Information-theoretic Justification Research Articles

Topological data analysis in information space

Various kinds of data are routinely represented as discrete probability distributions. Examples include text documents summarized by histograms of word occurrences and images represented as histograms of oriented gradients. Viewing a discrete probability distribution as a point in the standard simplex of the appropriate dimension, we can understand collections of such objects in geometric and topological terms. Importantly, instead of using the standard Euclidean distance, we look into dissimilarity measures with information-theoretic justification, and we develop the theory needed for applying topological data analysis in this setting. In doing so, we emphasize constructions that enable the usage of existing computational topology software in this context.

An information-theoretic approach to normal forms for relational and XML data

Normalization as a way of producing good relational database designs is a well-understood topic. However, the same problem of distinguishing well-designed databases from poorly designed ones arises in other data models, in particular, XML. While, in the relational world, the criteria for being well designed are usually very intuitive and clear to state, they become more obscure when one moves to more complex data models.Our goal is to provide a set of tools for testing when a condition on a database design, specified by a normal form , corresponds to a good design. We use techniques of information theory, and define a measure of information content of elements in a database with respect to a set of constraints. We first test this measure in the relational context, providing information-theoretic justification for familiar normal forms such as BCNF, 4NF, PJ/NF, 5NFR, DK/NF. We then show that the same measure applies in the XML context, which gives us a characterization of a recently introduced XML normal form called XNF. Finally, we look at information-theoretic criteria for justifying normalization algorithms.

Least and Most Powerful Phylogenetic Tests to Elucidate the Origin of the Seed Plants in the Presence of Conflicting Signals under Misspecified Models

Several tests of molecular phylogenies have been proposed over the last decades, but most of them lead to strikingly different P-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To support this hypothesis, two new tests are described. Both consider the composite null hypothesis that all the topologies are equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis at the least favorable distribution (frequentist significance test (FST)) or to the maximum likelihood topology (frequentist hypothesis test (FHT)). In both cases, the reduced null hypothesis is tested against each topology included in the analysis. The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a nonparametric bootstrap, adjusting P-values for multiple comparisons. I applied the new tests to the reanalysis of two chloroplast genes, psaA and psbB, and compared the results with those of previously described tests. As expected, the FST and the FHT behaved approximately like the Shimodaira-Hasegawa test and the bootstrap, respectively. Although the tests give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex models incorporating heterogeneity among codon positions resolve some conflicts. To further investigate the influence of the null hypothesis, a power study was conducted. Simulations showed that FST and the Shimodaira-Hasegawa test are the least powerful and FHT is the most powerful across the parameter space. Although the size of all the tests is affected by misspecification, the two new tests appear more robust against misspecification of the model of evolution and consistently supported the hypothesis that the Gnetales are nested within gymnosperms. (Approximately unbiased test; bootstrap proportion; hypothesis test; P-value adjustment; Shimodaira-Hasegawa test; significance test.)

Least and Most Powerful Phylogenetic Tests to Elucidate the Origin of the Seed Plants in the Presence of Conflicting Signals under Misspecified Models

Several tests of molecular phylogenies have been proposed over the last decades, but most of them lead to strikingly different P-values. I propose that such discrepancies are principally due to different forms of null hypotheses. To support this hypothesis, two new tests are described. Both consider the composite null hypothesis that all the topologies are equidistant from the true but unknown topology. This composite hypothesis can either be reduced to the simple hypothesis at the least favorable distribution (frequentist significance test [FST]) or to the maximum likelihood topology (frequentist hypothesis test [FHT]). In both cases, the reduced null hypothesis is tested against each topology included in the analysis. The tests proposed have an information-theoretic justification, and the distribution of their test statistic is estimated by a nonparametric bootstrap, adjusting P-values for multiple comparisons. I applied the new tests to the reanalysis of two chloroplast genes, psaA and psbB, and compared the results with those of previously described tests. As expected, the FST and the FHT behaved approximately like the Shimodaira-Hasegawa test and the bootstrap, respectively. Although the tests give overconfidence in a wrong tree when an overly simple nucleotide substitution model is assumed, more complex models incorporating heterogeneity among codon positions resolve some conflicts. To further investigate the influence of the null hypothesis, a power study was conducted. Simulations showed that FST and the Shimodaira-Hasegawa test are the least powerful and FHT is the most powerful across the parameter space. Although the size of all the tests is affected by misspecification, the two new tests appear more robust against misspecification of the model of evolution and consistently supported the hypothesis that the Gnetales are nested within gymnosperms.