Figure legends
Figure 1. PCA plot of yeast extract compositions. The percentages in brackets indicate the contributions of each component. Symbols: blue circles, E1; green circles, E2; red circles, E3; yellow circles, E4; blue triangles, M1; green triangles, M2; red triangles, M3; yellow triangles, M4; blue squares, mixture of E1 and E4; green squares, mixture of E2 and E4; red squares, mixture of E3 and E4; yellow squares, mixture of E4 and M1; blue diamonds, mixture of E4 and M2; green diamonds, mixture of E1 and M3; red diamonds, mixture of E2 and E3; yellow diamonds, mixture of E4 and M3; blue reverse triangles, mixture of E3 and M3; green reverse triangles, mixture of M3 and M1; red reverse triangles, mixture of M3 and M2; yellow reverse triangles, mixture of M3 and M4.
Figure 2. Comparison of MSEtrain, MSEtest, and MSEval for each machine learning algorithm. A, MSEtrain for estimating cell yields; B, MSEtrain for estimating GFP yields; C, MSEtest for estimating cell yields; D, MSEtest for estimating GFP yields; E, MSEval for estimating cell yields; F, MSEval for estimating GFP yields. The triangles indicate means, the dashed lines indicate medians, and the boxes indicate quantiles. Circles indicate outliers. Error bars indicate 1.5-fold standard deviations. The number of replication: n = 10.
Figure 3. Measured and predicted values by each machine learning algorithm. A, PLS model for cell yields; B, RF model for cell yields; C, NN model for cell yields; D, DNN model for cell yields; E, PLS model for GFP yields; F, RF model for GFP yields; G, NN model for GFP yields; H, DNN model for GFP yields; I, RF model for time courses of cell growth; J, DNN model for time courses of cell growth; K, RF model for time courses of GFP; L, DNN model for time courses of GFP. Symbols: yellow circles, training data; red circles, test data; blue circles, validation data.
Figure 4. Top 20 most important variables calculated by DNN-MIL. A, cell growth; B, GFP expression. Red dashed lines indicate minimal values of the averaged MSE in all variables.
Figure 5. The results of the validating cultivation. Each component was added at 0.05 g/L in basal medium with M4 yeast extract. Significance: *, 0.01 < p ≤ 0.05; **, p ≤ 0.01. Error bars indicate standard deviations.