DeepChem Minutes 5/12/2022

DeepChem Minutes

India/Asia/Pacific Call

Date: May 12th, 2022

Attendees: Bharath, Ashish,


Bharath has been busy this last week and has only worked on a couple of student calls.

Ashish explored cell profiler tutorial and docs and is now looking for an alternative tool that can be invoked more programmatically.

Americas/Europe/Africa/Middle East

Date: May 12th, 2022

Attendees: Bharath, Jose


Bharath gave the same update as at the previous call.

Jose has been working on the code for pytorch normalizing flows. Jose has also been looking at the deepbio repos.

Stanley has been looking at new transformer architectures and how they might be applied on the deepbio end.

DeepChem Bioinformatics Call

Date: May 16th, 2022

Attendees: Prashant, Saurav, Paulina, Stanley, Arun, Ashish


Prashant Kumar: basics of ML

Stanley: get a basic comparison system that David could help us develop and guide us to interesting properties. Shared bacterial bioinformatics resource:

Saurav maheshkar: RITA: a Study on Scaling Up Generative Protein Sequence Models

Paulina: read more about BERT, meeting with Galen this week for scVI-tools. Meeting with Stanley for follow up on David’s presentation.

Stanley - Shared about patric.

Saurav shared about RITA - a family of autoregressive protein models

Paulina had put up her draft PR on adding citation to tutorial. Arun suggested to wait for Bharath’s review.

Ashish explored Recursion’s dataset last week and shared his thoughts on it.

Prashanth was mostly busy this week with semester and shared that he is looking forward to contribute to deepbio over the summer.

Arun suggested that we should start building deepbio repo - adding necessary utils for data handling and model building. Here, Stanley mentioned that adding utilities like hyperparameter tuning to deepbio will be useful. Stanley also suggested to adding utilities large datasets via batch processing techniques.

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.