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theislab
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chemCPA
Code for "Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution", NeurIPS 2022.
https://arxiv.org/abs/2204.13545
MIT License
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Provide dataset to run an individual training round
#115
ggonzalezp
closed
10 months ago
2
question about reproducing the result
#114
huawen-poppy
closed
1 year ago
2
fail in running the rdkit hparam for lincs
#113
huawen-poppy
closed
1 year ago
2
How to calculate the uncertainty
#112
tuln128
closed
1 year ago
2
Usage of control cell gene expression in evaluation of chemCPA
#111
Dean-98543
closed
1 year ago
9
what's the differences between lincs_full.h5ad and lincs.h5ad?
#110
huawen-poppy
closed
1 year ago
3
Fold-change prediction on novel SMILES
#109
michal-pikusa
closed
1 year ago
3
Finetuning to SciPlex dataset.
#108
reem12345
closed
1 year ago
4
Neurips Update
#107
MxMstrmn
closed
1 year ago
2
Can not find “lincs_full.h5ad” file
#106
Dean-98543
closed
1 year ago
4
Creating chemCPA environemnt
#105
v-mahughes
closed
1 year ago
2
Theislab/neaten experiments folder
#104
MxMstrmn
closed
2 years ago
0
Data/neaten notebooks
#103
MxMstrmn
closed
2 years ago
1
Data/neaten preprocessing
#102
MxMstrmn
closed
2 years ago
1
Delete pp notebooks
#101
MxMstrmn
closed
2 years ago
1
Add figure notebooks
#100
MxMstrmn
closed
2 years ago
1
Get ready for publishing
#99
siboehm
closed
2 years ago
1
Get things ready for publication
#98
siboehm
closed
2 years ago
3
Separate adversary regularisation and make eval modular
#97
MxMstrmn
closed
2 years ago
2
BUG: Transfer of covariate embedding is broken
#96
siboehm
closed
2 years ago
1
Add code for covariate embedding state dict saving
#95
siboehm
closed
2 years ago
1
Add single loss evaluation
#94
MxMstrmn
closed
2 years ago
1
Add Chemical VAE
#93
siboehm
closed
2 years ago
2
Add notebook for loading models and low-dim UMAP embeddings
#92
siboehm
closed
2 years ago
2
Add ability to add layers (extended gene set finetuning)
#91
siboehm
closed
2 years ago
2
Evaluation: Add `evaluate_r2_sc` on per-cell level
#90
siboehm
closed
2 years ago
0
Properly calculate covariate disentanglement
#89
siboehm
closed
2 years ago
1
Add all zero embedding
#88
siboehm
closed
2 years ago
0
Sweep `sciplex_hparam`
#87
MxMstrmn
closed
2 years ago
4
Hparam sweep for finetuning parameters (`sciplex_hparam`)
#86
siboehm
closed
2 years ago
4
EXP: `finetuning_OOD_prediction`
#85
MxMstrmn
closed
2 years ago
2
EXP `finetuning_num_genes`
#84
MxMstrmn
closed
2 years ago
5
Calculate correlation betw. good reconstruction score & low disentanglement score
#83
siboehm
closed
2 years ago
2
EXP: "meaningfulness" of CCPAs low-dimensional embeddings
#82
siboehm
closed
2 years ago
0
Create 3 ood splits that exclude drugs of 3 different pathways
#81
MxMstrmn
closed
2 years ago
3
EXP: Clustering of low-dim drug embeddings (after drug embedder transformation) `drug_emb_ld_clustering`
#80
siboehm
closed
2 years ago
2
EXP `lincs_rdkit_hparam`
#79
siboehm
closed
2 years ago
9
Generate new Trapnell datasets with a large set of genes
#78
siboehm
closed
2 years ago
2
Generate Trapnell & LINCS splits for OOD drugs for each pathway
#77
siboehm
closed
2 years ago
1
EXP: Usefullness of LINCS pretraining for gene set expansion (`finetuning_num_genes`)
#76
siboehm
closed
2 years ago
2
EXP: OOD drug prediction (w/o pretraining)
#75
siboehm
closed
2 years ago
0
Fix DE genes for sciplex dataset dependent on available genes
#74
MxMstrmn
closed
2 years ago
1
Add notebook & csvs for Trapnell sim
#73
siboehm
closed
2 years ago
1
Make disentanglement model non-linear
#72
siboehm
closed
2 years ago
1
Add ChemicalVAE (following Aspuru Guzik)
#71
siboehm
closed
2 years ago
0
Repair the DE genes on the new large Trapnell dataset
#70
siboehm
closed
2 years ago
2
EXP: Better Sweeps on LINCS (`lincs_rdkit_hparam`)
#69
siboehm
closed
2 years ago
5
EXP: Make drug embedder bigger
#68
MxMstrmn
closed
2 years ago
2
EXP: OOD single cell drug prediction `finetuning_OOD_prediction`
#67
siboehm
closed
2 years ago
6
EXP: Drug embeddings show stronger disentanglement (`chemical_emb_disentangle`)
#66
MxMstrmn
closed
2 years ago
8
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