GearNet

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May I ask how Fmax and AUPRC are calculated? Can you share the code with me? Thank you

Qzhangyx

Hi, I would like to know if the fold weights in this [link ](https://zenodo.org/records/7723075)are the fine-tuned weights of the fc dataset, or the pre-trained weights used in the fc dataset

haniulu

A dataset not found when I run "python script/pretrain.py -c config/pretrain/mc_gearnet_edge.yaml --gpus [0]"

5

It seems that the file located in "https://ftp.ebi.ac.uk/pub/databases/alphafold/latest/UP000006548_3702_ARATH_v2.tar" really doesn't exist. When I entered this url in my browser, it also noticed me that the file doesn't exist. ``` 14:43:55...

horacehht

Problems in using FC dataset

2

Hello! Thank you for your great work of Torchdrug, GearNet, and ESM-GearNet! Sorry to bother you. I'm trying to extract feature embeddings using GearNet (as discussed in several former issues)...

Yangqy-16

Seeking help for dataset

4

Hi, thank you so much for your outstanding work! I'm interested in your models and would like to run them on. Could you please tell me how to generate or...

zsc2003

RuntimeError: shape '[31, 147]' is invalid for input of size 651 in extracting embbeding from pdb files

6

Thank you for your great work. When I followed the method in the [previous issue](https://github.com/DeepGraphLearning/GearNet/issues/23) to implement feature extraction for pdb files, I encountered the following problem. `Traceback (most recent...

blazexpire

Extract the structure embeddings

1

Dear Team of GearNet, Many many thanks for this wonderful package! I am new to programming (especially torchdrug and pytorch), so how to extract the structure representations confused me a...

Jerry888Chen

What is input (Tensor) – input node representations for GearNet

1

Dear Sir/Madam, Thank you for your fantastic paper GearNet. I wish to finetune Gearnet (distance prediction) for some other downstream tasks. Now I have all atom positions and residue type...

Heisenburger2020

Node classification tasks

3

Hi! First of all great job! I have been trying to do node classification in residue view, using my own node labels. However, I haven't been able to configure the...

mpedraza98

Pre-trained weight for ESM-GearNet

4

Howdy, thank you for sharing the amazing work, and may I ask if you have any plans on releasing the pre-trained weights for ESM-GearNet model? Many thanks!

hxu105