Advanced Knowledge Technologies at the Midterm: Tools and Methods for the Semantic Web

The University of Edinburgh and research sponsors are authorised to reproduce and distribute reprints and on-line copies for their purposes notwithstanding any copyright annotation hereon. The views and conclusions contained herein are the author’s and shouldn’t be interpreted as necessarily representing the official policies or endorsements, either expressed or implied, of other parties.In a celebrated essay on the new electronic media, Marshall McLuhan wrote in 1962:Our private senses are not closed systems but are endlessly translated into each other in that experience which we call consciousness. Our extended senses, tools, technologies, through the ages, have been closed systems incapable of interplay or collective awareness. Now, in the electric age, the very instantaneous nature of co-existence among our technological instruments has created a crisis quite new in human history. Our extended faculties and senses now constitute a single field of experience which demands that they become collectively conscious. Our technologies, like our private senses, now demand an interplay and ratio that makes rational co-existence possible. As long as our technologies were as slow as the wheel or the alphabet or money, the fact that they were separate, closed systems was socially and psychically supportable. This is not true now when sight and sound and movement are simultaneous and global in extent. (McLuhan 1962, p.5, emphasis in original)Over forty years later, the seamless interplay that McLuhan demanded between our technologies is still barely visible. McLuhan’s predictions of the spread, and increased importance, of electronic media have of course been borne out, and the worlds of business, science and knowledge storage and transfer have been revolutionised. Yet the integration of electronic systems as open systems remains in its infancy.Advanced Knowledge Technologies (AKT) aims to address this problem, to create a view of knowledge and its management across its lifecycle, to research and create the services and technologies that such unification will require. Half way through its sixyear span, the results are beginning to come through, and this paper will explore some of the services, technologies and methodologies that have been developed. We hope to give a sense in this paper of the potential for the next three years, to discuss the insights and lessons learnt in the first phase of the project, to articulate the challenges and issues that remain.The WWW provided the original context that made the AKT approach to knowledge management (KM) possible. AKT was initially proposed in 1999, it brought together an interdisciplinary consortium with the technological breadth and complementarity to create the conditions for a unified approach to knowledge across its lifecycle. The combination of this expertise, and the time and space afforded the consortium by the IRC structure, suggested the opportunity for a concerted effort to develop an approach to advanced knowledge technologies, based on the WWW as a basic infrastructure.The technological context of AKT altered for the better in the short period between the development of the proposal and the beginning of the project itself with the development of the semantic web (SW), which foresaw much more intelligent manipulation and querying of knowledge. The opportunities that the SW provided for e.g., more intelligent retrieval, put AKT in the centre of information technology innovation and knowledge management services; the AKT skill set would clearly be central for the exploitation of those opportunities.The SW, as an extension of the WWW, provides an interesting set of constraints to the knowledge management services AKT tries to provide. As a medium for the semantically-informed coordination of information, it has suggested a number of ways in which the objectives of AKT can be achieved, most obviously through the provision of knowledge management services delivered over the web as opposed to the creation and provision of technologies to manage knowledge.AKT is working on the assumption that many web services will be developed and provided for users. The KM problem in the near future will be one of deciding which services are needed and of coordinating them. Many of these services will be largely or entirely legacies of the WWW, and so the capabilities of the services will vary. As well as providing useful KM services in their own right, AKT will be aiming to exploit this opportunity, by reasoning over services, brokering between them, and providing essential meta-services for SW knowledge service management.Ontologies will be a crucial tool for the SW. The AKT consortium brings a lot of expertise on ontologies together, and ontologies were always going to be a key part of the strategy. All kinds of knowledge sharing and transfer activities will be mediated by ontologies, and ontology management will be an important enabling task. Different applications will need to cope with inconsistent ontologies, or with the problems that will follow the automatic creation of ontologies (e.g. merging of pre-existing ontologies to create a third). Ontology mapping, and the elimination of conflicts of reference, will be important tasks. All of these issues are discussed along with our proposed technologies.Similarly, specifications of tasks will be used for the deployment of knowledge services over the SW, but in general it cannot be expected that in the medium term there will be standards for task (or service) specifications. The brokering metaservices that are envisaged will have to deal with this heterogeneity.The emerging picture of the SW is one of great opportunity but it will not be a wellordered, certain or consistent environment. It will comprise many repositories of legacy data, outdated and inconsistent stores, and requirements for common understandings across divergent formalisms. There is clearly a role for standards to play to bring much of this context together; AKT is playing a significant role in these efforts. But standards take time to emerge, they take political power to enforce, and they have been known to stifle innovation (in the short term). AKT is keen to understand the balance between principled inference and statistical processing of web content. Logical inference on the Web is tough. Complex queries using traditional AI inference methods bring most distributed computer systems to their knees. Do we set up semantically well-behaved areas of the Web? Is any part of the Web in which semantic hygiene prevails interesting enough to reason in? These and many other questions need to be addressed if we are to provide effective knowledge technologies for our content on the web

Content-Based Organisation of Virtual Repositories of DICOM Objects

The integration of multi-centre medical image data to create knowledge repositories for research and training activities has been an aim targeted since long ago. This paper presents an environment to share, to process and to organise medical imaging data according to a structured framework in which the image reports play a key role. This environment has been validated on a clinical environment, facing problems such as firewalls and security restrictions, in the frame of the CVIMO (Valencian Cyberinfrastructure of Medical Imaging in Oncology) project. The environment uses a middleware called TRENCADIS (Towards a Grid Environment for Processing and Sharing DICOM Objects) that provides users with the management of multiple administrative domains, data encryption and decryption on the fly and semantic indexation of images. Data is structured into four levels: Global data available, virtual federated storages of studies shared across a vertical domain, subsets for projects or experiments on the virtual storage and individual searches on these subsets. This structure of levels gives the needed flexibility for organising authorisation, and hides data that are not relevant for a given experiment. The main components and interactions are shown in the document, outlining the workflows and explaining the different approaches considered, including the protocols used and the difficulties met. © 2009 Elsevier B.V. All rights reserved.The authors wish to thanks the financial support received from Valencia Region Ministry of Enterprises, University (Conselleria de Empresa, Universidad y Ciencia) to develop the project "Ciberinfraestructura Valenciana de Imagen medica Oncologica", with reference GVEMP06/04.Blanquer Espert, I.; Hernández García, V.; Meseguer Anastasio, JE.; Segrelles Quilis, JD. (2009). Content-Based Organisation of Virtual Repositories of DICOM Objects. Future Generation Computer Systems. 25(6):627-637. https://doi.org/10.1016/j.future.2008.12.004S62763725

Automation bias and prescribing decision support – rates, mediators and mitigators

Purpose: Computerised clinical decision support systems (CDSS) are implemented within healthcare settings as a method to improve clinical decision quality, safety and effectiveness, and ultimately patient outcomes. Though CDSSs tend to improve practitioner performance and clinical outcomes, relatively little is known about specific impact of inaccurate CDSS output on clinicians. Although there is high heterogeneity between CDSS types and studies, reviews of the ability of CDSS to prevent medication errors through incorrect decisions have generally been consistently positive, working by improving clinical judgement and decision making. However, it is known that the occasional incorrect advice given may tempt users to reverse a correct decision, and thus introduce new errors. These systematic errors can stem from Automation Bias (AB), an effect which has had little investigation within the healthcare field, where users have a tendency to use automated advice heuristically. Research is required to assess the rate of AB, identify factors and situations involved in overreliance and propose says to mitigate risk and refine the appropriate usage of CDSS; this can provide information to promote awareness of the effect, and ensure the maximisation of the impact of benefits gained from the implementation of CDSS. Background: A broader literature review was carried out coupled with a systematic review of studies investigating the impact of automated decision support on user decisions over various clinical and non-clinical domains. This aimed to identify gaps in the literature and build an evidence-based model of reliance on Decision Support Systems (DSS), particularly a bias towards over-using automation. The literature review and systematic review revealed a number of postulates - that CDSS are socio-technical systems, and that factors involved in CDSS misuse can vary from overarching social or cultural factors, individual cognitive variables to more specific technology design issues. However, the systematic review revealed there is a paucity of deliberate empirical evidence for this effect. The reviews identified the variables involved in automation bias to develop a conceptual model of overreliance, the initial development of an ontology for AB, and ultimately inform an empirical study to investigate persuasive potential factors involved: task difficulty, time pressure, CDSS trust, decision confidence, CDSS experience and clinical experience. The domain of primary care prescribing was chosen within which to carry out an empirical study, due to the evidence supporting CDSS usefulness in prescribing, and the high rate of prescribing error. Empirical Study Methodology: Twenty simulated prescribing scenarios with associated correct and incorrect answers were developed and validated by prescribing experts. An online Clinical Decision Support Simulator was used to display scenarios to users. NHS General Practitioners (GPs) were contacted via emails through associates of the Centre for Health Informatics, and through a healthcare mailing list company. Twenty-six GPs participated in the empirical study. The study was designed so each participant viewed and gave prescriptions for 20 prescribing scenarios, 10 coded as “hard” and 10 coded as “medium” prescribing scenarios (N = 520 prescribing cases were answered overall). Scenarios were accompanied by correct advice 70% of the time, and incorrect advice 30% of the time (in equal proportions in either task difficulty condition). Both the order of scenario presentation and the correct/incorrect nature of advice were randomised to prevent order effects. The planned time pressure condition was dropped due to low response rate. Results: To compare with previous literature which took overall decisions into account, taking individual cases into account (N=520), the pre advice accuracy rate of the clinicians was 50.4%, which improved to 58.3% post advice. The CDSS improved the decision accuracy in 13.1% of prescribing cases. The rate of AB, as measured by decision switches from correct pre advice, to incorrect post advice was 5.2% of all cases at a CDSS accuracy rate of 70% - leading to a net improvement of 8%. However, the above by-case type of analysis may not enable generalisation of results (but illustrates rates in this specific situation); individual participant differences must be taken into account. By participant (N = 26) when advice was correct, decisions were more likely to be switched to a correct prescription, when advice was incorrect decisions were more likely to be switched to an incorrect prescription. There was a significant correlation between decision switching and AB error. By participant, more immediate factors such as trust in the specific CDSS, decision confidence, and task difficulty influenced rate of decision switching. Lower clinical experience was associated with more decision switching (but not higher AB rate). The rate of AB was somewhat problematic to analyse due to low number of instances – the effect could potentially have been greater. The between subjects effect of time pressure could not be investigated due to low response rate. Age, DSS experience and trust in CDSS generally were not significantly associated with decision switching. Conclusion: There is a gap in the current literature investigating inappropriate CDSS use, but the general literature supports an interactive multi-factorial aetiology for automation misuse. Automation bias is a consistent effect with various potential direct and indirect causal factors. It may be mitigated by altering advice characteristics to aid clinicians’ awareness of advice correctness and support their own informed judgement – this needs further empirical investigation. Users’ own clinical judgement must always be maintained, and systems should not be followed unquestioningly

Eliciting Expertise

Since the last edition of this book there have been rapid developments in the use and exploitation of formally elicited knowledge. Previously, (Shadbolt and Burton, 1995) the emphasis was on eliciting knowledge for the purpose of building expert or knowledge-based systems. These systems are computer programs intended to solve real-world problems, achieving the same level of accuracy as human experts. Knowledge engineering is the discipline that has evolved to support the whole process of specifying, developing and deploying knowledge-based systems (Schreiber et al., 2000) This chapter will discuss the problem of knowledge elicitation for knowledge intensive systems in general

KneeTex: An ontology-driven system for information extraction from MRI reports

Background. In the realm of knee pathology, magnetic resonance imaging (MRI) has the advantage of visualising all structures within the knee joint, which makes it a valuable tool for increasing diagnostic accuracy and planning surgical treatments. Therefore, clinical narratives found in MRI reports convey valuable diagnostic information. A range of studies have proven the feasibility of natural language processing for information extraction from clinical narratives. However, no study focused specifically on MRI reports in relation to knee pathology, possibly due to the complexity of knee anatomy and a wide range of conditions that may be associated with different anatomical entities. In this paper we describe KneeTex, an information extraction system that operates in this domain. Methods. As an ontology–driven information extraction system, KneeTex makes active use of an ontology to strongly guide and constrain text analysis. We used automatic term recognition to facilitate the development of a domain–specific ontology with sufficient detail and coverage for text mining applications. In combination with the ontology, high regularity of the sublanguage used in knee MRI reports allowed us to model its processing by a set of sophisticated lexico–semantic rules with minimal syntactic analysis. The main processing steps involve named entity recognition combined with coordination, enumeration, ambiguity and co–reference resolution, followed by text segmentation. Ontology–based semantic typing is then used to drive the template filling process. Results. We adopted an existing ontology, TRAK (Taxonomy for RehAbilitation of Knee conditions), for use within KneeTex. The original TRAK ontology expanded from 1,292 concepts, 1,720 synonyms and 518 relationship instances to 1,621 concepts, 2,550 synonyms and 560 relationship instances. This provided KneeTex with a very fine–grained lexico–semantic knowledge base, which is highly attuned to the given sublanguage. Information extraction results were evaluated on a test set of 100 MRI reports. A gold standard consisted of 1,259 filled template records with the following slots: finding, finding qualifier, negation, certainty, anatomy and anatomy qualifier. KneeTex extracted information with precision of 98.00%, recall of 97.63% and F–measure of 97.81%, the values of which are in line with human–like performance. Conclusions. KneeTex is an open–source, stand–alone application for information extraction from narrative reports that describe an MRI scan of the knee. Given an MRI report as input, the system outputs the corresponding clinical findings in the form of JavaScript Object Notation objects. The extracted information is mapped onto TRAK, an ontology that formally models knowledge relevant for the rehabilitation of knee conditions. As a result, formally structured and coded information allows for complex searches to be conducted efficiently over the original MRI reports, thereby effectively supporting epidemiologic studies of knee conditions

Specialized Named Entity Recognition For Breast Cancer Subtyping

The amount of data and analysis being published and archived in the biomedical research community is more than can feasibly be sifted through manually, which limits the information an individual or small group can synthesize and integrate into their own research. This presents an opportunity for using automated methods, including Natural Language Processing (NLP), to extract important information from text on various topics. Named Entity Recognition (NER), is one way to automate knowledge extraction of raw text. NER is defined as the task of identifying named entities from text using labels such as people, dates, locations, diseases, and proteins. There are several NLP tools that are designed for entity recognition, but rely on large established corpus for training data. Biomedical research has the potential to guide diagnostic and therapeutic decisions, yet the overwhelming density of publications acts as a barrier to getting these results into a clinical setting. An exceptional example of this is the field of breast cancer biology where over 2 million people are diagnosed worldwide every year and billions of dollars are spent on research. Breast cancer biology literature and research relies on a highly specific domain with unique language and vocabulary, and therefore requires specialized NLP tools which can generate biologically meaningful results. This thesis presents a novel annotation tool, that is optimized for quickly creating training data for spaCy pipelines as well as exploring the viability of said data for analyzing papers with automated processing. Custom pipelines trained on these annotations are shown to be able to recognize custom entities at levels comparable to large corpus based recognition

RFID Technology in Intelligent Tracking Systems in Construction Waste Logistics Using Optimisation Techniques

Construction waste disposal is an urgent issue for protecting our environment. This paper proposes a waste management system and illustrates the work process using plasterboard waste as an example, which creates a hazardous gas when land filled with household waste, and for which the recycling rate is less than 10% in the UK. The proposed system integrates RFID technology, Rule-Based Reasoning, Ant Colony optimization and knowledge technology for auditing and tracking plasterboard waste, guiding the operation staff, arranging vehicles, schedule planning, and also provides evidence to verify its disposal. It h relies on RFID equipment for collecting logistical data and uses digital imaging equipment to give further evidence; the reasoning core in the third layer is responsible for generating schedules and route plans and guidance, and the last layer delivers the result to inform users. The paper firstly introduces the current plasterboard disposal situation and addresses the logistical problem that is now the main barrier to a higher recycling rate, followed by discussion of the proposed system in terms of both system level structure and process structure. And finally, an example scenario will be given to illustrate the system’s utilization

BIOMEDICAL ONTOLOGIES: EXAMINING ASPECTS OF INTEGRATION ACROSS BREAST CANCER KNOWLEDGE DOMAINS

The key ideas developed in this thesis lie at the intersection of epistemology, philosophy of molecular biology, medicine, and computer science. I examine how the epistemic and pragmatic needs of agents distributed across particular scientific disciplines influence the domain-specific reasoning, classification, and representation of breast cancer. The motivation to undertake an interdisciplinary approach, while addressing the problems of knowledge integration, originates in the peculiarity of the integrative endeavour of sciences that is fostered by information technologies and ontology engineering methods. I analyse what knowledge integration in this new field means and how it is possible to integrate diverse knowledge domains, such as clinical and molecular. I examine the extent and character of the integration achieved through the application of biomedical ontologies. While particular disciplines target certain aspects of breast cancer-related phenomena, biomedical ontologies target biomedical knowledge about phenomena that is often captured within diverse classificatory systems and domain-specific representations. In order to integrate dispersed pieces of knowledge, which is distributed across assorted research domains and knowledgebases, ontology engineers need to deal with the heterogeneity of terminological, conceptual, and practical aims that are not always shared among the domains. Accordingly, I analyse the specificities, similarities, and diversities across the clinical and biomedical domain conceptualisations and classifications of breast cancer. Instead of favouring a unifying approach to knowledge integration, my analysis shows that heterogeneous classifications and representations originate from different epistemic and pragmatic needs, each of which brings a fruitful insight into the problem. Thus, while embracing a pluralistic view on the ontologies that are capturing various aspects of knowledge, I argue that the resulting integration should be understood in terms of a coordinated social effort to bring knowledge together as needed and when needed, rather than in terms of a unity that represents domain-specific knowledge in a uniform manner. Furthermore, I characterise biomedical ontologies and knowledgebases as a novel socio-technological medium that allows representational interoperability across the domains. As an example, which also marks my own contribution to the collaborative efforts, I present an ontology for HER2+ breast cancer phenotypes that integrates clinical and molecular knowledge in an explicit way. Through this and a number of other examples, I specify how biomedical ontologies support a mutual enrichment of knowledge across the domains, thereby enabling the application of molecular knowledge into the clinics