Comparative analysis of knowledge representation and reasoning requirements across a range of life sciences textbooks.

BackgroundUsing knowledge representation for biomedical projects is now commonplace. In previous work, we represented the knowledge found in a college-level biology textbook in a fashion useful for answering questions. We showed that embedding the knowledge representation and question-answering abilities in an electronic textbook helped to engage student interest and improve learning. A natural question that arises from this success, and this paper's primary focus, is whether a similar approach is applicable across a range of life science textbooks. To answer that question, we considered four different textbooks, ranging from a below-introductory college biology text to an advanced, graduate-level neuroscience textbook. For these textbooks, we investigated the following questions: (1) To what extent is knowledge shared between the different textbooks? (2) To what extent can the same upper ontology be used to represent the knowledge found in different textbooks? (3) To what extent can the questions of interest for a range of textbooks be answered by using the same reasoning mechanisms?ResultsOur existing modeling and reasoning methods apply especially well both to a textbook that is comparable in level to the text studied in our previous work (i.e., an introductory-level text) and to a textbook at a lower level, suggesting potential for a high degree of portability. Even for the overlapping knowledge found across the textbooks, the level of detail covered in each textbook was different, which requires that the representations must be customized for each textbook. We also found that for advanced textbooks, representing models and scientific reasoning processes was particularly important.ConclusionsWith some additional work, our representation methodology would be applicable to a range of textbooks. The requirements for knowledge representation are common across textbooks, suggesting that a shared semantic infrastructure for the life sciences is feasible. Because our representation overlaps heavily with those already being used for biomedical ontologies, this work suggests a natural pathway to include such representations as part of the life sciences curriculum at different grade levels

Modal logics are coalgebraic

Applications of modal logics are abundant in computer science, and a large number of structurally different modal logics have been successfully employed in a diverse spectrum of application contexts. Coalgebraic semantics, on the other hand, provides a uniform and encompassing view on the large variety of specific logics used in particular domains. The coalgebraic approach is generic and compositional: tools and techniques simultaneously apply to a large class of application areas and can moreover be combined in a modular way. In particular, this facilitates a pick-and-choose approach to domain specific formalisms, applicable across the entire scope of application areas, leading to generic software tools that are easier to design, to implement, and to maintain. This paper substantiates the authors' firm belief that the systematic exploitation of the coalgebraic nature of modal logic will not only have impact on the field of modal logic itself but also lead to significant progress in a number of areas within computer science, such as knowledge representation and concurrency/mobility

Logics for approximate and strong entailments

We consider two kinds of similarity-based reasoning and formalise them in a logical setting. In one case, we are led by the principle that conclusions can be drawn even if they are only approximately correct. This leads to a graded approximate entailment, which is weaker than classical entailment. In the other case, we follow the principle that conclusions must remain correct even if the assumptions are slightly changed. This leads to a notion of a graded strong entailment, which is stronger than classical entailment. We develop two logical calculi based on the notions of approximate and of strong entailment, respectively. © 2011 Elsevier B.V.The authors acknowledge partial support of the bilateral Austrian-Spanish project HA2008-0017 and the Eurocores-LogICCC ESF project LoMoReVI. Esteva and Godo also acknowledge partial support of the Spanish project FFI2008-03126-E/FILO and Rodrıguez acknowledges the projects CyT-UBA X484 and the research CONICET program PIP 12-200801-02543 2009-2011. Finally, Esteva, Godo and Rodrıguez also acknowledge partial support of the MaToMUVI project (PIRSES-GA-2009- 247584).Peer Reviewe

Neurocognitive Informatics Manifesto.

Informatics studies all aspects of the structure of natural and artificial information systems. Theoretical and abstract approaches to information have made great advances, but human information processing is still unmatched in many areas, including information management, representation and understanding. Neurocognitive informatics is a new, emerging field that should help to improve the matching of artificial and natural systems, and inspire better computational algorithms to solve problems that are still beyond the reach of machines. In this position paper examples of neurocognitive inspirations and promising directions in this area are given

Barry Smith an sich

Festschrift in Honor of Barry Smith on the occasion of his 65th Birthday. Published as issue 4:4 of the journal Cosmos + Taxis: Studies in Emergent Order and Organization. Includes contributions by Wolfgang Grassl, Nicola Guarino, John T. Kearns, Rudolf Lüthe, Luc Schneider, Peter Simons, Wojciech Żełaniec, and Jan Woleński

On the semantics of fuzzy logic

AbstractThis paper presents a formal characterization of the major concepts and constructs of fuzzy logic in terms of notions of distance, closeness, and similarity between pairs of possible worlds. The formalism is a direct extension (by recognition of multiple degrees of accessibility, conceivability, or reachability) of the najor modal logic concepts of possible and necessary truth.Given a function that maps pairs of possible worlds into a number between 0 and 1, generalizing the conventional concept of an equivalence relation, the major constructs of fuzzy logic (conditional and unconditioned possibility distributions) are defined in terms of this similarity relation using familiar concepts from the mathematical theory of metric spaces. This interpretation is different in nature and character from the typical, chance-oriented, meanings associated with probabilistic concepts, which are grounded on the mathematical notion of set measure. The similarity structure defines a topological notion of continuity in the space of possible worlds (and in that of its subsets, i.e., propositions) that allows a form of logical “extrapolation” between possible worlds.This logical extrapolation operation corresponds to the major deductive rule of fuzzy logic — the compositional rule of inference or generalized modus ponens of Zadeh — an inferential operation that generalizes its classical counterpart by virtue of its ability to be utilized when propositions representing available evidence match only approximately the antecedents of conditional propositions. The relations between the similarity-based interpretation of the role of conditional possibility distributions and the approximate inferential procedures of Baldwin are also discussed.A straightforward extension of the theory to the case where the similarity scale is symbolic rather than numeric is described. The problem of generating similarity functions from a given set of possibility distributions, with the latter interpreted as defining a number of (graded) discernibility relations and the former as the result of combining them into a joint measure of distinguishability between possible worlds, is briefly discussed

Pragmatic factors of deontic reasoning

A thesis submitted in partial fulfilment of the requirements of the University of Wolverhamptonfor the degree of Doctor of PhilosophyThis thesis is concerned with pragmatic factors of deontic reasoning, namely scale of violation, aggravating and mitigating circumstances and power of source. Nine experiments are reported investigating deontic reasoning and judgement revision. Experiment 1 established scale of violation as a modifying factor of a working rule with an inferential reasoning task, however, the effects were not transferred to a deductive reasoning task in Experiment 2. Scale of violation and circumstances were found to influence the reasoning of motoring violations with a major offence and aggravating circumstances being rated as more serious and receiving greater fines than a minor offence or mitigating circumstances (Experiments 3 & 4). These effects were also observed with a judgement revision task (Experiment 5). Power of source was included as an additional pragmatic factor and was found to influence the reasoning of conditional statements (Experiment 6), inducements (Experiment 7) and ratings of credibility and probability of outcomes (Experiment 8). The final study (Experiment 9) found significant effects for scale of violation / compliance and power of source within a judgement revision task. However, no difference was observed in the reasoning of superordinate and non-superordinate statements. The findings are explained in terms of the conditional probability hypothesis

Core components for effective infection prevention and control programmes: new WHO evidence-based recommendations

Abstract Health care-associated infections (HAI) are a major public health problem with a significant impact on morbidity, mortality and quality of life. They represent also an important economic burden to health systems worldwide. However, a large proportion of HAI are preventable through effective infection prevention and control (IPC) measures. Improvements in IPC at the national and facility level are critical for the successful containment of antimicrobial resistance and the prevention of HAI, including outbreaks of highly transmissible diseases through high quality care within the context of universal health coverage. Given the limited availability of IPC evidence-based guidance and standards, the World Health Organization (WHO) decided to prioritize the development of global recommendations on the core components of effective IPC programmes both at the national and acute health care facility level, based on systematic literature reviews and expert consensus. The aim of the guideline development process was to identify the evidence and evaluate its quality, consider patient values and preferences, resource implications, and the feasibility and acceptability of the recommendations. As a result, 11 recommendations and three good practice statements are presented here, including a summary of the supporting evidence, and form the substance of a new WHO IPC guideline

An extended case study on the phenomenology of sequence-space synesthesia

Investigation of synesthesia phenomenology in adults is needed to constrain accounts of developmental trajectories of this trait. We report an extended phenomenological investigation of sequence-space synesthesia in a single case (AB). We used the Elicitation Interview (EI) method to facilitate repeated exploration of AB's synesthetic experience. During an EI the subject's attention is selectively guided by the interviewer in order to reveal precise details about the experience. Detailed analysis of the resulting 9 h of interview transcripts provided a comprehensive description of AB's synesthetic experience, including several novel observations. For example, we describe a specific spatial reference frame (a "mental room") in which AB's concurrents occur, and which overlays his perception of the real world (the "physical room"). AB is able to switch his attention voluntarily between this mental room and the physical room. Exemplifying the EI method, some of our observations were previously unknown even to AB. For example, AB initially reported to experience concurrents following visual presentation, yet we determined that in the majority of cases the concurrent followed an internal verbalization of the inducer, indicating an auditory component to sequence-space synesthesia. This finding is congruent with typical rehearsal of inducer sequences during development, implicating cross-modal interactions between auditory and visual systems in the genesis of this synesthetic form. To our knowledge, this paper describes the first application of an EI to synesthesia, and the first systematic longitudinal investigation of the first-person experience of synesthesia since the re-emergence of interest in this topic in the 1980's. These descriptions move beyond rudimentary graphical or spatial representations of the synesthetic spatial form, thereby providing new targets for neurobehavioral analysis