Query DAGs: A Practical Paradigm for Implementing Belief-Network Inference

We describe a new paradigm for implementing inference in belief networks, which consists of two steps: (1) compiling a belief network into an arithmetic expression called a Query DAG (Q-DAG); and (2) answering queries using a simple evaluation algorithm. Each node of a Q-DAG represents a numeric operation, a number, or a symbol for evidence. Each leaf node of a Q-DAG represents the answer to a network query, that is, the probability of some event of interest. It appears that Q-DAGs can be generated using any of the standard algorithms for exact inference in belief networks (we show how they can be generated using clustering and conditioning algorithms). The time and space complexity of a Q-DAG generation algorithm is no worse than the time complexity of the inference algorithm on which it is based. The complexity of a Q-DAG evaluation algorithm is linear in the size of the Q-DAG, and such inference amounts to a standard evaluation of the arithmetic expression it represents. The intended value of Q-DAGs is in reducing the software and hardware resources required to utilize belief networks in on-line, real-world applications. The proposed framework also facilitates the development of on-line inference on different software and hardware platforms due to the simplicity of the Q-DAG evaluation algorithm. Interestingly enough, Q-DAGs were found to serve other purposes: simple techniques for reducing Q-DAGs tend to subsume relatively complex optimization techniques for belief-network inference, such as network-pruning and computation-caching.Comment: See http://www.jair.org/ for any accompanying file

Polyhedral computational geometry for averaging metric phylogenetic trees

This paper investigates the computational geometry relevant to calculations of the Frechet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability measures on spaces of nonpositive curvature developed by Sturm. We show that the combinatorics of geodesics with a specified fixed endpoint in tree space are determined by the location of the varying endpoint in a certain polyhedral subdivision of tree space. The variance function associated to a finite subset of tree space has a fixed $C^\infty$ algebraic formula within each cell of the corresponding subdivision, and is continuously differentiable in the interior of each orthant of tree space. We use this subdivision to establish two iterative methods for producing sequences that converge to the Frechet mean: one based on Sturm's Law of Large Numbers, and another based on descent algorithms for finding optima of smooth functions on convex polyhedra. We present properties and biological applications of Frechet means and extend our main results to more general globally nonpositively curved spaces composed of Euclidean orthants.Comment: 43 pages, 6 figures; v2: fixed typos, shortened Sections 1 and 5, added counter example for polyhedrality of vistal subdivision in general CAT(0) cubical complexes; v1: 43 pages, 5 figure