snap-stanford / SATURN

snap-stanford/SATURN Issues

Which seed is the best in your frog_zebrafish_embryogenesis analysis?
Closed 23 days ago1
What are seeds? What is the optimal number of seeds to run?
Closed a month ago4
The meaning of weights in macrogene?
Closed 24 days ago1
Example of label transfer with saturn?
Closed 24 days ago1
SyntaxError while running saturn_multiple_seeds.py
Closed 24 days ago1
Out of memory error when using ESM2 for protein embeddings
Closed a month ago2
RuntimeError: indices should be either on cpu or on the same device as the indexed tensor (cpu)
Closed a month ago1
How to preserve all the metadata information in the Anndata from two species to the Final AnnData after integration?
Closed a month ago2
Looking for "publicly available protein embedding datasets we have provided."
Closed a month ago2
Error when training saturn
Closed 2 months ago2
Question: protein embedding, are we only using protein sequences?
Closed 2 months ago2
.append() does not exist anymore in pandas
Closed 10 months ago6
KeyError: 'species_gene_name'
Closed 2 months ago2
train.SATURN ERROR. Is a GPU necessary?
Closed 2 months ago1
New Data Integration
Closed 2 months ago3
issue with barcodes if species in the run.csv are provided in a non-alphabetic order
Closed 2 months ago1
ValueError: b'Extrapolation not allowed with blending'
Closed 2 months ago1
unexpected keyword argument 'miner_type'
Closed 2 months ago
Should I must provide the score_adata ?
Closed 2 months ago1
Similar to KeyError: 'cell_type' #4
Closed 2 months ago3
Failed for running frog_zebrafish_embryogenesis
Closed 2 months ago1
Within species integration
Closed 3 months ago1
Which ESM2 transformer should be used for proteome-wide embedding generation?
Closed 3 months ago1
Please help with GSE113074_Corrected_combined.annotated_counts.h5ad
Closed 3 months ago1
Error with installation？
Closed 3 months ago3
Question about centroid creation
Closed 3 months ago1
Help with file "zebrafish_cell_types_mapping"
Closed 3 months ago2
Where is the extract.py file used in protein embedding?
Closed 6 months ago2
Error at the biginning of the training step : centroid_weights.append(torch.tensor(species_genes_scores[sgn]))
Closed 3 months ago3
Question about availability
Closed 3 months ago1
creation of celltype_map csv
Closed 3 months ago5
train-saturn.py debugging
Closed 3 months ago2
Trouble creating protein embeddings
Closed 3 months ago1
Sapiens (~15gb) data not available
Closed 4 months ago1
Torch version not available
Closed 5 months ago1
How indices_tuple is always empty tensors?
Closed 8 months ago9
Precomputed embeddings
Closed a year ago15
Tunning Saturn
Closed 10 months ago3
where in the code the weights from the genes layer to the macrogenes layer are frozen?
Closed 10 months ago1
Are the species inputs fed to the model together?
Closed a year ago2
Ensuring cluster proximity in co-embedding for a selected subset
Closed a year ago6
species one hot encoding is the same for frog and zebrafish, shouldn't it be different?
Closed a year ago1
For which purpose is use_batch_labels used for?
Closed a year ago1
License?
Closed a year ago2
question about the zebrafish genome version
Closed a year ago4
Are the classes (OrthologPretrainModel, OrthologMetricModel) used to generate any data?, what is the use of the embeddings generated by SATURNMetricModel class?
Closed a year ago2
Cannot understand the means of result
Closed a year ago2
Are the classes OrthologPretrainModel, OrthologMetricModel used to generate any data?
Closed a year ago1
FileNotFoundError: [Errno 2] No such file or directory: 'saturn_results/fz_centroids.pkl'
Closed a year ago2
The pretraining process in Train SATURN does not start and no errors are shown
Closed a year ago13