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Development #67

Merged
merged 64 commits into from
Dec 18, 2023
Merged

Development #67

merged 64 commits into from
Dec 18, 2023

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jyaacoub
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@jyaacoub jyaacoub commented Dec 6, 2023

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@jyaacoub
results: davis protein kinase families #57
8e2506e
@jyaacoub
fix: sorted histplot for davis kinase families #57
5a8c306
@jyaacoub
fix(figures): added save code for combined violin
c69a38a
@jyaacoub
fix(dataset): RAISE exception missing fixed
7903d11
@jyaacoub
style(loader): less confusing naming for subsets
9225cce
@jyaacoub
feat(test.py): + save_predictions option
1fdba9e
@jyaacoub
results(davis): save predictions for DG model #57
b879cc6
@jyaacoub
results(davis): predictions EDI2-4
e4f0d20
@jyaacoub
results(davis): predictions EDI1-2
6d23697
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
ff93829 
… development
@jyaacoub
feat(stratify_protein): plots for #57
0f785c5
@jyaacoub
fix!: deprecate old train_val_test_split_kfold
2845292
@jyaacoub
feat(test): + --save_train argument
328621c
@jyaacoub
results: train pred EDI
ca5c0f8
@jyaacoub
results: train pred EDI0-1
aa553e4
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
d72e727 
… development
@jyaacoub
results: SPDM_davis0-2,4 narval
42f91c8
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
30a6a2f 
… development
@jyaacoub
fix(figures): prepare_df updated for foldseek #53
59ea267
@jyaacoub
style(test): informative save_pred args
3789d2f
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
21225b0 
… development
@jyaacoub
fix(test): update args call to save_pred_train
1fa782d
@jyaacoub
feat: clustring with mmseq2 #57
4daf011
@jyaacoub
results(kiba): predictions on Kiba #57
6ad1512
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
8783554 
… development
@jyaacoub
results(kiba): predictions on Kiba-EDI #57
7dbc5c2
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
0e20711 
… development
@jyaacoub
feat(raytune): init tuner for simple models
73b4d56
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
e3205cb 
… development
@jyaacoub
fix(tune): undef train_loss
f8f80f6
@jyaacoub
results(prot_strat): cluster stats
648dc80
@jyaacoub
fix: print num proteins and list in each clust #57
ac971ed
@jyaacoub
feat(rayTune_DDP): init RayTune env for DDP #68
67370ae
@jyaacoub
results(rayTune): tuned DGM on davis #68
aaffc34
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
0665f96 
… development
@jyaacoub
feat(prepare_df): parse lr and dropout
9f66e6d
@jyaacoub
results: davis train pred by DG #57
4d0854f
@jyaacoub
Merge branch 'development' of https://github.com/jyaacoub/MutDTA into…
93e1c84 
… development
@jyaacoub
results(prot_counts): Davis and kiba clusters #57
039beb3
@jyaacoub
feat(rayTune): using rayTrain for DDP instead #68
54960ac
@jyaacoub
fix(RayTeain): param_space is for PARAMS of the trainer (duh) #68
514c79c
@jyaacoub
fix: cuda mismatch, need torch==1.12.1
2dc9a6d
@jyaacoub
fix: send to default device pytorch
e549390
@jyaacoub
fix: get device from session #68
1bb8d45
@jyaacoub
fix(rayTrain): float has no attribute .item() #68
f58d614
@jyaacoub
fix(raytune_DDP): algo not defined #68
d58fcee
@jyaacoub
fix(SaProt): added dropout to gnn and extra fc
c3666f5 
This is initialized by superclass EsmDTA model
@jyaacoub
feat(rayTrainTune): updated search space for SPD #68
2f85c7f
@jyaacoub
fix(rayTrain): scaling config args #68
1f1cd72
@jyaacoub
fix(config): use absolute paths
ecf586c
@jyaacoub
style: print config info before run #68
c143c4b
@jyaacoub
fix(SaProt): explicitly define num_nodes for dropout_node for GCN #68
7bd318f
@jyaacoub
fix: rm dropout
7917602
@jyaacoub
temp fix
3400292
@jyaacoub
fix(SPD): SPD REQUIRES FOLDSEEK features #68
b197c96
@jyaacoub
feat(SPD): force extra fc layer for protein
ae9aa8a 
From Tuning this consistently improved model performance
@jyaacoub
feat(arg_parse): added dropout_prot and pro_emb_dim
e85aaa1
@jyaacoub
fix(arg_parse) unkown action 'stor'
c1137a6
@jyaacoub jyaacoub linked an issue Dec 18, 2023 that may be closed by this pull request
Implement RayTune for DDP #68
Closed
@jyaacoub jyaacoub merged commit 94b3048 into main Dec 18, 2023
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Implement RayTune for DDP
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@jyaacoub