DeepChem Minutes 6/10/2021

DeepChem Minutes

India/Asia/Pacific Call

Date: June 10th, 2021
Attendees: Bharath, Ashwin, Yuanqi, Peter, Alana
Summary: Bharath explained some of the issues with DeepChem 2.6.0 release. Numpy 1.20 doesn’t work with TensorFlow so we can’t make the release right now until TensorFlow fixes numpy 1.20.

Peter has been working on bugfixing and debugging. Peter figured out what happened with the uncertainty prediction and has a PR fix in place for that. Peter also has a PR in place for fixing mypy for numpy 1.20. Peter also tracked down what happened in the broken notebook.

Yuanqi has been busy recently and is organizing a new Neurips workshop.

Ashwin has been working on the loader method for the USPTO datasets. He’s currently working on getting the full dataset loaded.

Alana has been working on the protein tokenizer. Alana is running into some issues with figuring out how to handle the FASTA loader.

Americas/Europe/Africa/Middle East

India/Asia/Pacific Call

Date: May 28th, 2021
Attendees: Bharath, Atreya, James, Vignesh, David, Nathan, Seyone
Summary: Atreya is a 3rd year engineering undergrad who’s working on DeepChem for GSoC this summer.

Bharath gave the same update as at the last call.

Seyone has been busy this week but is getting back to getting the masked LM PR up.

Nathan has been on-boarding at his new job and is hoping to start running heavy duty DeepChem on some internal MIT clusters, mostly focusing on normalizing flows and atomic convs.

David has just finished his semester and hopes to work more on DeepChem and has been looking into adding SwissProt into MoleculeNet.

James is conducting some experiments for his paper using DeepChem but is seeing some GPU utilization issues.

Atreya has been working on developing his molecular attention transformer. He’s currently working on developing his molecular attention transformer and making tests.

Vignesh has been working on his JaxModel project for GSoC.

Joining the DeepChem Developer Calls

As a quick reminder to anyone reading along, the DeepChem developer calls are open to the public! If you’re interested in attending either or both of the calls, please send an email to, where X=bharath, Y=ramsundar.