epam / epam/Indigo

Tune atom and bonds featurisers to achieve best results for predicting AdrA1A_PCHEMBL_VALUE

Open
#624 0 comments 0 reactions 0 assignees View on GitHub
Improvement ML Priority: High python
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

Is blocked by #602 and #622.

**ToDo**
1. Take minimal set of featurisers (atom number and bond order) as a basis.
2. Write a simple engine that allows to add one or more featurisers to the mol2graph and concatenate them.

Next step is pretty creative, there could be different approaches. Just one of them as an example:
1. Write test code that automatically iterates over list of featurisers and adds them one by one.
2. Take minimal mol2graph and iterate over all featurisers to test what pair of featurisers act better: atom number and valence, atom number and mass etc.
2. Choose best model for two featurisers, then go back to step 3 and add one more featuriser from the rest of possible etc.
3. Stop when model is not achieving better results anymore.

After that add a ready preset of featurisers (as it's done in DGL-LifeSci).

Contributor guide

No contributing guide indexed for this repository

Research direction

Start with blocking issues #602 and #622, then inspect the minimal mol2graph and its atom-number and bond-order featurisers. Compare candidate featuriser combinations for AdrA1A_PCHEMBL_VALUE, and consider the requested DGL-LifeSci-style preset. Done means a working combination engine, comparison tests, and a selected preset.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
machine-learning
Issue type
Feature
Difficulty
5/5
Estimated time
Over a week
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
20/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.