Jon Williamson

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.

Key Terms in Logic offers the ideal introduction to this core area in the study of philosophy, providing detailed summaries of the important concepts in the study of logic and the application of logic to the rest of philosophy. A brief introduction provides context and background, while the following chapters offer detailed definitions of key terms and concepts, introductions to the work of key thinkers and lists of key texts. Designed specifically to meet the needs of students and assuming no prior knowledge of the subject, this is the ideal reference tool for those coming to Logic for the first time.

This paper discusses the issue of overriding the right of individual consent to participation in cluster randomised trials (CRTs). We focus on CRTs testing the efficacy of non-pharmaceutical interventions. As an example, we consider school closures during the COVID-19 pandemic. In Norway, a CRT was promoted as necessary for providing the best evidence to inform pandemic management policy. However, the proposal was rejected by the Norwegian Research Ethics Committee since it would violate the requirement for individual informed consent. This sparked debate about whether ethics stand in the way of evidence-based health policy, since the Norwegian Research Ethics law’s strict requirements for individual consent make it practically impossible to carry out CRTs of public health interventions. We argue that, in the case of the school closure trial, the suggested CRT would not have eliminated an epistemic gap and thus would not have justified the violation of consent rights. First, we focus on the methodological challenges to estimating quantifiable effects of school closures in the specific case of an airborne infectious disease. Second, in line with Evidential Pluralism, we highlight the value of alternative lines of evidence for informing school closure policy in a pandemic. In general, we propose that a trial requiring the waiver of participants’ consent rights must be highly likely to eliminate an epistemic gap. We elaborate on the practical aspects of this criterion and discuss the potential advantages of adding it to the Ottawa Statement on the Ethical Design and Conduct of Cluster Randomized Trials.

Key Terms in Logic offers the ideal introduction to this core area in the study of philosophy, providing detailed summaries of the important concepts in the study of logic and the application of logic to the rest of philosophy. A brief introduction provides context and background, while the following chapters offer detailed definitions of key terms and concepts, introductions to the work of key thinkers and lists of key texts. Designed specifically to meet the needs of students and assuming no prior knowledge of the subject, this is the ideal reference tool for those coming to Logic for the first time.

This paper addresses a data integration problem: given several mutually consistent datasets each of which measures a subset of the variables of interest, how can one construct a probabilistic model that fits the data and gives reasonable answers to questions which are under-determined by the data? Here we show how to obtain a Bayesian network model which represents the unique probability function that agrees with the probability distributions measured by the datasets and otherwise has maximum entropy. We provide a general algorithm, OBN-cDS, which offers substantial efficiency savings over the standard brute-force approach to determining the maximum entropy probability function. Furthermore, we develop modifications to the general algorithm which enable further efficiency savings but which are only applicable in particular situations. We show that there are circumstances in which one can obtain the model directly from the data; by solving algebraic problems; and by solving relatively simple independent optimisation problems.

Key Terms in Logic offers the ideal introduction to this core area in the study of philosophy, providing detailed summaries of the important concepts in the study of logic and the application of logic to the rest of philosophy. A brief introduction provides context and background, while the following chapters offer detailed definitions of key terms and concepts, introductions to the work of key thinkers and lists of key texts. Designed specifically to meet the needs of students and assuming no prior knowledge of the subject, this is the ideal reference tool for those coming to Logic for the first time.

Key Terms in Logic offers the ideal introduction to this core area in the study of philosophy, providing detailed summaries of the important concepts in the study of logic and the application of logic to the rest of philosophy. A brief introduction provides context and background, while the following chapters offer detailed definitions of key terms and concepts, introductions to the work of key thinkers and lists of key texts. Designed specifically to meet the needs of students and assuming no prior knowledge of the subject, this is the ideal reference tool for those coming to Logic for the first time.

Metabolism is a set of chemical reactions, used by living organisms to process chemical compounds in order to take energy and eliminate toxic compounds, for example. Its processes are referred as metabolic pathways. Understanding metabolism is imperative to biology, toxicology and medicine, but the number and complexity of metabolic pathways makes this a difficult task. In our paper, we investigate the use of causal Bayesian networks to model the pathways of yeast saccharomyces cerevisiae metabolism: such a network can be used to draw predictions about the levels of metabolites and enzymes in a particular specimen. We propose a two-stage methodology for causal networks, as follows. First construct a causal network from the network of metabolic pathways. The viability of this causal network depends on the validity of the causal Markov condition. If this condition fails, however, the principle of the common cause motivates the addition of a new causal arrow or a new `hidden' common cause to the network (stage 2 of the model formation process). Algorithms for adding arrows or hidden nodes have been developed separately in a number of papers, and in this paper we combine them, showing how the resulting procedure can be applied to the metabolic pathway problem. Our general approach was tested on neural cell morphology data and demonstrated noticeable improvements in both prediction and network accuracy.

The EBM+ programme is an attempt to improve the way in which present-day evidence-based medicine (EBM) assesses causal claims: according to EBM+, mechanistic studies should be scrutinised alongside association studies. This paper addresses two worries about EBM+: (i) that it is not feasible in practice, and (ii) that it is too malleable, i.e., its results depend on subjective choices that need to be made in order to implement the procedure. Several responses to these two worries are considered and evaluated. The paper also discusses the question of whether we should have confidence in medical interventions, in the light of Stegenga’s arguments for medical nihilism.

Key Terms in Logic offers the ideal introduction to this core area in the study of philosophy, providing detailed summaries of the important concepts in the study of logic and the application of logic to the rest of philosophy. A brief introduction provides context and background, while the following chapters offer detailed definitions of key terms and concepts, introductions to the work of key thinkers and lists of key texts. Designed specifically to meet the needs of students and assuming no prior knowledge of the subject, this is the ideal reference tool for those coming to Logic for the first time.

According to objective Bayesianism, an agent’s degrees of belief should be determined by a probability function, out of all those that satisfy constraints imposed by background knowledge, that maximises entropy. A Bayesian net offers a way of efficiently representing a probability function and efficiently drawing inferences from that function. An objective Bayesian net is a Bayesian net representation of the maximum entropy probability function. In this paper we apply the machinery of objective Bayesian nets to breast cancer prognosis. Background knowledge is diverse and comes from several different sources: a database of clinical data, a database of molecular data, and quantitative data from the literature. We show how an objective Bayesian net can be constructed from this background knowledge and how it can be applied to yield prognoses and aid translation of clinical knowledge to genomics research