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BioinfoMachineLearning/bio-diffusion
Train model with custom dataset

Hey, I am doing the exact same thing as #4 , that I want to train this model with my own custom dataset. I am wondering if you can provide some tutorials about this? I appreciate it really much.
  • yiyanliao
  • Opened 
    18 hours ago
  • #15

BioinfoMachineLearning/bio-diffusion
How to use the pre-trained classifier on QM9 properties without passing data to the diffusion model?

Hi, it is not really an issue, but I wonder if you can provide suggestions on how to do this? I want to generate molecule graphs and passing it directly to the classifier to predict molecular properties. ...
  • cengc13
  • 2
  • Opened 
    on Feb 16
  • #14

BioinfoMachineLearning/bio-diffusion
install local project as package

in README，maybe install pip3 install -e . to pip3 install -e . --no-deps, the conda env have pytorch
  • hotwa
  • 1
  • Opened 
    on Dec 6, 2024
  • #13

BioinfoMachineLearning/bio-diffusion
trian error

bio_diffusion
  • lfs119
  • 5
  • Opened 
    on Jul 8, 2024
  • #10

BioinfoMachineLearning/bio-diffusion
GEOM-Drugs train bio-diffusion

First，When I run this command python3 src/train.py experiment=geom_mol_gen_ddpm.yaml, set the parameter trainer.devices=1 datamodule.dataloader_cfg.batch_size=512 and compare trainer.devices=8 datamodule.dataloader_cfg.batch_size=512, ...
  • 18hfliu
  • 3
  • Opened 
    on Jun 24, 2024
  • #9

BioinfoMachineLearning/bio-diffusion
Is the adjacency matrix fully connected when it is first input to the GCPNet++?

Just like this link (https://github.com/BioinfoMachineLearning/bio-diffusion/blob/775a9760972f6ec254c44dd6e623c4451403ca4f/src/models/components/gcpnet.py#L1095-L1099) , I looked at the batch.edge_index ...
  • 18hfliu
  • 5
  • Opened 
    on Apr 28, 2024
  • #8

BioinfoMachineLearning/bio-diffusion
Provide a non-framework code?

Can you provide a non-framework code so that you can easily see the process, not just the functions? thanks! It stopped after this，and did not continue training ： Skipping training batch with index 43 ...
  • 18hfliu
  • 4
  • Opened 
    on Apr 26, 2024
  • #7

BioinfoMachineLearning/bio-diffusion
there might be errors in the egnn code

i found 6 unresolved references in the code of egnn,just like the picture error Perhaps you can provide a correct version，thanks！ I would greatly appreciate it if you could help
  • charlotte0104
  • 3
  • Opened 
    on Apr 26, 2024
  • #6

BioinfoMachineLearning/bio-diffusion
Diffusion model generalization ability

When I try to train DEM and GeoLDM with my own dataset, gradient norm is too large. an the gradient norm decrease when training a bio-diffusion model on my dataset? My custom data set is different from ...
  • 18hfliu
  • 4
  • Opened 
    on Apr 23, 2024
  • #5

BioinfoMachineLearning/bio-diffusion
Training on custom dataset

Hello,I am highly interested in using this diffusion model with my custom dataset, I am now trying to generate the .pkl files for my custom dataset. I understand that the default pkl files in this model ...
  • peonycabbage
  • 11
  • Opened 
    on Apr 27, 2023
  • #4
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