microsoft / microsoft/Graphormer

The collator function in collator.py will drop samples in train dataset, even validation/test dataset ?

Open
#101 2 comments 0 reactions 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
Python
Stars
2.5k
Forks
374
PR merge metrics
No merged PRs in 30d

Description

Hi authors,
Thank you for your great work! I'm working on PCBA dataset with your v1 code. But I noticed that the collator function used to load samples for Batch in collator.py would drop samples in training dataset, even validation/test dataset. The code snapshot is as blow:
def collator(items, max_node=512, multi_hop_max_dist=20, spatial_pos_max=20): items = [ item for item in items if item is not None and item.x.size(0) <= max_node]
Since the parameter max_node was set as 128 for PCBA dataset, it meant samples with item.x.size(0) larger than 128 wouldn't be loaded. I did a data exploration and found there were some samples whose x.size(0) is larger than 128 in both training dataset and validation/test dataset. I think it might also affect the evaluation score on the leaderboard. Or do I misunderstand it?. Thank you!

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start with collator.py and the PCBA dataset configuration where max_node is set to 128. Inspect how samples are filtered for the training, validation, and test splits, then measure which samples are omitted. Done means establishing whether the filtering is intentional and documenting or correcting its effect on evaluation.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data, machine-learning
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.