GO enrichment analysis of the gene sets associated with hidden variables.

<p>GO enrichment analysis of the gene sets associated with hidden variables.</p

GO enrichment analysis of the gene sets identified by NCA and our model.

<p>GO enrichment analysis of the gene sets identified by NCA and our model.</p

The graphical model

<p>Known and potential TFs are assumed to be mutually independent. Regulated genes are assumed to be mutually independent given the TFs.</p

Histogram of sizes of the gene sets associated with known and putative regulators.

<p>Histogram of sizes of the gene sets associated with known and putative regulators.</p

Four-loci, dbMHC Irish data.

<p>Abbreviations are: S = softmax, RM = regularized multinomial, M = non-regularized multinomial, AM = allele marginals. A total of 468 alleles were masked in the test set.</p

Summary of Private Data

<p>Summary of Private Data</p

Sensitivity to Variable Ordering.

<p>Top two rows are for the Hispanic data set; bottom two rows are for the European data set. Within each of these, the top row is the geometric mean probabilities, and the bottom row shows the percent correct MAP predictions. The number of masked alleles, respectively, in the Hispanic 30% and loci masks (A,B,C), was 306 and 354. The number of masked alleles, respectively, in the European 30% and loci masks (A,B,C), was 2669 and 3012.</p

Statistical Significance Results on Private Data, Separately for Each Ethnicity.

*<p>Denotes the method that performed better (except for the last row, where the allele marginals perform better than the unregularized multinomial on the log likelihood, but worse on the number of correct MAP predictions.</p

Locus-Specific Predictive Accuracy.

<p>Each set of grouped bars, from darkest to lightest, represents, respectively, A-masking, B-masking, and C-masking. The number of masked alleles in each masking was 3012, 1418, 528, and 354, respectively, for the European, African, Asian, and Hispanic test sets.</p

Results for population-augmented model.

<p>Abbreviations are: SSC = softmax+simple+conjunctive, SS = softmax+simple, S = simple, RM = regularized multinomial, M = non-regularized multinomial, AM = allele marginals, S = separate. The number of masked alleles in the test set was 514. For all methods, except ‘separate’, a single model was trained on data from all ethnicities.</p