Computing Competencies for Undergraduate Data Science Curricula: ACM Data Science Task Force

At the August 2017 ACM Education Council meeting, a task force was formed to explore a process to add to the broad, interdisciplinary conversation on data science, with an articulation of the role of computing discipline-specific contributions to this emerging field. Specifically, the task force would seek to define what the computing/computational contributions are to this new field, and provide guidance on computing-specific competencies in data science for departments offering such programs of study at the undergraduate level. There are many stakeholders in the discussion of data science – these include colleges and universities that (hope to) offer data science programs, employers who hope to hire a workforce with knowledge and experience in data science, as well as individuals and professional societies representing the fields of computing, statistics, machine learning, computational biology, computational social sciences, digital humanities, and others. There is a shared desire to form a broad interdisciplinary definition of data science and to develop curriculum guidance for degree programs in data science. This volume builds upon the important work of other groups who have published guidelines for data science education. There is a need to acknowledge the definition and description of the individual contributions to this interdisciplinary field. For instance, those interested in the business context for these concepts generally use the term “analytics”; in some cases, the abbreviation DSA appears, meaning Data Science and Analytics. This volume is the third draft articulation of computing-focused competencies for data science. It recognizes the inherent interdisciplinarity of data science and situates computing-specific competencies within the broader interdisciplinary space

Electronic Health Record Summarization over Heterogeneous and Irregularly Sampled Clinical Data

The increasing adoption of electronic health records (EHRs) has led to an unprecedented amount of patient health information stored in an electronic format. The ability to comb through this information is imperative, both for patient care and computational modeling. Creating a system to minimize unnecessary EHR data, automatically distill longitudinal patient information, and highlight salient parts of a patient’s record is currently an unmet need. However, summarization of EHR data is not a trivial task, as there exist many challenges with reasoning over this data. EHR data elements are most often obtained at irregular intervals as patients are more likely to receive medical care when they are ill, than when they are healthy. The presence of narrative documentation adds another layer of complexity as the notes are riddled with over-sampled text, often caused by the frequent copy-and-pasting during the documentation process. This dissertation synthesizes a set of challenges for automated EHR summarization identified in the literature and presents an array of methods for dealing with some of these challenges. We used hybrid data-driven and knowledge-based approaches to examine abundant redundancy in clinical narrative text, a data-driven approach to identify and mitigate biases in laboratory testing patterns with implications for using clinical data for research, and a probabilistic modeling approach to automatically summarize patient records and learn computational models of disease with heterogeneous data types. The dissertation also demonstrates two applications of the developed methods to important clinical questions: the questions of laboratory test overutilization and cohort selection from EHR data

Systematic Analysis of the Factors Contributing to the Variation and Change of the Microbiome

abstract: Understanding changes and trends in biomedical knowledge is crucial for individuals, groups, and institutions as biomedicine improves people’s lives, supports national economies, and facilitates innovation. However, as knowledge changes what evidence illustrates knowledge changes? In the case of microbiome, a multi-dimensional concept from biomedicine, there are significant increases in publications, citations, funding, collaborations, and other explanatory variables or contextual factors. What is observed in the microbiome, or any historical evolution of a scientific field or scientific knowledge, is that these changes are related to changes in knowledge, but what is not understood is how to measure and track changes in knowledge. This investigation highlights how contextual factors from the language and social context of the microbiome are related to changes in the usage, meaning, and scientific knowledge on the microbiome. Two interconnected studies integrating qualitative and quantitative evidence examine the variation and change of the microbiome evidence are presented. First, the concepts microbiome, metagenome, and metabolome are compared to determine the boundaries of the microbiome concept in relation to other concepts where the conceptual boundaries have been cited as overlapping. A collection of publications for each concept or corpus is presented, with a focus on how to create, collect, curate, and analyze large data collections. This study concludes with suggestions on how to analyze biomedical concepts using a hybrid approach that combines results from the larger language context and individual words. Second, the results of a systematic review that describes the variation and change of microbiome research, funding, and knowledge are examined. A corpus of approximately 28,000 articles on the microbiome are characterized, and a spectrum of microbiome interpretations are suggested based on differences related to context. The collective results suggest the microbiome is a separate concept from the metagenome and metabolome, and the variation and change to the microbiome concept was influenced by contextual factors. These results provide insight into how concepts with extensive resources behave within biomedicine and suggest the microbiome is possibly representative of conceptual change or a preview of new dynamics within science that are expected in the future.Dissertation/ThesisDoctoral Dissertation Biology 201

Cyber-Physical Threat Intelligence for Critical Infrastructures Security

Modern critical infrastructures can be considered as large scale Cyber Physical Systems (CPS). Therefore, when designing, implementing, and operating systems for Critical Infrastructure Protection (CIP), the boundaries between physical security and cybersecurity are blurred. Emerging systems for Critical Infrastructures Security and Protection must therefore consider integrated approaches that emphasize the interplay between cybersecurity and physical security techniques. Hence, there is a need for a new type of integrated security intelligence i.e., Cyber-Physical Threat Intelligence (CPTI). This book presents novel solutions for integrated Cyber-Physical Threat Intelligence for infrastructures in various sectors, such as Industrial Sites and Plants, Air Transport, Gas, Healthcare, and Finance. The solutions rely on novel methods and technologies, such as integrated modelling for cyber-physical systems, novel reliance indicators, and data driven approaches including BigData analytics and Artificial Intelligence (AI). Some of the presented approaches are sector agnostic i.e., applicable to different sectors with a fair customization effort. Nevertheless, the book presents also peculiar challenges of specific sectors and how they can be addressed. The presented solutions consider the European policy context for Security, Cyber security, and Critical Infrastructure protection, as laid out by the European Commission (EC) to support its Member States to protect and ensure the resilience of their critical infrastructures. Most of the co-authors and contributors are from European Research and Technology Organizations, as well as from European Critical Infrastructure Operators. Hence, the presented solutions respect the European approach to CIP, as reflected in the pillars of the European policy framework. The latter includes for example the Directive on security of network and information systems (NIS Directive), the Directive on protecting European Critical Infrastructures, the General Data Protection Regulation (GDPR), and the Cybersecurity Act Regulation. The sector specific solutions that are described in the book have been developed and validated in the scope of several European Commission (EC) co-funded projects on Critical Infrastructure Protection (CIP), which focus on the listed sectors. Overall, the book illustrates a rich set of systems, technologies, and applications that critical infrastructure operators could consult to shape their future strategies. It also provides a catalogue of CPTI case studies in different sectors, which could be useful for security consultants and practitioners as well

User-centric knowledge extraction and maintenance

An ontology is a machine readable knowledge collection. There is an abundance of information available for human consumption. Thus, large general knowledge ontologies are typically generated tapping into this information source using imperfect automatic extraction approaches that translate human readable text into machine readable semantic knowledge. This thesis provides methods for user-driven ontology generation and maintenance. In particular, this work consists of three main contributions: 1. An interactive human-supported extraction tool: LUKe. The system extends an automatic extraction framework to integrate human feedback on extraction decisions and extracted information on multiple levels. 2. A document retrieval approach based on semantic statements: S3K. While one application is the retrieval of documents that support extracted information to verify the correctness of the piece of information, another application in combination with an extraction system is a fact based indexing of a document corpus allowing statement based document retrieval. 3. A method for similarity based ontology navigation: QBEES. The approach enables search by example. That is, given a set of semantic entities, it provides the most similar entities with respect to their semantic properties considering different aspects. All three components are integrated into a modular architecture that also provides an interface for third-party components.Eine Ontologie ist eine Wissenssammlung in maschinenlesbarer Form. Da eine große Bandbreite an Informationen nur in natürlichsprachlicher Form verfügbar ist, werden maschinenlesbare Ontologien häufig durch imperfekte automatische Verfahren erzeugt, die eine Übersetzung in eine maschinenlesbare Darstellung vornehmen. In der vorliegenden Arbeit werden Methoden zur menschlichen Unterstützung des Extraktionsprozesses und Wartung der erzeugten Wissensbasen präsentiert. Dabei werden drei Beiträge geleistet: 1. Zum ersten wird ein interaktives Extraktionstool (LUKe) vorgestellt. Hierfür wird ein bestehendes Extraktionssystem um die Integration von Nutzerkorrekturen auf verschiedenen Ebenen der Extraktion erweitert und an ein beispielhaftes Szenario angepasst. 2. Zum zweiten wird ein Ansatz (S3K) zur Dokumentsuche basierend auf faktischen Aussagen beschrieben. Dieser erlaubt eine aussagenbasierte Suche nach Belegstellen oder weiteren Informationen im Zusammenhang mit diesen Aussagen in den Dokumentsammlungen die der Wissensbasis zugrunde liegen. 3. Zuletzt wird QBEES, eine Ähnlichkeitssuche in Ontologien, vorgestellt. QBEES ermöglicht die Suche bzw. Empfehlung von ähnlichen Entitäten auf Basis der semantischen Eigenschaften die sie mit einer als Beispiel angegebenen Menge von Entitäten gemein haben. Alle einzelnen Komponenten sind zudem in eine modulare Gesamtarchitektur integriert

Cyber-Physical Threat Intelligence for Critical Infrastructures Security

Modern critical infrastructures can be considered as large scale Cyber Physical Systems (CPS). Therefore, when designing, implementing, and operating systems for Critical Infrastructure Protection (CIP), the boundaries between physical security and cybersecurity are blurred. Emerging systems for Critical Infrastructures Security and Protection must therefore consider integrated approaches that emphasize the interplay between cybersecurity and physical security techniques. Hence, there is a need for a new type of integrated security intelligence i.e., Cyber-Physical Threat Intelligence (CPTI). This book presents novel solutions for integrated Cyber-Physical Threat Intelligence for infrastructures in various sectors, such as Industrial Sites and Plants, Air Transport, Gas, Healthcare, and Finance. The solutions rely on novel methods and technologies, such as integrated modelling for cyber-physical systems, novel reliance indicators, and data driven approaches including BigData analytics and Artificial Intelligence (AI). Some of the presented approaches are sector agnostic i.e., applicable to different sectors with a fair customization effort. Nevertheless, the book presents also peculiar challenges of specific sectors and how they can be addressed. The presented solutions consider the European policy context for Security, Cyber security, and Critical Infrastructure protection, as laid out by the European Commission (EC) to support its Member States to protect and ensure the resilience of their critical infrastructures. Most of the co-authors and contributors are from European Research and Technology Organizations, as well as from European Critical Infrastructure Operators. Hence, the presented solutions respect the European approach to CIP, as reflected in the pillars of the European policy framework. The latter includes for example the Directive on security of network and information systems (NIS Directive), the Directive on protecting European Critical Infrastructures, the General Data Protection Regulation (GDPR), and the Cybersecurity Act Regulation. The sector specific solutions that are described in the book have been developed and validated in the scope of several European Commission (EC) co-funded projects on Critical Infrastructure Protection (CIP), which focus on the listed sectors. Overall, the book illustrates a rich set of systems, technologies, and applications that critical infrastructure operators could consult to shape their future strategies. It also provides a catalogue of CPTI case studies in different sectors, which could be useful for security consultants and practitioners as well