141 karma · joined August 15, 2016
https://melwy.com/blog/black-female-scientist-timnit-gebru-f...
The MoleculeNet co-author gave another argument in the comments. My refutation is that you can't claim to lack time after 8*20 man-months have passed.
I also agree that there are many ways to work through the perfect discriminator problem for ORGAN. But it remains to be done (afaik).
Does it fit the Deepchem agenda? That's another question ;)
Look at the big list of exotic models they tried: http://moleculenet.ai/models
For me, this omission is a negligence. It is selective laziness.
The author (me) does not have 20 PhD students, postdocs and startuppers under his hand, to do the job for Stanford. With my limited resources, it is more cost-effective to do my job against Stanford ;)
1. I agree that graph convolutions make a lot of sense. However, it is not shown yet that they are better than SMILES, although it might just be a matter of time. A lot of graph variants are possible, or maybe we should look at molecules not as graphs, but as quantum objects (See the other Stanford paper on atom convolutions).
2. Yes, Deepchem is built on top of Tensorflow. This additional layer looks useful, but is it really the case? Using standard NLP models is simpler than using deepchem models, and NLP models might still be the state-of-the-art for chemistry tasks, via SMILES (until we get a reasonably comprehensive benchmark, which MoleculeNet is not).
I am not buying into a chemistry-specific library, until it is shown to be really necessary.