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)

In medicine and the social sciences, researchers must frequently integrate the findings of many observational studies, which measure overlapping collections of variables. For instance, learning how to prevent obesity requires combining studies that investigate obesity and diet with others that investigate obesity and exercise. Recently developed causal discovery algorithms provide techniques for integrating many studies, but little is known about what can be learned from such algorithms. This article argues that there are causal facts that one could learn by conducting (...) a large study but which could not be learned by combining many smaller studies. Moreover, I characterize the frequency with which combining many studies increases underdetermination and exactly how much information is lost. 1 Introduction2 Causal Inference from Observational Data3 Piecemeal Causal Inference4 The Extent and Frequency of the Problem of Piecemeal Induction5 Conclusion. (shrink)

Newsome ((2003). The debate between current versions of covariation and mechanism approaches to causal inference. Philosophical Psychology, 16, 87-107.) recently published a critical review of psychological theories of human causal inference. In that review, he characterized covariation and mechanism theories, the two dominant theory types, as competing, and offered possible ways to integrate them. I argue that Newsome has misunderstood the theoretical landscape, and that covariation and mechanism theories do not directly conflict. Rather, they rely on distinct sets of reliable (...) indicators of causation, and focus on different types of causation (type vs. token). There are certainly debates in the research field, but the theoretical landscape is not as fractured as Newsome suggests, and a potential unifying framework has already emerged using causal Bayes nets. Philosophical work on causal epistemology matters for psychologists, but not in the way Newsome suggests. (shrink)

A pervasive feature of the sciences, particularly the applied sciences, is an experimental focus on a few (often only one) possible causal connections. At the same time, scientists often advance and apply relatively broad models that incorporate many different causal mechanisms. We are naturally led to ask whether there are normative rules for integrating multiple local experimental conclusions into models covering many additional variables. In this paper, we provide a positive answer to this question by developing several inference rules that (...) use local causal models to place constraints on the integrated model, given quite general assumptions. We also demonstrate the practical value of these rules by applying them to a case study from ecology. Experimental scope in applied sciences Fusing the results of experiments A concrete example of the inference rules Application to a case study. (shrink)

Many approaches to evidence amalgamation focus on relatively static information or evidence: the data to be amalgamated involve different variables, contexts, or experiments, but not measurements over extended periods of time. However, much of scientific inquiry focuses on dynamical systems; the system’s behavior over time is critical. Moreover, novel problems of evidence amalgamation arise in these contexts. First, data can be collected at different measurement timescales, where potentially none of them correspond to the underlying system’s causal timescale. Second, missing variables (...) have a significantly different impact on time series measurements than they do in the traditional static setting; in particular, they make causal and structural inference much more difficult. In this paper, we argue that amalgamation should proceed by integrating causal knowledge, rather than at the level of “raw” evidence. We defend this claim by first outlining both of these problems, and then showing that they can be solved only if we operate on causal structures. We therefore must use causal discovery methods that are reliable given these problems. Such methods do exist, but their successful application requires careful consideration of the problems that we highlight. (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)