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Fig. 3 | Journal of Cheminformatics

Fig. 3

From: COMA: efficient structure-constrained molecular generation using contractive and margin losses

Fig. 3

Ablation studies of contractive and margin losses. a–d (Left) PCA plots for 10 molecular pairs sampled from the DRD2 training dataset and (Right) comparison of pairwise distance distributions between intra-(dis)similar molecular sets that constructed from the 20 molecules. For each box plot, the center line and box limits represent the quartiles of distance distributions, and whiskers represent 1.5x interquartile range. a The case when neither contractive nor margin losses was used. b The case when only contractive loss was used. c The case when only margin loss was used. d The case when both were used. e Comparison of molecular generation performances for three metrics (property, improvement, and similarity) in the DRD2 benchmark task. f Comparison of similar molecule generation performances on the DRD2 dataset among three regularization terms, contractive-and-margin, triplet, and contrastive loss functions. The score in parentheses is the mean value of the distribution. g Latent space analysis in the case when both contractive and margin losses were used. The green arrow represents a projective space containing three molecular pairs for analysing the effects of contractive and margin losses. h Analysis of the relationship between molecular structures and embedding positions via the Tanimoto similarity. A common molecular substructure between neighboring molecules was highlighted

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