Geneformer / geneformer /in_silico_perturber.py

Commit History

precommit formatting
f07bfd7

ctheodoris commited on

update with 12L and 20L i4096 gc95M models, multitask and quantiz code
933ca80

ctheodoris commited on

add typing list import
42053dc

ctheodoris commited on

move dicts to init
ea428cb

ctheodoris commited on

update get_embs with token_gene_dict arg
ace12e9
verified

ctheodoris commited on

fix cell state gene embeddings bug (#345)
c0e7b19
verified

ctheodoris commited on

add load model for train and fix validate anchor gene error
0d675a3

Christina Theodoris commited on

Handle case of single gene del for isp modeling of gene embs
316d817

Christina Theodoris commited on

edit docstring codeblock highlighting
d1931b1

Christina Theodoris commited on

change doc formatting
17f036a

Christina Theodoris commited on

add sphinx docs
2a0dcbe

Christina Theodoris commited on

update dependencies, reinstate compatibility with python<3.9 with typing for List
10d3f10

Christina Theodoris commited on

Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp
2f25aea

Christina Theodoris commited on

Add option to output embs as tensor
624349c

Christina Theodoris 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

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 function to extract and plot cell embeddings
d154fee

Christina Theodoris commited on

Fix min_genes to be >= tokens to perturb as a group
268e566

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

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

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 in silico perturbation module
efec1c4

Christina Theodoris commited on