Commit History
Re-update stats to handle case of empty alt_states
78517d8
Christina Theodoris
commited on
Add handling for case of alt_states being empty list
9e8dbe5
Christina Theodoris
commited on
Remove print statement from PR
c4b1f94
Fixed bug in gen_attention_mask with len > max_len (#158)
3a94209
Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)
9169bfd
Add error message for "gene" embedding extraction under development.
65b4915
Christina Theodoris
commited on
Update README.md
e820326
Rename heatmap legend to be correct label
badcca6
Christina Theodoris
commited on
Add function to extract and plot cell embeddings
d154fee
Christina Theodoris
commited on
Add fine-tuned CellClassifier for cardiomyopathy
1786b44
Christina Theodoris
commited on
Add error for no files found and suppress loompy import warning
abdf980
Christina Theodoris
commited on
Add sorting for aggregating data for goal state shifts
50e921d
Christina Theodoris
commited on
Fix min_genes to be >= tokens to perturb as a group
268e566
Christina Theodoris
commited on
Update tokenizer to allow tokenization without custom cell attributes
57b9778
Christina Theodoris
commited on
Update isp to allow modeling single perturbation in multiple cells as batches
acd253c
Christina Theodoris
commited on
Change list of individual IDs to set to ensure unique before subsetting into train/valid/test sets
45b9d69
Christina Theodoris
commited on
Update internal format of anchor token to list for consistency with genes to perturb
b36d210
Christina Theodoris
commited on
Add filtering for start state cells prior to in silico perturbation when modeling cell states
bb217cf
Christina Theodoris
commited on
Correct order of state dict in in silico perturber stats and tensor dims of alt state emb in in silico perturber
3d06203
Christina Theodoris
commited on
Add explanation of output columns and sort by largest shift
3072225
Christina Theodoris
commited on
Add note to recommend tuning hyperparameters for downstream applications
98ce6d7
Christina Theodoris
commited on
Add instructions to convert gene annotations w/ Ensembl Biomart
77eb432
Christina Theodoris
commited on
Update manuscript link to SharedIt
4f6115b
Update manuscript link in model card to ShareIt
dd016da
Modify tokenizer to allow renaming attr names btwn loom and .dataset
e78c44d
Christina Theodoris
commited on
Modify quant_layers to convert layer nums to integers before calculating max
2181aa4
Christina Theodoris
commited on
Remove unused evalset variable from cell classification example
879a878
Christina Theodoris
commited on
Modify documentation for modeling only 2 cell states
019165f
Christina Theodoris
commited on
Add instructions for modeling only 2 states and modify stats script for that option
912860d
Christina Theodoris
commited on
Update links including unsorted example lengths file
f0b6641
Christina Theodoris
commited on
Add function to create remainder emb for in silico overexpression batch
feeecd0
Christina Theodoris
commited on
Add mixture model option for gene-gene interaction stats
dc1481d
Christina Theodoris
commited on
Add uniform max len for padding for predictions
67f674c
Christina Theodoris
commited on
Add stats with mixture model to determine whether test perturbation is in impact component
d20ad0a
Christina Theodoris
commited on
Update model card for 12 layer Geneformer model
0637325
Update model card for 12 layer Geneformer
514c5fb
Upload 12 layer Geneformer model
9d41e70
Fix bug in clearing cache
8c2fae7
Christina Theodoris
commited on
Add example code for obtaining non-zero median digests
67b7f01
Christina Theodoris
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Update model card with license Apache 2.0
99b9a0a
Fix filter_data to allow value of None for no filtering
5fcf2b8
Christina Theodoris
commited on
Add further explanation regarding input file format for transcriptome tokenizer
c34ead6
Christina Theodoris
commited on
Update instructions in tokenizing example to clarify requirement for Ensembl ID
d468697
Christina Theodoris
commited on
Update instructions in tokenizing example to clarify requirement for Ensembl ID
e606e1c
Christina Theodoris
commited on
Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error
78dd83b
Christina Theodoris
commited on
Move example input files to dataset repository to include example datasets for fine-tuning
875ef33
Christina Theodoris
commited on
Update model card with information about fine-tuning
0a8c47b
Add example for tokenizing .loom dataset
f89f796
Christina Theodoris
commited on
Update gene classification example to create directory after training arguments are defined
ebe5ee8
Christina Theodoris
commited on