13,777 research outputs found
Induction of Word and Phrase Alignments for Automatic Document Summarization
Current research in automatic single document summarization is dominated by
two effective, yet naive approaches: summarization by sentence extraction, and
headline generation via bag-of-words models. While successful in some tasks,
neither of these models is able to adequately capture the large set of
linguistic devices utilized by humans when they produce summaries. One possible
explanation for the widespread use of these models is that good techniques have
been developed to extract appropriate training data for them from existing
document/abstract and document/headline corpora. We believe that future
progress in automatic summarization will be driven both by the development of
more sophisticated, linguistically informed models, as well as a more effective
leveraging of document/abstract corpora. In order to open the doors to
simultaneously achieving both of these goals, we have developed techniques for
automatically producing word-to-word and phrase-to-phrase alignments between
documents and their human-written abstracts. These alignments make explicit the
correspondences that exist in such document/abstract pairs, and create a
potentially rich data source from which complex summarization algorithms may
learn. This paper describes experiments we have carried out to analyze the
ability of humans to perform such alignments, and based on these analyses, we
describe experiments for creating them automatically. Our model for the
alignment task is based on an extension of the standard hidden Markov model,
and learns to create alignments in a completely unsupervised fashion. We
describe our model in detail and present experimental results that show that
our model is able to learn to reliably identify word- and phrase-level
alignments in a corpus of pairs
Probabilistic Clustering of Sequences: Inferring new bacterial regulons by comparative genomics
Genome wide comparisons between enteric bacteria yield large sets of
conserved putative regulatory sites on a gene by gene basis that need to be
clustered into regulons. Using the assumption that regulatory sites can be
represented as samples from weight matrices we derive a unique probability
distribution for assignments of sites into clusters. Our algorithm, 'PROCSE'
(probabilistic clustering of sequences), uses Monte-Carlo sampling of this
distribution to partition and align thousands of short DNA sequences into
clusters. The algorithm internally determines the number of clusters from the
data, and assigns significance to the resulting clusters. We place theoretical
limits on the ability of any algorithm to correctly cluster sequences drawn
from weight matrices (WMs) when these WMs are unknown. Our analysis suggests
that the set of all putative sites for a single genome (e.g. E. coli) is
largely inadequate for clustering. When sites from different genomes are
combined and all the homologous sites from the various species are used as a
block, clustering becomes feasible. We predict 50-100 new regulons as well as
many new members of existing regulons, potentially doubling the number of known
regulatory sites in E. coli.Comment: 27 pages including 9 figures and 3 table
Detection of recombination in DNA multiple alignments with hidden markov models
CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected
The Mathematics of Phylogenomics
The grand challenges in biology today are being shaped by powerful
high-throughput technologies that have revealed the genomes of many organisms,
global expression patterns of genes and detailed information about variation
within populations. We are therefore able to ask, for the first time,
fundamental questions about the evolution of genomes, the structure of genes
and their regulation, and the connections between genotypes and phenotypes of
individuals. The answers to these questions are all predicated on progress in a
variety of computational, statistical, and mathematical fields.
The rapid growth in the characterization of genomes has led to the
advancement of a new discipline called Phylogenomics. This discipline results
from the combination of two major fields in the life sciences: Genomics, i.e.,
the study of the function and structure of genes and genomes; and Molecular
Phylogenetics, i.e., the study of the hierarchical evolutionary relationships
among organisms and their genomes. The objective of this article is to offer
mathematicians a first introduction to this emerging field, and to discuss
specific mathematical problems and developments arising from phylogenomics.Comment: 41 pages, 4 figure
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