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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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Include all observations from the sciplex data
#65
MxMstrmn
closed
2 years ago
4
EXP: Experiment with very large models on LINCS
#64
siboehm
closed
2 years ago
3
Check for nans/infs in rdkit embedding and normalise features
#63
MxMstrmn
closed
2 years ago
2
Architecture surgery for transfer experiements
#62
MxMstrmn
closed
2 years ago
2
Remove Trapnell subsampling
#61
siboehm
closed
2 years ago
0
Adjust sweeps for better adv loss
#60
siboehm
closed
2 years ago
1
Transfer learning code
#59
siboehm
closed
2 years ago
9
Update noteboks
#58
MxMstrmn
closed
2 years ago
4
Adjust adversarial parameters
#57
siboehm
closed
2 years ago
3
Adjust RDKit embeddings
#56
siboehm
closed
2 years ago
5
LINCS Trapnell gene overlap
#55
siboehm
closed
2 years ago
1
Small changes to LINCS config
#54
siboehm
closed
2 years ago
1
Exclude DMSO perturbation when running r2 eval
#53
siboehm
closed
2 years ago
1
Check differentially expressed genes
#52
siboehm
closed
2 years ago
2
Fix control + (+)-JQ1
#51
siboehm
closed
2 years ago
3
Add notebooks to align genes in sciplex and lincs datasets
#50
MxMstrmn
closed
2 years ago
2
This adds the JunctionTree VAE
#49
siboehm
closed
2 years ago
1
Fix NaNs
#48
siboehm
closed
2 years ago
3
Deal with apparent NaNs during eval
#47
siboehm
closed
2 years ago
3
Add rdkit embedding
#46
MxMstrmn
closed
2 years ago
0
Stop training early on NaNs
#45
siboehm
closed
2 years ago
2
Implement early stopping on NaN
#44
siboehm
closed
2 years ago
0
Add amortized doser
#43
siboehm
closed
2 years ago
0
Check LINCS splits
#42
siboehm
closed
2 years ago
3
Calc disentanglement loss on GPU
#41
siboehm
closed
2 years ago
0
Improve model saving
#40
siboehm
closed
2 years ago
0
Faster disentangle
#39
siboehm
closed
2 years ago
1
Add profiling
#38
siboehm
closed
2 years ago
2
Delete some code
#37
siboehm
closed
2 years ago
0
First runs with GROVER
#36
siboehm
closed
2 years ago
0
Speeding up evaluation on LINCS
#35
siboehm
closed
2 years ago
3
Deal with different genes in LINCS vs Trapnell during transfer learning
#34
siboehm
closed
2 years ago
3
Add gnn embeddings from pretraing models (dgl)
#33
MxMstrmn
closed
2 years ago
2
Add Seq2seq embedding
#32
siboehm
closed
2 years ago
1
Generate & use once-canonical SMILES
#31
siboehm
closed
2 years ago
2
Figure out canoncialization
#30
siboehm
closed
2 years ago
3
Add more Embeddings
#29
siboehm
closed
2 years ago
4
Delete unused code
#28
siboehm
closed
2 years ago
0
Setup finetuning workflow
#27
siboehm
closed
2 years ago
1
Add class imbalance to BCE loss.
#26
siboehm
closed
2 years ago
0
Check that SMILES are canonical
#25
MxMstrmn
closed
2 years ago
2
Add chemical representation
#24
siboehm
closed
2 years ago
3
Remove the one hot encoding
#23
siboehm
closed
2 years ago
1
Adapt Adversarial predictor for large number of classes
#22
siboehm
closed
2 years ago
5
Add Grover
#21
siboehm
closed
2 years ago
2
Remove One-Hot-Encoding
#20
siboehm
closed
2 years ago
2
GPU Evaluation
#19
siboehm
closed
2 years ago
1
Add a `environment.yml`
#18
siboehm
closed
2 years ago
0
Reduce time spent on evaluation during training
#17
siboehm
closed
2 years ago
4
Meta Class for Predictor
#16
siboehm
closed
2 years ago
1
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