Table 2.

Performance of the proposed method on the traumatic injury application and comparison with other methods.

Method		Size	Rand Index	Test Set
				Error rate	BCM1	AUPR2
Proposed methods	Sign Avg. & LASSO/CD3	32	19.58%	0.351	0.605	0.626
	Sign Avg. & TGDR4	30	25.21%	0.378	0.590	0.662
Existing methods	limma	47	21.40%	0.432	0.542	0.628
	EDGE	453	13.67%	0.432	0.543	0.622
	glmmLASSO	8	34.99%	0.432	0.519	0.532
	LASSO/CD separately5	28	13.59%	0.486	0.498	0.508
	TGDR separately6	133	22.58%	0.378	0.520	0.579
	Mean & LASSO/CD7	29	17.95%	0.405	0.536	0.560
Using other summary scores	Mean & TGDR8	36	27.37%	0.405	0.562	0.617
	Median & LASSO/CD9	22	7.76%	0.351	0.543	0.617
	Median & TGDR10	43	18.58%	0.405	0.578	0.626
	PC1 & LASSO/CD11	3	13.59%	0.405	0.504	0.541
	PC1 & TGDR12	29	32.68%	0.432	0.539	0.548

¹BCM captures the average confidence that a sample belongs to class i when it indeed belongs to that class;

²AUPR is the average of AUPR_k for each class and it captures the ability of correctly ranking the samples known to belong in a given class;

³Sign Avg. & LASSO/CD: pseudo genes were obtained by calculating the sign average of a gene's expression values across time, and the feature selection method is LASSO in which the optimization method used is coordinate descent;

⁴Sign Avg. & TGDR: pseudo genes were obtained by calculating the sign average of a gene's expression values across time, and the feature selection/optimization method is threshold gradient descent regularization;

⁵LASSO/CD separately: separate LASSO models were trained at individual time points; the optimization method is CD;

⁶TGDR separately: separate TGDR models were trained at individual time points; the optimization method is TGDR;

⁷Mean & LASSO/CD: pseudo genes were obtained by calculating the average of a gene's expression values across time, and the optimization method is CD;

⁸Mean & TGDR: pseudo genes were obtained by calculating the average of a gene's expression values across time, and the optimization method is TGDR;

⁹Median & LASSO/CD: pseudo genes were obtained by calculating the median of a gene's expression values across time, and the optimization method is CD;

¹⁰Median & TGDR: pseudo genes were obtained by calculating the median of a gene's expression values across time, and the optimization method is TGDR;

¹¹PC1 & LASSO/CD: pseudo genes obtained by calculating the first principal component of a gene's expression values across time, and the optimization method is CD;

¹²PC1 & TGDR: pseudo genes were obtained by calculating the first principal component of a gene's expression values across time, and the optimization method is TGDR.