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flatironinstitute
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cryoSBI
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implement usage of CSV file for the MRCDataLoader
#65
DSilva27
opened
1 month ago
0
Improve unitests for simulator
#64
DSilva27
opened
1 month ago
0
Set up a docker image for cryoSBI
#63
DSilva27
opened
1 month ago
0
Set up pre-commit, mypy, ruff, etc
#62
DSilva27
opened
1 month ago
0
Write micrograph utils to load sliding window with dataloader
#61
Dingel321
opened
1 month ago
0
Create documentation website
#60
DSilva27
opened
1 month ago
1
Bugs found while running tutorial
#59
DSilva27
closed
1 month ago
1
orientations should follow cryoSpark or relion convention
#58
Dingel321
opened
4 months ago
0
Accessing parameters from a simulation
#57
aevans1
opened
4 months ago
0
New cmd tools to generate models for simulation and training
#56
Dingel321
closed
5 months ago
0
Automatically compute normalization for theta
#55
Dingel321
opened
5 months ago
2
Things to add in README
#54
Dingel321
closed
1 month ago
5
New main
#53
Dingel321
closed
7 months ago
1
User-specfied conformational indices not returned in simulator
#52
aevans1
closed
7 months ago
1
Clean up prior. Confusing notation
#51
Dingel321
closed
4 months ago
3
Warning in CryoEM simulator
#50
Dingel321
closed
7 months ago
0
print total training time in main training script
#49
Dingel321
closed
1 month ago
0
add cmd script for pdb and traj parser
#48
Dingel321
closed
5 months ago
0
Implement implicit solvent model
#47
DSilva27
closed
7 months ago
1
bug in typehints forNPEwithEmbedding
#46
Dingel321
closed
1 month ago
0
add function to compute power spectrum
#45
Dingel321
closed
1 month ago
0
Make activation function a parameter in the training config file
#44
Dingel321
opened
1 year ago
0
Iss42
#43
DSilva27
closed
6 months ago
1
Change Sigma for Res
#42
DSilva27
closed
10 months ago
0
include physical information in simulator and implement pdb/traj parser
#41
DSilva27
closed
6 months ago
0
Include tensor board summary writer for training
#40
Dingel321
opened
1 year ago
0
Use torch.compile on encoder to speed up training.
#39
Dingel321
closed
1 month ago
0
include cudnn benchmarking in training and inference scripts
#38
Dingel321
closed
1 month ago
0
MRCDataset bug loading images
#37
Dingel321
closed
5 months ago
0
add more assertions in code, with proper error massages.
#36
Dingel321
closed
1 month ago
2
add easy way to identify particles in MRC loader to load them with MRCdataset
#35
Dingel321
opened
1 year ago
1
add function in estimator utils for extracting map value
#34
Dingel321
opened
1 year ago
1
Think about torch data parallel to run training code on multiple gpus
#33
Dingel321
closed
1 month ago
0
Add logging to the important parts of the code
#32
Dingel321
closed
5 months ago
0
refactor priors
#31
Dingel321
closed
1 month ago
0
add command line tool for inference (similar to train_npe)
#30
Dingel321
closed
1 month ago
0
improve function for checking parameter files
#29
Dingel321
closed
1 month ago
0
Rewrite tests
#28
Dingel321
closed
7 months ago
0
Maybe include per residue std of gaussians in simulation
#27
Dingel321
closed
7 months ago
0
refactor simulator class to include automatic batching in simulation method
#26
Dingel321
closed
7 months ago
0
Improve MRCdataset
#25
Dingel321
closed
7 months ago
0
write function to extract CA models from pdb
#24
Dingel321
closed
10 months ago
1
write function to evaluate log posterior
#23
Dingel321
closed
7 months ago
0
remover experiment and notebook folder
#22
Dingel321
closed
7 months ago
0
Implement per image whitening (similar to aspire cryo em)
#21
Dingel321
closed
7 months ago
0
Finish writing documentation
#20
DSilva27
closed
5 months ago
0
Change n_pixels to box_size (variable name)
#19
DSilva27
closed
1 month ago
0
Fix embedding net input by making it receive box size
#18
DSilva27
opened
1 year ago
3
Develop
#17
DSilva27
closed
6 months ago
0
Clean up functions and documentation
#16
Dingel321
closed
1 year ago
0
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