Crammer, Koby
Email Address
ORCID
Disciplines
Search Results
Now showing 1 - 2 of 2
Publication Learning from Multiple Sources(2008-06-01) Crammer, Koby; Kearns, Michael; Wortman, JenniferWe consider the problem of learning accurate models from multiple sources of "nearby" data. Given distinct samples from multiple data sources and estimates of the dissimilarities between these sources, we provide a general theory of which samples should be used to learn models for each source. This theory is applicable in a broad decision-theoretic learning framework, and yields general results for classification and regression. A key component of our approach is the development of approximate triangle inequalities for expected loss, which may be of independent interest. We discuss the related problem of learning parameters of a distribution from multiple data sources. Finally, we illustrate our theory through a series of synthetic simulations.Publication Reranking candidate gene models with cross-species comparison for improved gene prediction(2008-10-14) Liu, Qian; Crammer, Koby; Roos, David S; Pereira, Fernando CNBackground: Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar state-based scores may be distinguishable with additional information. In particular, functional and comparative genomics datasets may help to select among competing models of comparable probability by exploiting features likely to be associated with the correct gene models, such as conserved exon/intron structure or protein sequence features. Results: We have investigated the utility of a simple post-processing step for selecting among a set of alternative gene models, using global scoring rules to rerank competing models for more accurate prediction. For each gene locus, we first generate the K best candidate gene models using the gene finder Evigan, and then rerank these models using comparisons with putative orthologous genes from closely-related species. Candidate gene models with lower scores in the original gene finder may be selected if they exhibit strong similarity to probable orthologs in coding sequence, splice site location, or signal peptide occurrence. Experiments on Drosophila melanogaster demonstrate that reranking based on cross-species comparison outperforms the best gene models identified by Evigan alone, and also outperforms the comparative gene finders GeneWise and Augustus+. Conclusion: Reranking gene models with cross-species comparison improves gene prediction accuracy. This straightforward method can be readily adapted to incorporate additional lines of evidence, as it requires only a ranked source of candidate gene models.