Data-Driven Shape Analysis and Processing

Data-driven methods play an increasingly important role in discovering geometric, structural, and semantic relationships between 3D shapes in collections, and applying this analysis to support intelligent modeling, editing, and visualization of geometric data. In contrast to traditional approaches, a key feature of data-driven approaches is that they aggregate information from a collection of shapes to improve the analysis and processing of individual shapes. In addition, they are able to learn models that reason about properties and relationships of shapes without relying on hard-coded rules or explicitly programmed instructions. We provide an overview of the main concepts and components of these techniques, and discuss their application to shape classification, segmentation, matching, reconstruction, modeling and exploration, as well as scene analysis and synthesis, through reviewing the literature and relating the existing works with both qualitative and numerical comparisons. We conclude our report with ideas that can inspire future research in data-driven shape analysis and processing.Comment: 10 pages, 19 figure

Analyzing Visual Mappings of Traditional and Alternative Music Notation

In this paper, we postulate that combining the domains of information visualization and music studies paves the ground for a more structured analysis of the design space of music notation, enabling the creation of alternative music notations that are tailored to different users and their tasks. Hence, we discuss the instantiation of a design and visualization pipeline for music notation that follows a structured approach, based on the fundamental concepts of information and data visualization. This enables practitioners and researchers of digital humanities and information visualization, alike, to conceptualize, create, and analyze novel music notation methods. Based on the analysis of relevant stakeholders and their usage of music notation as a mean of communication, we identify a set of relevant features typically encoded in different annotations and encodings, as used by interpreters, performers, and readers of music. We analyze the visual mappings of musical dimensions for varying notation methods to highlight gaps and frequent usages of encodings, visual channels, and Gestalt laws. This detailed analysis leads us to the conclusion that such an under-researched area in information visualization holds the potential for fundamental research. This paper discusses possible research opportunities, open challenges, and arguments that can be pursued in the process of analyzing, improving, or rethinking existing music notation systems and techniques.Comment: 5 pages including references, 3rd Workshop on Visualization for the Digital Humanities, Vis4DH, IEEE Vis 201

A survey of visual preprocessing and shape representation techniques

Many recent theories and methods proposed for visual preprocessing and shape representation are summarized. The survey brings together research from the fields of biology, psychology, computer science, electrical engineering, and most recently, neural networks. It was motivated by the need to preprocess images for a sparse distributed memory (SDM), but the techniques presented may also prove useful for applying other associative memories to visual pattern recognition. The material of this survey is divided into three sections: an overview of biological visual processing; methods of preprocessing (extracting parts of shape, texture, motion, and depth); and shape representation and recognition (form invariance, primitives and structural descriptions, and theories of attention)

Visualization Techniques for Neuroscience-Inspired Dynamic Architectures

This work introduces visualization tools for Neuroscience-Inspired Dynamic Architecture (NIDA) networks and for the Dynamic Adaptive Neural Network Array (DANNA) hardware implementation of NIDA. A NIDA network is a novel type of artificial neural network that has performed well on control, anomaly detection, and classification tasks. We introduce a three dimensional visualization of software NIDA networks that represents network structure and simulates activity on networks. We present some of the analysis tasks for which the tool has been used, including the identification of useful substructures within NIDA networks through activity analysis and through the tracing of causality paths from events to their respective sources. We discuss features of the visualization that allow for the exploration of dense networks and subnetworks. We define analysis goals for the tools, in particular the definition of similarity between networks and substructures and the objectives for the recognition of similar substructures. We also introduce a two dimensional visual interface for DANNAs, which includes representation of the physical arrangement of elements on DANNAs, as well as interactions to configure and save the networks. We explore various representations of elements and connections within DANNAs, and we demonstrate the interactions that assist users in evaluating and modifying the networks. Finally, we propose extensions to the tools that will further aid in the exploration and understanding of NIDA and DANNA structure and behavior

Multi-faceted Structure-Activity Relationship Analysis Using Graphical Representations

A core focus in medicinal chemistry is the interpretation of structure-activity relationships (SARs) of small molecules. SAR analysis is typically carried out on a case-by-case basis for compound sets that share activity against a given target. Although SAR investigations are not a priori dependent on computational approaches, limitations imposed by steady rise in activity information have necessitated the use of such methodologies. Moreover, understanding SARs in multi-target space is extremely difficult. Conceptually different computational approaches are reported in this thesis for graphical SAR analysis in single- as well as multi-target space. Activity landscape models are often used to describe the underlying SAR characteristics of compound sets. Theoretical activity landscapes that are reminiscent of topological maps intuitively represent distributions of pair-wise similarity and potency difference information as three-dimensional surfaces. These models provide easy access to identification of various SAR features. Therefore, such landscapes for actual data sets are generated and compared with graph-based representations. Existing graphical data structures are adapted to include mechanism of action information for receptor ligands to facilitate simultaneous SAR and mechanism-related analyses with the objective of identifying structural modifications responsible for switching molecular mechanisms of action. Typically, SAR analysis focuses on systematic pair-wise relationships of compound similarity and potency differences. Therefore, an approach is reported to calculate SAR feature probabilities on the basis of these pair-wise relationships for individual compounds in a ligand set. The consequent expansion of feature categories improves the analysis of local SAR environments. Graphical representations are designed to avoid a dependence on preconceived SAR models. Such representations are suitable for systematic large-scale SAR exploration. Methods for the navigation of SARs in multi-target space using simple and interpretable data structures are introduced. In summary, multi-faceted SAR analysis aided by computational means forms the primary objective of this dissertation