Information Retrieval for Multivariate Research Data Repositories

In this dissertation, I tackle the challenge of information retrieval for multivariate research data by providing novel means of content-based access. Large amounts of multivariate data are produced and collected in different areas of scientific research and industrial applications, including the human or natural sciences, the social or economical sciences and applications like quality control, security and machine monitoring. Archival and re-use of this kind of data has been identified as an important factor in the supply of information to support research and industrial production. Due to increasing efforts in the digital library community, such multivariate data are collected, archived and often made publicly available by specialized research data repositories. A multivariate research data document consists of tabular data with $m$ columns (measurement parameters, e.g., temperature, pressure, humidity, etc.) and $n$ rows (observations). To render such data-sets accessible, they are annotated with meta-data according to well-defined meta-data standard when being archived. These annotations include time, location, parameters, title, author (and potentially many more) of the document under concern. In particular for multivariate data, each column is annotated with the parameter name and unit of its data (e.g., water depth [m]). The task of retrieving and ranking the documents an information seeker is looking for is an important and difficult challenge. To date, access to this data is primarily provided by means of annotated, textual meta-data as described above. An information seeker can search for documents of interest, by querying for the annotated meta-data. For example, an information seeker can retrieve all documents that were obtained in a specific region or within a certain period of time. Similarly, she can search for data-sets that contain a particular measurement via its parameter name or search for data-sets that were produced by a specific scientist. However, retrieval via textual annotations is limited and does not allow for content-based search, e.g., retrieving data which contains a particular measurement pattern like a linear relationship between water depth and water pressure, or which is similar to example data the information seeker provides. In this thesis, I deal with this challenge and develop novel indexing and retrieval schemes, to extend the established, meta-data based access to multivariate research data. By analyzing and indexing the data patterns occurring in multivariate data, one can support new techniques for content-based retrieval and exploration, well beyond meta-data based query methods. This allows information seekers to query for multivariate data-sets that exhibit patterns similar to an example data-set they provide. Furthermore, information seekers can specify one or more particular patterns they are looking for, to retrieve multivariate data-sets that contain similar patterns. To this end, I also develop visual-interactive techniques to support information seekers in formulating such queries, which inherently are more complex than textual search strings. These techniques include providing an over-view of potentially interesting patterns to search for, that interactively adapt to the user's query as it is being entered. Furthermore, based on the pattern description of each multivariate data document, I introduce a similarity measure for multivariate data. This allows scientists to quickly discover similar (or contradictory) data to their own measurements

Exploratory search in time-oriented primary data

In a variety of research fields, primary data that describes scientific phenomena in an original condition is obtained. Time-oriented primary data, in particular, is an indispensable data type, derived from complex measurements depending on time. Today, time-oriented primary data is collected at rates that exceed the domain experts’ abilities to seek valuable information undiscovered in the data. It is widely accepted that the magnitudes of uninvestigated data will disclose tremendous knowledge in data-driven research, provided that domain experts are able to gain insight into the data. Domain experts involved in data-driven research urgently require analytical capabilities. In scientific practice, predominant activities are the generation and validation of hypotheses. In analytical terms, these activities are often expressed in confirmatory and exploratory data analysis. Ideally, analytical support would combine the strengths of both types of activities. Exploratory search (ES) is a concept that seamlessly includes information-seeking behaviors ranging from search to exploration. ES supports domain experts in both gaining an understanding of huge and potentially unknown data collections and the drill-down to relevant subsets, e.g., to validate hypotheses. As such, ES combines predominant tasks of domain experts applied to data-driven research. For the design of useful and usable ES systems (ESS), data scientists have to incorporate different sources of knowledge and technology. Of particular importance is the state-of-the-art in interactive data visualization and data analysis. Research in these factors is at heart of Information Visualization (IV) and Visual Analytics (VA). Approaches in IV and VA provide meaningful visualization and interaction designs, allowing domain experts to perform the information-seeking process in an effective and efficient way. Today, bestpractice ESS almost exclusively exist for textual data content, e.g., put into practice in digital libraries to facilitate the reuse of digital documents. For time-oriented primary data, ES mainly remains at a theoretical state. Motivation and Problem Statement. This thesis is motivated by two main assumptions. First, we expect that ES will have a tremendous impact on data-driven research for many research fields. In this thesis, we focus on time-oriented primary data, as a complex and important data type for data-driven research. Second, we assume that research conducted to IV and VA will particularly facilitate ES. For time-oriented primary data, however, novel concepts and techniques are required that enhance the design and the application of ESS. In particular, we observe a lack of methodological research in ESS for time-oriented primary data. In addition, the size, the complexity, and the quality of time-oriented primary data hampers the content-based access, as well as the design of visual interfaces for gaining an overview of the data content. Furthermore, the question arises how ESS can incorporate techniques for seeking relations between data content and metadata to foster data-driven research. Overarching challenges for data scientists are to create usable and useful designs, urgently requiring the involvement of the targeted user group and support techniques for choosing meaningful algorithmic models and model parameters. Throughout this thesis, we will resolve these challenges from conceptual, technical, and systemic perspectives. In turn, domain experts can benefit from novel ESS as a powerful analytical support to conduct data-driven research. Concepts for Exploratory Search Systems (Chapter 3). We postulate concepts for the ES in time-oriented primary data. Based on a survey of analysis tasks supported in IV and VA research, we present a comprehensive selection of tasks and techniques relevant for search and exploration activities. The assembly guides data scientists in the choice of meaningful techniques presented in IV and VA. Furthermore, we present a reference workflow for the design and the application of ESS for time-oriented primary data. The workflow divides the data processing and transformation process into four steps, and thus divides the complexity of the design space into manageable parts. In addition, the reference workflow describes how users can be involved in the design. The reference workflow is the framework for the technical contributions of this thesis. Visual-Interactive Preprocessing of Time-Oriented Primary Data (Chapter 4). We present a visual-interactive system that enables users to construct workflows for preprocessing time-oriented primary data. In this way, we introduce a means of providing content-based access. Based on a rich set of preprocessing routines, users can create individual solutions for data cleansing, normalization, segmentation, and other preprocessing tasks. In addition, the system supports the definition of time series descriptors and time series distance measures. Guidance concepts support users in assessing the workflow generalizability, which is important for large data sets. The execution of the workflows transforms time-oriented primary data into feature vectors, which can subsequently be used for downstream search and exploration techniques. We demonstrate the applicability of the system in usage scenarios and case studies. Content-Based Overviews (Chapter 5). We introduce novel guidelines and techniques for the design of contentbased overviews. The three key factors are the creation of meaningful data aggregates, the visual mapping of these aggregates into the visual space, and the view transformation providing layouts of these aggregates in the display space. For each of these steps, we characterize important visualization and interaction design parameters allowing the involvement of users. We introduce guidelines supporting data scientists in choosing meaningful solutions. In addition, we present novel visual-interactive quality assessment techniques enhancing the choice of algorithmic model and model parameters. Finally, we present visual interfaces enabling users to formulate visual queries of the time-oriented data content. In this way, we provide means of combining content-based exploration with content-based search. Relation Seeking Between Data Content and Metadata (Chapter 6). We present novel visual interfaces enabling domain experts to seek relations between data content and metadata. These interfaces can be integrated into ESS to bridge analytical gaps between the data content and attached metadata. In three different approaches, we focus on different types of relations and define algorithmic support to guide users towards most interesting relations. Furthermore, each of the three approaches comprises individual visualization and interaction designs, enabling users to explore both the data and the relations in an efficient and effective way. We demonstrate the applicability of our interfaces with usage scenarios, each conducted together with domain experts. The results confirm that our techniques are beneficial for seeking relations between data content and metadata, particularly for data-centered research. Case Studies - Exploratory Search Systems (Chapter 7). In two case studies, we put our concepts and techniques into practice. We present two ESS constructed in design studies with real users, and real ES tasks, and real timeoriented primary data collections. The web-based VisInfo ESS is a digital library system facilitating the visual access to time-oriented primary data content. A content-based overview enables users to explore large collections of time series measurements and serves as a baseline for content-based queries by example. In addition, VisInfo provides a visual interface for querying time oriented data content by sketch. A result visualization combines different views of the data content and metadata with faceted search functionality. The MotionExplorer ESS supports domain experts in human motion analysis. Two content-based overviews enhance the exploration of large collections of human motion capture data from two perspectives. MotionExplorer provides a search interface, allowing domain experts to query human motion sequences by example. Retrieval results are depicted in a visual-interactive view enabling the exploration of variations of human motions. Field study evaluations performed for both ESS confirm the applicability of the systems in the environment of the involved user groups. The systems yield a significant improvement of both the effectiveness and the efficiency in the day-to-day work of the domain experts. As such, both ESS demonstrate how large collections of time-oriented primary data can be reused to enhance data-centered research. In essence, our contributions cover the entire time series analysis process starting from accessing raw time-oriented primary data, processing and transforming time series data, to visual-interactive analysis of time series. We present visual search interfaces providing content-based access to time-oriented primary data. In a series of novel explorationsupport techniques, we facilitate both gaining an overview of large and complex time-oriented primary data collections and seeking relations between data content and metadata. Throughout this thesis, we introduce VA as a means of designing effective and efficient visual-interactive systems. Our VA techniques empower data scientists to choose appropriate models and model parameters, as well as to involve users in the design. With both principles, we support the design of usable and useful interfaces which can be included into ESS. In this way, our contributions bridge the gap between search systems requiring exploration support and exploratory data analysis systems requiring visual querying capability. In the ESS presented in two case studies, we prove that our techniques and systems support data-driven research in an efficient and effective way

Prognostication and New Treatment Strategies for Esophageal and Junctional Cancer

The research described in this thesis addresses prediction of survival and new treatment strategies for patients with esophageal or junctional cancer

Retrieval and exploratory search in multivariate research data repositories using regressional features

Increasing amounts of data are collected in many areas of research and application. The degree to which this data can be accessed, retrieved, and analyzed is decisive to obtain progress in fields such as scientific research or industrial production. We present a novel method supporting content-based retrieval and exploratory search in repositories of multivariate research data. In particular, functional dependencies are a key characteristic of data that researchers are often interested in. Our methods are able to describe the functional form of such dependencies, e.g., the relationship between inflation and unemployment in economics. Our basic idea is to use feature vectors based on the goodness-of-fit of a set of regression models, to describe the data mathematically. We denote this approach Regressional Features and use it for content-based search and, since our approach motivates an intuitive definition of interestingness, for exploring the most interesting data. We apply our method on considerable real-world research datasets, showing the usefulness of our approach for user-centered access to research data in a Digital Library system