Online research in philosophy

In his Bayesian Nets and Causality, Jon Williamson presents an ‘Objective Bayesian’ interpretation of probability, which he endeavours to distance from the logical interpretation yet associate with the subjective interpretation. In doing so, he suggests that the logical interpretation suffers from severe epistemological problems that do not affect his alternative. In this paper, I present a challenge to his analysis. First, I closely examine the relationship between the logical and ‘Objective Bayesian’ views, and show how, and why, they are highly similar. Second, I argue that the logical interpretation is not manifestly inferior, at least for the reasons that Williamson offers. I suggest that the key difference between the logical and ‘Objective Bayesian’ views is in the domain of the philosophy of logic; and that the genuine disagreement appears to be over Platonism versus nominalism (within weak psychologism).

The paper displays the similarity between the theory of probabilistic causation developed by Glymour et al. since 1983 and mine developed since 1976: the core of both is that causal graphs are Bayesian nets. The similarity extends to the treatment of actions or interventions in the two theories. But there is also a crucial difference. Glymour et al. take causal dependencies as primitive and argue them to behave like Bayesian nets under wide circumstances. By contrast, I argue the behavior of Bayesian nets to be ultimately the defining characteristic of causal dependence.

To write about the disease of breast cancer from both scientific and spiritual perspectives is to reflect upon our genetic and spiritual ancestry. We examine the issues involved in breast cancer at the intersections of spirituality, technology, and science, using the fundamental thing we know about being human: our bodies. Our goal in this essay is to offer close readings of women's spiritual and bodily journeys through the disease of breast cancer. We have discovered that both illness and health come within the stories of particular people and particular disciplines. And to learn more about breast cancer, both scientific and spiritual aspects, one must be attentive to such particularities. Medicine and religion are bodily experiences, and being a body-self is what it means to be human.

This paper develops connections between objective Bayesian epistemology—which holds that the strengths of an agent’s beliefs should be representable by probabilities, should be calibrated with evidence of empirical probability, and should otherwise be equivocal—and probabilistic logic. After introducing objective Bayesian epistemology over propositional languages, the formalism is extended to handle predicate languages. A rather general probabilistic logic is formulated and then given a natural semantics in terms of objective Bayesian epistemology. The machinery of objective Bayesian nets and objective credal nets is introduced and this machinery is applied to provide a calculus for probabilistic logic that meshes with the objective Bayesian semantics.

How should we reason with causal relationships? Much recent work on this question has been devoted to the theses (i) that Bayesian nets provide a calculus for causal reasoning and (ii) that we can learn causal relationships by the automated learning of Bayesian nets from observational data. The aim of this book is to..

this paper we argue that the formalism can also be applied to modelling the hierarchical structure of physical mechanisms. The resulting network contains quantitative information about probabilities, as well as qualitative information about mechanistic structure and causal relations. Since information about probabilities, mechanisms and causal relations are vital for prediction, explanation and control respectively, a recursive Bayesian net can be applied to all these tasks. We show how a Recursive Bayesian Net can be used to model mechanisms in cancer science. The highest level of the proposed model will contain variables at the clinical level, while a middle level will map the structure of the DNA damage response mechanism and the lowest level will contain information about gene expression.

I present a formalism that combines two methodologies: objective Bayesianism and Bayesian nets. According to objective Bayesianism, an agent’s degrees of belief (i) ought to satisfy the axioms of probability, (ii) ought to satisfy constraints imposed by background knowledge, and (iii) should otherwise be as non-committal as possible (i.e. have maximum entropy). Bayesian nets offer an efficient way of representing and updating probability functions. An objective Bayesian net is a Bayesian net representation of the maximum entropy probability function.

Cancer treatment decisions should be based on all available evidence. But this evidence is complex and varied: it includes not only the patient’s symptoms and expert knowledge of the relevant causal processes, but also clinical databases relating to past patients, databases of observations made at the molecular level, and evidence encapsulated in scientific papers and medical informatics systems. Objective Bayesian nets offer a principled path to knowledge integration, and we show in this chapter how they can be applied to integrate various kinds of evidence in the cancer domain. This is important from the systems biology perspective, which needs to integrate data that concern different levels of analysis, and is also important from the point of view of medical informatics.

Cancer treatment decisions should be based on all available evidence. But this evidence is complex and varied: it includes not only the patient’s symptoms and expert knowledge of the relevant causal processes, but also clinical databases relating to past patients, databases of observations made at the molecular level, and evidence encapsulated in scientific papers and medical informatics systems. Objective Bayesian nets offer a principled path to knowledge integration, and we show in this chapter how they can be applied to integrate various kinds of evidence in the cancer domain. This is important from the systems biology perspective, which needs to integrate data that concern different levels of analysis, and is also important from the point of view of medical informatics.

We present a new framework for combining logic with probability, and demonstrate the application of this framework to breast cancer prognosis. Background knowledge concerning breast cancer prognosis is represented using logical arguments. This background knowledge and a database are used to build a Bayesian net that captures the probabilistic relationships amongst the variables. Causal hypotheses gleaned from the Bayesian net in turn generate new arguments. The Bayesian net can be queried to help decide when one argument attacks another. The Bayesian net is used to perform the prognosis, while the argumentation framework is used to provide a qualitative explanation of the prognosis.