Perceiving and Knowing as Activities

According to the tradition of most empiricists, perception is the basis for all our knowledge (at least of the world). The tradition also assumes that perception by humans is a passive activity resulting in some static states pertaining perception and belief, which are then, in some versions, modified by the mind before being passed onto memory and knowledge. Following the work of J. J. Gibson, we argue that perceiving involves many activities and actions. This is true of both visual as well as olfactory-taste perception. The main moral of this paper is that perceiving and knowing are best thought of not as involving static states, but rather as ongoing temporal activities involving change. This presumably means giving up a frozen ontology of states and moving towards something like a dynamic ontology as a basis

Overcoming the Newtonian Paradigm: The Unfinished Project of Theoretical Biology from a Schellingian Perspective

Defending Robert Rosen’s claim that in every confrontation between physics and biology it is physics that has always had to give ground, it is shown that many of the most important advances in mathematics and physics over the last two centuries have followed from Schelling’s demand for a new physics that could make the emergence of life intelligible. Consequently, while reductionism prevails in biology, many biophysicists are resolutely anti-reductionist. This history is used to identify and defend a fragmented but progressive tradition of anti-reductionist biomathematics. It is shown that the mathematicoephysico echemical morphology research program, the biosemiotics movement, and the relational biology of Rosen, although they have developed independently of each other, are built on and advance this antireductionist tradition of thought. It is suggested that understanding this history and its relationship to the broader history of post-Newtonian science could provide guidance for and justify both the integration of these strands and radically new work in post-reductionist biomathematics

User and Developer Interaction with Editable and Readable Ontologies

The process of building ontologies is a difficult task that involves collaboration between ontology developers and domain experts and requires an ongoing interaction between them. This collaboration is made more difficult, because they tend to use different tool sets, which can hamper this interaction. In this paper, we propose to decrease this distance between domain experts and ontology developers by creating more readable forms of ontologies, and further to enable editing in normal office environments. Building on a programmatic ontology development environment, such as Tawny-OWL, we are now able to generate these readable/editable from the raw ontological source and its embedded comments. We have this translation to HTML for reading; this environment provides rich hyperlinking as well as active features such as hiding the source code in favour of comments. We are now working on translation to a Word document that also enables editing. Taken together this should provide a significant new route for collaboration between the ontologist and domain specialist.Comment: 5 pages, 5 figures, accepted at ICBO 2017, License update

Towards automated knowledge-based mapping between individual conceptualisations to empower personalisation of Geospatial Semantic Web

Geospatial domain is characterised by vagueness, especially in the semantic disambiguation of the concepts in the domain, which makes defining universally accepted geo- ontology an onerous task. This is compounded by the lack of appropriate methods and techniques where the individual semantic conceptualisations can be captured and compared to each other. With multiple user conceptualisations, efforts towards a reliable Geospatial Semantic Web, therefore, require personalisation where user diversity can be incorporated. The work presented in this paper is part of our ongoing research on applying commonsense reasoning to elicit and maintain models that represent users' conceptualisations. Such user models will enable taking into account the users' perspective of the real world and will empower personalisation algorithms for the Semantic Web. Intelligent information processing over the Semantic Web can be achieved if different conceptualisations can be integrated in a semantic environment and mismatches between different conceptualisations can be outlined. In this paper, a formal approach for detecting mismatches between a user's and an expert's conceptual model is outlined. The formalisation is used as the basis to develop algorithms to compare models defined in OWL. The algorithms are illustrated in a geographical domain using concepts from the SPACE ontology developed as part of the SWEET suite of ontologies for the Semantic Web by NASA, and are evaluated by comparing test cases of possible user misconceptions

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: NL

Proceedings ICPW'07: 2nd International Conference on the Pragmatic Web, 22-23 Oct. 2007, Tilburg: N

A Process Modelling Framework Based on Point Interval Temporal Logic with an Application to Modelling Patient Flows

This thesis considers an application of a temporal theory to describe and model the patient journey in the hospital accident and emergency (A&E) department. The aim is to introduce a generic but dynamic method applied to any setting, including healthcare. Constructing a consistent process model can be instrumental in streamlining healthcare issues. Current process modelling techniques used in healthcare such as flowcharts, unified modelling language activity diagram (UML AD), and business process modelling notation (BPMN) are intuitive and imprecise. They cannot fully capture the complexities of the types of activities and the full extent of temporal constraints to an extent where one could reason about the flows. Formal approaches such as Petri have also been reviewed to investigate their applicability to the healthcare domain to model processes. Additionally, to schedule patient flows, current modelling standards do not offer any formal mechanism, so healthcare relies on critical path method (CPM) and program evaluation review technique (PERT), that also have limitations, i.e. finish-start barrier. It is imperative to specify the temporal constraints between the start and/or end of a process, e.g., the beginning of a process A precedes the start (or end) of a process B. However, these approaches failed to provide us with a mechanism for handling these temporal situations. If provided, a formal representation can assist in effective knowledge representation and quality enhancement concerning a process. Also, it would help in uncovering complexities of a system and assist in modelling it in a consistent way which is not possible with the existing modelling techniques. The above issues are addressed in this thesis by proposing a framework that would provide a knowledge base to model patient flows for accurate representation based on point interval temporal logic (PITL) that treats point and interval as primitives. These objects would constitute the knowledge base for the formal description of a system. With the aid of the inference mechanism of the temporal theory presented here, exhaustive temporal constraints derived from the proposed axiomatic system’ components serves as a knowledge base. The proposed methodological framework would adopt a model-theoretic approach in which a theory is developed and considered as a model while the corresponding instance is considered as its application. Using this approach would assist in identifying core components of the system and their precise operation representing a real-life domain deemed suitable to the process modelling issues specified in this thesis. Thus, I have evaluated the modelling standards for their most-used terminologies and constructs to identify their key components. It will also assist in the generalisation of the critical terms (of process modelling standards) based on their ontology. A set of generalised terms proposed would serve as an enumeration of the theory and subsume the core modelling elements of the process modelling standards. The catalogue presents a knowledge base for the business and healthcare domains, and its components are formally defined (semantics). Furthermore, a resolution theorem-proof is used to show the structural features of the theory (model) to establish it is sound and complete. After establishing that the theory is sound and complete, the next step is to provide the instantiation of the theory. This is achieved by mapping the core components of the theory to their corresponding instances. Additionally, a formal graphical tool termed as point graph (PG) is used to visualise the cases of the proposed axiomatic system. PG facilitates in modelling, and scheduling patient flows and enables analysing existing models for possible inaccuracies and inconsistencies supported by a reasoning mechanism based on PITL. Following that, a transformation is developed to map the core modelling components of the standards into the extended PG (PG*) based on the semantics presented by the axiomatic system. A real-life case (from the King’s College hospital accident and emergency (A&E) department’s trauma patient pathway) is considered to validate the framework. It is divided into three patient flows to depict the journey of a patient with significant trauma, arriving at A&E, undergoing a procedure and subsequently discharged. Their staff relied upon the UML-AD and BPMN to model the patient flows. An evaluation of their representation is presented to show the shortfalls of the modelling standards to model patient flows. The last step is to model these patient flows using the developed approach, which is supported by enhanced reasoning and scheduling