Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space
Paper summary I found this paper a bit difficult to fully understand. Its premise, as far as I can follow, is that we may want to use genetic algorithms (GA), where we make modifications to elements in a population, and keep elements around at a rate proportional to some set of their desirable properties. In particular we might want to use this approach for constructing molecules that have properties (or predicted properties) we want. However, a downside of GA is that its easy to end up in local minima, where a single molecule, or small modifications to that molecule, end up dominating your population, because everything else gets removed for having less-high reward. The authors proposed fix for this is by training a discriminator to tell the difference between molecules from the GA population and those from a reference dataset, and then using that discriminator loss, GAN-style, as part of the "fitness" term that's used to determine if elements stay in the population. The rest of the "fitness" term is made up of chemical desiderata - solubility, how easy a molecule is to synthesize, binding efficacy, etc. I think the intuition here is that if the GA produces the same molecule (or similar ones) over and over again, the discriminator will have an easy time telling the difference between the GA molecules and the reference ones. One confusion I had with this paper is that it only really seems to have one experiment supporting its idea of using a discriminator as part of the loss - where the discriminator wasn't used at all unless the chemical fitness terms plateaued for some defined period (shown below). https://i.imgur.com/sTO0Asc.png The other constrained optimization experiments in section 4.4 (generating a molecule with specific properties, improving a desired property while staying similar to a reference molecule, and drug discovery). They also specifically say that they'd like to be the case that the beta parameter - which controls the weight of the discriminator relative to the chemical fitness properties - lets you smoothly interpolate between prioritizing properties and prioritizing diversity/realness of images, but they find that's not the case, and that, in fact, there's a point at which you move beta a small amount and switch sharply to a regime where chemical fitness values are a lot lower. Plots of eventual chemical fitness found over time seem to be the highest for models with beta set to 0, which isn't what you'd expect if the discriminator was in fact useful for getting you out of plateaus and into long-term better solutions. Overall, I found this paper an interesting idea, but, especially since it was accepted into ICLR, found it had confusingly little empirical support behind it.
arxiv.org
scholar.google.com
Augmenting Genetic Algorithms with Deep Neural Networks for Exploring the Chemical Space
Nigam, AkshatKumar and Friederich, Pascal and Krenn, Mario and Aspuru-Guzik, Alán
arXiv e-Print archive - 2019 via Local Bibsonomy
Keywords: dblp


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Summary by CodyWild 1 month ago
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