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I checked again, and found a short section in the supplemental that I hadn't noticed, which is enough to decipher it. Turns out the 50 dimensions are known chemical and medicinal properties, so it's not really "auto-encoding"; instead they're giving it a ton and a half of data.
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As regards reversibility, they just train a forward network to map one way, and a reverse network (with very different shape) to map the other way. Not perfect reversibility, but they don't care; they discard the outputs that make no sense.
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