BACKGROUND: Computing exact multipoint LOD scores for extended pedigrees rapidly becomes infeasible as the number of markers and untyped individuals increase. When markers are excluded from the computation, significant power may be lost. Therefore accurate approximate methods which take into account all markers are desirable. METHODS: We present a novel method for efficient estimation of LOD scores on extended pedigrees. Our approach is based on the Cluster Variation Method, which deterministically estimates likelihoods by performing exact computations on tractable subsets of variables (clusters) of a Bayesian network. First a distribution over inheritances on the marker loci is approximated with the Cluster Variation Method. Then this distribution is used to estimate the LOD score for each location of the trait locus. RESULTS: First we demonstrate that significant power may be lost if markers are ignored in the multi-point analysis. On a set of pedigrees where exact computation is possible we compare the estimates of the LOD scores obtained with our method to the exact LOD scores. Secondly, we compare our method to a state of the art MCMC sampler. When both methods are given equal computation time, our method is more efficient. Finally, we show that CVM scales to large problem instances. CONCLUSION: We conclude that the Cluster Variation Method is as accurate as MCMC and generally is more efficient. Our method is a promising alternative to approaches based on MCMC sampling.

In this article we present an algorithm to compute bounds on the marginals of a graphical model. For several small clusters of nodes upper and lower bounds on the marginal values are computed independently of the rest of the network. The range of allowed probability distributions over the surrounding nodes is restricted using earlier computed bounds. As we will show, this can be considered as a set of constraints in a linear programming problem of which the objective function is the marginal probability of the center nodes. In this way knowledge about the maginals of neighbouring clusters is passed to other clusters thereby tightening the bounds on their marginals. We show that sharp bounds can be obtained for undirected and directed graphs that are used for practical applications, but for which exact computations are infeasible.

The partition function for a Boltzmann machine can be bounded from above and below. We can use this to bound the means and the correlations. For networks with small weights, the values of these statistics can be restricted to non-trivial regions (i.e. a subset of [-1 , 1]). Experimental results show that reasonable bounding occurs for weight sizes where mean field expansions generally give good results.

We present a method to bound the partition function of a Boltzmann machine neural network with any odd-order polynomial. This is a direct extension of the mean-field bound, which is first order. We show that the third-order bound is strictly better than mean field. Additionally, we derive a third-order bound for the likelihood of sigmoid belief networks. Numerical experiments indicate that an error reduction of a factor of two is easily reached in the region where expansion-based approximations are useful.

We present a method to bound the partition function of a Boltz(cid:173) mann machine neural network with any odd order polynomial. This is a direct extension of the mean field bound, which is first order. We show that the third order bound is strictly better than mean field. Additionally we show the rough outline how this bound is applicable to sigmoid belief networks. Numerical experiments in(cid:173) dicate that an error reduction of a factor two is easily reached in the region where expansion based approximations are useful.