When studying multi-body protein complexes, biochemists use computational tools that can suggest hundreds or thousands of their possible spatial configurations. However, it is not feasible to experimentally verify more than only a very small subset of them. In this paper, we propose a novel multiscale visual drilldown approach that was designed in tight collaboration with proteomic experts, enabling a systematic exploration of the configuration space. Our approach takes advantage of the hierarchical structure of the data -- from the whole ensemble of protein complex configurations to the individual configurations, their contact interfaces, and the interacting amino acids. Our new solution is based on interactively linked 2D and 3D views for individual hierarchy levels and at each level, we offer a set of selection and filtering operations enabling the user to narrow down the number of configurations that need to be manually scrutinized. Furthermore, we offer a dedicated filter interface, which provides the users with an overview of the applied filtering operations and enables them to examine their impact on the explored ensemble. This way, we maintain the history of the exploration process and thus enable the user to return to an earlier point of the exploration. We demonstrate the effectiveness of our approach on two case studies conducted by collaborating proteomic experts.
In our case, we were not only concerned with designing proper visual representations of the individual hierarchy levels of large ensembles of multi-body complexes, but also with how to interactively explore and filter these ensembles to support the identification of biochemically most relevant instances. @cite_34 focus on the problem of interactive visual steering of hierarchical simulation ensembles. In their substantially different application case, they also deal with linking representations on different levels of detail as well as with the challenge that the ensemble can grow during the exploration process.
@cite_34
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Multi-level simulation models, i.e., models where different components are simulated using sub-models of varying levels of complexity, belong to the current state-of-the-art in simulation. The existing analysis practice for multi-level simulation results is to manually compare results from different levels of complexity, amounting to a very tedious and error-prone, trial-and-error exploration process. In this paper, we introduce hierarchical visual steering, a new approach to the exploration and design of complex systems. Hierarchical visual steering makes it possible to explore and analyze hierarchical simulation ensembles at different levels of complexity. At each level, we deal with a dynamic simulation ensemble — the ensemble grows during the exploration process. There is at least one such ensemble per simulation level, resulting in a collection of dynamic ensembles, analyzed simultaneously. The key challenge is to map the multi-dimensional parameter space of one ensemble to the multi-dimensional parameter space of another ensemble (from another level). In order to support the interactive visual analysis of such complex data we propose a novel approach to interactive and semi-automatic parameter space segmentation and comparison. The approach combines a novel interaction technique and automatic, computational methods — clustering, concave hull computation, and concave polygon overlapping — to support the analysts in the cross-ensemble parameter space mapping. In addition to the novel parameter space segmentation we also deploy coordinated multiple views with standard plots. We describe the abstract analysis tasks, identified during a case study, i.e., the design of a variable valve actuation system of a car engine. The study is conducted in cooperation with experts from the automotive industry. Very positive feedback indicates the usefulness and efficiency of the newly proposed approach. Systems biologists and cancer researchers require interactive visualization tools that enable them to more easily navigate and discover patterns at different levels of the biological hierarchy of signaling pathways. Furthermore, biologists are often interested in understanding and exploring the causal biochemical links between processes. When exploring the literature of particular biological pathways or specific proteins within those pathways, biologists find it useful to know the contexts in which biochemical links are active and, importantly, to be aware of potential conflicts when different experiments introduce alternative interpretations of the function of a pathway or biochemical reaction. We introduce BioLinker, a interactive visualization system that helps users to perform bottom-up exploration of complex protein interaction networks. Five interconnected views provide the user with a range of ways to explore pathway data, including views that show potential conflicts within pathway databases and publications and that highlight contextual information about individual proteins. Additionally, we discuss system details to show how our system manages the large amount of protein interactions extracted from the literature of biological pathways. The comparison of many members of an ensemble is difficult, tedious, and error-prone, which is aggravated by often just subtle differences. In this paper, we introduce Dynamic Volume Lines for the interactive visual analysis and comparison of sets of 3D volumes. Each volume is linearized along a Hilbert space-filling curve into a 1D Hilbert line plot, which depicts the intensities over the Hilbert indices. We present a nonlinear scaling of these 1D Hilbert line plots based on the intensity variations in the ensemble of 3D volumes, which enables a more effective use of the available screen space. The nonlinear scaling builds the basis for our interactive visualization techniques. An interactive histogram heatmap of the intensity frequencies serves as overview visualization. When zooming in, the frequencies are replaced by detailed 1D Hilbert line plots and optional functional boxplots. To focus on important regions of the volume ensemble, nonlinear scaling is incorporated into the plots. An interactive scaling widget depicts the local ensemble variations. Our brushing and linking interface reveals, for example, regions with a high ensemble variation by showing the affected voxels in a 3D spatial view. We show the applicability of our concepts using two case studies on ensembles of 3D volumes resulting from tomographic reconstruction. In the first case study, we evaluate an artificial specimen from simulated industrial 3D X-ray computed tomography (XCT). In the second case study, a real-world XCT foam specimen is investigated. Our results show that Dynamic Volume Lines can identify regions with high local intensity variations, allowing the user to draw conclusions, for example, about the choice of reconstruction parameters. Furthermore, it is possible to detect ring artifacts in reconstructions volumes. Ensembles of numerical simulations are used in a variety of applications, such as meteorology or computational solid mechanics, in order to quantify the uncertainty or possible error in a model or simulation. Deriving robust statistics and visualizing the variability of an ensemble is a challenging task and is usually accomplished through direct visualization of ensemble members or by providing aggregate representations such as an average or pointwise probabilities. In many cases, the interesting quantities in a simulation are not dense fields, but are sets of features that are often represented as thresholds on physical or derived quantities. In this paper, we introduce a generalization of boxplots, called contour boxplots, for visualization and exploration of ensembles of contours or level sets of functions. Conventional boxplots have been widely used as an exploratory or communicative tool for data analysis, and they typically show the median, mean, confidence intervals, and outliers of a population. The proposed contour boxplots are a generalization of functional boxplots, which build on the notion of data depth. Data depth approximates the extent to which a particular sample is centrally located within its density function. This produces a center-outward ordering that gives rise to the statistical quantities that are essential to boxplots. Here we present a generalization of functional data depth to contours and demonstrate methods for displaying the resulting boxplots for two-dimensional simulation data in weather forecasting and computational fluid dynamics. There is growing interest in multiplex networks where individual nodes take part in several layers of networks simultaneously. This is the case for example in social networks where each individual node has different kind of social ties or transportation systems where each location is connected to another location by different types of transport. Many of these multiplex are characterized by a significant overlap of the links in different layers. In this paper we introduce a statistical mechanics framework to describe multiplex ensembles. A multiplex is a system formed by N nodes and M layers of interactions where each node belongs to the M layers at the same time. Each layer @math is formed by a network @math . Here we introduce the concept of correlated multiplex ensembles in which the existence of a link in one layer is correlated with the existence of a link in another layer. This implies that a typical multiplex of the ensemble can have a significant overlap of the links in the different layers. Moreover we characterize microcanonical and canonical multiplex ensembles satisfying respectively hard and soft constraints and we discuss how to construct multiplex in these ensembles. Finally we provide the expression for the entropy of these ensembles that can be useful to address different inference problems involving multiplexes. We present the zoomable adjacency matrix explorer (ZAME), a visualization tool for exploring graphs at a scale of millions of nodes and edges. ZAME is based on an adjacency matrix graph representation aggregated at multiple scales. It allows analysts to explore a graph at many levels, zooming and panning with interactive performance from an overview to the most detailed views. Several components work together in the ZAME tool to make this possible. Efficient matrix ordering algorithms group related elements. Individual data cases are aggregated into higher-order meta-representations. Aggregates are arranged into a pyramid hierarchy that allows for on-demand paging to GPU shader programs to support smooth multiscale browsing. Using ZAME, we are able to explore the entire French Wikipedia - over 500,000 articles and 6,000,000 links - with interactive performance on standard consumer-level computer hardware. Abstract Visualizing high-dimensional labeled data on a two-dimensional plane can quickly result in visual clutter and information overload. To address this problem, the data usually needs to be structured, so that only parts of it are displayed at a time. We present a hierarchy-based approach that projects labeled data on different levels of detail on a two-dimensional plane, whilst keeping the user׳s cognitive load between the level changes as low as possible. The approach consists of three steps: First, the data is hierarchically clustered; second, the user can determine levels of detail; third, the levels of detail are visualized one at a time on a two-dimensional plane. Animations make transitions between the levels of detail traceable, while the exploration on each level is supported by several interaction techniques, including halos, a darts view, and a magic lens. We demonstrate the applicability and usefulness of the approach with use cases from the patent domain and a question-and-answer website. In addition, we conducted a qualitative evaluation to assess the usefulness and comprehensibility of our approach. Based on negative correlation learning and evolutionary learning, this paper presents evolutionary ensembles with negative correlation learning (EENCL) to address the issues of automatic determination of the number of individual neural networks (NNs) in an ensemble and the exploitation of the interaction between individual NN design and combination. The idea of EENCL is to encourage different individual NNs in the ensemble to learn different parts or aspects of the training data so that the ensemble can learn better the entire training data. The cooperation and specialization among different individual NNs are considered during the individual NN design. This provides an opportunity for different NNs to interact with each other and to specialize. Experiments on two real-world problems demonstrate that EENCL can produce NN ensembles with good generalization ability. The exploration and analysis of scientific literature collections is an important task for effective knowledge management. Past interest in such document sets has spurred the development of numerous visualization approaches for their interactive analysis. They either focus on the textual content of publications, or on document metadata including authors and citations. Previously presented approaches for citation analysis aim primarily at the visualization of the structure of citation networks and their exploration. We extend the state-of-the-art by presenting an approach for the interactive visual analysis of the contents of scientific documents, and combine it with a new and flexible technique to analyze their citations. This technique facilitates user-steered aggregation of citations which are linked to the content of the citing publications using a highly interactive visualization approach. Through enriching the approach with additional interactive views of other important aspects of the data, we support the exploration of the dataset over time and enable users to analyze citation patterns, spot trends, and track long-term developments. We demonstrate the strengths of our approach through a use case and discuss it based on expert user feedback. Ensemble methods are state of the art for many NLP tasks. Recent work by Banko and Brill (2001) suggests that this would not necessarily be true if very large training corpora were available. However, their results are limited by the simplicity of their evaluation task and individual classifiers.Our work explores ensemble efficacy for the more complex task of automatic thesaurus extraction on up to 300 million words. We examine our conflicting results in terms of the constraints on, and complexity of, different contextual representations, which contribute to the sparseness-and noise-induced bias behaviour of NLP systems on very large corpora. Visual analytics plays a key role in the era of connected industry (or industry 4.0, industrial internet) as modern machines and assembly lines generate large amounts of data and effective visual exploration techniques are needed for troubleshooting, process optimization, and decision making. However, developing effective visual analytics solutions for this application domain is a challenging task due to the sheer volume and the complexity of the data collected in the manufacturing processes. We report the design and implementation of a comprehensive visual analytics system, ViDX. It supports both real-time tracking of assembly line performance and historical data exploration to identify inefficiencies, locate anomalies, and form hypotheses about their causes and effects. The system is designed based on a set of requirements gathered through discussions with the managers and operators from manufacturing sites. It features interlinked views displaying data at different levels of detail. In particular, we apply and extend the Marey's graph by introducing a time-aware outlier-preserving visual aggregation technique to support effective troubleshooting in manufacturing processes. We also introduce two novel interaction techniques, namely the quantiles brush and samples brush, for the users to interactively steer the outlier detection algorithms. We evaluate the system with example use cases and an in-depth user interview, both conducted together with the managers and operators from manufacturing plants. The result demonstrates its effectiveness and reports a successful pilot application of visual analytics for manufacturing in smart factories. Machine learning is an increasingly used computational tool within human-computer interaction research. While most researchers currently utilize an iterative approach to refining classifier models and performance, we propose that ensemble classification techniques may be a viable and even preferable alternative. In ensemble learning, algorithms combine multiple classifiers to build one that is superior to its components. In this paper, we present EnsembleMatrix, an interactive visualization system that presents a graphical view of confusion matrices to help users understand relative merits of various classifiers. EnsembleMatrix allows users to directly interact with the visualizations in order to explore and build combination models. We evaluate the efficacy of the system and the approach in a user study. Results show that users are able to quickly combine multiple classifiers operating on multiple feature sets to produce an ensemble classifier with accuracy that approaches best-reported performance classifying images in the CalTech-101 dataset. Over the last decades, there have been a rich variety of approaches towards modeling student knowledge and skill within interactive learning environments. There have recently been several empirical comparisons as to which types of student models are better at predicting future performance, both within and outside of the interactive learning environment. However, these comparisons have produced contradictory results. Within this paper, we examine whether ensemble methods, which integrate multiple models, can produce prediction results comparable to or better than the best of nine student modeling frameworks, taken individually. We ensemble model predictions within a Cognitive Tutor for Genetics, at the level of predicting knowledge action-by-action within the tutor. We evaluate the predictions in terms of future performance within the tutor and on a paper post-test. Within this data set, we do not find evidence that ensembles of models are significantly better. Ensembles of models perform comparably to or slightly better than the best individual models, at predicting future performance within the tutor software. However, the ensembles of models perform marginally significantly worse than the best individual models, at predicting post-test performance. The need to visualize large social networks is growing as hardware capabilities make analyzing large networks feasible and many new data sets become available. Unfortunately, the visualizations in existing systems do not satisfactorily resolve the basic dilemma of being readable both for the global structure of the network and also for detailed analysis of local communities. To address this problem, we present NodeTrix, a hybrid representation for networks that combines the advantages of two traditional representations: node-link diagrams are used to show the global structure of a network, while arbitrary portions of the network can be shown as adjacency matrices to better support the analysis of communities. A key contribution is a set of interaction techniques. These allow analysts to create a NodeTrix visualization by dragging selections to and from node-link and matrix forms, and to flexibly manipulate the NodeTrix representation to explore the dataset and create meaningful summary visualizations of their findings. Finally, we present a case study applying NodeTrix to the analysis of the InfoVis 2004 coauthorship dataset to illustrate the capabilities of NodeTrix as both an exploration tool and an effective means of communicating results. We present a biologically motivated architecture for object recognition that is capable of online learning of several objects based on interaction with a human teacher. The system combines biological principles such as appearance-based representation in topographical feature detection hierarchies and context-driven transfer between different levels of object memory. Training can be performed in an unconstrained environment by presenting objects in front of a stereo camera system and labeling them by speech input. The learning is fully online and thus avoids an artificial separation of the interaction into training and test phases. We demonstrate the performance on a challenging ensemble of 50 objects. General regression and classification models are constructed as linear combinations of simple rules derived from the data. Each rule consists of a conjunction of a small number of simple statements concerning the values of individual input variables. These rule ensembles are shown to produce predictive accuracy comparable to the best methods. However, their principal advantage lies in interpretation. Because of its simple form, each rule is easy to understand, as is its influence on individual predictions, selected subsets of predictions, or globally over the entire space of joint input variable values. Similarly, the degree of relevance of the respective input variables can be assessed globally, locally in different regions of the input space, or at individual prediction points. Techniques are presented for automatically identifying those variables that are involved in interactions with other variables, the strength and degree of those interactions, as well as the identities of the other variables with which they interact. Graphical representations are used to visualize both main and interaction effects. In visual analytics, sensemaking is facilitated through interactive visual exploration of data. Throughout this dynamic process, users combine their domain knowledge with the dataset to create insight. Therefore, visual analytic tools exist that aid sensemaking by providing various interaction techniques that focus on allowing users to change the visual representation through adjusting parameters of the underlying statistical model. However, we postulate that the process of sensemaking is not focused on a series of parameter adjustments, but instead, a series of perceived connections and patterns within the data. Thus, how can models for visual analytic tools be designed, so that users can express their reasoning on observations (the data), instead of directly on the model or tunable parameters? Observation level (and thus “observation”) in this paper refers to the data points within a visualization. In this paper, we explore two possible observation-level interactions, namely exploratory and expressive, within the context of three statistical methods, Probabilistic Principal Component Analysis (PPCA), Multidimensional Scaling (MDS), and Generative Topographic Mapping (GTM). We discuss the importance of these two types of observation level interactions, in terms of how they occur within the sensemaking process. Further, we present use cases for GTM, MDS, and PPCA, illustrating how observation level interaction can be incorporated into visual analytic tools. The ASCENS project deals with designing systems as ensembles of adaptive components. Among the outputs of the ASCENS project are multiple tools that address particular issues in designing the ensembles, ranging from support for early stage formal modeling to runtime environment for executing and monitoring ensemble implementations. The goal of this chapter is to provide a compact description of the individual tools, which is supplemented by additional downloadable material on the project website. In this paper, we have developed a new scheme for achieving multilevel annotations of large-scale images automatically. To achieve more sufficient representation of various visual properties of the images, both the global visual features and the local visual features are extracted for image content representation. To tackle the problem of huge intraconcept visual diversity, multiple types of kernels are integrated to characterize the diverse visual similarity relationships between the images more precisely, and a multiple kernel learning algorithm is developed for SVM image classifier training. To address the problem of huge interconcept visual similarity, a novel multitask learning algorithm is developed to learn the correlated classifiers for the sibling image concepts under the same parent concept and enhance their discrimination and adaptation power significantly. To tackle the problem of huge intraconcept visual diversity for the image concepts at the higher levels of the concept ontology, a novel hierarchical boosting algorithm is developed to learn their ensemble classifiers hierarchically. In order to assist users on selecting more effective hypotheses for image classifier training, we have developed a novel hyperbolic framework for large-scale image visualization and interactive hypotheses assessment. Our experiments on large-scale image collections have also obtained very positive results. This paper studies efficient means in dealing with intracategory diversity in object detection. Strategies for occlusion and orientation handling are explored by learning an ensemble of detection models from visual and geometrical clusters of object instances. An AdaBoost detection scheme is employed with pixel lookup features for fast detection. The analysis provides insight into the design of a robust vehicle detection system, showing promise in terms of detection performance and orientation estimation accuracy.