This paper (which is mainly expository) sets up graphical models for causation, having a bit less than the usual complement of hypothetical counterfactuals. Assuming the invariance of error distributions may be essential for causal inference, but the errors themselves need not be invariant. Graphs can be interpreted using conditional distributions, so that we can better address connections between the mathematical framework and causality in the world. The identification problem is posed in terms of conditionals. As will be seen, causal relationships cannot be inferred from a data set by running regressions unless there is substantial prior knowledge about the mechanisms that generated the data. There are few successful applications of graphical models, mainly because few causal pathways can be excluded on a priori grounds. The invariance conditions themselves remain to be assessed.

Bayesian networks are normally given one of two types of foundations: they are either treated purely formally as an abstract way of representing probability functions, or they are interpreted, with some causal interpretation given to the graph in a network and some standard interpretation of probability given to the probabilities specified in the network. In this chapter I argue that current foundations are problematic, and put forward new foundations which involve aspects of both the interpreted and the formal approaches. One standard approach is to interpret a Bayesian network objectively: the graph in a Bayesian network represents causality in the world and the specified probabilities are objective, empirical probabilities. Such an interpretation founders when the Bayesian network independence assumption (often called the causal Markov condition) fails to hold. In §2 I catalogue the occasions when the independence assumption fails, and show that such failures are pervasive. Next, in §3, I show that even where the independence assumption does hold objectively, an agent’s causal knowledge is unlikely to satisfy the assumption with respect to her subjective probabilities, and that slight differences between an agent’s subjective Bayesian network and an objective Bayesian network can lead to large differences between probability distributions determined by these networks. To overcome these difficulties I put forward logical Bayesian foundations in §5. I show that if the graph and probability specification in a Bayesian network are thought of as an agent’s background knowledge, then the agent is most rational if she adopts the probability distribution determined by the

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