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

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

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

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

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

Results on private data, separately for each ethnicity.

<p>Each set of grouped bars represents the four different modeling approaches. From darkest to lightest: softmax, regularized multinomial, unregularized multinomial, allele marginal. The number of masked alleles, respectively, in the European, African, Asian, and Hispanic data sets was 2669, 1287, 477, and 306, respectively.</p

Summary of dbMHC Data

<p>Summary of dbMHC Data</p

Low Resolution Prediction.

<p>Each set of grouped bars represents, from darkest to lightest, respectively, 100% mask with softmax model, 100% mask with allele marginals model, 30% mask with softmax model, 30% mask with allele marginals model. The number of masked alleles for the 100% mask was 4254, 1429, and 1062, and for the 30% mask, 1287, 477, and 306, in the African, Asian, and Hispanic test sets, respectively.</p

Sensitivity to training data set size for the European and African data sets.

<p>Top row shows the geometric mean probabilities; the bottom row shows the percentage of correct MAP predictions.</p