IEEE Computational Intelligence Magazine - May 2022 - 21

with a very small value of b is poor at learning latent representations.
In fact, [52] shows that in
b-VAE , small values of b
tend to encourage disentangled representations and form latent
clusters. Finally, it should be clarified that the validity, novelty,
and diversity of generated molecules are usually used for a " sanity
check " of generative models in molecular design. These three
measures should not be used as dominant performance indicators
of a design algorithm, as the algorithm should be evaluated
in terms of the quality of solutions.
The property distributions of generated samples can be
important indicators of the proximity of generated samples to
actual samples. Figure 3 shows the distributions of QED, SAS,
0.2
2
0.5
QED
0.5
ZINC
Atoms
20
10
20
β = 1
(a)
Bonds
2
Rings
β = 0.1
1 246 -10 -5 05 10
SAS
LOGP
β = 0.01
00 0
ZINC β = 1 β = 0.1 β = 0.01
CF NO Other
2
0.5
QED
PCBA
Atoms
20
10
20
1
β = 1
(c)
Bonds
2
Rings
0.5
1
SAS
β = 0.1
ZINC β = 1 β = 0.1 β = 0.01
Single Double
(b)
Triple
0.2
ZINC β = 1 β = 0.1 β = 0.01
Tri Quad Pent Hex
510 -10 -5 05 10
LOGP
β = 0.01
00 0
PCBA β = 1 β = 0.1 β = 0.01
CF NO Other
PCBA β = 1 β = 0.1 β = 0.01
Single Double
(d)
Triple
PCBA β = 1 β = 0.1 β = 0.01
Tri Quad Pent Hex
FIGURE 3 Property and structural feature distributions over 20K randomly sampled molecules by FragVAE without evolution. (a) Property
distributions over ZINC. (b) Structural feature distributions over ZINC. (c) Property distributions over PCBA. (d) Structural feature distributions
over PCBA.
MAY 2022 | IEEE COMPUTATIONAL INTELLIGENCE MAGAZINE 21

IEEE Computational Intelligence Magazine - May 2022

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