Commit History
Add option to output embs as tensor
624349c
Christina Theodoris
commited on
anndata_tokenizer (#170)
4302f48
Fixed bugs related to overexpressing genes (#229)
39ab62e
Add memory-efficient method for computing emb summary statistics
6caf480
Christina Theodoris
commited on
Fixed bug with the double removing of indices when cell_states_to_model is false (#188)
0adfe67
Upload in_silico_perturber.py (#187)
8180caa
Added feature to perturb a set of indices to help with debugging and with very large runtimes (#175)
f115e8f
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
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 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
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
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
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
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 stats with mixture model to determine whether test perturbation is in impact component
d20ad0a
Christina Theodoris
commited on
Fix bug in clearing cache
8c2fae7
Christina Theodoris
commited on
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
Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error
78dd83b
Christina Theodoris
commited on
Subclass collator for cell classification
402ba9b
Christina Theodoris
commited on
Update pretrainer for transformers==4.28.0
b925dcc
Christina Theodoris
commited on
Upload gene_name_id_dict.pkl (#14)
8ce598f
Fixes to stats and adding gene dict attempt number 2 (#13)
42e9bf9
Rename isp stats methods to clarify mode.
188029e
Reorder/sort isp stats output in vs_null mode
f4fea1e
add in silico perturbation module
d4fe544
Christina Theodoris
commited on
add in silico perturbation module
efec1c4
Christina Theodoris
commited on
Add gene name : Ensembl ID dictionary
09276dd
Fix bug with metadata when processing multiple .loom files (#3)
044d737
Update token_dictionary.pkl
1987df4
Delete geneformer/token_dictionary.pkl
870b99b
Add data collator for gene classification and example for gene classification
edacd12
Christina Theodoris
commited on
Add data collator for cell classification and example for cell classification
088ea6e
Christina Theodoris
commited on