GearNet

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Custom dataset. Data preprocessing

1

Thank you so much for your outstanding work! I'm interested in your models and would like to run them on some custom datasets. Unfortunately, I haven't found any instructions on...

Chicky-Picky

The pre-trained GearNet-Edge model for Fold Classification

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Thank you for your amazing work! I found that for the Fold Classification task, the GearNet-Edge model was implemented based on the GearNetIEConv script rather than the GearNet script, which...

arantir123

Solution when alpha carbon coordinate is missing

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Hi, since GearNet models each residue in the protein by the C_alpha coordinates, how do you handle the situation when the coordinate for alpha carbon is missing?

YanjingLiLi

confusion on epochs

3

Hi! I am wondering the number of epochs in experiment. The epoch is set to 200 for EC stated in the paper, but in the config the epoch is set...

Siirui

atom view

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I was wondering how atom view is implemented? I'm getting a shape mismatch. In mc-gearnet_edge.yaml I changed the view and entity level to 'atom' and input dimension to 38. As...

karel-w

Explainability

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Hello, Is there any code available for the explainability experiment in Section K in the appendix of your paper https://arxiv.org/pdf/2203.06125.pdf? Thank you.

MichailChatzianastasis

error in mc_esm_gearnet

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Howdy, thank u for ur awesome work in Enhancing Protein Language Models with Structure-based Encoder and Pre-training. I am running the pretaining experiment now, and I am facing an issue...

hxu105

ERROR:torch.distributed.elastic.multiprocessing.api:failed (exitcode: -6) local_rank: 0 (pid: 20) of binary....

1

When I run python -m torch.distributed.launch --nproc_per_node=4 script/downstream.py -c config/downstream/GO-BP/gearnet_edge.yaml --gpus [0,1,2,3] --ckpt on worker*1 Tesla-V100-SXM2-32GB:4 GPU, 47 CPU, I got the error: [219013] [E ProcessGroupNCCL.cpp:587] [Rank 0] Watchdog caught...

bozhenhhu

I currently have a LoRA fine-tuned ESM-3b model and want to evaluate its performance on the downstream task of EC number prediction. How should I modify the YAML file and...

fourier20laplace

Is there a way to work with proteins with different number of residues in a the same batch? I don't want to use the trimming transformation since I need the...

mpedraza98