Instance-driven TBox revision in DL-Lite

The development and maintenance of large and complex ontologies are often time-consuming and error-prone. Thus, automated ontology learning and revision have attracted intensive research interest. In data-centric applications where ontologies are designed or automatically learnt from the data, when new data instances are added that contradict to the ontology, it is often desirable to incrementally revise the ontology according to the added data. This problem can be intuitively formulated as the problem of revising a TBox by an ABox. In this paper we introduce a model-theoretic approach to such an ontology revision problem by using a novel alternative semantic characterisation of DL-Lite ontologies. We show some desired properties for our ontology revision. We have also developed an algorithm for reasoning with the ontology revision without computing the revision result. The algorithm is efficient as its computational complexity is in coNP in the worst case and in PTIME when the size of the new data is bounded.

The space of make: A topological account of the studio

Approaches to art-practice-as-research tend to draw a distinction between the processes of creative practice and scholarly reflection. According to this template, the two sites of activity – studio/desk, work/writing, body/mind – form the ‘correlative’ entity known as research. Creative research is said to be produced by the navigation of world and thought: spaces that exist in a continual state of tension with one another. Either we have the studio tethered to brute reality while the desk floats free as a site for the fluid cross-pollination of texts and concepts. Or alternatively, the studio is characterized by the amorphous, intuitive play of forms and ideas, while the desk represents its cartography, mapping and fixing its various fluidities. In either case, the research status of art practice is figured as a fundamentally riven space. However, the nascent philosophy of Speculative Realism proposes a different ontology – one in which the space of human activity comprises its own reality, independent of human perception. The challenge it poses to traditional metaphysics is to rethink the world as if it were a real space. When applied to practice-led research, this reconceptualization challenges the creative researcher to consider creative research as a contiguous space – a topology where thinking and making are not dichotomous points but inflections in an amorphous and dynamic field. Instead of being subject to the vertical tension between earth and air, a topology of practice emphasizes its encapsulated, undulating reality – an agentive ‘object’ formed according to properties of connectedness, movement and differentiation. Taking the central ideas of Quentin Meillassoux and Graham Harman as a point of departure, this paper will provide a speculative account of the interplay of spatialities that characterise the author’s studio practice. In so doing, the paper will model the innovative methodological potential produced by the analysis of topological dimensions of the studio and the way they can be said to move beyond the ‘geo-critical’ divide.

Communication and essentialism: Grounding the shared reality of a social category

Essentialism is an ontological belief that there exists an underlying essence to a category. This article advances and tests in three studies the hypothesis that communication about a social category, and expected or actual mutual validation, promotes essentialism about a social category. In Study 1, people who wrote communications about a social category to their ingroup audiences essentialized it more strongly than those who simply memorized about it. In Study 2, communicators whose messages about a novel social category were more elaborately discussed with a confederate showed a stronger tendency to essentialize it. In Study 3, communicators who elaborately talked about a social category with a naive conversant also essentialized the social category. A meta-analysis of the results supported the hypothesis that communication promotes essentialism. Although essentialism has been discussed primarily in perceptual and cognitive domains, the role of social processes as its antecedent deserves greater attention.

Permanent shift: the topology of Didier Vermeiren's Cariatide à la Pierre

Photographic documentation of sculpture produces significant consequences for the way in which sculptural space is conceived. When viewed as discrete mediums the interaction of the photograph and its sculptural subject is always framed by notions of loss. However, when taken as a composite system, the sculpture-photograph proposes a new ontology of space. In place of the fixity of medium, we can observe a topology at play: a theory drawn from mathematics in which space is understood not as a static field but in terms of properties of connectedness, movement and differentiation. Refracted through the photographic medium, sculpture becomes not a field of fixed points in space, but rather as a fluid set of relations - a continuous sequence of multiple ‘surfaces’, a network of shifting views. This paper will develop a topological account of studio practice through an examination of the work of the contemporary Belgian sculptor Didier Vermeiren (b. 1951). Since the 1980s, Vermeiren has made extensive use of photography in his sculptural practice. By analysing a series of iterations of his work Cariatide à la Pierre (1997-1998), this paper proposes that Vermeiren’s use of photography reveals patterns of connection that expand and complicate the language of sculpture, while also emphasising the broader topology of the artist’s practice as a network of ‘backward glances’ to previous works from the artist’s oeuvre and the art-historical canon. In this context, photography is not simply a method of documentation, but rather a means of revealing the intrinsic condition of sculpture as medium shaped by dynamic patterns of connection and change. In Vermeiren’s work the sculpture-photograph, has a composite identity that exceeds straightforward categories of medium. In their place, we can observe a practice based upon the complex interactions of objects whose ontology is always underpinned by a certain contingency. It is in this fundamental mobility, that the topology of Vermeiren’s practice can be said to rest.

The ways of things: Objects in the studio

Conventions of the studio presuppose the artist as the active agent, imposing his/her will upon and through objects that remain essentially inert. However, this characterisation of practice overlooks the complex object dynamics that underpin the art-making process. Far from passive entities, objects are resistant, ‘speaking back’ to the artist, impressing their will upon their surroundings. Objects stick to one another, fall over, drip, spill, spatter and chip one another. Objects support, dismantle, cover and transform one another. Objects are both the apparatus of the studio and its products. It can be argued that the work of art is as much shaped by objects as it is by human impulse. Within this alternate ontology, the artist becomes but one element in a constellation of objects. Drawing upon Graham Harman’s Object-Oriented Ontology and a selection of photographs of my studio processes, this practice-led paper will explore the notion of agentive objects and the ways in which the contemporary art studio can be reconsidered as a primary site for the production of new object relationships.

Medical semantic similarity with a neural language model

Advances in neural network language models have demonstrated that these models can effectively learn representations of words meaning. In this paper, we explore a variation of neural language models that can learn on concepts taken from structured ontologies and extracted from free-text, rather than directly from terms in free-text. This model is employed for the task of measuring semantic similarity between medical concepts, a task that is central to a number of techniques in medical informatics and information retrieval. The model is built with two medical corpora (journal abstracts and patient records) and empirically validated on two ground-truth datasets of human-judged concept pairs assessed by medical professionals. Empirically, our approach correlates closely with expert human assessors ($\approx$ 0.9) and outperforms a number of state-of-the-art benchmarks for medical semantic similarity. The demonstrated superiority of this model for providing an effective semantic similarity measure is promising in that this may translate into effectiveness gains for techniques in medical information retrieval and medical informatics (e.g., query expansion and literature-based discovery).

Normative requirements for regulatory compliance: An abstract formal framework

By definition, regulatory rules (in legal context called norms) intend to achieve specific behaviour from business processes, and might be relevant to the whole or part of a business process. They can impose conditions on different aspects of process models, e.g., control-flow, data and resources etc. Based on the rules sets, norms can be classified into various classes and sub-classes according to their effects. This paper presents an abstract framework consisting of a list of norms and a generic compliance checking approach on the idea of (possible) execution of processes. The proposed framework is independent of any existing formalism, and provides a conceptually rich and exhaustive ontology and semantics of norms needed for business process compliance checking. The possible uses of the proposed framework include to compare different compliance management frameworks (CMFs).

An application of fuzzy DL-Based semantic perception to soil container classification

Semantic perception and object labeling are key requirements for robots interacting with objects on a higher level. Symbolic annotation of objects allows the usage of planning algorithms for object interaction, for instance in a typical fetchand-carry scenario. In current research, perception is usually based on 3D scene reconstruction and geometric model matching, where trained features are matched with a 3D sample point cloud. In this work we propose a semantic perception method which is based on spatio-semantic features. These features are defined in a natural, symbolic way, such as geometry and spatial relation. In contrast to point-based model matching methods, a spatial ontology is used where objects are rather described how they "look like", similar to how a human would described unknown objects to another person. A fuzzy based reasoning approach matches perceivable features with a spatial ontology of the objects. The approach provides a method which is able to deal with senor noise and occlusions. Another advantage is that no training phase is needed in order to learn object features. The use-case of the proposed method is the detection of soil sample containers in an outdoor environment which have to be collected by a mobile robot. The approach is verified using real world experiments.

The tumour-promoting receptor tyrosine kinase, EphB4, regulates expression of Integrin-β8 in prostate cancer cells

Background The EphB4 receptor tyrosine kinase is overexpressed in many cancers including prostate cancer. The molecular mechanisms by which this ephrin receptor influences cancer progression are complex as there are tumor-promoting ligand-independent mechanisms in place as well as ligand-dependent tumor suppressive pathways. Methods We employed transient knockdown of EPHB4 in prostate cancer cells, coupled with gene microarray analysis, to identify genes that were regulated by EPHB4 and may represent linked tumor-promoting factors. We validated target genes using qRT-PCR and employed functional assays to determine their role in prostate cancer migration and invasion. Results We discovered that over 500 genes were deregulated upon EPHB4 siRNA knockdown, with integrin β8 (ITGB8) being the top hit (29-fold down-regulated compared to negative non-silencing siRNA). Gene ontology analysis found that the process of cell adhesion was highly deregulated and two other integrin genes, ITGA3 and ITGA10, were also differentially expressed. In parallel, we also discovered that over-expression of EPHB4 led to a concomitant increase in ITGB8 expression. In silico analysis of a prostate cancer progression microarray publically available in the Oncomine database showed that both EPHB4 and ITGB8 are highly expressed in prostatic intraepithelial neoplasia, the precursor to prostate cancer. Knockdown of ITGB8 in PC-3 and 22Rv1 prostate cancer cells in vitro resulted in significant reduction of cell migration and invasion. Conclusions These results reveal that EphB4 regulates integrin β8 expression and that integrin β8 plays a hitherto unrecognized role in the motility of prostate cancer cells and thus targeting integrin β8 may be a new treatment strategy for prostate cancer.

Integration of Opinion Mining into customer analysis model

This research proposes a multi-dimensional model for Opinion Mining, which integrates customers' characteristics and their opinions about products (or services). Customer opinions are valuable for companies to deliver right products or services to their customers. This research presents a comprehensive framework to evaluate opinions' orientation based on products' hierarchy attributes. It also provides an alternative way to obtain opinion summaries for different groups of customers and different categories of produces.

Linking business goals to process models in semantic business process modeling

Broad knowledge is required when a business process is modeled by a business analyst. We argue that existing Business Process Management methodologies do not consider business goals at the appropriate level. In this paper we present an approach to integrate business goals and business process models. We design a Business Goal Ontology for modeling business goals. Furthermore, we devise a modeling pattern for linking the goals to process models and show how the ontology can be used in query answering. In this way, we integrate the intentional perspective into our business process ontology framework, enriching the process description and enabling new types of business process analysis. © 2008 IEEE.

Analysis, characterisation and expression of gill-expressed carbonic anhydrase genes in the freshwater crayfish Cherax quadricarinatus

Changes in water quality parameters such as pH and salinity can have a significant effect on productivity of aquaculture species. Similarly, relative osmotic pressure influences various physiological processes and regulates expression of a number of osmoregulatory genes. Among those, carbonic anhydrase (CA) plays a key role in systemic acid–base balance and ion regulation. Redclaw crayfish (Cherax quadricarinatus) are unique in their ability to thrive in environments with naturally varied pH levels, suggesting unique adaptation to pH stress. To date, however, no studies have focused on identification and characterisation of CA or other osmoregulatory genes in C. quadricarinatus. Here, we analysed the redclaw gill transcriptome and characterized CA genes along with a number of other key osmoregulatory genes that were identified in the transcriptome. We also examined patterns of gene expression of these CA genes when exposed to three pH treatments. In total, 72,382,710 paired end Illumina reads were assembled into 36,128 contigs with an average length of 800 bp. Approximately 37% of contigs received significant BLAST hits and 22% were assigned gene ontology terms. Three full length CA isoforms; cytoplasmic CA (ChqCAc), glycosyl-phosphatidylinositol-linked CA (ChqCAg), and β-CA (ChqCA-beta) as well as two partial CA gene sequences were identified. Both partial CA genes showed high similarity to ChqCAg and appeared to be duplicated from the ChqCAg. Full length coding sequences of Na+/K+-ATPase, V-type H+-ATPase, sarcoplasmic Ca+-ATPase, arginine kinase, calreticulin and Cl− channel protein 2 were also identified. Only the ChqCAc gene showed significant differences in expression across the three pH treatments. These data provide valuable information on the gill expressed CA genes and their expression patterns in freshwater crayfish. Overall our data suggest an important role for the ChqCAc gene in response to changes in pH and in systemic acid–base balance in freshwater crayfish.

Quality-aware review selection based on product feature taxonomy

As of today, user-generated information such as online reviews has become increasingly significant for customers in decision making process. Meanwhile, as the volume of online reviews proliferates, there is an insistent demand to help the users tackle the information overload problem. In order to extract useful information from overwhelming reviews, considerable work has been proposed such as review summarization and review selection. Particularly, to avoid the redundant information, researchers attempt to select a small set of reviews to represent the entire review corpus by preserving its statistical properties (e.g., opinion distribution). However, one significant drawback of the existing works is that they only measure the utility of the extracted reviews as a whole without considering the quality of each individual review. As a result, the set of chosen reviews may consist of low-quality ones even its statistical property is close to that of the original review corpus, which is not preferred by the users. In this paper, we proposed a review selection method which takes review quality into consideration during the selection process. Specifically, we examine the relationships between product features based upon a domain ontology to capture the review characteristics based on which to select reviews that have good quality and preserve the opinion distribution as well. Our experimental results based on real world review datasets demonstrate that our proposed approach is feasible and able to improve the performance of the review selection effectively.

Excessive bone formation in a mouse model of ankylosing spondylitis is associated with decreases in Wnt pathway inhibitors

Introduction: Ankylosing spondylitis (AS) is unique in its pathology where inflammation commences at the entheses before progressing to an osteoproliferative phenotype generating excessive bone formation that can result in joint fusion. The underlying mechanisms of this progression are poorly understood. Recent work has suggested that changes in Wnt signalling, a key bone regulatory pathway, may contribute to joint ankylosis in AS. Using the proteoglycan-induced spondylitis (PGISp) mouse model which displays spondylitis and eventual joint fusion following an initial inflammatory stimulus, we have characterised the structural and molecular changes that underlie disease progression. Methods: PGISp mice were characterised 12 weeks after initiation of inflammation using histology, immunohistochemistry (IHC) and expression profiling. Results: Inflammation initiated at the periphery of the intervertebral discs progressing to disc destruction followed by massively excessive cartilage and bone matrix formation, as demonstrated by toluidine blue staining and IHC for collagen type I and osteocalcin, leading to syndesmophyte formation. Expression levels of DKK1 and SOST, Wnt signalling inhibitors highly expressed in joints, were reduced by 49% and 63% respectively in the spine PGISp compared with control mice (P < 0.05) with SOST inhibition confirmed by IHC. Microarray profiling showed genes involved in inflammation and immune-regulation were altered. Further, a number of genes specifically involved in bone regulation including other members of the Wnt pathway were also dysregulated. Conclusions: This study implicates the Wnt pathway as a likely mediator of the mechanism by which inflammation induces bony ankylosis in spondyloarthritis, raising the potential that therapies targeting this pathway may be effective in preventing this process.

A method for matching patients to advanced prostate cancer clinical trials

Objective: To illustrate a new method for simplifying patient recruitment for advanced prostate cancer clinical trials using natural language processing techniques. Background: The identification of eligible participants for clinical trials is a critical factor to increase patient recruitment rates and an important issue for discovery of new treatment interventions. The current practice of identifying eligible participants is highly constrained due to manual processing of disparate sources of unstructured patient data. Informatics-based approaches can simplify the complex task of evaluating patient’s eligibility for clinical trials. We show that an ontology-based approach can address the challenge of matching patients to suitable clinical trials. Methods: The free-text descriptions of clinical trial criteria as well as patient data were analysed. A set of common inclusion and exclusion criteria was identified through consultations with expert clinical trial coordinators. A research prototype was developed using Unstructured Information Management Architecture (UIMA) that identified SNOMED CT concepts in the patient data and clinical trial description. The SNOMED CT concepts model the standard clinical terminology that can be used to represent and evaluate patient’s inclusion/exclusion criteria for the clinical trial. Results: Our experimental research prototype describes a semi-automated method for filtering patient records using common clinical trial criteria. Our method simplified the patient recruitment process. The discussion with clinical trial coordinators showed that the efficiency in patient recruitment process measured in terms of information processing time could be improved by 25%. Conclusion: An UIMA-based approach can resolve complexities in patient recruitment for advanced prostate cancer clinical trials.