Explorative visual analytics on interval-based genomic data and their metadata

Background: With the wide-spreading of public repositories of NGS processed data, the availability of user-friendly and effective tools for data exploration, analysis and visualization is becoming very relevant. These tools enable interactive analytics, an exploratory approach for the seamless "sense-making" of data through on-the-fly integration of analysis and visualization phases, suggested not only for evaluating processing results, but also for designing and adapting NGS data analysis pipelines. Results: This paper presents abstractions for supporting the early analysis of NGS processed data and their implementation in an associated tool, named GenoMetric Space Explorer (GeMSE). This tool serves the needs of the GenoMetric Query Language, an innovative cloud-based system for computing complex queries over heterogeneous processed data. It can also be used starting from any text files in standard BED, BroadPeak, NarrowPeak, GTF, or general tab-delimited format, containing numerical features of genomic regions; metadata can be provided as text files in tab-delimited attribute-value format. GeMSE allows interactive analytics, consisting of on-the-fly cycling among steps of data exploration, analysis and visualization that help biologists and bioinformaticians in making sense of heterogeneous genomic datasets. By means of an explorative interaction support, users can trace past activities and quickly recover their results, seamlessly going backward and forward in the analysis steps and comparative visualizations of heatmaps. Conclusions: GeMSE effective application and practical usefulness is demonstrated through significant use cases of biological interest. GeMSE is available at http://www.bioinformatics.deib.polimi.it/GeMSE/ , and its source code is available at https://github.com/Genometric/GeMSEunder GPLv3 open-source license

Experiences in the development of a data management system for genomics

GMQL is a high-level query language for genomics, which operates on datasets described through GDM, a unifying data model for processed data formats. They are ingredients for the integration of processed genomic datasets, i.e. of signals produced by the genome after sequencing and long data extraction pipelines. While most of the processing load of today’s genomic platforms is due to data extraction pipelines, we anticipate soon a shift of attention towards processed datasets, as such data are being collected by large consortia and are becoming increasingly available. In our view, biology and personalized medicine will increasingly rely on data extraction and analysis methods for inferring new knowledge from existing heterogeneous repositories of processed datasets, typically augmented with the results of experimental data targeting individuals or small populations. While today’s big data are raw reads of the sequencing machines, tomorrow’s big data will also include billions or trillions of genomic regions, each featuring specific values depending on the processing conditions. Coherently, GMQL is a high-level, declarative language inspired by big data management, and its execution engines include classic cloud-based systems, from Pig to Flink to SciDB to Spark. In this paper, we discuss how the GMQL execution environment has been developed, by going through a major version change that marked a complete system redesign; we also discuss our experiences in comparatively evaluating the four platforms

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further

Explorative Graph Visualization

Netzwerkstrukturen (Graphen) sind heutzutage weit verbreitet. Ihre Untersuchung dient dazu, ein besseres Verständnis ihrer Struktur und der durch sie modellierten realen Aspekte zu gewinnen. Die Exploration solcher Netzwerke wird zumeist mit Visualisierungstechniken unterstützt. Ziel dieser Arbeit ist es, einen Überblick über die Probleme dieser Visualisierungen zu geben und konkrete Lösungsansätze aufzuzeigen. Dabei werden neue Visualisierungstechniken eingeführt, um den Nutzen der geführten Diskussion für die explorative Graphvisualisierung am konkreten Beispiel zu belegen.Network structures (graphs) have become a natural part of everyday life and their analysis helps to gain an understanding of their inherent structure and the real-world aspects thereby expressed. The exploration of graphs is largely supported and driven by visual means. The aim of this thesis is to give a comprehensive view on the problems associated with these visual means and to detail concrete solution approaches for them. Concrete visualization techniques are introduced to underline the value of this comprehensive discussion for supporting explorative graph visualization

24th International Conference on Information Modelling and Knowledge Bases

In the last three decades information modelling and knowledge bases have become essentially important subjects not only in academic communities related to information systems and computer science but also in the business area where information technology is applied. The series of European – Japanese Conference on Information Modelling and Knowledge Bases (EJC) originally started as a co-operation initiative between Japan and Finland in 1982. The practical operations were then organised by professor Ohsuga in Japan and professors Hannu Kangassalo and Hannu Jaakkola in Finland (Nordic countries). Geographical scope has expanded to cover Europe and also other countries. Workshop characteristic - discussion, enough time for presentations and limited number of participants (50) / papers (30) - is typical for the conference. Suggested topics include, but are not limited to: 1. Conceptual modelling: Modelling and specification languages; Domain-specific conceptual modelling; Concepts, concept theories and ontologies; Conceptual modelling of large and heterogeneous systems; Conceptual modelling of spatial, temporal and biological data; Methods for developing, validating and communicating conceptual models. 2. Knowledge and information modelling and discovery: Knowledge discovery, knowledge representation and knowledge management; Advanced data mining and analysis methods; Conceptions of knowledge and information; Modelling information requirements; Intelligent information systems; Information recognition and information modelling. 3. Linguistic modelling: Models of HCI; Information delivery to users; Intelligent informal querying; Linguistic foundation of information and knowledge; Fuzzy linguistic models; Philosophical and linguistic foundations of conceptual models. 4. Cross-cultural communication and social computing: Cross-cultural support systems; Integration, evolution and migration of systems; Collaborative societies; Multicultural web-based software systems; Intercultural collaboration and support systems; Social computing, behavioral modeling and prediction. 5. Environmental modelling and engineering: Environmental information systems (architecture); Spatial, temporal and observational information systems; Large-scale environmental systems; Collaborative knowledge base systems; Agent concepts and conceptualisation; Hazard prediction, prevention and steering systems. 6. Multimedia data modelling and systems: Modelling multimedia information and knowledge; Contentbased multimedia data management; Content-based multimedia retrieval; Privacy and context enhancing technologies; Semantics and pragmatics of multimedia data; Metadata for multimedia information systems. Overall we received 56 submissions. After careful evaluation, 16 papers have been selected as long paper, 17 papers as short papers, 5 papers as position papers, and 3 papers for presentation of perspective challenges. We thank all colleagues for their support of this issue of the EJC conference, especially the program committee, the organising committee, and the programme coordination team. The long and the short papers presented in the conference are revised after the conference and published in the Series of “Frontiers in Artificial Intelligence” by IOS Press (Amsterdam). The books “Information Modelling and Knowledge Bases” are edited by the Editing Committee of the conference. We believe that the conference will be productive and fruitful in the advance of research and application of information modelling and knowledge bases. Bernhard Thalheim Hannu Jaakkola Yasushi Kiyok

Deriving statistical inference from the application of artificial neural networks to clinical metabolomics data

Metabolomics data are complex with a high degree of multicollinearity. As such, multivariate linear projection methods, such as partial least squares discriminant analysis (PLS-DA) have become standard. Non-linear projections methods, typified by Artificial Neural Networks (ANNs) may be more appropriate to model potential nonlinear latent covariance; however, they are not widely used due to difficulty in deriving statistical inference, and thus biological interpretation. Herein, we illustrate the utility of ANNs for clinical metabolomics using publicly available data sets and develop an open framework for deriving and visualising statistical inference from ANNs equivalent to standard PLS-DA methods

Front-Line Physicians' Satisfaction with Information Systems in Hospitals

Day-to-day operations management in hospital units is difficult due to continuously varying situations, several actors involved and a vast number of information systems in use. The aim of this study was to describe front-line physicians' satisfaction with existing information systems needed to support the day-to-day operations management in hospitals. A cross-sectional survey was used and data chosen with stratified random sampling were collected in nine hospitals. Data were analyzed with descriptive and inferential statistical methods. The response rate was 65 % (n = 111). The physicians reported that information systems support their decision making to some extent, but they do not improve access to information nor are they tailored for physicians. The respondents also reported that they need to use several information systems to support decision making and that they would prefer one information system to access important information. Improved information access would better support physicians' decision making and has the potential to improve the quality of decisions and speed up the decision making process.Peer reviewe

Next Generation Indexing for Genomic Intervals

Di4 (1D intervals incremental inverted index) is a multi-resolution, single-dimension indexing framework for efficient, scalable, and extensible computation of genomic interval expressions. The framework has a tri-layer architecture: the semantic layer provides orthogonal and generic means (including the support of user-defined function) of sense-making and higher-lever reasoning from region-based datasets; the logical layer provides building blocks for region calculus and topological relations between intervals; the physical layer abstracts from persistence technology and makes the model adaptable to variety of persistence technologies, spanning from small-scale (e.g., B+tree) to large-scale (e.g., LevelDB). The extensibility of Di4 to application scenarios is shown with an example of comparative evaluation of ChIP-seq and DNase-Seq replicates. Performance of Di4 is benchmarked for small and large scale scenarios under common bioinformatics application scenarios. Di4 is freely available from https://genometric.github.io/Di4

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

Close and Distant Reading Visualizations for the Comparative Analysis of Digital Humanities Data

Traditionally, humanities scholars carrying out research on a specific or on multiple literary work(s) are interested in the analysis of related texts or text passages. But the digital age has opened possibilities for scholars to enhance their traditional workflows. Enabled by digitization projects, humanities scholars can nowadays reach a large number of digitized texts through web portals such as Google Books or Internet Archive. Digital editions exist also for ancient texts; notable examples are PHI Latin Texts and the Perseus Digital Library. This shift from reading a single book “on paper” to the possibility of browsing many digital texts is one of the origins and principal pillars of the digital humanities domain, which helps developing solutions to handle vast amounts of cultural heritage data – text being the main data type. In contrast to the traditional methods, the digital humanities allow to pose new research questions on cultural heritage datasets. Some of these questions can be answered with existent algorithms and tools provided by the computer science domain, but for other humanities questions scholars need to formulate new methods in collaboration with computer scientists. Developed in the late 1980s, the digital humanities primarily focused on designing standards to represent cultural heritage data such as the Text Encoding Initiative (TEI) for texts, and to aggregate, digitize and deliver data. In the last years, visualization techniques have gained more and more importance when it comes to analyzing data. For example, Saito introduced her 2010 digital humanities conference paper with: “In recent years, people have tended to be overwhelmed by a vast amount of information in various contexts. Therefore, arguments about ’Information Visualization’ as a method to make information easy to comprehend are more than understandable.” A major impulse for this trend was given by Franco Moretti. In 2005, he published the book “Graphs, Maps, Trees”, in which he proposes so-called distant reading approaches for textual data that steer the traditional way of approaching literature towards a completely new direction. Instead of reading texts in the traditional way – so-called close reading –, he invites to count, to graph and to map them. In other words, to visualize them. This dissertation presents novel close and distant reading visualization techniques for hitherto unsolved problems. Appropriate visualization techniques have been applied to support basic tasks, e.g., visualizing geospatial metadata to analyze the geographical distribution of cultural heritage data items or using tag clouds to illustrate textual statistics of a historical corpus. In contrast, this dissertation focuses on developing information visualization and visual analytics methods that support investigating research questions that require the comparative analysis of various digital humanities datasets. We first take a look at the state-of-the-art of existing close and distant reading visualizations that have been developed to support humanities scholars working with literary texts. We thereby provide a taxonomy of visualization methods applied to show various aspects of the underlying digital humanities data. We point out open challenges and we present our visualizations designed to support humanities scholars in comparatively analyzing historical datasets. In short, we present (1) GeoTemCo for the comparative visualization of geospatial-temporal data, (2) the two tag cloud designs TagPies and TagSpheres that comparatively visualize faceted textual summaries, (3) TextReuseGrid and TextReuseBrowser to explore re-used text passages among the texts of a corpus, (4) TRAViz for the visualization of textual variation between multiple text editions, and (5) the visual analytics system MusikerProfiling to detect similar musicians to a given musician of interest. Finally, we summarize our and the collaboration experiences of other visualization researchers to emphasize the ingredients required for a successful project in the digital humanities, and we take a look at future challenges in that research field