Motivation: Algorithms that discover variables which are causally related to a target may inform the design of experiments. With observational gene expression data, many methods discover causal variables by measuring each variable's degree of statistical dependence with the target using dependence measures (DMs). However, other methods measure each variable's ability to explain the statistical dependence between the target and the remaining variables in the data using conditional dependence measures (CDMs), since this strategy is guaranteed to find the target's direct causes, direct effects, and direct causes of the direct effects in the infinite sample limit. In this paper, we design a new algorithm in order to systematically compare the relative abilities of DMs and CDMs in discovering causal variables from gene expression data. Results: The proposed algorithm using a CDM is sample efficient, since it consistently outperforms other state-of-the-art local causal discovery algorithms when samples sizes are small. However, the proposed algorithm using a CDM outperforms the proposed algorithm using a DM only when sample sizes are above several hundred. These results suggest that accurate causal discovery from gene expression data using current CDM-based algorithms requires datasets with at least several hundred samples. Availability: The proposed algorithm is freely available at https://github.com/ericstrobl/DvCD.

We propose a general algorithm for approximating nonstandard Bayesian posterior distributions. The algorithm minimizes the Kullback-Leibler divergence of an approximating distribution to the intractable posterior distribution. Our method can be used to approximate any posterior distribution, provided that it is given in closed form up to the proportionality constant. The approximation can be any distribution in the exponential family or any mixture of such distributions, which means that it can be made arbitrarily precise. Several examples illustrate the speed and accuracy of our approximation method in practice.

As examples such as the Monty Hall puzzle show, applying conditioning to update a probability distribution on a ``naive space', which does not take into account the protocol used, can often lead to counterintuitive results. Here we examine why. A criterion known as CAR (coarsening at random) in the statistical literature characterizes when ``naive' conditioning in a naive space works. We show that the CAR condition holds rather infrequently. We then consider more generalized notions of update such as Jeffrey conditioning and minimizing relative entropy (MRE). We give a generalization of the CAR condition that characterizes when Jeffrey conditioning leads to appropriate answers, but show that there are no such conditions for MRE. This generalizes and interconnects previous results obtained in the literature on CAR and MRE.

It is commonly-accepted wisdom that more information is better, and that information should never be ignored. Here we argue, using both a Bayesian and a non-Bayesian analysis, that in some situations you are better off ignoring information if your uncertainty is represented by a set of probability measures. These include situations in which the information is relevant for the prediction task at hand. In the non-Bayesian analysis, we show how ignoring information avoids dilation, the phenomenon that additional pieces of information sometimes lead to an increase in uncertainty. In the Bayesian analysis, we show that for small sample sizes and certain prediction tasks, the Bayesian posterior based on a noninformative prior yields worse predictions than simply ignoring the given information.

We consider how an agent should update her uncertainty when it is represented by a set P of probability distributions and the agent observes that a random variable X takes on value x, given that the agent makes decisions using the minimax criterion, perhaps the best-studied and most commonly-used criterion in the literature. We adopt a game-theoretic framework, where the agent plays against a bookie, who chooses some distribution from P. We consider two reasonable games that differ in what the bookie knows when he makes his choice. Anomalies that have been observed before, like time inconsistency, can be understood as arising because different games are being played, against bookies with different information. We characterize the important special cases in which the optimal decision rules according to the minimax criterion amount to either conditioning or simply ignoring the information. Finally, we consider the relationship between conditioning and calibration when uncertainty is described by sets of probabilities.

Expectation is a central notion in probability theory. The notion of expectation also makes sense for other notions of uncertainty. We introduce a propositional logic for reasoning about expectation, where the semantics depends on the underlying representation of uncertainty. We give sound and complete axiomatizations for the logic in the case that the underlying representation is (a) probability, (b) sets of probability measures, (c) belief functions, and (d) possibility measures. We show that this logic is more expressive than the corresponding logic for reasoning about likelihood in the case of sets of probability measures, but equi-expressive in the case of probability, belief, and possibility. Finally, we show that satisfiability for these logics is NP-complete, no harder than satisfiability for propositional logic.

We introduce a logic for reasoning about evidence, that essentially views evidence as a function from prior beliefs (before making an observation) to posterior beliefs (after making the observation). We provide a sound and complete axiomatization for the logic, and consider the complexity of the decision problem. Although the reasoning in the logic is mainly propositional, we allow variables representing numbers and quantification over them. This expressive power seems necessary to capture important properties of evidence

Over the last decade, there has been growing interest in the use or measures or change in belief for reasoning with uncertainty in artificial intelligence research. An important characteristic of several methodologies that reason with changes in belief or belief updates, is a property that we term modularity. We call updates that satisfy this property modular updates. Whereas probabilistic measures of belief update - which satisfy the modularity property were first discovered in the nineteenth century, knowledge and discussion of these quantities remains obscure in artificial intelligence research. We define modular updates and discuss their inappropriate use in two influential expert systems.

An agent often has a number of hypotheses, and must choose among them based on observations, or outcomes of experiments. Each of these observations can be viewed as providing evidence for or against various hypotheses. All the attempts to formalize this intuition up to now have assumed that associated with each hypothesis h there is a likelihood function {\mu}h, which is a probability measure that intuitively describes how likely each observation is, conditional on h being the correct hypothesis. We consider an extension of this framework where there is uncertainty as to which of a number of likelihood functions is appropriate, and discuss how one formal approach to defining evidence, which views evidence as a function from priors to posteriors, can be generalized to accommodate this uncertainty.

A general notion of algebraic conditional plausibility measures is defined. Probability measures, ranking functions, possibility measures, and (under the appropriate definitions) sets of probability measures can all be viewed as defining algebraic conditional plausibility measures. It is shown that the technology of Bayesian networks can be applied to algebraic conditional plausibility measures.