UIMA in the Biocuration Workflow: A coherent framework for cooperation between biologists and computational linguists

As collaborating partners, Barcelona Media Innovation Centre and GRIB (Universitat Pompeu Fabra) seek to combine strengths from Computational Linguistics and Biomedicine to produce a robust Text Mining system to generate data that will help biocurators in their daily work. The first version of this system will focus on the discovery of relationships between genes, SNPs (Single Nucleotide Polymorphisms) and diseases from the literature.

A first challenge that we were faced with during the setup of this project is the fact that most current tools that support the curation workflow are complex, ad-hoc built applications which sometimes make difficult the interoperability and results sharing between research groups from different and unrelated expert fields. Often, biologists (even computer-savvy ones) are hard pressed to use and adapt sophisticated Natural Language Processing systems, and computational linguists are challenged by the intricacies of biology in applying their processing pipelines to elicit knowledge from texts. The flow of knowledge (needed to develop a usable, practical tool) to and from the parties involved in the development of such systems is not always easy or straightforward.

The modular and versatile architecture of UIMA (Unstructed Information Management Architecture) provides a framework to address these challenges. UIMA is a component architecture and software framework implementation (including a UIMA SDK) to develop applications that analyse large volumes of unstructured information, and has been increasingly adopted by a significant part of the BioNLP community that needs industrial-grade and robust applications to exploit the whole bibliome. The use of UIMA to develop Text Mining applications useful for curation purposes allows the combination of diverse expertises which is beyond the individual know-how of biologists, computer scientists or linguists in isolation. A good synergy and circulation of knowledge between these experts is fundamental to the development of a successful curation tool

Embedding Requirements within the Model Driven Architecture

The Model Driven Architecture (MDA) brings benefits to software development, among them the potential for connecting software models with the business domain. This paper focuses on the upstream or Computation Independent Model (CIM) phase of the MDA. Our contention is that, whilst there are many models and notations available within the CIM Phase, those that are currently popular and supported by the Object Management Group (OMG), may not be the most useful notations for business analysts nor sufficient to fully support software requirements and specification. Therefore, with specific emphasis on the value of the Business Process Modelling Notation (BPMN) for business analysts, this paper provides an example of a typical CIM approach before describing an approach which incorporates specific requirements techniques. A framework extension to the MDA is then introduced; which embeds requirements and specification within the CIM, thus further enhancing the utility of MDA by providing a more complete method for business analysis

The future of technology enhanced active learning – a roadmap

The notion of active learning refers to the active involvement of learner in the learning process, capturing ideas of learning-by-doing and the fact that active participation and knowledge construction leads to deeper and more sustained learning. Interactivity, in particular learnercontent interaction, is a central aspect of technology-enhanced active learning. In this roadmap, the pedagogical background is discussed, the essential dimensions of technology-enhanced active learning systems are outlined and the factors that are expected to influence these systems currently and in the future are identified. A central aim is to address this promising field from a best practices perspective, clarifying central issues and formulating an agenda for future developments in the form of a roadmap

BIMing the architectural curricula: integrating Building Information Modelling (BIM) in architectural education

Building Information Modelling (BIM) reflects the current heightened transformation within the Architectural, Engineering and Construction (AEC) Industry and the Facilities and Management (FM) sector, offering a host of benefits from increased efficiency, accuracy, speed, co-ordination, consistency, energy analysis, project cost reduction etc to various stake holders from owners to architects, engineers, contractors and other built environment professionals. Many countries around the world are responding to this paradigm shift including the United Kingdom (UK). The Cabinet office took the decision in 2011 to make the use of collaborative 3D BIM technology mandatory for all public sector construction contracts by 2016 (Cabinet Office, 2011). According to Smith and Tardif, despite certain myths and misconceptions surrounding BIM, its rate of implementation has been much faster in comparison to the availability of professionals skilled in use of BIM, thus creating a skill gap in the design and construction industry (Smith and Tardif, cited in Barison and Santos, 2010a). This article aims at bridging the gap between the graduate skill sets and the changing needs of the profession. The research methodology adopted consists of thoroughly reviewing the existing literature in this subject area coupled with carrying out a survey of accredited Schools of Architecture in the UK. The analysis of the survey questionnaire results shows the extent to which BIM is currently being taught and identifies the barriers where its implementation has either been slow or not yet started. The paper highlights the fact that there has been considerable delay in the successful integration of BIM in the Schools of Architecture in the UK, thus emphasising the need for expeditiously training and preparing students in the use of BIM making them ready to effectively perform in a BIM enabled work arena

Specification of vertical semantic consistency rules of UML class diagram refinement using logical approach

Unified Modelling Language (UML) is the most popular modelling language use for software design in software development industries with a class diagram being the most frequently use diagram. Despite the popularity of UML, it is being affected by inconsistency problems of its diagrams at the same or different abstraction levels. Inconsistency in UML is mostly caused by existence of various views on the same system and sometimes leads to potentially conflicting system specifications. In general, syntactic consistency can be automatically checked and therefore is supported by current UML Computer-aided Software Engineering (CASE) tools. Semantic consistency problems, unlike syntactic consistency problems, there exists no specific method for specifying semantic consistency rules and constraints. Therefore, this research has specified twenty-four abstraction rules of class‟s relation semantic among any three related classes of a refined class diagram to semantically equivalent relations of two of the classes using a logical approach. This research has also formalized three vertical semantic consistency rules of a class diagram refinement identified by previous researchers using a logical approach and a set of formalized abstraction rules. The results were successfully evaluated using hotel management system and passenger list system case studies and were found to be reliable and efficient

A New Constructivist AI: From Manual Methods to Self-Constructive Systems

The development of artificial intelligence (AI) systems has to date been largely one of manual labor. This constructionist approach to AI has resulted in systems with limited-domain application and severe performance brittleness. No AI architecture to date incorporates, in a single system, the many features that make natural intelligence general-purpose, including system-wide attention, analogy-making, system-wide learning, and various other complex transversal functions. Going beyond current AI systems will require significantly more complex system architecture than attempted to date. The heavy reliance on direct human specification and intervention in constructionist AI brings severe theoretical and practical limitations to any system built that way. One way to address the challenge of artificial general intelligence (AGI) is replacing a top-down architectural design approach with methods that allow the system to manage its own growth. This calls for a fundamental shift from hand-crafting to self-organizing architectures and self-generated code – what we call a constructivist AI approach, in reference to the self-constructive principles on which it must be based. Methodologies employed for constructivist AI will be very different from today’s software development methods; instead of relying on direct design of mental functions and their implementation in a cog- nitive architecture, they must address the principles – the “seeds” – from which a cognitive architecture can automatically grow. In this paper I describe the argument in detail and examine some of the implications of this impending paradigm shift