Geneformer / geneformer

Commit History

Fixed bugs related to overexpressing genes
72c6501

davidjwen commited on

Fixed bug with the double removing of indices when cell_states_to_model is false (#188)
0adfe67

ctheodoris davidjwen commited on

Added feature to perturb a set of indices to help with debugging and with very large runtimes (#175)
f115e8f

ctheodoris davidjwen commited on

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

ctheodoris commited on

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)
9169bfd

ctheodoris davidjwen commited on

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

Fixes to stats and adding gene dict attempt number 2 (#13)
42e9bf9

ctheodoris commited on

Rename isp stats methods to clarify mode.
188029e

ctheodoris commited on

Reorder/sort isp stats output in vs_null mode
f4fea1e

ctheodoris commited on

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

ctheodoris commited on

Fix bug with metadata when processing multiple .loom files (#3)
044d737

ctheodoris davidjwen commited on

Update token_dictionary.pkl
1987df4

ctheodoris commited on

Delete geneformer/token_dictionary.pkl
870b99b

ctheodoris commited on

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

Add Geneformer trainer and pretraining example
bcc03e8

Christina Theodoris commited on

Add Geneformer tokenizer and updated model card
5426788

Christina Theodoris commited on