microsoft/Graphormer

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Graphormer is a general-purpose deep learning backbone for molecular modeling.

Stars: 2.5k
Forks: 374
Open beginner issues: 0
Indexed issues: 92

Dominant language: Python
License: MIT
Last GitHub push: Jun 12, 2026
Latest indexed: Sep 19, 2026
Contributing guide: No contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue help wanted
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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92 open issues indexed

3D graphormer model on PCQM4M-v2 Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#135 · 3 comments · Opened Aug 18, 2022
Graphormer module Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

microsoft/Graphormer#133 · 10 comments · 2 reactions · Opened Aug 11, 2022
Issue running `bash zinc.sh` after fresh install (Ubuntu) Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

microsoft/Graphormer#130 · 2 comments · Opened Aug 6, 2022
Can't load the pretrain model Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#129 · 7 comments · Opened Jul 27, 2022
Molecule-level features Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#128 · 1 comment · Opened Jul 15, 2022
Reproducing ZINC result with v2 Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

microsoft/Graphormer#127 · 5 comments · Opened Jul 13, 2022
ImportError: No module named setuptools Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

microsoft/Graphormer#125 · 4 comments · Opened Jun 22, 2022
error: command ':/usr/local/cuda/bin/nvcc' failed: No such file or directory Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

microsoft/Graphormer#124 · 3 comments · Opened Jun 21, 2022
Simple/Basic tutorial Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#120 · 4 comments · Opened Jun 10, 2022
I want to rewrite the grapher model into a generative model, but I don't have any ideas now. Open

Difficulty 5/5 Over a week Newbie friendliness 10/100

microsoft/Graphormer#118 · Opened Jun 7, 2022
run_ zinc. sh: line 26: 648 aborted (core dumped) Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

microsoft/Graphormer#117 · 2 comments · Opened Jun 6, 2022
An error occurs"TypeError: 'type' object is not subscriptable" when I run an example。 Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

microsoft/Graphormer#116 · 4 comments · Opened May 27, 2022
What is the maximum number of nodes a graphormer can handle? Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

microsoft/Graphormer#113 · 8 comments · Opened Apr 22, 2022
CUDA Error when adding new GIN model Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#112 · Opened Apr 21, 2022
Example script hangs without output Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#111 · 4 comments · Opened Apr 20, 2022
Cannot Assign Requested Address Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

microsoft/Graphormer#110 · 1 comment · Opened Apr 19, 2022
How to convert the molecular graph in SDF/JSON format to the input of graphormer? Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

microsoft/Graphormer#108 · 4 comments · Opened Apr 8, 2022
How to train Graphormer for autoregressive task? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#107 · 1 comment · Opened Apr 5, 2022
[Bug] Load Pre-trained Graphormer-3d from OC20 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#104 · Opened Mar 28, 2022
can not reproduce PCQM4M-LSC results Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#103 · 12 comments · Opened Mar 22, 2022
How can I train my new dataset？ Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

microsoft/Graphormer#102 · 3 comments · Opened Mar 22, 2022
The collator function in collator.py will drop samples in train dataset, even validation/test dataset ? Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

microsoft/Graphormer#101 · 2 comments · Opened Mar 18, 2022
About the results on ogbp-pcba in the process of finetune Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#97 · 3 comments · Opened Mar 13, 2022
About the resullt in ogbg-molhiv Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#90 · 12 comments · Opened Feb 27, 2022
Question about graphormer version 1 Open

Difficulty 1/5 Under an hour Newbie friendliness 20/100

microsoft/Graphormer#88 · 1 comment · Opened Feb 4, 2022
Hi, can your work be migrated to an undirected graph？ Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

microsoft/Graphormer#86 · 1 comment · Opened Jan 13, 2022
How to evaluate for dataset zinc? Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

microsoft/Graphormer#85 · 9 comments · 2 reactions · Opened Jan 10, 2022
Inputs for evaluate.py Open

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

microsoft/Graphormer#84 · 3 comments · Opened Jan 8, 2022
[Feature request] Supports Sparse Graph Representation Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

microsoft/Graphormer#82 · 2 reactions · Opened Jan 6, 2022
Could upgrade and support torch-geometric 2.0 ? Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

microsoft/Graphormer#77 · 4 comments · Opened Dec 30, 2021
Can Graphormer be modified to accommodate node classification and link prediction problems? Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#75 · 3 comments · Opened Dec 29, 2021
[Feature Request] Pre-trained Graphormer-large v2.0 on PCQM4M Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#74 · Opened Dec 29, 2021
[Feature Request] Package Graphormer code for PyPI Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#72 · 2 reactions · Opened Dec 29, 2021
[Feature Request] Molecule Feature Extraction by RDKit Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

microsoft/Graphormer#71 · Opened Dec 29, 2021
[Feature Request] Pre-trained Graphormer v2.0 model for OGBG-MolPCBA Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

microsoft/Graphormer#70 · 1 comment · Opened Dec 29, 2021
[Feature Request] High Efficient Shortest Path Implementation Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

microsoft/Graphormer#69 · Opened Dec 29, 2021
Customizing number of epochs for training. Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

microsoft/Graphormer#65 · 3 comments · Opened Dec 27, 2021
Feature Requests & Voting Hub Open

enhancement help wanted

Difficulty 5/5 Over a week Newbie friendliness 15/100

microsoft/Graphormer#63 · Opened Dec 24, 2021
How to evaluate the model with V.2? Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

microsoft/Graphormer#60 · 5 comments · Opened Dec 23, 2021
unable to import PygPCQN4MDataset Open

Difficulty 3/5 1-2 days Newbie friendliness 30/100

microsoft/Graphormer#43 · 10 comments · Opened Dec 1, 2021
train from scratch on molecule datasets Open

good first issue

Difficulty 5/5 Over a week Newbie friendliness 18/100

microsoft/Graphormer#39 · 4 comments · Opened Nov 30, 2021
Evidential deep learning and other feature requests Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

microsoft/Graphormer#23 · Opened Sep 8, 2021

microsoft/Graphormer

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