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AJResearchGroup
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nsphs_ml_qt
R package for nsphs_ml_qt
GNU General Public License v3.0
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[RUNNING] What does GCAE converge to? Why to a NMSE of 1?
#61
richelbilderbeek
opened
2 years ago
24
Plot NMSE versus r_squared
#60
richelbilderbeek
opened
2 years ago
0
[RUNNING] Partially re-run 42
#59
richelbilderbeek
opened
2 years ago
10
No matches found for 'gcae_experiment_params_filename'
#58
richelbilderbeek
opened
2 years ago
0
Do Keras demos on Rackham
#57
richelbilderbeek
closed
2 years ago
0
Run with autoencoder-only for 2,3,5,10,25
#56
richelbilderbeek
opened
2 years ago
0
Do autoencode-only with latent layer of 3 neurons
#55
richelbilderbeek
opened
2 years ago
6
Plot in delta-AUC
#54
richelbilderbeek
closed
2 years ago
3
Plot in R2
#53
richelbilderbeek
closed
2 years ago
7
Plot end of phenotype predictions
#52
richelbilderbeek
closed
2 years ago
2
What is the relation between genotype concordance and R2?
#51
richelbilderbeek
opened
2 years ago
0
[RUNNING] Do a long run with M3d and p1
#50
richelbilderbeek
opened
2 years ago
4
Determine if a SNP is kept in the autoencoder when used for prediction
#49
richelbilderbeek
opened
2 years ago
0
Compare with regular prediction: UMAP and linear regression
#48
richelbilderbeek
closed
2 years ago
1
Compare with regular prediction: PLINK PCA and fit linearly
#47
richelbilderbeek
closed
2 years ago
1
Compare with regular prediction: PLINK assoc_qt and betas
#46
richelbilderbeek
opened
2 years ago
0
[RUNNING] Filter out M and p models that do not work
#45
richelbilderbeek
closed
2 years ago
5
Change the `trainingdir`
#44
richelbilderbeek
closed
2 years ago
0
Allow parameters to store more info
#43
richelbilderbeek
closed
2 years ago
0
[RUNNING] Do a run on the many-SNPs data with for all combinations of autoencoder and phenotypic models
#42
richelbilderbeek
closed
2 years ago
34
Do a run on the many-SNPs data with only autoencoder functionality for all models
#41
richelbilderbeek
opened
2 years ago
0
Notes meeting Daniil 2022-05-12
#40
richelbilderbeek
opened
2 years ago
0
Completely separate internal/training and external/validation sets
#39
richelbilderbeek
opened
2 years ago
0
Do a SNP injection, to see if NN has learned genotypes
#38
richelbilderbeek
opened
2 years ago
1
Compare with regular prediction: latent layer and linear regression
#37
richelbilderbeek
opened
2 years ago
0
Compare with regular prediction: UMAP and linear regression
#36
richelbilderbeek
opened
2 years ago
0
Fix zipping
#35
richelbilderbeek
opened
2 years ago
1
Compare with regular prediction: PLINK PCA and fit linearly
#34
richelbilderbeek
opened
2 years ago
0
Always plot the distribution of the phenotype input data
#33
richelbilderbeek
closed
2 years ago
6
Remove GenoCAE folder from starter zip
#32
richelbilderbeek
closed
2 years ago
0
Remove labels
#31
richelbilderbeek
closed
2 years ago
2
Always do a PLINK analysis on the data
#30
richelbilderbeek
closed
2 years ago
8
[RUNNING] Run with IL17-RA, as the biomarker has (1 primary and) 6 conditional cis signals
#29
richelbilderbeek
closed
2 years ago
18
[RUNNING] Use window of 10k, 100k and 1Mb around SNP from #5
#28
richelbilderbeek
closed
2 years ago
42
Do PLINK analysis on subset data of #5
#27
richelbilderbeek
closed
2 years ago
1
Create nsphs_ml_qt.sif
#26
richelbilderbeek
closed
2 years ago
5
Fake Bianca
#25
richelbilderbeek
opened
2 years ago
0
Extract subset of SNPs
#24
richelbilderbeek
closed
2 years ago
5
sbatch: error: Invalid directive found in batch script: defined
#23
richelbilderbeek
closed
2 years ago
1
Feedback Daniil
#22
richelbilderbeek
closed
2 years ago
1
Plot the phenotype prediction through time
#21
richelbilderbeek
closed
2 years ago
2
Measure NMSE through time
#20
richelbilderbeek
closed
2 years ago
1
Allow save/load of gcaer params
#19
richelbilderbeek
closed
2 years ago
1
Do full workflow with gcaer
#18
richelbilderbeek
closed
2 years ago
8
Devise measure of trait prediction quality: NMSE
#17
richelbilderbeek
closed
2 years ago
2
Copy autoencoder models into Singularity container
#16
richelbilderbeek
closed
2 years ago
1
Create phenotypic models with different number of neurons in latent layer
#15
richelbilderbeek
closed
2 years ago
2
Analyse 100k SNP run on Bianca
#14
richelbilderbeek
closed
2 years ago
3
Run NSPHS for 100, 1k, 10k and 100k random SNPs on Bianca
#13
richelbilderbeek
closed
2 years ago
1
Run simple settings with different autoencoder neural network settings
#12
richelbilderbeek
closed
2 years ago
4
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