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NYarvin's profile
Norman Yarvin
Norman Yarvin
Norman Yarvin
@NYarvin

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Norman Yarvin

@NYarvin

yarchive.net/blog
Joined April 2013

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    1. whitequark‏ @whitequark 20 Nov 2019
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      ouchpic.twitter.com/j3SCBS5YMW

      2 replies 4 retweets 20 likes
    2. Norman Yarvin‏ @NYarvin 20 Nov 2019
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      Replying to @whitequark

      I had a look at the GENTRL paper recently, wondering how they got from three-dimensional chemical structure space to a vector that could be fed into a machine learning algorithm... and even harder, how they made that mapping reversible. Couldn't figure it out.

      1 reply 0 retweets 0 likes
    3. Norman Yarvin‏ @NYarvin 20 Nov 2019
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      Replying to @NYarvin @whitequark

      And I don't think that's my fault. They say approximately one word about how the transformation starts: SMILES. https://en.wikipedia.org/wiki/Simplified_molecular-input_line-entry_system …

      1 reply 0 retweets 0 likes
    4. Norman Yarvin‏ @NYarvin 20 Nov 2019
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      Replying to @NYarvin @whitequark

      But from there, how they get to "a continous space of 50 dimensions" (i.e. a 50-element vector) is left almost completely undescribed, even in the supplementary information.

      1 reply 0 retweets 1 like
    5. Norman Yarvin‏ @NYarvin 20 Nov 2019
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      Replying to @NYarvin @whitequark

      And the real trick is making all this reversible. I was expecting about 20 pages of describing how they did that, and found bupkis.

      1 reply 0 retweets 1 like
      Norman Yarvin‏ @NYarvin 20 Nov 2019
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      Replying to @NYarvin @whitequark

      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.

      9:33 PM - 20 Nov 2019
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      • whitequark
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        2. Norman Yarvin‏ @NYarvin 20 Nov 2019
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          Replying to @NYarvin @whitequark

          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.

          1 reply 0 retweets 0 likes
        3. Norman Yarvin‏ @NYarvin 20 Nov 2019
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          Replying to @NYarvin @whitequark

          One of the 50 properties is "this is a drug that does exactly what we want", so to have the end result be an almost identical chemical is unsurprising. The corollary of garbage in, garbage out: solved problem in, solved problem out.

          0 replies 0 retweets 1 like
        4. End of conversation

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