Evolutionary framework for DNA Microarry Cluster Analysis

En esta investigación se propone un framework evolutivo donde se fusionan un método de clustering jerárquico basado en un modelo evolutivo, un conjunto de medidas de validación de agrupamientos (clusters) de datos y una herramienta de visualización de clusterings. El objetivo es crear un marco apropiado para la extracción de conocimiento a partir de datos provenientes de DNA-microarrays. Por una parte, el modelo evolutivo de clustering de nuestro framework es una alternativa novedosa que intenta resolver algunos de los problemas presentes en los métodos de clustering existentes. Por otra parte, nuestra alternativa de visualización de clusterings, materializada en una herramienta, incorpora nuevas propiedades y nuevos componentes de visualización, lo cual permite validar y analizar los resultados de la tarea de clustering. De este modo, la integración del modelo evolutivo de clustering con el modelo visual de clustering, convierta a nuestro framework evolutivo en una aplicación novedosa de minería de datos frente a los métodos convencionales

Feedback-Driven Data Clustering

The acquisition of data and its analysis has become a common yet critical task in many areas of modern economy and research. Unfortunately, the ever-increasing scale of datasets has long outgrown the capacities and abilities humans can muster to extract information from them and gain new knowledge. For this reason, research areas like data mining and knowledge discovery steadily gain importance. The algorithms they provide for the extraction of knowledge are mandatory prerequisites that enable people to analyze large amounts of information. Among the approaches offered by these areas, clustering is one of the most fundamental. By finding groups of similar objects inside the data, it aims to identify meaningful structures that constitute new knowledge. Clustering results are also often used as input for other analysis techniques like classification or forecasting. As clustering extracts new and unknown knowledge, it obviously has no access to any form of ground truth. For this reason, clustering results have a hypothetical character and must be interpreted with respect to the application domain. This makes clustering very challenging and leads to an extensive and diverse landscape of available algorithms. Most of these are expert tools that are tailored to a single narrowly defined application scenario. Over the years, this specialization has become a major trend that arose to counter the inherent uncertainty of clustering by including as much domain specifics as possible into algorithms. While customized methods often improve result quality, they become more and more complicated to handle and lose versatility. This creates a dilemma especially for amateur users whose numbers are increasing as clustering is applied in more and more domains. While an abundance of tools is offered, guidance is severely lacking and users are left alone with critical tasks like algorithm selection, parameter configuration and the interpretation and adjustment of results. This thesis aims to solve this dilemma by structuring and integrating the necessary steps of clustering into a guided and feedback-driven process. In doing so, users are provided with a default modus operandi for the application of clustering. Two main components constitute the core of said process: the algorithm management and the visual-interactive interface. Algorithm management handles all aspects of actual clustering creation and the involved methods. It employs a modular approach for algorithm description that allows users to understand, design, and compare clustering techniques with the help of building blocks. In addition, algorithm management offers facilities for the integration of multiple clusterings of the same dataset into an improved solution. New approaches based on ensemble clustering not only allow the utilization of different clustering techniques, but also ease their application by acting as an abstraction layer that unifies individual parameters. Finally, this component provides a multi-level interface that structures all available control options and provides the docking points for user interaction. The visual-interactive interface supports users during result interpretation and adjustment. For this, the defining characteristics of a clustering are communicated via a hybrid visualization. In contrast to traditional data-driven visualizations that tend to become overloaded and unusable with increasing volume/dimensionality of data, this novel approach communicates the abstract aspects of cluster composition and relations between clusters. This aspect orientation allows the use of easy-to-understand visual components and makes the visualization immune to scale related effects of the underlying data. This visual communication is attuned to a compact and universally valid set of high-level feedback that allows the modification of clustering results. Instead of technical parameters that indirectly cause changes in the whole clustering by influencing its creation process, users can employ simple commands like merge or split to directly adjust clusters. The orchestrated cooperation of these two main components creates a modus operandi, in which clusterings are no longer created and disposed as a whole until a satisfying result is obtained. Instead, users apply the feedback-driven process to iteratively refine an initial solution. Performance and usability of the proposed approach were evaluated with a user study. Its results show that the feedback-driven process enabled amateur users to easily create satisfying clustering results even from different and not optimal starting situations

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