Fig. 6: Two pairs of molecules (s1, t1), (s2, t2) with Tanimoto similarity 0.71 and 0.76, respectively, are shown.
From: Exhaustive local chemical space exploration using a transformer model
The Tanimoto similarity is represented by κ in the Figure, and s1 and s2 denote two source molecules, while t1 and t2 two targets molecules. NLL1 and NLL2 are the negative log-likelihood associated with (s1, t1) and (s2, t2), respectively. In the left example NLL2 > NLL1, therefore the regularization term Ω (see Eq. (3)) is greater than 0. This indicates that NLL1 and NLL2 are incorrectly ordered, which we emphasize by enclosing Ω = 1.8 in a red box in the left picture. In the right example NLL1 > NLL2. In this case, Ω = 0 as the similarities and NLLs have the same rank-order, which we emphasize by enclosing Ω = 0.0 in a green box in the right picture.
