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This paper presents a plausible reasoning system to illustrate some broad issues in knowledge representation: dualities between different reasoning forms, the difficulty of unifying complementary reasoning styles, and the approximate nature…
We consider biological individuality in terms of information theoretic and graphical principles. Our purpose is to extract through an algorithmic decomposition system-environment boundaries supporting individuality. We infer or detect…
Biological systems are generally complicated and/or complex. In the former approach, one sets up a model with a large number of parameters to describe the system in detail. The latter approach focuses on understanding the universal aspects…
The rich and varied ways that genetic material can be passed between species has motivated extensive research into the theory of phylogenetic networks. Features that align with biological processes, or with desirable mathematical…
Explainable AI has garnered considerable attention in recent years, as understanding the reasons behind decisions or predictions made by AI systems is crucial for their successful adoption. Explaining classifiers' behavior is one prominent…
Understanding soccer as a complex system we base on nature and the collective behavior of many organisms that "do calculations," seeking to generate solutions in a bioinspired way. When soccer mysteries appear, complex systems science…
Reproducibility has been consistently identified as an important component of scientific research. Although there is a general consensus on the importance of reproducibility along with the other commonly used 'R' terminology (i.e.,…
Knowledge representation and reasoning in law are essential to facilitate the automation of legal analysis and decision-making tasks. In this paper, we propose a new approach based on legal science, specifically legal taxonomy, for…
Formulating data science problems is an uncertain and difficult process. It requires various forms of discretionary work to translate high-level objectives or strategic goals into tractable problems, necessitating, among other things, the…
Traditionally, semantics has been seen as a feature of human language. The advent of the information era has led to its widespread redefinition as an information feature. Contrary to this praxis, I define semantics as a special kind of…
The term {\em complexity} is used informally both as a quality and as a quantity. As a quality, complexity has something to do with our ability to understand a system or object -- we understand simple systems, but not complex ones. On…
The study of complex systems through the lens of category theory consistently proves to be a powerful approach. We propose that cognition deserves the same category-theoretic treatment. We show that by considering a highly-compact cognitive…
We explain and explore class-theoretic potentialism -- the view that one can always individuate more classes over a set-theoretic universe. We examine some motivations for class-theoretic potentialism, before proving some results concerning…
Reproducible research---by its many names---has come to be regarded as a key concern across disciplines and stakeholder groups. Funding agencies and journals, professional societies and even mass media are paying attention, often focusing…
Reproducibility is a confused terminology. In this paper, I take a fundamental view on reproducibility rooted in the scientific method. The scientific method is analysed and characterised in order to develop the terminology required to…
Explaining why the species lives at a particular location is important for understanding ecological systems and conserving biodiversity. However, existing ecological workflows are fragmented and often inaccessible to non-specialists. We…
We contemplate the notion of ambiguity in mathematical discourse. We consider a general method of resolving ambiguity and semantic options for sustaining a resolution. The general discussion is applied to the case of `fraction' which is…
Orthology is a central concept in evolutionary and comparative genomics, used to relate corresponding genes in different species. In particular, orthologs are needed to infer species trees. In this chapter, we introduce the fundamental…
Why is language vague? Vagueness may be explained and rationalized if it can be shown that vague language is more useful to speaker and hearer than precise language. In a well-known paper, Lipman proposes a game-theoretic account of…
Prominent ethical and policy issues such as affirmative action and female enrollment in science and engineering revolve around the idea that diversity is good. However, even though diversity is an ambiguous concept, a precise definition is…