper, we present an analysis of cross-lingual citations based on over one million English papers, spanning three scientific disciplines and a time span of three decades. Our investigation covers differences between cited languages and disciplines, trends over time, and the usage characteristics as well as impact of cross-lingual citations. Among our findings are an increasing rate of citations to publications written in Chinese, citations being primarily to local non-English languages, and consistency in citation intent between cross- and monolingual citations. To facilitate further research, we make our collected data and source code publicly available.
A good data visualization is not only a distortion-free graphical representation of data but also a way to reveal underlying statistical properties of the data. Despite its common use across various stages of data analysis, selecting a good visualization often is a manual process involving many iterations. Recently there has been interest in reducing this effort by developing models that can recommend visualizations, but they are of limited use since they require large training samples (data and visualization pairs) and focus primarily on the design aspects rather than on assessing the effectiveness of the selected visualization. In this paper, we present VizAI, a generative-discriminative framework that first generates various statistical properties of the data from a number of alternative visualizations of the data. It is linked to a discriminative model that selects the visualization that best matches the true statistics of the data being visualized. VizAI can easily be trained with minimal supervision and adapts to settings with varying degrees of supervision easily. Using crowd-sourced judgements and a large repository of publicly available visualizations, we demonstrate that VizAI outperforms the state of the art methods that learn to recommend visualizations.
Annual ranking of higher educational institutions (HEIs) is a global phenomenon and have significant impact on higher education landscape. Most of the HEIs pay close attention to ranking results and look forward to improving their ranks. However, maintaining a good rank and ascending in the rankings is a difficult task because it requires considerable resources, efforts and performance improvement plan. In this work, firstly, we show how exploratory data analysis (EDA) using correlation heatmaps and box plots can aid in understanding the broad trends in the ranking data. Subsequently, we present a novel idea of classifying the rankings data using Decision Tree (DT) based algorithms and retrieve decision paths for rank improvement using data visualization techniques. Using Laplace correction to the probability estimate, we quantify the amount of certainty attached with different decision paths obtained from interpretable DT models. The proposed methodology can aid Universities and HEIs to quantitatively assess the scope of improvement, adumbrate a fine-grained long-term action plan and prepare a suitable road-map.
Innovative developments in data processing, archiving, analysis, and visualization are nowadays unavoidable to deal with the data deluge expected in next-generation facilities for radio astronomy, such as the Square Kilometre Array (SKA) and its precursors. In this context, the integration of source extraction and analysis algorithms into data visualization tools could significantly improve and speed up the cataloguing process of large area surveys, boosting astronomer productivity and shortening publication time. To this aim, we are developing a visual analytic platform (CIRASA) for advanced source finding and classification, integrating state-of-the-art tools, such as the CAESAR source finder, the ViaLactea Visual Analytic (VLVA) and Knowledge Base (VLKB). In this work, we present the project objectives and the platform architecture, focusing on the implemented source finding services.
With the rapid development of data collection techniques, complex data objects that are not in the Euclidean space are frequently encountered in new statistical applications. Fr\'echet regression model (Peterson & M\"uller 2019) provides a promising framework for regression analysis with metric space-valued responses. In this paper, we introduce a flexible sufficient dimension reduction (SDR) method for Fr\'echet regression to achieve two purposes: to mitigate the curse of dimensionality caused by high-dimensional predictors and to provide a visual inspection tool for Fr\'echet regression. Our approach is flexible enough to turn any existing SDR method for Euclidean (X,Y) into one for Euclidean X and metric space-valued Y. The basic idea is to first map the metric-space valued random object $Y$ to a real-valued random variable $f(Y)$ using a class of functions, and then perform classical SDR to the transformed data. If the class of functions is sufficiently rich, then we are guaranteed to uncover the Fr\'echet SDR space. We showed that such a class, which we call an ensemble, can be generated by a universal kernel. We established the consistency and asymptotic convergence rate of the proposed methods. The finite-sample performance of the proposed methods is illustrated through simulation studies for several commonly encountered metric spaces that include Wasserstein space, the space of symmetric positive definite matrices, and the sphere. We illustrated the data visualization aspect of our method by exploring the human mortality distribution data across countries and by studying the distribution of hematoma density.
A fundamental task in machine learning involves visualizing high-dimensional data sets that arise in high-impact application domains. When considering the context of large imbalanced data, this problem becomes much more challenging. In this paper, the t-Distributed Stochastic Neighbor Embedding (t-SNE) algorithm is used to reduce the dimensions of an earthquake engineering related data set for visualization purposes. Since imbalanced data sets greatly affect the accuracy of classifiers, we employ Synthetic Minority Oversampling Technique (SMOTE) to tackle the imbalanced nature of such data set. We present the result obtained from t-SNE and SMOTE and compare it to the basic approaches with various aspects. Considering four options and six classification algorithms, we show that using t-SNE on the imbalanced data and SMOTE on the training data set, neural network classifiers have promising results without sacrificing accuracy. Hence, we can transform the studied scientific data into a two-dimensional (2D) space, enabling the visualization of the classifier and the resulting decision surface using a 2D plot.
Uniform Manifold Approximation and Projection (UMAP) is one of the state-of-the-art methods for dimensionality reduction and data visualization. This is a tutorial and survey paper on UMAP and its variants. We start with UMAP algorithm where we explain probabilities of neighborhood in the input and embedding spaces, optimization of cost function, training algorithm, derivation of gradients, and supervised and semi-supervised embedding by UMAP. Then, we introduce the theory behind UMAP by algebraic topology and category theory. Then, we introduce UMAP as a neighbor embedding method and compare it with t-SNE and LargeVis algorithms. We discuss negative sampling and repulsive forces in UMAP's cost function. DensMAP is then explained for density-preserving embedding. We then introduce parametric UMAP for embedding by deep learning and progressive UMAP for streaming and out-of-sample data embedding.
Here we will give a perspective on new possible interplays between Machine Learning and Quantum Physics, including also practical cases and applications. We will explore the ways in which machine learning could benefit from new quantum technologies and algorithms to find new ways to speed up their computations by breakthroughs in physical hardware, as well as to improve existing models or devise new learning schemes in the quantum domain. Moreover, there are lots of experiments in quantum physics that do generate incredible amounts of data and machine learning would be a great tool to analyze those and make predictions, or even control the experiment itself. On top of that, data visualization techniques and other schemes borrowed from machine learning can be of great use to theoreticians to have better intuition on the structure of complex manifolds or to make predictions on theoretical models. This new research field, named as Quantum Machine Learning, is very rapidly growing since it is expected to provide huge advantages over its classical counterpart and deeper investigations are timely needed since they can be already tested on the already commercially available quantum machines.
Neighbor Embedding (NE) aims to preserve pairwise similarities between data items and has been shown to yield an effective principle for data visualization. However, even the best existing NE methods such as Stochastic Neighbor Embedding (SNE) may leave large-scale patterns hidden, for example clusters, despite strong signals being present in the data. To address this, we propose a new cluster visualization method based on the Neighbor Embedding principle. We first present a family of Neighbor Embedding methods that generalizes SNE by using non-normalized Kullback-Leibler divergence with a scale parameter. In this family, much better cluster visualizations often appear with a parameter value different from the one corresponding to SNE. We also develop an efficient software that employs asynchronous stochastic block coordinate descent to optimize the new family of objective functions. Our experimental results demonstrate that the method consistently and substantially improves the visualization of data clusters compared with the state-of-the-art NE approaches.
We use graphical methods to probe neural nets that classify images. Plots of t-SNE outputs at successive layers in a network reveal increasingly organized arrangement of the data points. They can also reveal how a network can diminish or even forget about within-class structure as the data proceeds through layers. We use class-specific analogues of principal components to visualize how succeeding layers separate the classes. These allow us to sort images from a given class from most typical to least typical (in the data) and they also serve as very useful projection coordinates for data visualization. We find them especially useful when defining versions guided tours for animated data visualization.
The efficiency of modern computer graphics allows us to explore collections of space curves simultaneously with "drag-to-rotate" interfaces. This inspires us to replace "scatterplots of points" with "scatterplots of curves" to simultaneously visualize relationships across an entire dataset. Since spaces of curves are infinite dimensional, scatterplots of curves avoid the "lossy" nature of scatterplots of points. In particular, if two points are close in a scatterplot of points derived from high-dimensional data, it does not generally follow that the two associated data points are close in the data space. Standard Andrews plots provide scatterplots of curves that perfectly preserve Euclidean distances, but simultaneous visualization of these graphs over an entire dataset produces visual clutter because graphs of functions generally overlap in 2D. We mitigate this visual clutter issue by constructing computationally inexpensive 3D extensions of Andrews plots. First, we construct optimally smooth 3D Andrews plots by considering linear isometries from Euclidean data spaces to spaces of planar parametric curves. We rigorously parametrize the linear isometries that produce (on average) optimally smooth curves over a given dataset. This parameterization of optimal isometries reveals many degrees of freedom, and (using recent results on generalized Gauss sums) we identify a particular member of this set which admits an asymptotic "tour" property that avoids certain local degeneracies as well. Finally, we construct unit-length 3D curves (filaments) by numerically solving Frenet-Serret systems given data from these 3D Andrews plots. We conclude with examples of filament plots for several standard datasets, illustrating how filament plots avoid visual clutter. Code and examples available at https://github.com/n8epi/filaments/ and https://n8epi.github.io/filaments/
The deployment of various networks (e.g., Internet of Things [IoT] and mobile networks), databases (e.g., nutrition tables and food compositional databases), and social media (e.g., Instagram and Twitter) generates huge amounts of food data, which present researchers with an unprecedented opportunity to study various problems and applications in food science and industry via data-driven computational methods. However, these multi-source heterogeneous food data appear as information silos, leading to difficulty in fully exploiting these food data. The knowledge graph provides a unified and standardized conceptual terminology in a structured form, and thus can effectively organize these food data to benefit various applications. In this review, we provide a brief introduction to knowledge graphs and the evolution of food knowledge organization mainly from food ontology to food knowledge graphs. We then summarize seven representative applications of food knowledge graphs, such as new recipe development, diet-disease correlation discovery, and personalized dietary recommendation. We also discuss future directions in this field, such as multimodal food knowledge graph construction and food knowledge graphs for human health.
As the complexity of machine learning (ML) models increases, resulting in a lack of prediction explainability, several methods have been developed to explain a model's behavior in terms of the training data points that most influence the model. However, these methods tend to mark outliers as highly influential points, limiting the insights that practitioners can draw from points that are not representative of the training data. In this work, we take a step towards finding influential training points that also represent the training data well. We first review methods for assigning importance scores to training points. Given importance scores, we propose a method to select a set of DIVerse INfluEntial (DIVINE) training points as a useful explanation of model behavior. As practitioners might not only be interested in finding data points influential with respect to model accuracy, but also with respect to other important metrics, we show how to evaluate training data points on the basis of group fairness. Our method can identify unfairness-inducing training points, which can be removed to improve fairness outcomes. Our quantitative experiments and user studies show that visualizing DIVINE points helps practitioners understand and explain model behavior better than earlier approaches.
Machine learning algorithms often produce models considered as complex black-box models by both end users and developers. They fail to explain the model in terms of the domain they are designed for. The proposed Iterative Visual Logical Classifier (IVLC) is an interpretable machine learning algorithm that allows end users to design a model and classify data with more confidence and without having to compromise on the accuracy. Such technique is especially helpful when dealing with sensitive and crucial data like cancer data in the medical domain with high cost of errors. With the help of the proposed interactive and lossless multidimensional visualization, end users can identify the pattern in the data based on which they can make explainable decisions. Such options would not be possible in black box machine learning methodologies. The interpretable IVLC algorithm is supported by the Interactive Shifted Paired Coordinates Software System (SPCVis). It is a lossless multidimensional data visualization system with user interactive features. The interactive approach provides flexibility to the end user to perform data classification as self-service without having to rely on a machine learning expert. Interactive pattern discovery becomes challenging while dealing with large data sets with hundreds of dimensions/features. To overcome this problem, this chapter proposes an automated classification approach combined with new Coordinate Order Optimizer (COO) algorithm and a Genetic algorithm. The COO algorithm automatically generates the coordinate pair sequences that best represent the data separation and the genetic algorithm helps optimizing the proposed IVLC algorithm by automatically generating the areas for data classification. The feasibility of the approach is shown by experiments on benchmark datasets covering both interactive and automated processes used for data classification.
Persistence diagrams have been widely used to quantify the underlying features of filtered topological spaces in data visualization. In many applications, computing distances between diagrams is essential; however, computing these distances has been challenging due to the computational cost. In this paper, we propose a persistence diagram hashing framework that learns a binary code representation of persistence diagrams, which allows for fast computation of distances. This framework is built upon a generative adversarial network (GAN) with a diagram distance loss function to steer the learning process. Instead of using standard representations, we hash diagrams into binary codes, which have natural advantages in large-scale tasks. The training of this model is domain-oblivious in that it can be computed purely from synthetic, randomly created diagrams. As a consequence, our proposed method is directly applicable to various datasets without the need for retraining the model. These binary codes, when compared using fast Hamming distance, better maintain topological similarity properties between datasets than other vectorized representations. To evaluate this method, we apply our framework to the problem of diagram clustering and we compare the quality and performance of our approach to the state-of-the-art. In addition, we show the scalability of our approach on a dataset with 10k persistence diagrams, which is not possible with current techniques. Moreover, our experimental results demonstrate that our method is significantly faster with the potential of less memory usage, while retaining comparable or better quality comparisons.
This paper investigates the theoretical foundations of the t-distributed stochastic neighbor embedding (t-SNE) algorithm, a popular nonlinear dimension reduction and data visualization method. A novel theoretical framework for the analysis of t-SNE based on the gradient descent approach is presented. For the early exaggeration stage of t-SNE, we show its asymptotic equivalence to power iterations based on the underlying graph Laplacian, characterize its limiting behavior, and uncover its deep connection to Laplacian spectral clustering, and fundamental principles including early stopping as implicit regularization. The results explain the intrinsic mechanism and the empirical benefits of such a computational strategy. For the embedding stage of t-SNE, we characterize the kinematics of the low-dimensional map throughout the iterations, and identify an amplification phase, featuring the intercluster repulsion and the expansive behavior of the low-dimensional map, and a stabilization phase. The general theory explains the fast convergence rate and the exceptional empirical performance of t-SNE for visualizing clustered data, brings forth interpretations of the t-SNE visualizations, and provides theoretical guidance for applying t-SNE and selecting its tuning parameters in various applications.
This paper presents maplet, an open-source R package for the creation of highly customizable, fully reproducible statistical pipelines for omics data analysis, with a special focus on metabolomics-based methods. It builds on the SummarizedExperiment data structure to create a centralized pipeline framework for storing data, analysis steps, results, and visualizations. maplet's key design feature is its modularity, which offers several advantages, such as ensuring code quality through the individual maintenance of functions and promoting collaborative development by removing technical barriers to code contribution. With over 90 functions, the package includes a wide range of functionalities, covering many widely used statistical approaches and data visualization techniques.
Plot-based Graphic API recommendation (Plot2API) is an unstudied but meaningful issue, which has several important applications in the context of software engineering and data visualization, such as the plotting guidance of the beginner, graphic API correlation analysis, and code conversion for plotting. Plot2API is a very challenging task, since each plot is often associated with multiple APIs and the appearances of the graphics drawn by the same API can be extremely varied due to the different settings of the parameters. Additionally, the samples of different APIs also suffer from extremely imbalanced. Considering the lack of technologies in Plot2API, we present a novel deep multi-task learning approach named Semantic Parsing Guided Neural Network (SPGNN) which translates the Plot2API issue as a multi-label image classification and an image semantic parsing tasks for the solution. In SPGNN, the recently advanced Convolutional Neural Network (CNN) named EfficientNet is employed as the backbone network for API recommendation. Meanwhile, a semantic parsing module is complemented to exploit the semantic relevant visual information in feature learning and eliminate the appearance-relevant visual information which may confuse the visual-information-based API recommendation. Moreover, the recent data augmentation technique named random erasing is also applied for alleviating the imbalance of API categories. We collect plots with the graphic APIs used to drawn them from Stack Overflow, and release three new Plot2API datasets corresponding to the graphic APIs of R and Python programming languages for evaluating the effectiveness of Plot2API techniques. Extensive experimental results not only demonstrate the superiority of our method over the recent deep learning baselines but also show the practicability of our method in the recommendation of graphic APIs.
Interpretability in machine learning (ML) is crucial for high stakes decisions and troubleshooting. In this work, we provide fundamental principles for interpretable ML, and dispel common misunderstandings that dilute the importance of this crucial topic. We also identify 10 technical challenge areas in interpretable machine learning and provide history and background on each problem. Some of these problems are classically important, and some are recent problems that have arisen in the last few years. These problems are: (1) Optimizing sparse logical models such as decision trees; (2) Optimization of scoring systems; (3) Placing constraints into generalized additive models to encourage sparsity and better interpretability; (4) Modern case-based reasoning, including neural networks and matching for causal inference; (5) Complete supervised disentanglement of neural networks; (6) Complete or even partial unsupervised disentanglement of neural networks; (7) Dimensionality reduction for data visualization; (8) Machine learning models that can incorporate physics and other generative or causal constraints; (9) Characterization of the "Rashomon set" of good models; and (10) Interpretable reinforcement learning. This survey is suitable as a starting point for statisticians and computer scientists interested in working in interpretable machine learning.