Systems medicine is a promising new paradigm for discovering associations, causal relationships and mechanisms in medicine. But it faces some tough challenges that arise from the use of big data: in particular, the problem of how to integrate evidence and the problem of how to structure the development of models. I argue that objective Bayesian models offer one way of tackling the evidence integration problem. I also offer a general methodology for structuring the development of models, within which the objective (...) Bayesian approach fits rather naturally. (shrink)

This article connects recent work in formal epistemology to work in economics and computer science. Analysing the Dutch Book Arguments, Epistemic Utility Theory and Objective Bayesian Epistemology we discover that formal epistemologists employ the same argument structure as economists and computer scientists. Since similar approaches often have similar problems and have shared solutions, opportunities for cross-fertilisation abound.

According to the objective Bayesian approach to inductive logic, premisses inductively entail a conclusion just when every probability function with maximal entropy, from all those that satisfy the premisses, satisfies the conclusion. When premisses and conclusion are constraints on probabilities of sentences of a first-order predicate language, however, it is by no means obvious how to determine these maximal entropy functions. This paper makes progress on the problem in the following ways. Firstly, we introduce the concept of a limit in (...) entropy and show that, if the set of probability functions satisfying the premisses contains a limit in entropy, then this limit point is unique and is the maximal entropy probability function. Next, we turn to the special case in which the premisses are categorical sentences of the logical language. We show that if the uniform probability function gives the premisses positive probability, then the maximal entropy function can be found by simply conditionalising this uniform prior on the premisses. We generalise our results to demonstrate agreement between the maximal entropy approach and Jeffrey conditionalisation in the case in which there is a single premiss that specifies the probability of a sentence of the language. We show that, after learning such a premiss, certain inferences are preserved, namely inferences to inductive tautologies. Finally, we consider potential pathologies of the approach: we explore the extent to which the maximal entropy approach is invariant under permutations of the constants of the language, and we discuss some cases in which there is no maximal entropy probability function. (shrink)

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. (shrink)