ynuozhang
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Commit
·
43ed8e5
1
Parent(s):
df85e24
update new models
Browse filesThis view is limited to 50 files because it contains too many changes.
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- training_classifiers/half_life/cnn_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/cnn_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/cnn_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/cnn_unpooled_smiles/best_model.pt +3 -0
- training_classifiers/half_life/cnn_unpooled_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/cnn_unpooled_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/cnn_unpooled_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/{enet_smiles → enet_gpu_smiles}/best_model.joblib +0 -0
- training_classifiers/half_life/enet_gpu_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/enet_gpu_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/enet_gpu_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/mlp_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/mlp_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/mlp_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/mlp_unpooled_smiles/best_model.pt +3 -0
- training_classifiers/half_life/mlp_unpooled_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/mlp_unpooled_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/mlp_unpooled_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/{svr_smiles → svr_gpu_smiles}/best_model.joblib +0 -0
- training_classifiers/half_life/svr_gpu_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/svr_gpu_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/svr_gpu_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/transformer_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/transformer_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/transformer_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/transformer_unpooled_smiles/best_model.pt +3 -0
- training_classifiers/half_life/transformer_unpooled_smiles/cv_fold_metrics.csv +3 -0
- training_classifiers/half_life/transformer_unpooled_smiles/cv_oof_predictions.csv +3 -0
- training_classifiers/half_life/transformer_unpooled_smiles/cv_oof_summary.json +5 -0
- training_classifiers/half_life/transformer_wt_log/best_model.pt +3 -0
- training_classifiers/half_life/transformer_wt_log/best_params.json +6 -0
- training_classifiers/half_life/transformer_wt_log/cv_fold_reports.json +73 -0
- training_classifiers/half_life/transformer_wt_log/final_model_benchmark.json +39 -0
- training_classifiers/half_life/transformer_wt_log/oof_pred_vs_true.png +0 -0
- training_classifiers/half_life/transformer_wt_log/oof_predictions.csv +3 -0
- training_classifiers/half_life/transformer_wt_log/oof_residual_hist.png +0 -0
- training_classifiers/half_life/transformer_wt_log/oof_residual_vs_pred.png +0 -0
- training_classifiers/half_life/transformer_wt_log/optimization_summary.txt +33 -0
- training_classifiers/half_life/{xgb_wt → transformer_wt_log}/study_trials.csv +2 -2
- training_classifiers/half_life/transformer_wt_raw/best_model.pt +3 -0
- training_classifiers/half_life/transformer_wt_raw/best_params.json +6 -0
- training_classifiers/half_life/transformer_wt_raw/cv_fold_reports.json +73 -0
- training_classifiers/half_life/transformer_wt_raw/final_model_benchmark.json +39 -0
- training_classifiers/half_life/transformer_wt_raw/oof_pred_vs_true.png +0 -0
- training_classifiers/half_life/transformer_wt_raw/oof_predictions.csv +3 -0
- training_classifiers/half_life/transformer_wt_raw/oof_residual_hist.png +0 -0
- training_classifiers/half_life/transformer_wt_raw/oof_residual_vs_pred.png +0 -0
- training_classifiers/half_life/transformer_wt_raw/optimization_summary.txt +33 -0
- training_classifiers/half_life/transformer_wt_raw/study_trials.csv +3 -0
- training_classifiers/half_life/xgb_smiles/cv_fold_metrics.csv +3 -0
training_classifiers/half_life/cnn_smiles/cv_fold_metrics.csv
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size 338
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training_classifiers/half_life/cnn_smiles/cv_oof_predictions.csv
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size 13748
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training_classifiers/half_life/cnn_smiles/cv_oof_summary.json
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{
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"rmse": 12.29292849687051,
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"r2": 0.4231074242264117,
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"spearman": 0.5538544385243245
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}
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training_classifiers/half_life/cnn_unpooled_smiles/best_model.pt
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size 16525563
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training_classifiers/half_life/cnn_unpooled_smiles/cv_fold_metrics.csv
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size 343
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training_classifiers/half_life/cnn_unpooled_smiles/cv_oof_predictions.csv
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size 13705
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training_classifiers/half_life/cnn_unpooled_smiles/cv_oof_summary.json
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{
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"rmse": 20.300619293077894,
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"r2": -0.5732683735737854,
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"spearman": 0.46115584341635735
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}
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training_classifiers/half_life/{enet_smiles → enet_gpu_smiles}/best_model.joblib
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training_classifiers/half_life/enet_gpu_smiles/cv_fold_metrics.csv
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size 325
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training_classifiers/half_life/enet_gpu_smiles/cv_oof_predictions.csv
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size 13649
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training_classifiers/half_life/enet_gpu_smiles/cv_oof_summary.json
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{
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"rmse": 16.22447469657455,
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"r2": -0.0049062048184822515,
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"spearman": 0.42804994066462665
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}
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training_classifiers/half_life/mlp_smiles/cv_fold_metrics.csv
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size 342
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training_classifiers/half_life/mlp_smiles/cv_oof_predictions.csv
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size 13724
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training_classifiers/half_life/mlp_smiles/cv_oof_summary.json
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{
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"rmse": 14.71665917646266,
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"r2": 0.17319574457366238,
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"spearman": 0.5522206032780749
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}
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training_classifiers/half_life/mlp_unpooled_smiles/best_model.pt
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size 2368455
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training_classifiers/half_life/mlp_unpooled_smiles/cv_fold_metrics.csv
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size 350
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training_classifiers/half_life/mlp_unpooled_smiles/cv_oof_predictions.csv
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size 13745
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training_classifiers/half_life/mlp_unpooled_smiles/cv_oof_summary.json
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{
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"rmse": 16.337643510468396,
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"r2": -0.018973922742636873,
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"spearman": 0.4671870079986837
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}
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training_classifiers/half_life/{svr_smiles → svr_gpu_smiles}/best_model.joblib
RENAMED
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training_classifiers/half_life/svr_gpu_smiles/cv_fold_metrics.csv
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size 322
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training_classifiers/half_life/svr_gpu_smiles/cv_oof_predictions.csv
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size 13746
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training_classifiers/half_life/svr_gpu_smiles/cv_oof_summary.json
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"spearman": 0.4912202789443222
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training_classifiers/half_life/transformer_smiles/cv_fold_metrics.csv
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size 344
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training_classifiers/half_life/transformer_smiles/cv_oof_predictions.csv
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size 13694
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training_classifiers/half_life/transformer_smiles/cv_oof_summary.json
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{
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"rmse": 15.394577527810586,
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"spearman": 0.47733675985880863
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training_classifiers/half_life/transformer_unpooled_smiles/best_model.pt
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training_classifiers/half_life/transformer_unpooled_smiles/cv_fold_metrics.csv
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size 343
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training_classifiers/half_life/transformer_unpooled_smiles/cv_oof_predictions.csv
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size 13683
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training_classifiers/half_life/transformer_unpooled_smiles/cv_oof_summary.json
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{
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"spearman": 0.46445104717472613
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training_classifiers/half_life/transformer_wt_log/best_model.pt
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size 5923915
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training_classifiers/half_life/transformer_wt_log/best_params.json
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{
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"lr": 0.0003603824115240561,
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"weight_decay": 2.9442493502916885e-09,
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"dropout": 0.3851371373367485,
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"batch_size": 16
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}
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training_classifiers/half_life/transformer_wt_log/cv_fold_reports.json
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{
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"folds": [
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{
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"fold": 1,
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"val_size": 26,
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"score": 0.7069292577972689,
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"metrics": {
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| 12 |
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| 13 |
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|
| 14 |
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| 15 |
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{
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| 16 |
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|
| 17 |
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|
| 18 |
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| 19 |
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| 20 |
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| 24 |
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| 25 |
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|
| 26 |
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| 27 |
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|
| 28 |
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"fold": 3,
|
| 29 |
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|
| 30 |
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|
| 31 |
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"metrics": {
|
| 32 |
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"rmse": 1.2359933853149414,
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| 33 |
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| 34 |
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|
| 35 |
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|
| 36 |
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|
| 37 |
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|
| 38 |
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|
| 39 |
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{
|
| 40 |
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|
| 41 |
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|
| 42 |
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|
| 43 |
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"metrics": {
|
| 44 |
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|
| 48 |
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| 49 |
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|
| 50 |
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|
| 51 |
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{
|
| 52 |
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"fold": 5,
|
| 53 |
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"val_size": 26,
|
| 54 |
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|
| 55 |
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| 56 |
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|
| 60 |
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| 61 |
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|
| 62 |
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|
| 63 |
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|
| 64 |
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"oof": {
|
| 65 |
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"score": 0.5818272477094295,
|
| 66 |
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"metrics": {
|
| 67 |
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|
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"spearman_rho": 0.5818272477094295
|
| 71 |
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}
|
| 72 |
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}
|
| 73 |
+
}
|
training_classifiers/half_life/transformer_wt_log/final_model_benchmark.json
ADDED
|
@@ -0,0 +1,39 @@
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|
| 1 |
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{
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| 2 |
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|
| 3 |
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| 4 |
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|
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| 11 |
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|
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|
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|
| 15 |
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|
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|
| 18 |
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|
| 19 |
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|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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},
|
| 24 |
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|
| 25 |
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|
| 26 |
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|
| 27 |
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|
| 28 |
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|
| 29 |
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|
| 30 |
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| 31 |
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|
| 32 |
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|
| 33 |
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"gpu_mem_total_MB": 49140.0,
|
| 34 |
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"gpu_sm_clock_MHz": 210,
|
| 35 |
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"gpu_mem_clock_MHz": 405,
|
| 36 |
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"gpu_power_W": 22.767,
|
| 37 |
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"gpu_temp_C": 29
|
| 38 |
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}
|
| 39 |
+
}
|
training_classifiers/half_life/transformer_wt_log/oof_pred_vs_true.png
ADDED
|
training_classifiers/half_life/transformer_wt_log/oof_predictions.csv
ADDED
|
@@ -0,0 +1,3 @@
|
|
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|
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|
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|
|
|
|
| 1 |
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version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:8ec7b8dee908ef43ba7633a887a988834e24f952711b906472e1b41b833de714
|
| 3 |
+
size 14100
|
training_classifiers/half_life/transformer_wt_log/oof_residual_hist.png
ADDED
|
training_classifiers/half_life/transformer_wt_log/oof_residual_vs_pred.png
ADDED
|
training_classifiers/half_life/transformer_wt_log/optimization_summary.txt
ADDED
|
@@ -0,0 +1,33 @@
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|
|
|
|
|
| 1 |
+
========================================================================
|
| 2 |
+
MODEL: transformer
|
| 3 |
+
Dataset: /scratch/pranamlab/tong/data/halflife/halflife_embedding_unpooled
|
| 4 |
+
Target column: log_label
|
| 5 |
+
CV folds: 5
|
| 6 |
+
Optuna objective: spearman (direction=maximize)
|
| 7 |
+
Best trial: 45
|
| 8 |
+
OOF metrics:
|
| 9 |
+
{
|
| 10 |
+
"rmse": 1.0389505624771118,
|
| 11 |
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"mae": 0.722099244594574,
|
| 12 |
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"r2": 0.30950748920440674,
|
| 13 |
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"spearman_rho": 0.5818272477094295
|
| 14 |
+
}
|
| 15 |
+
OOF score (spearman): 0.581827
|
| 16 |
+
Best params:
|
| 17 |
+
{
|
| 18 |
+
"lr": 0.0003603824115240561,
|
| 19 |
+
"weight_decay": 2.9442493502916885e-09,
|
| 20 |
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"dropout": 0.3851371373367485,
|
| 21 |
+
"batch_size": 16
|
| 22 |
+
}
|
| 23 |
+
Final refit epochs (all data): 15
|
| 24 |
+
Saved final model: /scratch/pranamlab/tong/PeptiVerse/src/halflife/finetune_stability_transformer/final_model.pt
|
| 25 |
+
Benchmark (final model on full data):
|
| 26 |
+
{
|
| 27 |
+
"n_samples": 130,
|
| 28 |
+
"wall_time_s": 1.9577592574059963,
|
| 29 |
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"throughput_samples_per_s": 66.40244427818372,
|
| 30 |
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"gpu_ms_per_sample": 0.28296443315652703,
|
| 31 |
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"gpu_peak_mem_MB": 77.5693359375
|
| 32 |
+
}
|
| 33 |
+
========================================================================
|
training_classifiers/half_life/{xgb_wt → transformer_wt_log}/study_trials.csv
RENAMED
|
@@ -1,3 +1,3 @@
|
|
| 1 |
version https://git-lfs.github.com/spec/v1
|
| 2 |
-
oid sha256:
|
| 3 |
-
size
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|
| 1 |
version https://git-lfs.github.com/spec/v1
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| 2 |
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oid sha256:5726f6b8541c7ca85eda9f0e526db0cb10156eadb2c440fd7a66f7a7d1209175
|
| 3 |
+
size 10154
|
training_classifiers/half_life/transformer_wt_raw/best_model.pt
ADDED
|
@@ -0,0 +1,3 @@
|
|
|
|
|
|
|
|
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|
|
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|
| 1 |
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version https://git-lfs.github.com/spec/v1
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|
| 3 |
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size 5923851
|
training_classifiers/half_life/transformer_wt_raw/best_params.json
ADDED
|
@@ -0,0 +1,6 @@
|
|
|
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|
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|
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|
| 1 |
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{
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| 2 |
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| 3 |
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|
| 4 |
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|
| 5 |
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"batch_size": 16
|
| 6 |
+
}
|
training_classifiers/half_life/transformer_wt_raw/cv_fold_reports.json
ADDED
|
@@ -0,0 +1,73 @@
|
|
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|
|
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|
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|
|
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|
|
|
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|
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|
|
|
|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
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{
|
| 2 |
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"folds": [
|
| 3 |
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{
|
| 4 |
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"fold": 1,
|
| 5 |
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"val_size": 26,
|
| 6 |
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"score": 0.6042773810600081,
|
| 7 |
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|
| 8 |
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|
| 9 |
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|
| 10 |
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|
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|
| 12 |
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},
|
| 13 |
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|
| 14 |
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},
|
| 15 |
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{
|
| 16 |
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"fold": 2,
|
| 17 |
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"val_size": 26,
|
| 18 |
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"score": 0.4960634572452323,
|
| 19 |
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"metrics": {
|
| 20 |
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|
| 21 |
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|
| 22 |
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|
| 23 |
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|
| 24 |
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},
|
| 25 |
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"best_epoch": 18
|
| 26 |
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},
|
| 27 |
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{
|
| 28 |
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"fold": 3,
|
| 29 |
+
"val_size": 26,
|
| 30 |
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"score": 0.35664216626559203,
|
| 31 |
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"metrics": {
|
| 32 |
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"rmse": 40.16226577758789,
|
| 33 |
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"mae": 16.82233428955078,
|
| 34 |
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"r2": -0.056325674057006836,
|
| 35 |
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|
| 36 |
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},
|
| 37 |
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"best_epoch": 15
|
| 38 |
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},
|
| 39 |
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{
|
| 40 |
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"fold": 4,
|
| 41 |
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"val_size": 26,
|
| 42 |
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"score": 0.32158748547360894,
|
| 43 |
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"metrics": {
|
| 44 |
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"rmse": 12.541864395141602,
|
| 45 |
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|
| 46 |
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|
| 47 |
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|
| 48 |
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},
|
| 49 |
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"best_epoch": 20
|
| 50 |
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},
|
| 51 |
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{
|
| 52 |
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"fold": 5,
|
| 53 |
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"val_size": 26,
|
| 54 |
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"score": 0.5868265620146739,
|
| 55 |
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"metrics": {
|
| 56 |
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"rmse": 19.025236129760742,
|
| 57 |
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"mae": 6.9760541915893555,
|
| 58 |
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"r2": -0.12794995307922363,
|
| 59 |
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"spearman_rho": 0.5868265620146739
|
| 60 |
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},
|
| 61 |
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"best_epoch": 1
|
| 62 |
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}
|
| 63 |
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],
|
| 64 |
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"oof": {
|
| 65 |
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"score": 0.3759734508605516,
|
| 66 |
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"metrics": {
|
| 67 |
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"rmse": 45.00321578979492,
|
| 68 |
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|
| 69 |
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"r2": 0.02070075273513794,
|
| 70 |
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"spearman_rho": 0.3759734508605516
|
| 71 |
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}
|
| 72 |
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}
|
| 73 |
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}
|
training_classifiers/half_life/transformer_wt_raw/final_model_benchmark.json
ADDED
|
@@ -0,0 +1,39 @@
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|
|
|
|
|
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|
|
|
|
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|
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|
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|
|
|
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|
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|
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|
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|
|
|
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|
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|
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|
|
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|
|
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|
| 1 |
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{
|
| 2 |
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"n_samples": 130,
|
| 3 |
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"wall_time_s": 1.6299039730802178,
|
| 4 |
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|
| 5 |
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|
| 6 |
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|
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|
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|
| 9 |
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|
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|
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|
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|
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|
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|
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|
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|
| 21 |
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|
| 22 |
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| 23 |
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},
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|
| 31 |
+
"gpu_mem_util_pct": 0,
|
| 32 |
+
"gpu_mem_used_MB": 632.125,
|
| 33 |
+
"gpu_mem_total_MB": 49140.0,
|
| 34 |
+
"gpu_sm_clock_MHz": 210,
|
| 35 |
+
"gpu_mem_clock_MHz": 405,
|
| 36 |
+
"gpu_power_W": 23.065,
|
| 37 |
+
"gpu_temp_C": 29
|
| 38 |
+
}
|
| 39 |
+
}
|
training_classifiers/half_life/transformer_wt_raw/oof_pred_vs_true.png
ADDED
|
training_classifiers/half_life/transformer_wt_raw/oof_predictions.csv
ADDED
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@@ -0,0 +1,3 @@
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| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:c3df70b094757f34fa380a28727877694fcb1ec367bbbef28c63b257ecec74e6
|
| 3 |
+
size 13516
|
training_classifiers/half_life/transformer_wt_raw/oof_residual_hist.png
ADDED
|
training_classifiers/half_life/transformer_wt_raw/oof_residual_vs_pred.png
ADDED
|
training_classifiers/half_life/transformer_wt_raw/optimization_summary.txt
ADDED
|
@@ -0,0 +1,33 @@
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|
| 1 |
+
========================================================================
|
| 2 |
+
MODEL: transformer
|
| 3 |
+
Dataset: /scratch/pranamlab/tong/data/halflife/halflife_embedding_unpooled
|
| 4 |
+
Target column: label
|
| 5 |
+
CV folds: 5
|
| 6 |
+
Optuna objective: spearman (direction=maximize)
|
| 7 |
+
Best trial: 22
|
| 8 |
+
OOF metrics:
|
| 9 |
+
{
|
| 10 |
+
"rmse": 45.00321578979492,
|
| 11 |
+
"mae": 11.352466583251953,
|
| 12 |
+
"r2": 0.02070075273513794,
|
| 13 |
+
"spearman_rho": 0.3759734508605516
|
| 14 |
+
}
|
| 15 |
+
OOF score (spearman): 0.375973
|
| 16 |
+
Best params:
|
| 17 |
+
{
|
| 18 |
+
"lr": 0.00019977882554167927,
|
| 19 |
+
"weight_decay": 1.102955470301081e-07,
|
| 20 |
+
"dropout": 1.2707176359392082e-05,
|
| 21 |
+
"batch_size": 16
|
| 22 |
+
}
|
| 23 |
+
Final refit epochs (all data): 14
|
| 24 |
+
Saved final model: /scratch/pranamlab/tong/PeptiVerse/src/halflife/finetune_stability_transformer_raw/final_model.pt
|
| 25 |
+
Benchmark (final model on full data):
|
| 26 |
+
{
|
| 27 |
+
"n_samples": 130,
|
| 28 |
+
"wall_time_s": 1.6299039730802178,
|
| 29 |
+
"throughput_samples_per_s": 79.7593000244818,
|
| 30 |
+
"gpu_ms_per_sample": 0.23774326214423547,
|
| 31 |
+
"gpu_peak_mem_MB": 77.5693359375
|
| 32 |
+
}
|
| 33 |
+
========================================================================
|
training_classifiers/half_life/transformer_wt_raw/study_trials.csv
ADDED
|
@@ -0,0 +1,3 @@
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7c38352854ad4142c02a4bcb33caee9fe8fa22fca86dcb8c17c05c24f3fa5bca
|
| 3 |
+
size 10895
|
training_classifiers/half_life/xgb_smiles/cv_fold_metrics.csv
ADDED
|
@@ -0,0 +1,3 @@
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|
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|
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|
| 1 |
+
version https://git-lfs.github.com/spec/v1
|
| 2 |
+
oid sha256:7a01d5b7fd8bea75667a1ae1e508ab11ff65b9bbea56839adb549971c16bb1af
|
| 3 |
+
size 353
|