Probabilistic Parsing Strategies

We present new results on the relation between purely symbolic context-free parsing strategies and their probabilistic counter-parts. Such parsing strategies are seen as constructions of push-down devices from grammars. We show that preservation of probability distribution is possible under two conditions, viz. the correct-prefix property and the property of strong predictiveness. These results generalize existing results in the literature that were obtained by considering parsing strategies in isolation. From our general results we also derive negative results on so-called generalized LR parsing.Comment: 36 pages, 1 figur

Accurate reconstruction of insertion-deletion histories by statistical phylogenetics

The Multiple Sequence Alignment (MSA) is a computational abstraction that represents a partial summary either of indel history, or of structural similarity. Taking the former view (indel history), it is possible to use formal automata theory to generalize the phylogenetic likelihood framework for finite substitution models (Dayhoff's probability matrices and Felsenstein's pruning algorithm) to arbitrary-length sequences. In this paper, we report results of a simulation-based benchmark of several methods for reconstruction of indel history. The methods tested include a relatively new algorithm for statistical marginalization of MSAs that sums over a stochastically-sampled ensemble of the most probable evolutionary histories. For mammalian evolutionary parameters on several different trees, the single most likely history sampled by our algorithm appears less biased than histories reconstructed by other MSA methods. The algorithm can also be used for alignment-free inference, where the MSA is explicitly summed out of the analysis. As an illustration of our method, we discuss reconstruction of the evolutionary histories of human protein-coding genes.Comment: 28 pages, 15 figures. arXiv admin note: text overlap with arXiv:1103.434