Doo Nam Kim
Doo Nam Kim
### Checklist - [X] I have searched for [similar issues](https://github.com/isl-org/Open3D-ML/issues). - [X] I have tested with the [latest development wheel](http://www.open3d.org/docs/latest/getting_started.html#development-version-pip). - [X] I have checked the [release documentation](http://www.open3d.org/docs/release/) and the...
I mean training sample in https://github.com/rosinality/vq-vae-2-pytorch/#stage-1 Even when I ran train_vqvae with my own data set, many image files in sample folder showed as duplicate. Initially, I thought that images...
I ran `python /people/kimd999/script/python/cryoEM/vq-vae-2-pytorch/train_vqvae.py /people/kimd999/MARScryo/dn/data/part/PDX_label_correct/exp_coexp/input --size 256` It seems to generate sample images and checkpoint files in checkpoint folder well. However, `python /people/kimd999/script/python/cryoEM/vq-vae-2-pytorch/extract_code.py --size 256 --ckpt checkpoint/vqvae_560.pt --name small256 /people/kimd999/MARScryo/dn/data/part/PDX_label_correct/exp_coexp/input`...
Thank you for sharing this great code. I have used infovae as a subsitute of beta-vae and traditional vae (beta=1). However, I think that your vq-vae-2 better reconstructs images. Unfortunately,...
I downloaded some FFHQ images from https://drive.google.com/drive/folders/1tZUcXDBeOibC6jcMCtgRRz67pzrAHeHL Then, I ran python /people/kimd999/script/python/cryoEM/vq-vae-2-pytorch/train_vqvae.py /people/kimd999/MARScryo/dn/data/devel/FFHQ/data Since it is a default running, --size should be 256 (line 142 of train_vqvae.py). I think that...
Maybe this is not cryodrgn specific issue, but more general vae problem???. Anyway, have you ever seen "nan" like below? Thank you -- ``` 2020-08-15 07:13:21 # =====> Epoch: 2457...
With published 50S ribosome set, and some of my own sets, I have no problem. However, for two of my own sets, I have a problem with backproject_voxel (all other...
https://github.com/torch-points3d/torch-points-kernels' readme says `poetry add torch-points-kernels` However, my centos can't use it as ``` (RandLA) [kimd999@tlogin2 python]$ ~/.poetry/bin/poetry add torch-points-kernels RuntimeError Poetry could not find a pyproject.toml file in /home/kimd999/script/python...
After running HIV data tutorial, I am trying neuronal synapse data tutorial. I could run commandline tutorial up to refine well. However, when I used GUI, I can't see any...
[2023_Cyclic peptide structure prediction and design using AlphaFold](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9980166/ ) mentions `"Example scripts for structure prediction, sequence design, and hallucination are available at https://github.com/sokrypton/ColabDesign/blob/main/af/examples/af_cyc_design.ipynb"` However, I can't see prediction of cyclic...