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snap-stanford
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SATURN
MIT License
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Torch version not available
#28
dariotommasini
closed
10 months ago
1
Where is the extract.py file used in protein embedding?
#27
vinettey
closed
11 months ago
2
BugFix
#26
moinfar
closed
9 months ago
1
Tunning Saturn
#25
Hrovatin
closed
1 year ago
3
How indices_tuple is always empty tensors?
#24
MohammedZidane
closed
1 year ago
9
where in the code the weights from the genes layer to the macrogenes layer are frozen?
#23
MohammedZidane
closed
1 year ago
1
.append() does not exist anymore in pandas
#22
anaellle
closed
1 year ago
6
Are the species inputs fed to the model together?
#21
MohammedZidane
closed
1 year ago
2
For which purpose is use_batch_labels used for?
#20
cam1flag
closed
1 year ago
1
Precomputed embeddings
#19
bschilder
closed
1 year ago
15
License?
#18
tristanic
closed
1 year ago
2
question about the zebrafish genome version
#17
huawen-poppy
closed
1 year ago
4
species one hot encoding is the same for frog and zebrafish, shouldn't it be different?
#16
MohammedZidane
closed
1 year ago
1
Are the classes (OrthologPretrainModel, OrthologMetricModel) used to generate any data?, what is the use of the embeddings generated by SATURNMetricModel class?
#15
MohammedZidane
closed
1 year ago
2
Are the classes OrthologPretrainModel, OrthologMetricModel used to generate any data?
#14
MohammedZidane
closed
1 year ago
1
FileNotFoundError: [Errno 2] No such file or directory: 'saturn_results/fz_centroids.pkl'
#13
MohammedZidane
closed
1 year ago
2
Cannot understand the means of result
#12
houruiyan
closed
1 year ago
2
Ensuring cluster proximity in co-embedding for a selected subset
#11
lijinbio
closed
1 year ago
6
The pretraining process in Train SATURN does not start and no errors are shown
#10
cam1flag
closed
1 year ago
13
FileNotFoundError: [Errno 2] No such file or directory: '/dfs/project/cross-species/yanay/data/proteome/embeddings/Xenopus_tropicalis.Xenopus_tropicalis_v9.1.gene_symbol_to_embedding_ESM2.pt'
#9
MohammedZidane
closed
1 year ago
5
kernel dies while running 'frog = generate_frog_h5ad()' in dataloader.ipynb
#8
MohammedZidane
closed
1 year ago
1
pretrain error
#7
huawen-poppy
closed
1 year ago
6
train-saturn.py: error: unrecognized arguments: \
#6
MohammedZidane
closed
1 year ago
5
Are there any strategies available for preserving cell type similarity when conducting cross-species co-embedding?
#5
lijinbio
closed
1 year ago
8
KeyError: 'cell_type'
#4
houruiyan
closed
1 year ago
32
ImportError: cannot import name 'QuantStub' from 'torch.ao.quantization'
#3
houruiyan
closed
1 year ago
2
cannot find the extract.py file in esm
#2
houruiyan
closed
1 year ago
0
Host count data as h5ad
#1
cdedonno
closed
1 year ago
2
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