Visual Exploration And Information Analytics Of High-Dimensional Medical Images

Data visualization has transformed how we analyze increasingly large and complex data sets. Advanced visual tools logically represent data in a way that communicates the most important information inherent within it and culminate the analysis with an insightful conclusion. Automated analysis disciplines - such as data mining, machine learning, and statistics - have traditionally been the most dominant fields for data analysis. It has been complemented with a near-ubiquitous adoption of specialized hardware and software environments that handle the storage, retrieval, and pre- and postprocessing of digital data. The addition of interactive visualization tools allows an active human participant in the model creation process. The advantage is a data-driven approach where the constraints and assumptions of the model can be explored and chosen based on human insight and confirmed on demand by the analytic system. This translates to a better understanding of data and a more effective knowledge discovery. This trend has become very popular across various domains, not limited to machine learning, simulation, computer vision, genetics, stock market, data mining, and geography. In this dissertation, we highlight the role of visualization within the context of medical image analysis in the field of neuroimaging. The analysis of brain images has uncovered amazing traits about its underlying dynamics. Multiple image modalities capture qualitatively different internal brain mechanisms and abstract it within the information space of that modality. Computational studies based on these modalities help correlate the high-level brain function measurements with abnormal human behavior. These functional maps are easily projected in the physical space through accurate 3-D brain reconstructions and visualized in excellent detail from different anatomical vantage points. Statistical models built for comparative analysis across subject groups test for significant variance within the features and localize abnormal behaviors contextualizing the high-level brain activity. Currently, the task of identifying the features is based on empirical evidence, and preparing data for testing is time-consuming. Correlations among features are usually ignored due to lack of insight. With a multitude of features available and with new emerging modalities appearing, the process of identifying the salient features and their interdependencies becomes more difficult to perceive. This limits the analysis only to certain discernible features, thus limiting human judgments regarding the most important process that governs the symptom and hinders prediction. These shortcomings can be addressed using an analytical system that leverages data-driven techniques for guiding the user toward discovering relevant hypotheses. The research contributions within this dissertation encompass multidisciplinary fields of study not limited to geometry processing, computer vision, and 3-D visualization. However, the principal achievement of this research is the design and development of an interactive system for multimodality integration of medical images. The research proceeds in various stages, which are important to reach the desired goal. The different stages are briefly described as follows: First, we develop a rigorous geometry computation framework for brain surface matching. The brain is a highly convoluted structure of closed topology. Surface parameterization explicitly captures the non-Euclidean geometry of the cortical surface and helps derive a more accurate registration of brain surfaces. We describe a technique based on conformal parameterization that creates a bijective mapping to the canonical domain, where surface operations can be performed with improved efficiency and feasibility. Subdividing the brain into a finite set of anatomical elements provides the structural basis for a categorical division of anatomical view points and a spatial context for statistical analysis. We present statistically significant results of our analysis into functional and morphological features for a variety of brain disorders. Second, we design and develop an intelligent and interactive system for visual analysis of brain disorders by utilizing the complete feature space across all modalities. Each subdivided anatomical unit is specialized by a vector of features that overlap within that element. The analytical framework provides the necessary interactivity for exploration of salient features and discovering relevant hypotheses. It provides visualization tools for confirming model results and an easy-to-use interface for manipulating parameters for feature selection and filtering. It provides coordinated display views for visualizing multiple features across multiple subject groups, visual representations for highlighting interdependencies and correlations between features, and an efficient data-management solution for maintaining provenance and issuing formal data queries to the back end

Doctor of Philosophy

dissertationWith the ever-increasing amount of available computing resources and sensing devices, a wide variety of high-dimensional datasets are being produced in numerous fields. The complexity and increasing popularity of these data have led to new challenges and opportunities in visualization. Since most display devices are limited to communication through two-dimensional (2D) images, many visualization methods rely on 2D projections to express high-dimensional information. Such a reduction of dimension leads to an explosion in the number of 2D representations required to visualize high-dimensional spaces, each giving a glimpse of the high-dimensional information. As a result, one of the most important challenges in visualizing high-dimensional datasets is the automatic filtration and summarization of the large exploration space consisting of all 2D projections. In this dissertation, a new type of algorithm is introduced to reduce the exploration space that identifies a small set of projections that capture the intrinsic structure of high-dimensional data. In addition, a general framework for summarizing the structure of quality measures in the space of all linear 2D projections is presented. However, identifying the representative or informative projections is only part of the challenge. Due to the high-dimensional nature of these datasets, obtaining insights and arriving at conclusions based solely on 2D representations are limited and prone to error. How to interpret the inaccuracies and resolve the ambiguity in the 2D projections is the other half of the puzzle. This dissertation introduces projection distortion error measures and interactive manipulation schemes that allow the understanding of high-dimensional structures via data manipulation in 2D projections

Parallel Hierarchies: Interactive Visualization of Multidimensional Hierarchical Aggregates

Exploring multi-dimensional hierarchical data is a long-standing problem present in a wide range of fields such as bioinformatics, software systems, social sciences and business intelligence. While each hierarchical dimension within these data structures can be explored in isolation, critical information lies in the relationships between dimensions. Existing approaches can either simultaneously visualize multiple non-hierarchical dimensions, or only one or two hierarchical dimensions. Yet, the challenge of visualizing multi-dimensional hierarchical data remains open. To address this problem, we developed a novel data visualization approach -- Parallel Hierarchies -- that we demonstrate on a real-life SAP SE product called SAP Product Lifecycle Costing. The starting point of the research is a thorough customer-driven requirement engineering phase including an iterative design process. To avoid restricting ourselves to a domain-specific solution, we abstract the data and tasks gathered from users, and demonstrate the approach generality by applying Parallel Hierarchies to datasets from bioinformatics and social sciences. Moreover, we report on a qualitative user study conducted in an industrial scenario with 15 experts from 9 different companies. As a result of this co-innovation experience, several SAP customers requested a product feature out of our solution. Moreover, Parallel Hierarchies integration as a standard diagram type into SAP Analytics Cloud platform is in progress. This thesis further introduces different uncertainty representation methods applicable to Parallel Hierarchies and in general to flow diagrams. We also present a visual comparison taxonomy for time-series of hierarchically structured data with one or multiple dimensions. Moreover, we propose several visual solutions for comparing hierarchies employing flow diagrams. Finally, after presenting two application examples of Parallel Hierarchies on industrial datasets, we detail two validation methods to examine the effectiveness of the visualization solution. Particularly, we introduce a novel design validation table to assess the perceptual aspects of eight different visualization solutions including Parallel Hierarchies.:1 Introduction 1.1 Motivation and Problem Statement 1.2 Research Goals 1.3 Outline and Contributions 2 Foundations of Visualization 2.1 Information Visualization 2.1.1 Terms and Definition 2.1.2 What: Data Structures 2.1.3 Why: Visualization Tasks 2.1.4 How: Visualization Techniques 2.1.5 How: Interaction Techniques 2.2 Visual Perception 2.2.1 Visual Variables 2.2.2 Attributes of Preattentive and Attentive Processing 2.2.3 Gestalt Principles 2.3 Flow Diagrams 2.3.1 Classifications of Flow Diagrams 2.3.2 Main Visual Features 2.4 Summary 3 Related Work 3.1 Cross-tabulating Hierarchical Categories 3.1.1 Visualizing Categorical Aggregates of Item Sets 3.1.2 Hierarchical Visualization of Categorical Aggregates 3.1.3 Visualizing Item Sets and Their Hierarchical Properties 3.1.4 Hierarchical Visualization of Categorical Set Aggregates 3.2 Uncertainty Visualization 3.2.1 Uncertainty Taxonomies 3.2.2 Uncertainty in Flow Diagrams 3.3 Time-Series Data Visualization 3.3.1 Time & Data 3.3.2 User Tasks 3.3.3 Visual Representation 3.4 Summary ii Contents 4 Requirement Engineering Phase 4.1 Introduction 4.2 Environment 4.2.1 The Product 4.2.2 The Customers and Development Methodology 4.2.3 Lessons Learned 4.3 Visualization Requirements for Product Costing 4.3.1 Current Visualization Practice 4.3.2 Visualization Tasks 4.3.3 Data Structure and Size 4.3.4 Early Visualization Prototypes 4.3.5 Challenges and Lessons Learned 4.4 Data and Task Abstraction 4.4.1 Data Abstraction 4.4.2 Task Abstraction 4.5 Summary and Outlook 5 Parallel Hierarchies 5.1 Introduction 5.2 The Parallel Hierarchies Technique 5.2.1 The Individual Axis: Showing Hierarchical Categories 5.2.2 Two Interlinked Axes: Showing Pairwise Frequencies 5.2.3 Multiple Linked Axes: Propagating Frequencies 5.2.4 Fine-tuning Parallel Hierarchies through Reordering 5.3 Design Choices 5.4 Applying Parallel Hierarchies 5.4.1 US Census Data 5.4.2 Yeast Gene Ontology Annotations 5.5 Evaluation 5.5.1 Setup of the Evaluation 5.5.2 Procedure of the Evaluation 5.5.3 Results from the Evaluation 5.5.4 Validity of the Evaluation 5.6 Summary and Outlook 6 Visualizing Uncertainty in Flow Diagrams 6.1 Introduction 6.2 Uncertainty in Product Costing 6.2.1 Background 6.2.2 Main Causes of Bad Quality in Costing Data 6.3 Visualization Concepts 6.4 Uncertainty Visualization using Ribbons 6.4.1 Selected Visualization Techniques 6.4.2 Study Design and Procedure 6.4.3 Results 6.4.4 Discussion 6.5 Revised Visualization Approach using Ribbons 6.5.1 Application to Sankey Diagram 6.5.2 Application to Parallel Sets 6.5.3 Application to Parallel Hierarchies 6.6 Uncertainty Visualization using Nodes 6.6.1 Visual Design of Nodes 6.6.2 Expert Evaluation 6.7 Summary and Outlook 7 Visual Comparison Task 7.1 Introduction 7.2 Comparing Two One-dimensional Time Steps 7.2.1 Problem Statement 7.2.2 Visualization Design 7.3 Comparing Two N-dimensional Time Steps 7.4 Comparing Several One-dimensional Time Steps 7.5 Summary and Outlook 8 Parallel Hierarchies in Practice 8.1 Application to Plausibility Check Task 8.1.1 Plausibility Check Process 8.1.2 Visual Exploration of Machine Learning Results 8.2 Integration into SAP Analytics Cloud 8.2.1 SAP Analytics Cloud 8.2.2 Ocean to Table Project 8.3 Summary and Outlook 9 Validation 9.1 Introduction 9.2 Nested Model Validation Approach 9.3 Perceptual Validation of Visualization Techniques 9.3.1 Design Validation Table 9.3.2 Discussion 9.4 Summary and Outlook 10 Conclusion and Outlook 10.1 Summary of Findings 10.2 Discussion 10.3 Outlook A Questionnaires of the Evaluation B Survey of the Quality of Product Costing Data C Questionnaire of Current Practice Bibliograph

Ontology based data warehousing for mining of heterogeneous and multidimensional data sources

Heterogeneous and multidimensional big-data sources are virtually prevalent in all business environments. System and data analysts are unable to fast-track and access big-data sources. A robust and versatile data warehousing system is developed, integrating domain ontologies from multidimensional data sources. For example, petroleum digital ecosystems and digital oil field solutions, derived from big-data petroleum (information) systems, are in increasing demand in multibillion dollar resource businesses worldwide. This work is recognized by Industrial Electronic Society of IEEE and appeared in more than 50 international conference proceedings and journals

New Fundamental Technologies in Data Mining

The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. The series of books entitled by "Data Mining" address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters. The contributing authors have highlighted many future research directions that will foster multi-disciplinary collaborations and hence will lead to significant development in the field of data mining

Multi-tier framework for the inferential measurement and data-driven modeling

A framework for the inferential measurement and data-driven modeling has been proposed and assessed in several real-world application domains. The architecture of the framework has been structured in multiple tiers to facilitate extensibility and the integration of new components. Each of the proposed four tiers has been assessed in an uncoupled way to verify their suitability. The first tier, dealing with exploratory data analysis, has been assessed with the characterization of the chemical space related to the biodegradation of organic chemicals. This analysis has established relationships between physicochemical variables and biodegradation rates that have been used for model development. At the preprocessing level, a novel method for feature selection based on dissimilarity measures between Self-Organizing maps (SOM) has been developed and assessed. The proposed method selected more features than others published in literature but leads to models with improved predictive power. Single and multiple data imputation techniques based on the SOM have also been used to recover missing data in a Waste Water Treatment Plant benchmark. A new dynamic method to adjust the centers and widths of in Radial basis Function networks has been proposed to predict water quality. The proposed method outperformed other neural networks. The proposed modeling components have also been assessed in the development of prediction and classification models for biodegradation rates in different media. The results obtained proved the suitability of this approach to develop data-driven models when the complex dynamics of the process prevents the formulation of mechanistic models. The use of rule generation algorithms and Bayesian dependency models has been preliminary screened to provide the framework with interpretation capabilities. Preliminary results obtained from the classification of Modes of Toxic Action (MOA) indicate that this could be a promising approach to use MOAs as proxy indicators of human health effects of chemicals.Finally, the complete framework has been applied to three different modeling scenarios. A virtual sensor system, capable of inferring product quality indices from primary process variables has been developed and assessed. The system was integrated with the control system in a real chemical plant outperforming multi-linear correlation models usually adopted by chemical manufacturers. A model to predict carcinogenicity from molecular structure for a set of aromatic compounds has been developed and tested. Results obtained after the application of the SOM-dissimilarity feature selection method yielded better results than models published in the literature. Finally, the framework has been used to facilitate a new approach for environmental modeling and risk management within geographical information systems (GIS). The SOM has been successfully used to characterize exposure scenarios and to provide estimations of missing data through geographic interpolation. The combination of SOM and Gaussian Mixture models facilitated the formulation of a new probabilistic risk assessment approach.Aquesta tesi proposa i avalua en diverses aplicacions reals, un marc general de treball per al desenvolupament de sistemes de mesurament inferencial i de modelat basats en dades. L'arquitectura d'aquest marc de treball s'organitza en diverses capes que faciliten la seva extensibilitat així com la integració de nous components. Cadascun dels quatre nivells en que s'estructura la proposta de marc de treball ha estat avaluat de forma independent per a verificar la seva funcionalitat. El primer que nivell s'ocupa de l'anàlisi exploratòria de dades ha esta avaluat a partir de la caracterització de l'espai químic corresponent a la biodegradació de certs compostos orgànics. Fruit d'aquest anàlisi s'han establert relacions entre diverses variables físico-químiques que han estat emprades posteriorment per al desenvolupament de models de biodegradació. A nivell del preprocés de les dades s'ha desenvolupat i avaluat una nova metodologia per a la selecció de variables basada en l'ús del Mapes Autoorganitzats (SOM). Tot i que el mètode proposat selecciona, en general, un major nombre de variables que altres mètodes proposats a la literatura, els models resultants mostren una millor capacitat predictiva. S'han avaluat també tot un conjunt de tècniques d'imputació de dades basades en el SOM amb un conjunt de dades estàndard corresponent als paràmetres d'operació d'una planta de tractament d'aigües residuals. Es proposa i avalua en un problema de predicció de qualitat en aigua un nou model dinàmic per a ajustar el centre i la dispersió en xarxes de funcions de base radial. El mètode proposat millora els resultats obtinguts amb altres arquitectures neuronals. Els components de modelat proposat s'han aplicat també al desenvolupament de models predictius i de classificació de les velocitats de biodegradació de compostos orgànics en diferents medis. Els resultats obtinguts demostren la viabilitat d'aquesta aproximació per a desenvolupar models basats en dades en aquells casos en els que la complexitat de dinàmica del procés impedeix formular models mecanicistes. S'ha dut a terme un estudi preliminar de l'ús de algorismes de generació de regles i de grafs de dependència bayesiana per a introduir una nova capa que faciliti la interpretació dels models. Els resultats preliminars obtinguts a partir de la classificació dels Modes d'acció Tòxica (MOA) apunten a que l'ús dels MOA com a indicadors intermediaris dels efectes dels compostos químics en la salut és una aproximació factible.Finalment, el marc de treball proposat s'ha aplicat en tres escenaris de modelat diferents. En primer lloc, s'ha desenvolupat i avaluat un sensor virtual capaç d'inferir índexs de qualitat a partir de variables primàries de procés. El sensor resultant ha estat implementat en una planta química real millorant els resultats de les correlacions multilineals emprades habitualment. S'ha desenvolupat i avaluat un model per a predir els efectes carcinògens d'un grup de compostos aromàtics a partir de la seva estructura molecular. Els resultats obtinguts desprès d'aplicar el mètode de selecció de variables basat en el SOM milloren els resultats prèviament publicats. Aquest marc de treball s'ha usat també per a proporcionar una nova aproximació al modelat ambiental i l'anàlisi de risc amb sistemes d'informació geogràfica (GIS). S'ha usat el SOM per a caracteritzar escenaris d'exposició i per a desenvolupar un nou mètode d'interpolació geogràfica. La combinació del SOM amb els models de mescla de gaussianes dona una nova formulació al problema de l'anàlisi de risc des d'un punt de vista probabilístic

Reading the news through its structure: new hybrid connectivity based approaches

In this thesis a solution for the problem of identifying the structure of news published by online newspapers is presented. This problem requires new approaches and algorithms that are capable of dealing with the massive number of online publications in existence (and that will grow in the future). The fact that news documents present a high degree of interconnection makes this an interesting and hard problem to solve. The identification of the structure of the news is accomplished both by descriptive methods that expose the dimensionality of the relations between different news, and by clustering the news into topic groups. To achieve this analysis this integrated whole was studied using different perspectives and approaches. In the identification of news clusters and structure, and after a preparatory data collection phase, where several online newspapers from different parts of the globe were collected, two newspapers were chosen in particular: the Portuguese daily newspaper Público and the British newspaper The Guardian. In the first case, it was shown how information theory (namely variation of information) combined with adaptive networks was able to identify topic clusters in the news published by the Portuguese online newspaper Público. In the second case, the structure of news published by the British newspaper The Guardian is revealed through the construction of time series of news clustered by a kmeans process. After this approach an unsupervised algorithm, that filters out irrelevant news published online by taking into consideration the connectivity of the news labels entered by the journalists, was developed. This novel hybrid technique is based on Qanalysis for the construction of the filtered network followed by a clustering technique to identify the topical clusters. Presently this work uses a modularity optimisation clustering technique but this step is general enough that other hybrid approaches can be used without losing generality. A novel second order swarm intelligence algorithm based on Ant Colony Systems was developed for the travelling salesman problem that is consistently better than the traditional benchmarks. This algorithm is used to construct Hamiltonian paths over the news published using the eccentricity of the different documents as a measure of distance. This approach allows for an easy navigation between published stories that is dependent on the connectivity of the underlying structure. The results presented in this work show the importance of taking topic detection in large corpora as a multitude of relations and connectivities that are not in a static state. They also influence the way of looking at multi-dimensional ensembles, by showing that the inclusion of the high dimension connectivities gives better results to solving a particular problem as was the case in the clustering problem of the news published online.Neste trabalho resolvemos o problema da identificação da estrutura das notícias publicadas em linha por jornais e agências noticiosas. Este problema requer novas abordagens e algoritmos que sejam capazes de lidar com o número crescente de publicações em linha (e que se espera continuam a crescer no futuro). Este facto, juntamente com o elevado grau de interconexão que as notícias apresentam tornam este problema num problema interessante e de difícil resolução. A identificação da estrutura do sistema de notícias foi conseguido quer através da utilização de métodos descritivos que expõem a dimensão das relações existentes entre as diferentes notícias, quer através de algoritmos de agrupamento das mesmas em tópicos. Para atingir este objetivo foi necessário proceder a ao estudo deste sistema complexo sob diferentes perspectivas e abordagens. Após uma fase preparatória do corpo de dados, onde foram recolhidos diversos jornais publicados online optou-se por dois jornais em particular: O Público e o The Guardian. A escolha de jornais em línguas diferentes deve-se à vontade de encontrar estratégias de análise que sejam independentes do conhecimento prévio que se tem sobre estes sistemas. Numa primeira análise é empregada uma abordagem baseada em redes adaptativas e teoria de informação (nomeadamente variação de informação) para identificar tópicos noticiosos que são publicados no jornal português Público. Numa segunda abordagem analisamos a estrutura das notícias publicadas pelo jornal Britânico The Guardian através da construção de séries temporais de notícias. Estas foram seguidamente agrupadas através de um processo de k-means. Para além disso desenvolveuse um algoritmo que permite filtrar de forma não supervisionada notícias irrelevantes que apresentam baixa conectividade às restantes notícias através da utilização de Q-analysis seguida de um processo de clustering. Presentemente este método utiliza otimização de modularidade, mas a técnica é suficientemente geral para que outras abordagens híbridas possam ser utilizadas sem perda de generalidade do método. Desenvolveu-se ainda um novo algoritmo baseado em sistemas de colónias de formigas para solução do problema do caixeiro viajante que consistentemente apresenta resultados melhores que os tradicionais bancos de testes. Este algoritmo foi aplicado na construção de caminhos Hamiltonianos das notícias publicadas utilizando a excentricidade obtida a partir da conectividade do sistema estudado como medida da distância entre notícias. Esta abordagem permitiu construir um sistema de navegação entre as notícias publicadas que é dependente da conectividade observada na estrutura de notícias encontrada. Os resultados apresentados neste trabalho mostram a importância de analisar sistemas complexos na sua multitude de relações e conectividades que não são estáticas e que influenciam a forma como tradicionalmente se olha para sistema multi-dimensionais. Mostra-se que a inclusão desta dimensões extra produzem melhores resultados na resolução do problema de identificar a estrutura subjacente a este problema da publicação de notícias em linha

Probabilistic analysis of the human transcriptome with side information

Understanding functional organization of genetic information is a major challenge in modern biology. Following the initial publication of the human genome sequence in 2001, advances in high-throughput measurement technologies and efficient sharing of research material through community databases have opened up new views to the study of living organisms and the structure of life. In this thesis, novel computational strategies have been developed to investigate a key functional layer of genetic information, the human transcriptome, which regulates the function of living cells through protein synthesis. The key contributions of the thesis are general exploratory tools for high-throughput data analysis that have provided new insights to cell-biological networks, cancer mechanisms and other aspects of genome function. A central challenge in functional genomics is that high-dimensional genomic observations are associated with high levels of complex and largely unknown sources of variation. By combining statistical evidence across multiple measurement sources and the wealth of background information in genomic data repositories it has been possible to solve some the uncertainties associated with individual observations and to identify functional mechanisms that could not be detected based on individual measurement sources. Statistical learning and probabilistic models provide a natural framework for such modeling tasks. Open source implementations of the key methodological contributions have been released to facilitate further adoption of the developed methods by the research community.Comment: Doctoral thesis. 103 pages, 11 figure