A method, apparatus, and computer-readable medium for efficiently optimizing a phenotype with a specialized prediction model, including receiving constraints, encoding genotype information in experimental data points corresponding to the constraints experiential genotype vectors, the experimental data points comprising the genotype information and phenotype information corresponding to the genotype information, training a phenotype prediction model based on the experiential genotype vectors, the corresponding phenotype information, and the one or more constraints, applying the phenotype prediction model to available genotypes corresponding to the constrains to generate scores, determining result genotypes based on a ranking of the available genotypes according to the scores, and generating, a result based on the result genotypes, the result indicating one or more genetic constructs for testing.