Additional file 1 of MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra

Additional file 1. MS2DeepScore: a novel deep learning similarity measure to compare tandem mass spectra. Figure S1. Score comparisons with respect to precision-recall in highly unbalanced dataset. Figure S2–S8. Hyperparameter search. Figure S9 Early stopping. Figure S10 Assessing prediction uncertainty using Monte-Carlo Dropout. Table S1. Measuring the linear correlation between actual and predicted scores. Figure S11 t-SNE using MS2DeepScore or modified cosine score.