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round like in MoleculeNet paper (Lipophilicity to 3 decimal places, F…
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…reeeSolv and ESOL to 2 dp)
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@GeorgeBatch
GeorgeBatch committed Sep 8, 2020
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Showing 9 changed files with 876 additions and 839 deletions.
1,651 changes: 844 additions & 807 deletions notebooks/prepare_reproducing_grid_search_results.ipynb
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8 changes: 4 additions & 4 deletions tables/esol_original_reproducing_random_search_best_means.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,38.156,0.081,0.484,1.286,1.246,0.338,0.931,0.928,0.946,0.604,0.67,0.977,0.783,0.819
xgb,10.217,0.025,0.456,1.236,1.185,0.297,0.902,0.872,0.952,0.633,0.704,0.977,0.8,0.841
krr,0.172,0.027,0.742,1.289,1.299,0.535,0.96,0.962,0.873,0.602,0.641,0.939,0.782,0.803
gp,8.643,0.13,0.438,1.138,1.098,0.29,0.859,0.806,0.956,0.69,0.744,0.981,0.836,0.866
rf,38.16,0.08,0.48,1.29,1.25,0.34,0.93,0.93,0.95,0.6,0.67,0.98,0.78,0.82
xgb,10.22,0.03,0.46,1.24,1.19,0.3,0.9,0.87,0.95,0.63,0.7,0.98,0.8,0.84
krr,0.17,0.03,0.74,1.29,1.3,0.53,0.96,0.96,0.87,0.6,0.64,0.94,0.78,0.8
gp,8.64,0.13,0.44,1.14,1.1,0.29,0.86,0.81,0.96,0.69,0.74,0.98,0.84,0.87
8 changes: 4 additions & 4 deletions tables/esol_original_reproducing_random_search_best_means_pm_stds.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,38.156 +/- 8.906,0.081 +/- 0.019,0.484 +/- 0.012,1.286 +/- 0.049,1.246 +/- 0.08,0.338 +/- 0.003,0.931 +/- 0.022,0.928 +/- 0.047,0.946 +/- 0.003,0.604 +/- 0.042,0.67 +/- 0.063,0.977 +/- 0.001,0.783 +/- 0.027,0.819 +/- 0.039
xgb,10.217 +/- 1.86,0.025 +/- 0.005,0.456 +/- 0.003,1.236 +/- 0.048,1.185 +/- 0.039,0.297 +/- 0.004,0.902 +/- 0.051,0.872 +/- 0.01,0.952 +/- 0.001,0.633 +/- 0.047,0.704 +/- 0.033,0.977 +/- 0.0,0.8 +/- 0.029,0.841 +/- 0.02
krr,0.172 +/- 0.035,0.027 +/- 0.006,0.742 +/- 0.009,1.289 +/- 0.058,1.299 +/- 0.094,0.535 +/- 0.005,0.96 +/- 0.041,0.962 +/- 0.054,0.873 +/- 0.004,0.602 +/- 0.047,0.641 +/- 0.07,0.939 +/- 0.002,0.782 +/- 0.027,0.803 +/- 0.042
gp,8.643 +/- 0.963,0.13 +/- 0.015,0.438 +/- 0.035,1.138 +/- 0.024,1.098 +/- 0.058,0.29 +/- 0.023,0.859 +/- 0.027,0.806 +/- 0.042,0.956 +/- 0.007,0.69 +/- 0.038,0.744 +/- 0.041,0.981 +/- 0.003,0.836 +/- 0.024,0.866 +/- 0.024
rf,38.16 +/- 8.91,0.08 +/- 0.02,0.48 +/- 0.01,1.29 +/- 0.05,1.25 +/- 0.08,0.34 +/- 0.0,0.93 +/- 0.02,0.93 +/- 0.05,0.95 +/- 0.0,0.6 +/- 0.04,0.67 +/- 0.06,0.98 +/- 0.0,0.78 +/- 0.03,0.82 +/- 0.04
xgb,10.22 +/- 1.86,0.03 +/- 0.01,0.46 +/- 0.0,1.24 +/- 0.05,1.19 +/- 0.04,0.3 +/- 0.0,0.9 +/- 0.05,0.87 +/- 0.01,0.95 +/- 0.0,0.63 +/- 0.05,0.7 +/- 0.03,0.98 +/- 0.0,0.8 +/- 0.03,0.84 +/- 0.02
krr,0.17 +/- 0.03,0.03 +/- 0.01,0.74 +/- 0.01,1.29 +/- 0.06,1.3 +/- 0.09,0.53 +/- 0.01,0.96 +/- 0.04,0.96 +/- 0.05,0.87 +/- 0.0,0.6 +/- 0.05,0.64 +/- 0.07,0.94 +/- 0.0,0.78 +/- 0.03,0.8 +/- 0.04
gp,8.64 +/- 0.96,0.13 +/- 0.01,0.44 +/- 0.04,1.14 +/- 0.02,1.1 +/- 0.06,0.29 +/- 0.02,0.86 +/- 0.03,0.81 +/- 0.04,0.96 +/- 0.01,0.69 +/- 0.04,0.74 +/- 0.04,0.98 +/- 0.0,0.84 +/- 0.02,0.87 +/- 0.02
8 changes: 4 additions & 4 deletions tables/esol_original_reproducing_random_search_best_means_pm_stds_rmse.csv
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,train_RMSE,val_RMSE,test_RMSE
rf,0.484 +/- 0.012,1.286 +/- 0.049,1.246 +/- 0.08
xgb,0.456 +/- 0.003,1.236 +/- 0.048,1.185 +/- 0.039
krr,0.742 +/- 0.009,1.289 +/- 0.058,1.299 +/- 0.094
gp,0.438 +/- 0.035,1.138 +/- 0.024,1.098 +/- 0.058
rf,0.48 +/- 0.01,1.29 +/- 0.05,1.25 +/- 0.08
xgb,0.46 +/- 0.0,1.24 +/- 0.05,1.19 +/- 0.04
krr,0.74 +/- 0.01,1.29 +/- 0.06,1.3 +/- 0.09
gp,0.44 +/- 0.04,1.14 +/- 0.02,1.1 +/- 0.06
8 changes: 4 additions & 4 deletions tables/esol_original_reproducing_random_search_best_stds.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,8.906,0.019,0.012,0.049,0.08,0.003,0.022,0.047,0.003,0.042,0.063,0.001,0.027,0.039
xgb,1.86,0.005,0.003,0.048,0.039,0.004,0.051,0.01,0.001,0.047,0.033,0.0,0.029,0.02
krr,0.035,0.006,0.009,0.058,0.094,0.005,0.041,0.054,0.004,0.047,0.07,0.002,0.027,0.042
gp,0.963,0.015,0.035,0.024,0.058,0.023,0.027,0.042,0.007,0.038,0.041,0.003,0.024,0.024
rf,8.91,0.02,0.01,0.05,0.08,0.0,0.02,0.05,0.0,0.04,0.06,0.0,0.03,0.04
xgb,1.86,0.01,0.0,0.05,0.04,0.0,0.05,0.01,0.0,0.05,0.03,0.0,0.03,0.02
krr,0.03,0.01,0.01,0.06,0.09,0.01,0.04,0.05,0.0,0.05,0.07,0.0,0.03,0.04
gp,0.96,0.01,0.04,0.02,0.06,0.02,0.03,0.04,0.01,0.04,0.04,0.0,0.02,0.02
8 changes: 4 additions & 4 deletions tables/freesolv_original_reproducing_random_search_best_means.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,13.819,0.065,0.749,2.411,2.399,0.451,1.32,1.307,0.961,0.633,0.665,0.985,0.809,0.825
xgb,3.862,0.023,0.423,2.081,2.103,0.297,1.274,1.284,0.988,0.725,0.742,0.994,0.856,0.863
krr,0.079,0.015,1.014,2.133,2.122,0.715,1.306,1.266,0.929,0.713,0.737,0.969,0.856,0.865
gp,3.8,0.056,0.059,2.1,1.999,0.03,1.224,1.17,1.0,0.722,0.765,1.0,0.863,0.883
rf,13.82,0.06,0.75,2.41,2.4,0.45,1.32,1.31,0.96,0.63,0.66,0.98,0.81,0.82
xgb,3.86,0.02,0.42,2.08,2.1,0.3,1.27,1.28,0.99,0.73,0.74,0.99,0.86,0.86
krr,0.08,0.02,1.01,2.13,2.12,0.72,1.31,1.27,0.93,0.71,0.74,0.97,0.86,0.86
gp,3.8,0.06,0.06,2.1,2.0,0.03,1.22,1.17,1.0,0.72,0.77,1.0,0.86,0.88
8 changes: 4 additions & 4 deletions tables/freesolv_original_reproducing_random_search_best_means_pm_stds.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,13.819 +/- 2.877,0.065 +/- 0.015,0.749 +/- 0.024,2.411 +/- 0.269,2.399 +/- 0.452,0.451 +/- 0.012,1.32 +/- 0.083,1.307 +/- 0.131,0.961 +/- 0.002,0.633 +/- 0.041,0.665 +/- 0.063,0.985 +/- 0.001,0.809 +/- 0.03,0.825 +/- 0.037
xgb,3.862 +/- 0.755,0.023 +/- 0.006,0.423 +/- 0.02,2.081 +/- 0.073,2.103 +/- 0.329,0.297 +/- 0.014,1.274 +/- 0.079,1.284 +/- 0.166,0.988 +/- 0.001,0.725 +/- 0.012,0.742 +/- 0.031,0.994 +/- 0.0,0.856 +/- 0.008,0.863 +/- 0.019
krr,0.079 +/- 0.022,0.015 +/- 0.001,1.014 +/- 0.015,2.133 +/- 0.148,2.122 +/- 0.277,0.715 +/- 0.007,1.306 +/- 0.042,1.266 +/- 0.072,0.929 +/- 0.0,0.713 +/- 0.007,0.737 +/- 0.018,0.969 +/- 0.0,0.856 +/- 0.005,0.865 +/- 0.009
gp,3.8 +/- 0.37,0.056 +/- 0.006,0.059 +/- 0.0,2.1 +/- 0.163,1.999 +/- 0.222,0.03 +/- 0.001,1.224 +/- 0.061,1.17 +/- 0.115,1.0 +/- 0.0,0.722 +/- 0.012,0.765 +/- 0.004,1.0 +/- 0.0,0.863 +/- 0.006,0.883 +/- 0.002
rf,13.82 +/- 2.88,0.06 +/- 0.01,0.75 +/- 0.02,2.41 +/- 0.27,2.4 +/- 0.45,0.45 +/- 0.01,1.32 +/- 0.08,1.31 +/- 0.13,0.96 +/- 0.0,0.63 +/- 0.04,0.66 +/- 0.06,0.98 +/- 0.0,0.81 +/- 0.03,0.82 +/- 0.04
xgb,3.86 +/- 0.76,0.02 +/- 0.01,0.42 +/- 0.02,2.08 +/- 0.07,2.1 +/- 0.33,0.3 +/- 0.01,1.27 +/- 0.08,1.28 +/- 0.17,0.99 +/- 0.0,0.73 +/- 0.01,0.74 +/- 0.03,0.99 +/- 0.0,0.86 +/- 0.01,0.86 +/- 0.02
krr,0.08 +/- 0.02,0.02 +/- 0.0,1.01 +/- 0.01,2.13 +/- 0.15,2.12 +/- 0.28,0.72 +/- 0.01,1.31 +/- 0.04,1.27 +/- 0.07,0.93 +/- 0.0,0.71 +/- 0.01,0.74 +/- 0.02,0.97 +/- 0.0,0.86 +/- 0.0,0.86 +/- 0.01
gp,3.8 +/- 0.37,0.06 +/- 0.01,0.06 +/- 0.0,2.1 +/- 0.16,2.0 +/- 0.22,0.03 +/- 0.0,1.22 +/- 0.06,1.17 +/- 0.11,1.0 +/- 0.0,0.72 +/- 0.01,0.77 +/- 0.0,1.0 +/- 0.0,0.86 +/- 0.01,0.88 +/- 0.0
8 changes: 4 additions & 4 deletions tables/freesolv_original_reproducing_random_search_best_means_pm_stds_rmse.csv
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,train_RMSE,val_RMSE,test_RMSE
rf,0.749 +/- 0.024,2.411 +/- 0.269,2.399 +/- 0.452
xgb,0.423 +/- 0.02,2.081 +/- 0.073,2.103 +/- 0.329
krr,1.014 +/- 0.015,2.133 +/- 0.148,2.122 +/- 0.277
gp,0.059 +/- 0.0,2.1 +/- 0.163,1.999 +/- 0.222
rf,0.75 +/- 0.02,2.41 +/- 0.27,2.4 +/- 0.45
xgb,0.42 +/- 0.02,2.08 +/- 0.07,2.1 +/- 0.33
krr,1.01 +/- 0.01,2.13 +/- 0.15,2.12 +/- 0.28
gp,0.06 +/- 0.0,2.1 +/- 0.16,2.0 +/- 0.22
8 changes: 4 additions & 4 deletions tables/freesolv_original_reproducing_random_search_best_stds.csv
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,fit_time,score_time,train_RMSE,val_RMSE,test_RMSE,train_MAE,val_MAE,test_MAE,train_R^2,val_R^2,test_R^2,train_pearson_r,val_pearson_r,test_pearson_r
rf,2.877,0.015,0.024,0.269,0.452,0.012,0.083,0.131,0.002,0.041,0.063,0.001,0.03,0.037
xgb,0.755,0.006,0.02,0.073,0.329,0.014,0.079,0.166,0.001,0.012,0.031,0.0,0.008,0.019
krr,0.022,0.001,0.015,0.148,0.277,0.007,0.042,0.072,0.0,0.007,0.018,0.0,0.005,0.009
gp,0.37,0.006,0.0,0.163,0.222,0.001,0.061,0.115,0.0,0.012,0.004,0.0,0.006,0.002
rf,2.88,0.01,0.02,0.27,0.45,0.01,0.08,0.13,0.0,0.04,0.06,0.0,0.03,0.04
xgb,0.76,0.01,0.02,0.07,0.33,0.01,0.08,0.17,0.0,0.01,0.03,0.0,0.01,0.02
krr,0.02,0.0,0.01,0.15,0.28,0.01,0.04,0.07,0.0,0.01,0.02,0.0,0.0,0.01
gp,0.37,0.01,0.0,0.16,0.22,0.0,0.06,0.11,0.0,0.01,0.0,0.0,0.01,0.0

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