Editorial: biological ontologies and semantic biology

As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account

The SP theory of intelligence: benefits and applications

This article describes existing and expected benefits of the "SP theory of intelligence", and some potential applications. The theory aims to simplify and integrate ideas across artificial intelligence, mainstream computing, and human perception and cognition, with information compression as a unifying theme. It combines conceptual simplicity with descriptive and explanatory power across several areas of computing and cognition. In the "SP machine" -- an expression of the SP theory which is currently realized in the form of a computer model -- there is potential for an overall simplification of computing systems, including software. The SP theory promises deeper insights and better solutions in several areas of application including, most notably, unsupervised learning, natural language processing, autonomous robots, computer vision, intelligent databases, software engineering, information compression, medical diagnosis and big data. There is also potential in areas such as the semantic web, bioinformatics, structuring of documents, the detection of computer viruses, data fusion, new kinds of computer, and the development of scientific theories. The theory promises seamless integration of structures and functions within and between different areas of application. The potential value, worldwide, of these benefits and applications is at least $190 billion each year. Further development would be facilitated by the creation of a high-parallel, open-source version of the SP machine, available to researchers everywhere.Comment: arXiv admin note: substantial text overlap with arXiv:1212.022

Crisis Analytics: Big Data Driven Crisis Response

Disasters have long been a scourge for humanity. With the advances in technology (in terms of computing, communications, and the ability to process and analyze big data), our ability to respond to disasters is at an inflection point. There is great optimism that big data tools can be leveraged to process the large amounts of crisis-related data (in the form of user generated data in addition to the traditional humanitarian data) to provide an insight into the fast-changing situation and help drive an effective disaster response. This article introduces the history and the future of big crisis data analytics, along with a discussion on its promise, challenges, and pitfalls

Big Data and the Internet of Things

Advances in sensing and computing capabilities are making it possible to embed increasing computing power in small devices. This has enabled the sensing devices not just to passively capture data at very high resolution but also to take sophisticated actions in response. Combined with advances in communication, this is resulting in an ecosystem of highly interconnected devices referred to as the Internet of Things - IoT. In conjunction, the advances in machine learning have allowed building models on this ever increasing amounts of data. Consequently, devices all the way from heavy assets such as aircraft engines to wearables such as health monitors can all now not only generate massive amounts of data but can draw back on aggregate analytics to "improve" their performance over time. Big data analytics has been identified as a key enabler for the IoT. In this chapter, we discuss various avenues of the IoT where big data analytics either is already making a significant impact or is on the cusp of doing so. We also discuss social implications and areas of concern.Comment: 33 pages. draft of upcoming book chapter in Japkowicz and Stefanowski (eds.) Big Data Analysis: New algorithms for a new society, Springer Series on Studies in Big Data, to appea

Research and Education in Computational Science and Engineering

Over the past two decades the field of computational science and engineering (CSE) has penetrated both basic and applied research in academia, industry, and laboratories to advance discovery, optimize systems, support decision-makers, and educate the scientific and engineering workforce. Informed by centuries of theory and experiment, CSE performs computational experiments to answer questions that neither theory nor experiment alone is equipped to answer. CSE provides scientists and engineers of all persuasions with algorithmic inventions and software systems that transcend disciplines and scales. Carried on a wave of digital technology, CSE brings the power of parallelism to bear on troves of data. Mathematics-based advanced computing has become a prevalent means of discovery and innovation in essentially all areas of science, engineering, technology, and society; and the CSE community is at the core of this transformation. However, a combination of disruptive developments---including the architectural complexity of extreme-scale computing, the data revolution that engulfs the planet, and the specialization required to follow the applications to new frontiers---is redefining the scope and reach of the CSE endeavor. This report describes the rapid expansion of CSE and the challenges to sustaining its bold advances. The report also presents strategies and directions for CSE research and education for the next decade.Comment: Major revision, to appear in SIAM Revie

How will the Internet of Things enable Augmented Personalized Health?

Internet-of-Things (IoT) is profoundly redefining the way we create, consume, and share information. Health aficionados and citizens are increasingly using IoT technologies to track their sleep, food intake, activity, vital body signals, and other physiological observations. This is complemented by IoT systems that continuously collect health-related data from the environment and inside the living quarters. Together, these have created an opportunity for a new generation of healthcare solutions. However, interpreting data to understand an individual's health is challenging. It is usually necessary to look at that individual's clinical record and behavioral information, as well as social and environmental information affecting that individual. Interpreting how well a patient is doing also requires looking at his adherence to respective health objectives, application of relevant clinical knowledge and the desired outcomes. We resort to the vision of Augmented Personalized Healthcare (APH) to exploit the extensive variety of relevant data and medical knowledge using Artificial Intelligence (AI) techniques to extend and enhance human health to presents various stages of augmented health management strategies: self-monitoring, self-appraisal, self-management, intervention, and disease progress tracking and prediction. kHealth technology, a specific incarnation of APH, and its application to Asthma and other diseases are used to provide illustrations and discuss alternatives for technology-assisted health management. Several prominent efforts involving IoT and patient-generated health data (PGHD) with respect converting multimodal data into actionable information (big data to smart data) are also identified. Roles of three components in an evidence-based semantic perception approach- Contextualization, Abstraction, and Personalization are discussed

RoboChain: A Secure Data-Sharing Framework for Human-Robot Interaction

Robots have potential to revolutionize the way we interact with the world around us. One of their largest potentials is in the domain of mobile health where they can be used to facilitate clinical interventions. However, to accomplish this, robots need to have access to our private data in order to learn from these data and improve their interaction capabilities. Furthermore, to enhance this learning process, the knowledge sharing among multiple robot units is the natural step forward. However, to date, there is no well-established framework which allows for such data sharing while preserving the privacy of the users (e.g., the hospital patients). To this end, we introduce RoboChain - the first learning framework for secure, decentralized and computationally efficient data and model sharing among multiple robot units installed at multiple sites (e.g., hospitals). RoboChain builds upon and combines the latest advances in open data access and blockchain technologies, as well as machine learning. We illustrate this framework using the example of a clinical intervention conducted in a private network of hospitals. Specifically, we lay down the system architecture that allows multiple robot units, conducting the interventions at different hospitals, to perform efficient learning without compromising the data privacy.Comment: 7 pages, 6 figure

Searching Data: A Review of Observational Data Retrieval Practices in Selected Disciplines

A cross-disciplinary examination of the user behaviours involved in seeking and evaluating data is surprisingly absent from the research data discussion. This review explores the data retrieval literature to identify commonalities in how users search for and evaluate observational research data. Two analytical frameworks rooted in information retrieval and science technology studies are used to identify key similarities in practices as a first step toward developing a model describing data retrieval