def get_prev_train_test_data(prev_data_version=None, prev_trial_no=None):
file_folder = '../input'
train = pd.read_csv(f'{file_folder}/train.csv')
sample_loaded = False
prev_folder = f"../processed/{prev_data_version}/{prev_data_version}_{prev_trial_no}"
if DEBUG:
# v003_033
train_path = Path(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J_sampled.pkl"
)
test_path = Path(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J_sampled.pkl"
)
if train_path.exists() and test_path.exists():
print("sample loading")
train = unpickle(train_path)
test = unpickle(test_path)
sample_loaded = True
print("sample load finish")
if not sample_loaded:
print(f"loading previous dataest")
print("train loading")
train: pd.DataFrame = unpickle(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J.pkl",
)
assert "scalar_coupling_constant" in train.columns
print("test loading")
test: pd.DataFrame = unpickle(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J.pkl",
)
print(f"loading finished")
if DEBUG and not sample_loaded:
n_sample = 5000
print(f"sampling {n_sample} rows.")
train = train.sample(n=n_sample)
test = test.sample(n=n_sample)
Path(
f"../processed/{prev_data_version}/{prev_data_version}_{prev_trial_no}"
).mkdir(parents=True, exist_ok=True)
to_pickle(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J_sampled.pkl",
train)
to_pickle(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_yiemon_123J_sampled.pkl",
test)
print("saved.")
###################################################################################################
# add additional feature for trying
# Path(save_path / f"{DATA_VERSION}_{TRIAL_NO}").mkdir(parents=True, exist_ok=True)
# to_pickle(save_path / f"{DATA_VERSION}_{TRIAL_NO}/train_concat_{DATA_VERSION}_{TRIAL_NO}.pkl", train)
# to_pickle(save_path / f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl", test)
return train, test
def feat(data, num=5):
try:
number = data["number"]
df = data["df"]
mols = data["mols"]
#mols = df['molecule_name'].unique()
# dist_mat = np.zeros([0, num*5])
# atoms_idx = np.zeros([0], dtype=np.int32)
# molecule_names = np.empty([0])
start = time.time()
mp_data = [{"mol": mol, "df": df} for mol in mols]
dist_mats = [get_dist_mat(d) for d in mp_data]
#dist_mats = Parallel(n_jobs=NCORES)(delayed(get_dist_mat)(data) for data in mp_data)
molecule_names = np.hstack([x[0] for x in dist_mats])
atoms_idx = np.hstack([x[1] for x in dist_mats])
dist_mat = np.vstack([x[2] for x in dist_mats])
col_name_list = []
atoms = ['H', 'C', 'N', 'O', 'F']
for a in atoms:
for n in range(num):
col_name_list.append('dist_{}_{}'.format(a, n))
se_mole = pd.Series(molecule_names, name='molecule_name')
se_atom_idx = pd.Series(atoms_idx, name='atom_index')
df_dist = pd.DataFrame(dist_mat, columns=col_name_list)
df_distance = pd.concat([se_mole, se_atom_idx, df_dist], axis=1)
elapsed_time = time.time() - start
print("elapsed_time:{0:.2f}".format(elapsed_time) + "[sec]")
first_mol_name = df.molecule_name.iloc[0].replace("dsgdb9nsd_", "")
last_mol_name = df.molecule_name.iloc[-1].replace("dsgdb9nsd_", "")
np.save(f"mols_{first_mol_name}_{last_mol_name}.npy", mols)
to_pickle(
coulomb_feat /
f"coulomb_train_{number}_{first_mol_name}_{last_mol_name}.pkl",
df_distance)
except Exception as e:
print(e)
print(mols[:5])
print(mols[-5:])
display(df.head())
display(df.tail())
raise e
ss = StandardScaler()
df_ss = pd.DataFrame(ss.fit_transform(df.iloc[:, 2:]), columns=df.columns[2:])
decomp_cols = []
comp_results = []
comp_names = ["fa", "pca", "tsvd", "ica", "grp", "srp",
"mbkm"] #, "tsne"] # removing tsne
for name, transform in zip(comp_names,
[fa, pca, tsvd, ica, grp, srp, mbkm, tsne]):
print(current_time(), "{} converting...".format(name), flush=True)
n_components = N_COMP
if name == 'mbkm':
n_components = num_clusters2
elif name == "tsne":
n_components = 2
df_results = pd.DataFrame(transform.fit_transform(df_ss))
decomp_col = ["{0}_{1:02d}".format(name, i) for i in range(n_components)]
df_results.columns = decomp_col
decomp_cols.extend(decomp_col)
df_results.reset_index(inplace=True)
del df_results['index']
comp_results.append(df_results)
comp_results_df = pd.concat(comp_results, axis=1)
comp_results_df = pd.concat([
df.iloc[:, :2].reset_index(drop=True),
comp_results_df.reset_index(drop=True)
],
axis=1)
to_pickle(f"../processed/v003/comp_results_df_{N_COMP}.pkl", comp_results_df)
train = train.merge(rdkit_train, on="id", how="left")
test = test.merge(rdkit_test, on="id", how="left")
ob_charges = pd.read_csv("../processed/v003/ob_charges.csv", index_col=0)
train = map_ob_charges(train, 0)
train = map_ob_charges(train, 1)
test = map_ob_charges(test, 0)
test = map_ob_charges(test, 1)
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
Path(save_path / f"{DATA_VERSION}_{TRIAL_NO}").mkdir(parents=True,
exist_ok=True)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
train)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
test)
else:
train = unpickle(save_path / f"v003_010/train_concat_v003_010.pkl", )
test = unpickle(save_path / f"v003_010/test_concat_v003_010.pkl", )
if AUGMENT:
augmented_train = unpickle(save_path / f"augmented_train_v001.pkl", ).drop(
["Unnamed: 0_x", "Unnamed: 0_y"], axis=1)
augmented_train['id'] += train["id"].max() + 1
train = pd.concat([train, augmented_train], axis=0).reset_index(drop=True)
def train_main(seed, type_):
print(f"==================== seed: {seed} ====================")
params = { #'num_leaves': 128,
'min_child_samples': 79,
'objective': 'regression',
'max_depth': -1, #9,
'learning_rate': 0.2,
"boosting_type": "gbdt",
"subsample_freq": 1,
"subsample": 0.9,
"metric": 'mae',
"verbosity": -1,
'reg_alpha': 0.1,
'reg_lambda': 0.3,
'colsample_bytree': 1.0,
'num_threads' : -1,
}
params["seed"] = seed
params["bagging_seed"] = seed + 1
params["feature_fraction_seed"] = seed + 2
n_estimators = 5 #10000
params["num_leaves"] = 256
if DEBUG:
n_estimators = 5
X_short = pd.DataFrame({
'ind': list(X.index),
'type': X['type'].values,
'oof': [0] * len(X),
'target': y.values,
'fc': y_fc.values
})
X_short_test = pd.DataFrame({
'ind': list(X_test.index),
'type': X_test['type'].values,
'prediction': [0] * len(X_test)
})
print(f'{current_time()} Training of type {type_} / {X["type"].unique()}')
X_t = X.loc[X['type'] == type_]
X_test_t = X_test.loc[X_test['type'] == type_]
y_fc_t = X_short.loc[X_short['type'] == type_, 'fc']
y_t = X_short.loc[X_short['type'] == type_, 'target']
mol_name_t = mol_name.loc[X['type'] == type_][
X_t.index] if GROUP_K_FOLD else None
print(
f"X_t.shape: {X_t.shape}, X_test_t.shape: {X_test_t.shape}, y_t.shape: {y_t.shape}"
)
########################################################################################################
# fc
print("=" * 30 + " fc " + "=" * 30)
result_dict_lgb1 = train_model_regression(X=X_t,
X_test=X_test_t,
y=y_fc_t,
params=params,
folds=folds,
model_type='lgb',
eval_metric='group_mae',
plot_feature_importance=False,
verbose=1000,
early_stopping_rounds=200,
n_estimators=n_estimators,
fold_group=mol_name.values)
X['oof_fc'] = result_dict_lgb1['oof']
X_test['oof_fc'] = result_dict_lgb1['prediction']
to_pickle(
submit_path /
f"train_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.pkl",
X['oof_fc'])
to_pickle(
submit_path /
f"test_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.pkl",
X_test['oof_fc'])
to_pickle(
model_path /
f"first_model_list_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.pkl",
result_dict_lgb1["models"])
#########################################################################################################
# 2nd layer model
params["seed"] = seed + 3
params["bagging_seed"] = seed + 4
params["feature_fraction_seed"] = seed + 5
params["num_leaves"] = 256 # num_leaves_dict[t]
start_time = current_time()
bairitsu = 256 / params["num_leaves"]
n_estimators = 5 #int(15000 * bairitsu)
if DEBUG:
n_estimators = 5
if TRAIN_ALL_DATA:
print("============= 2nd layer TRIAN ALL DATA ================")
result_dict = train_lgb_regression_alldata(
X=X_t,
X_test=X_test_t,
y=y_t,
params=params,
eval_metric='group_mae',
plot_feature_importance=True,
verbose=5000,
n_estimators=int(n_estimators * 1.6),
mol_type=type_)
X_short_test.loc[X_short_test['type'] == type_,
'prediction'] = result_dict['prediction']
X_short_test.to_csv(
submit_path / f"sub_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.csv")
elif CV_FOLD:
print("============= 2nd layer CV ================")
result_dict = train_model_regression(X_t,
X_test_t,
y_t,
params,
folds,
model_type='lgb',
eval_metric='mae',
columns=None,
plot_feature_importance=True,
model=None,
verbose=1000,
early_stopping_rounds=200,
n_estimators=n_estimators,
mol_type=-1,
fold_group=mol_name_t)
result_dict["start_time"] = start_time
result_dict["n_estimator"] = n_estimators
result_dict["X_t_len"] = X_t.shape[0]
result_dict["type"] = type_
result_dict["type_name"] = type_name[type_]
X_short.loc[X_short['type'] == type_, 'oof'] = result_dict['oof']
X_short.to_csv(submit_path /
f"oof_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.csv")
X_short_test.loc[X_short_test['type'] == type_,
'prediction'] = result_dict['prediction']
X_short_test.to_csv(
submit_path / f"sub_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.csv")
else:
print("============= 2nd layer hold out ================")
result_dict = hold_out_lgb_validation(X=X_t,
y=y_t,
params=params,
eval_metric='mae',
plot_feature_importance=True,
verbose=5000,
early_stopping_rounds=200,
n_estimators=n_estimators)
result_dict["start_time"] = start_time
result_dict["n_estimator"] = n_estimators
result_dict["X_t_len"] = X_t.shape[0]
result_dict["type"] = type_
result_dict["type_name"] = type_name[type_]
eval_result: list = result_dict["eval_result"]["valid_1"]["l1"]
training_log_df: pd.DataFrame = pd.DataFrame(
eval_result, index=np.arange(len(eval_result)) + 1)
training_log_df.columns = ["l1"]
training_log_df.index.name = "iter"
training_log_df.to_csv(
log_path / f"train_log_{DATA_VERSION}_{TRIAL_NO}_{type_}.csv")
to_pickle(
model_path /
f"hold_out_model_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.pkl",
result_dict["model"])
#
#
# to_pickle(log_path / f"result_dict_{type_}_{seed}.pkl", result_dict)
# importance_path = log_path / f'importance_{DATA_VERSION}_{TRIAL_NO}_{type_}_{seed}.csv'
# result_dict["importance"].to_csv(importance_path, index=True)
#
# for type_, s in zip(X['type'].unique(), score_list):
# print(f"type {type_}, score: {s:0.5f}")
if TRAIN_ALL_DATA or CV_FOLD:
#########################################################################################################
# create oof & submission file.
sub = pd.read_csv(f'../input/sample_submission.csv')
sub['scalar_coupling_constant'] = X_short_test['prediction']
sub.to_csv(submit_path /
f'submission_t_{DATA_VERSION}_{TRIAL_NO}_{seed}.csv',
index=False)
print(sub.head())
send_message(f"finish all_data train_{DATA_VERSION}_{TRIAL_NO}_{seed}")
if CV_FOLD:
oof_log_mae = group_mean_log_mae(X_short['target'],
X_short['oof'],
X_short['type'],
floor=1e-9)
print(f"oof_log_mae: {oof_log_mae}")
df_oof = pd.DataFrame(index=train.id)
df_oof["scalar_coupling_constant"] = X_short['oof']
df_oof.to_csv(submit_path /
f'oof_{DATA_VERSION}_{TRIAL_NO}_{seed}.csv',
index=True)
send_message(
f"finish train_{DATA_VERSION}_{TRIAL_NO}_{seed}, oof_log_mae: {oof_log_mae}"
)
train['abs_dist'] = np.linalg.norm(train_p_0 - train_p_1, axis=1, ord=1)
dist12('dist_xy', 'x', 'y')
dist12('dist_xz', 'x', 'z')
dist12('dist_yz', 'y', 'z')
atom_count = structures.groupby(['molecule_name',
'atom']).size().unstack(fill_value=0)
train = pd.merge(train,
atom_count,
how='left',
left_on='molecule_name',
right_on='molecule_name')
train = create_features(train)
angle_df_train = angle_feature_conv()
train = train.merge(angle_df_train, on="id", how="left")
train = train.merge(train_add, on="id", how="left")
train = train.merge(babel_train, on="id", how="left")
train = train.merge(rdkit_train, on="id", how="left")
ob_charges = pd.read_csv("../processed/v003/ob_charges_augmented.csv",
index_col=0)
train = map_ob_charges(train, 0)
train = map_ob_charges(train, 1)
train = reduce_mem_usage(train)
to_pickle(save_path / f"augmented_train_v001.pkl", train)
print("finished.")
X=X,
X_test=X_test,
y=mullkan_0,
params=params,
folds=folds,
model_type='lgb',
eval_metric='group_mae',
plot_feature_importance=False,
verbose=500,
early_stopping_rounds=200,
n_estimators=n_estimators,
fold_group=mol_name.values)
oof_mullkan_0_train = result_dict_lgb_m0['oof']
oof_mullkan_0_test = result_dict_lgb_m0['prediction']
to_pickle(
submit_path /
f"train_oof_mullkan_0_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
oof_mullkan_0_train)
to_pickle(
submit_path /
f"test_oof_mullkan_0_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
oof_mullkan_0_test)
to_pickle(
model_path /
f"first_model_list_mullkan_0_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
result_dict_lgb_m0["models"])
########################################################################################################
# mullken 1
print("=" * 30 + " mullken 1 " + "=" * 30)
result_dict_lgb_m1 = train_model_regression(
X=X,
categorical_feature=categorical,
folds=folds,
num_boost_round=30000,
verbose_eval = 500,
early_stopping_rounds=200,
callbacks=callbacks,
)
df_ret = pd.DataFrame(ret)
display(df_ret)
print("finish fitting.")
# Retrieving booster and training information.
proxy = extraction_cb.boosters_proxy
boosters = extraction_cb.raw_boosters
best_iteration = extraction_cb.best_iteration
to_pickle(model_path/'extraction_cb.pkl', extraction_cb)
# Create oof prediction result
print("create oof preds.")
fold_iter = folds.split(train, y)
oof_preds = np.zeros_like(y)
for n_fold, ((trn_idx, val_idx), booster) in enumerate(zip(fold_iter, boosters)):
print(val_idx)
valid = train.iloc[val_idx]
oof_preds[val_idx] = booster.predict(valid, num_iteration=best_iteration)
print(f"mae on oof preds: {mean_absolute_error(y, oof_preds)}")
np.save(submit_path/'oof.npy', oof_preds)
# Averaging prediction result for test data.
y_pred_proba_list = proxy.predict(test, num_iteration=best_iteration)
y_pred_proba_avg = np.array(y_pred_proba_list).mean(axis=0)
# train = train.merge(train_angle_add, on="id", how="left")
# test = test.merge(test_angle_add, on="id", how="left")
train = train.merge(train_add, on="id", how="left")
test = test.merge(test_add, on="id", how="left")
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
for f in ['atom_1', 'type_0', 'type']:
if f in good_columns:
lbl = LabelEncoder()
lbl.fit(list(train[f].values) + list(test[f].values))
train[f] = lbl.transform(list(train[f].values))
test[f] = lbl.transform(list(test[f].values))
to_pickle(save_path / f"train_v003_{DATA_VERSION}_{TRIAL_NO}.pkl", train)
to_pickle(save_path / f"test_v003_{DATA_VERSION}_{TRIAL_NO}.pkl", test)
X = train[good_columns].copy()
y = train['scalar_coupling_constant']
y_fc = train['fc']
X_test = test[good_columns].copy()
# export colnames
pd.DataFrame({
"columns": X.columns.tolist()
}).to_csv(log_path / f"use_cols.csv")
####################################################################################################
# Model Fitting
n_fold = 5
folds=folds,
model_type='lgb',
eval_metric='group_mae',
plot_feature_importance=True,
verbose=500,
early_stopping_rounds=200,
n_estimators=n_estimators,
fold_group=mol_name_t)
importance_path = log_path / f'importance_fc_{DATA_VERSION}_{TRIAL_NO}_{t}_{seed}.csv'
result_dict_lgb1["importance"].to_csv(importance_path, index=True)
X_t['oof_fc'] = result_dict_lgb1['oof']
X_test_t['oof_fc'] = result_dict_lgb1['prediction']
to_pickle(
submit_path /
f"train_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{t}_{seed}.pkl",
X_t['oof_fc'])
to_pickle(
submit_path /
f"test_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{t}_{seed}.pkl",
X_test_t['oof_fc'])
params["num_leaves"] = 256 # num_leaves_dict[t]
start_time = current_time()
bairitsu = 256 / params["num_leaves"]
n_estimators = int(15000 * bairitsu)
if DEBUG:
n_estimators = 5
if TRAIN_ALL_DATA:
# result_dict["start_time"] = start_time
# result_dict["n_estimator"] = n_estimators
# result_dict["X_t_len"] = X_t.shape[0]
# result_dict["type"] = t
# result_dict["type_name"] = type_name[t]
# score_list += [result_dict["score"]]
#
# eval_result: list = result_dict["eval_result"]["valid_1"]["l1"]
# training_log_df: pd.DataFrame = pd.DataFrame(eval_result, index=np.arange(len(eval_result)) + 1)
# training_log_df.columns = ["l1"]
# training_log_df.index.name = "iter"
# training_log_df.to_csv(log_path / f"train_log_{DATA_VERSION}_{TRIAL_NO}_{t}.csv")
#
# to_pickle(model_path / f"hold_out_model_{DATA_VERSION}_{TRIAL_NO}_{t}_{seed}.pkl", result_dict["model"])
to_pickle(log_path / f"result_dict_{t}_{seed}.pkl", result_dict)
importance_path = log_path / f'importance_{DATA_VERSION}_{TRIAL_NO}_{t}_{seed}.csv'
result_dict["importance"].to_csv(importance_path, index=True)
for t, s in zip(X['type'].unique(), score_list):
print(f"type {t}, score: {s:0.5f}")
if TRAIN_ALL_DATA or CV_FOLD:
#########################################################################################################
# create oof & submission file.
sub = pd.read_csv(f'../input/sample_submission.csv')
sub['scalar_coupling_constant'] = X_short_test['prediction']
submit_file_path = str(
submit_path / f'submission_t_{DATA_VERSION}_{TRIAL_NO}_{seed}.csv')
sub.to_csv(submit_file_path, index=False)
rgs = RankGaussScalar()
rgs.fit(X_fillna)
X_rgs = rgs.transform(X_fillna)
del X
gc.collect()
X_test_rgs = rgs.transform(X_test.fillna(0))
del X_test
gc.collect()
X_rgs.fillna(0, inplace=True)
X_test_rgs.fillna(0, inplace=True)
X_rgs["type"] = type_train
X_test_rgs["type"] = type_test
to_pickle(train_data_path, X_rgs)
to_pickle(test_data_path, X_test_rgs)
to_pickle(y_data_path, y)
to_pickle(mol_name_data_path, mol_name)
print("saved files for model train.")
####################################################################################################
# Model Fitting
print("start fitting")
n_fold = 5
if DEBUG:
n_fold = 3
if GROUP_K_FOLD:
folds = GroupKFold(n_splits=n_fold)
else:
folds=folds,
num_boost_round=30000,
verbose_eval = 500,
early_stopping_rounds=500,
callbacks=callbacks,
)
df_ret = pd.DataFrame(ret)
display(df_ret.tail())
print("finish fitting.")
# Retrieving booster and training information.
proxy = extraction_cb.boosters_proxy
boosters = extraction_cb.raw_boosters
best_iteration = extraction_cb.best_iteration
print(f"best_iteration: {best_iteration}")
to_pickle(model_path/f'extraction_cb_{mol_type}.pkl', extraction_cb)
to_pickle(model_path/f'boosters.pkl_{mol_type}', boosters)
to_pickle(model_path/f'proxy.pkl_{mol_type}', proxy)
# Create oof prediction result
print("create oof preds.")
fold_iter = folds.split(train, y)
oof_preds = np.zeros_like(y)
for n_fold, ((trn_idx, val_idx), booster) in enumerate(zip(fold_iter, boosters)):
print(val_idx)
valid = train.iloc[val_idx]
oof_preds[val_idx] = booster.predict(valid, num_iteration=best_iteration)
print(f"mae on oof preds: {mean_absolute_error(y, oof_preds)}")
df_oof = pd.DataFrame(index=train.index)
df_oof["scalar_coupling_constant"] = oof_preds
axis=1)
ret_list.append(acsf_df)
return pd.concat(ret_list, axis=0)
print("loading structures")
structures = pd.read_csv("../input/structures.csv")
molecule_names = np.sort(structures.molecule_name.unique())
gb_structure = structures.groupby("molecule_name")
n_split = mp.cpu_count()
unit = np.ceil(len(molecule_names) / n_split).astype(int)
indexer = [[unit * (i), unit * (i + 1)] for i in range(n_split)]
split_mol_names = []
for idx in indexer:
split_mol_names.append(molecule_names[idx[0]:idx[1]])
mp_data = [{"mol_names": m} for m in split_mol_names]
print("start multiprocessing")
num_workers = mp.cpu_count()
with mp.Pool(num_workers) as executor:
features_chunk = executor.map(get_scsf, mp_data)
df = pd.concat(features_chunk)
to_pickle("../processed/v003/acsf_feat.pkl", df)
#df.to_csv("../processed/v003/acsf_feat.csv")
print("finished.")
'molecule_atom_index_1_dist_std_diff',
'molecule_atom_index_0_dist_mean_diff',
'molecule_atom_index_1_dist_mean_div',
'molecule_atom_index_1_dist_min_diff', 'rc_A', 'rc_B', 'rc_C', 'mu',
'alpha', 'h**o', 'lumo', 'gap', 'zpve', 'Cv', 'freqs_min', 'freqs_max',
'freqs_mean', 'mulliken_min', 'mulliken_max', 'mulliken_atom_0',
'mulliken_atom_1', 'dist_C_0_x', 'dist_C_1_x', 'dist_C_2_x', 'dist_C_3_x',
'dist_C_4_x', 'dist_F_0_x', 'dist_F_1_x', 'dist_F_2_x', 'dist_H_0_x',
'dist_H_1_x', 'dist_H_2_x', 'dist_H_3_x', 'dist_H_4_x', 'dist_N_0_x',
'dist_N_1_x', 'dist_N_2_x', 'dist_N_3_x', 'dist_N_4_x', 'dist_O_0_x',
'dist_O_1_x', 'dist_O_2_x', 'dist_O_3_x', 'dist_O_4_x', 'dist_C_0_y',
'dist_C_1_y', 'dist_C_2_y', 'dist_C_3_y', 'dist_C_4_y', 'dist_F_0_y',
'dist_F_1_y', 'dist_F_2_y', 'dist_F_3_y', 'dist_F_4_y', 'dist_H_0_y',
'dist_H_1_y', 'dist_H_2_y', 'dist_H_3_y', 'dist_H_4_y', 'dist_N_0_y',
'dist_N_1_y', 'dist_N_2_y', 'dist_N_3_y', 'dist_N_4_y', 'dist_O_0_y',
'dist_O_1_y', 'dist_O_2_y', 'dist_O_3_y', 'dist_O_4_y',
'distance_closest_0', 'distance_closest_1', 'distance_farthest_0',
'distance_farthest_1', 'cos_c0_c1', 'cos_f0_f1', 'cos_c0_f0', 'cos_c1_f1',
'cos_center0_center1', 'cos_c0', 'cos_c1', 'cos_f0', 'cos_f1',
'cos_center0', 'cos_center1'
] + giba_columns
cat_features = ['atom_y']
to_pickle("../processed/v003/train_kernel_plus_more_feats.pkl",
train[all_features])
to_pickle("../processed/v003/test_kernel_plus_more_feats.pkl",
test[all_features])
print("finished.")
g = unpickle(graph_list[j])
node_df = pd.concat([structure[structure.molecule_name==graph_name][["molecule_name", "atom_index"]].reset_index(drop=True),
pd.DataFrame(np.concatenate(g.node, -1), columns=[f"node_{i}" for i in range(13)])], axis=1)
node_list += [node_df]
return node_list
structure = pd.read_csv("../input/structures.csv")
graph_list = glob("../input/graph/*.pickle")
print(len(graph_list))
n_split = mp.cpu_count()
unit = np.ceil(len(graph_list) / n_split).astype(int)
indexer = [[unit * (i), unit * (i + 1)] for i in range(n_split)]
split_graph_list = []
for idx in indexer:
split_graph_list.append(graph_list[idx[0]:idx[1]])
mp_data = [{"graph_list": m} for m in split_graph_list]
num_workers = mp.cpu_count()
with mp.Pool(num_workers) as executor:
features_chunk = executor.map(func, mp_data)
concat_list = []
for i in range(len(features_chunk)):
concat_list += features_chunk[i]
node_df = pd.concat(concat_list, axis=0)
to_pickle("../processed/v003/node_df.pkl", node_df)
test = map_ob_charges(test, 1)
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
for f in ['atom_1', 'type_0', 'type']:
if f in use_cols.good_columns:
lbl = LabelEncoder()
lbl.fit(list(train[f].values) + list(test[f].values))
train[f] = lbl.transform(list(train[f].values))
test[f] = lbl.transform(list(test[f].values))
Path(save_path / f"{DATA_VERSION}_{TRIAL_NO}").mkdir(parents=True,
exist_ok=True)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/train_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
train)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
test)
else:
train = unpickle(save_path / f"v003_024/train_concat_v003_024.pkl", )
test = unpickle(save_path / f"v003_024/test_concat_v003_024.pkl", )
###################################################################################################
# add additional feature for trying
###################################################################################################
# final data preparation for train
X = train[use_cols.good_columns].copy()
axis=1,
inplace=True)
print("test 1")
test = map_atom_info(test, 0)
print("test 2")
test = map_atom_info(test, 1)
print("test 3")
test.rename(
{
"mass_x": "f006:mass_0",
"mass_y": "f006:mass_1",
"dist_from_origin_x": "f006:dist_from_origin_0",
"dist_from_origin_y": "f006:dist_from_origin_1",
},
axis=1,
inplace=True)
Path("../processed/v003").mkdir(parents=True, exist_ok=True)
to_pickle(
"../processed/v003/train_augmented_006.df.pkl", train[[
"id", "f006:dist_origin_mean", "f006:mass_0", "f006:mass_1",
"f006:dist_from_origin_0", "f006:dist_from_origin_1"
]])
# to_pickle("../processed/v004/aug_test_006.df.pkl",test[["id",
# "f006:dist_origin_mean", "f006:mass_0", "f006:mass_1",
# "f006:dist_from_origin_0", "f006:dist_from_origin_1"]])
print("finished")
plot_feature_importance=True,
verbose=500,
early_stopping_rounds=200,
n_estimators=n_estimators,
fold_group=mol_name.values,
phase_mark="_fc")
importance_path = log_path / f'importance_fc_{DATA_VERSION}_{TRIAL_NO}_{seed}.csv'
result_dict_lgb1["importance"].to_csv(importance_path, index=True)
########################################################################################################
X['oof_fc'] = result_dict_lgb1['oof']
X_test['oof_fc'] = result_dict_lgb1['prediction']
to_pickle(
submit_path / f"train_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
X['oof_fc'])
to_pickle(
submit_path / f"test_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
X_test['oof_fc'])
to_pickle(
model_path /
f"first_model_list_{DATA_VERSION}_{TRIAL_NO}_{seed}.pkl",
result_dict_lgb1["models"])
else:
X['oof_fc'] = unpickle(
submit_path /
f"train_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{current_seed}.pkl")
X_test['oof_fc'] = unpickle(
submit_path /
f"test_oof_fc_{DATA_VERSION}_{TRIAL_NO}_{current_seed}.pkl")
folds=folds,
num_boost_round=30000,
verbose_eval=500,
early_stopping_rounds=500,
callbacks=callbacks,
)
df_ret = pd.DataFrame(ret)
display(df_ret.tail())
print("finish fitting.")
# Retrieving booster and training information.
proxy = extraction_cb.boosters_proxy
boosters = extraction_cb.raw_boosters
best_iteration = extraction_cb.best_iteration
print(f"best_iteration: {best_iteration}")
to_pickle(model_path / 'extraction_cb.pkl', extraction_cb)
to_pickle(model_path / 'boosters.pkl', boosters)
to_pickle(model_path / 'proxy.pkl', proxy)
# Create oof prediction result
print("create oof preds.")
fold_iter = folds.split(train, y)
oof_preds = np.zeros_like(y)
for n_fold, ((trn_idx, val_idx),
booster) in enumerate(zip(fold_iter, boosters)):
print(val_idx)
valid = train.iloc[val_idx]
oof_preds[val_idx] = booster.predict(valid, num_iteration=best_iteration)
print(f"mae on oof preds: {mean_absolute_error(y, oof_preds)}")
df_oof = pd.DataFrame(index=train.index)
train = map_ob_charges(train, 0)
train = map_ob_charges(train, 1)
test = map_ob_charges(test, 0)
test = map_ob_charges(test, 1)
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
for f in ['atom_1', 'type_0', 'type']:
if f in good_columns:
lbl = LabelEncoder()
lbl.fit(list(train[f].values) + list(test[f].values))
train[f] = lbl.transform(list(train[f].values))
test[f] = lbl.transform(list(test[f].values))
to_pickle(save_path / f"train_concat_v003_{DATA_VERSION}_{TRIAL_NO}.pkl",
train)
to_pickle(save_path / f"test_concat_v003_{DATA_VERSION}_{TRIAL_NO}.pkl", test)
X = train[good_columns].copy()
y = train['scalar_coupling_constant']
y_fc = train['fc']
X_test = test[good_columns].copy()
# export colnames
pd.DataFrame({
"columns": X.columns.tolist()
}).to_csv(log_path / f"use_cols.csv")
####################################################################################################
# Model Fitting
n_fold = 5
def train_model_regression(X, X_test, y, params, folds, model_type='lgb', eval_metric='mae', columns=None,
plot_feature_importance=False, model=None,
verbose=10000, early_stopping_rounds=200, n_estimators=50000, mol_type=-1,
fold_group=None, skip_folds=None, phase_mark="", skipped_mark=[]):
"""
A function to train a variety of regression models.
Returns dictionary with oof predictions, test predictions, scores and, if necessary, feature importances.
:params: X - training data, can be pd.DataFrame or np.ndarray (after normalizing)
:params: X_test - test data, can be pd.DataFrame or np.ndarray (after normalizing)
:params: y - target
:params: folds - folds to split data
:params: model_type - type of model to use
:params: eval_metric - metric to use
:params: columns - columns to use. If None - use all columns
:params: plot_feature_importance - whether to plot feature importance of LGB
:params: model - sklearn model, works only for "sklearn" model type
"""
assert isinstance(skip_folds, list) or skip_folds is None
print(f"skip_folds :{skip_folds}")
columns = X.columns if columns is None else columns
X_test = X_test[columns]
# to set up scoring parameters
metrics_dict = {'mae': {'lgb_metric_name': 'mae',
'catboost_metric_name': 'MAE',
'sklearn_scoring_function': metrics.mean_absolute_error},
'group_mae': {'lgb_metric_name': 'mae',
'catboost_metric_name': 'MAE',
'scoring_function': group_mean_log_mae},
'mse': {'lgb_metric_name': 'mse',
'catboost_metric_name': 'MSE',
'sklearn_scoring_function': metrics.mean_squared_error}
}
result_dict = {}
# out-of-fold predictions on train data
oof = np.zeros(len(X))
# averaged predictions on train data
prediction = np.zeros(len(X_test))
# list of scores on folds
scores = []
feature_importance = pd.DataFrame()
model_list = []
# split and train on folds
for fold_n, (train_index, valid_index) in enumerate(folds.split(X, groups=fold_group)):
if skip_folds is not None and fold_n in skip_folds and phase_mark in skipped_mark:
print(f'Fold {fold_n + 1} is skipped!!! at {time.ctime()}')
oof = unpickle(mid_path / f"oof_cv{phase_mark}_{fold_n}.pkl", )
y_pred = unpickle(mid_path / f"prediction_cv{phase_mark}_{fold_n}.pkl", )
model = unpickle(mid_path / f"model_cv{phase_mark}_{fold_n}.pkl", )
fold_importance = unpickle(mid_path / f"importance_cv{phase_mark}_{fold_n}.pkl", )
feature_importance = pd.concat([feature_importance, fold_importance], axis=0)
prediction += y_pred
model_list += [model]
continue
print(f'Fold {fold_n + 1} started at {time.ctime()}')
if type(X) == np.ndarray:
X_train, X_valid = X[columns][train_index], X[columns][valid_index]
y_train, y_valid = y[train_index], y[valid_index]
else:
X_train, X_valid = X[columns].iloc[train_index], X[columns].iloc[valid_index]
y_train, y_valid = y.iloc[train_index], y.iloc[valid_index]
if model_type == 'lgb':
model = lgb.LGBMRegressor(**params, n_estimators=n_estimators, n_jobs=-1, importance_type='gain')
print(model)
model.fit(X_train, y_train,
eval_set=[(X_train, y_train), (X_valid, y_valid)],
eval_metric=metrics_dict[eval_metric]['lgb_metric_name'],
verbose=verbose, early_stopping_rounds=early_stopping_rounds)
y_pred_valid = model.predict(X_valid)
y_pred = model.predict(X_test, num_iteration=model.best_iteration_)
if model_type == 'xgb':
train_data = xgb.DMatrix(data=X_train, label=y_train, feature_names=X.columns)
valid_data = xgb.DMatrix(data=X_valid, label=y_valid, feature_names=X.columns)
watchlist = [(train_data, 'train'), (valid_data, 'valid_data')]
params["objective"] = "reg:linear"
params["eval_metric"] = metrics_dict[eval_metric]['lgb_metric_name']
model = xgb.train(dtrain=train_data, num_boost_round=20000, evals=watchlist, early_stopping_rounds=200,
verbose_eval=verbose, params=params)
y_pred_valid = model.predict(xgb.DMatrix(X_valid, feature_names=X.columns),
ntree_limit=model.best_ntree_limit)
y_pred = model.predict(xgb.DMatrix(X_test, feature_names=X.columns), ntree_limit=model.best_ntree_limit)
if model_type == 'sklearn':
model = model
model.fit(X_train, y_train)
y_pred_valid = model.predict(X_valid).reshape(-1, )
score = metrics_dict[eval_metric]['sklearn_scoring_function'](y_valid, y_pred_valid)
print(f'Fold {fold_n}. {eval_metric}: {score:.4f}.')
print('')
y_pred = model.predict(X_test).reshape(-1, )
if model_type == 'cat':
model = CatBoostRegressor(iterations=20000, eval_metric=metrics_dict[eval_metric]['catboost_metric_name'],
**params,
loss_function=metrics_dict[eval_metric]['catboost_metric_name'])
model.fit(X_train, y_train, eval_set=(X_valid, y_valid), cat_features=[], use_best_model=True,
verbose=False)
y_pred_valid = model.predict(X_valid)
y_pred = model.predict(X_test)
oof[valid_index] = y_pred_valid.reshape(-1, )
if eval_metric != 'group_mae':
scores.append(metrics_dict[eval_metric]['sklearn_scoring_function'](y_valid, y_pred_valid))
else:
scores.append(metrics_dict[eval_metric]['scoring_function'](y_valid, y_pred_valid, X_valid['type']))
prediction += y_pred
if model_type == 'lgb' and plot_feature_importance:
# feature importance
fold_importance = pd.DataFrame()
fold_importance["feature"] = columns
fold_importance["importance"] = model.feature_importances_
fold_importance["fold"] = fold_n + 1
try:
fold_importance.to_csv(mid_path / f"importance_cv_{fold_n}.csv")
except Exception as e:
print("failed to save importance...")
print(e)
feature_importance = pd.concat([feature_importance, fold_importance], axis=0)
model_list += [model]
try:
to_pickle(mid_path / f"oof_cv{phase_mark}_{fold_n}.pkl", oof)
to_pickle(mid_path / f"prediction_cv{phase_mark}_{fold_n}.pkl", y_pred)
to_pickle(mid_path / f"model_cv{phase_mark}_{fold_n}.pkl", model)
to_pickle(mid_path / f"importance_cv{phase_mark}_{fold_n}.pkl", fold_importance)
except Exception as e:
print("failed to save intermediate data...")
print(e)
if model_type == 'lgb' and plot_feature_importance:
result_dict['importance'] = feature_importance
prediction /= folds.n_splits
try:
cv_score_msg = f'{DATA_VERSION}_{TRIAL_NO}' +' CV mean score: {0:.4f}, std: {1:.4f}.'.format(np.mean(scores), np.std(scores))
print(cv_score_msg)
send_message(cv_score_msg)
except Exception as e:
print(e)
pass
result_dict["models"] = model_list
result_dict['oof'] = oof
result_dict['prediction'] = prediction
result_dict['scores'] = scores
return result_dict
def get_train_test_data(use_prev=False,
prev_data_version=None,
prev_trial_no=None):
if use_prev:
assert prev_data_version is not None
assert prev_trial_no is not None
file_folder = '../input'
train = pd.read_csv(f'{file_folder}/train.csv')
if not use_prev:
test = pd.read_csv(f'{file_folder}/test.csv')
structures = pd.read_csv(f'{file_folder}/structures.csv')
scalar_coupling_contributions = pd.read_csv(
f'{file_folder}/scalar_coupling_contributions.csv')
# train_cos = unpickle(save_path / "train_003.df.pkl", )[["id", "f003:cos_0_1", "f003:cos_1"]]
# test_cos = unpickle(save_path / "test_003.df.pkl", )[["id", "f003:cos_0_1", "f003:cos_1"]]
train_add = unpickle(save_path / "train_006.df.pkl", )
test_add = unpickle(save_path / "test_006.df.pkl", )
babel_train = pd.read_csv(save_path / "babel_train.csv",
usecols=use_cols.babel_cols)
babel_test = pd.read_csv(save_path / "babel_test.csv",
usecols=use_cols.babel_cols)
use_cols.good_columns += [c for c in use_cols.rdkit_cols if c != 'id']
rdkit_train = pd.read_csv(save_path / "rdkit_train.csv",
usecols=use_cols.rdkit_cols)
rdkit_test = pd.read_csv(save_path / "rdkit_test.csv",
usecols=use_cols.rdkit_cols)
coulomb_train = pd.read_csv(save_path /
"coulomb_interaction_train.csv")
coulomb_test = pd.read_csv(save_path / "coulomb_interaction_test.csv")
bond_calc_train = unpickle(save_path / "bond_calc_feat_train.pkl")
bond_calc_test = unpickle(save_path / "bond_calc_feat_test.pkl")
ob_charges = pd.read_csv(save_path / "ob_charges.csv", index_col=0)
tda_radius_df = pd.read_csv(save_path / "tda_radius_df.csv",
index_col=0)
tda_radius_df_03 = pd.read_csv(save_path / "tda_radius_df_v003.csv",
index_col=0)
pca_feat = unpickle(save_path / "pca_feat_df.pkl")
####################################################################################################
# Feature Engineering
train = pd.merge(
train,
scalar_coupling_contributions,
how='left',
left_on=['molecule_name', 'atom_index_0', 'atom_index_1', 'type'],
right_on=['molecule_name', 'atom_index_0', 'atom_index_1', 'type'])
train = map_atom_info(train, 0, structures)
train = map_atom_info(train, 1, structures)
test = map_atom_info(test, 0, structures)
test = map_atom_info(test, 1, structures)
train_p_0 = train[['x_0', 'y_0', 'z_0']].values
train_p_1 = train[['x_1', 'y_1', 'z_1']].values
test_p_0 = test[['x_0', 'y_0', 'z_0']].values
test_p_1 = test[['x_1', 'y_1', 'z_1']].values
train['dist'] = np.linalg.norm(train_p_0 - train_p_1, axis=1)
test['dist'] = np.linalg.norm(test_p_0 - test_p_1, axis=1)
train['dist_x'] = (train['x_0'] - train['x_1'])**2
test['dist_x'] = (test['x_0'] - test['x_1'])**2
train['dist_y'] = (train['y_0'] - train['y_1'])**2
test['dist_y'] = (test['y_0'] - test['y_1'])**2
train['dist_z'] = (train['z_0'] - train['z_1'])**2
test['dist_z'] = (test['z_0'] - test['z_1'])**2
train['type_0'] = train['type'].apply(lambda x: x[0])
test['type_0'] = test['type'].apply(lambda x: x[0])
train['abs_dist'] = np.linalg.norm(train_p_0 - train_p_1,
axis=1,
ord=1)
test['abs_dist'] = np.linalg.norm(test_p_0 - test_p_1, axis=1, ord=1)
dist12('dist_xy', 'x', 'y')
dist12('dist_xz', 'x', 'z')
dist12('dist_yz', 'y', 'z')
atom_count = structures.groupby(['molecule_name',
'atom']).size().unstack(fill_value=0)
train = pd.merge(train,
atom_count,
how='left',
left_on='molecule_name',
right_on='molecule_name')
test = pd.merge(test,
atom_count,
how='left',
left_on='molecule_name',
right_on='molecule_name')
train = create_features(train)
test = create_features(test)
angle_df_train, angle_df_test = angle_feature_conv(structures)
train = train.merge(angle_df_train, on="id", how="left")
test = test.merge(angle_df_test, on="id", how="left")
train = train.merge(train_add, on="id", how="left")
test = test.merge(test_add, on="id", how="left")
# train = train.merge(train_cos, on="id", how="left")
# test = test.merge(test_cos, on="id", how="left")
train = train.merge(babel_train, on="id", how="left")
test = test.merge(babel_test, on="id", how="left")
train = train.merge(rdkit_train, on="id", how="left")
test = test.merge(rdkit_test, on="id", how="left")
train = train.merge(coulomb_train, on="id", how="left")
test = test.merge(coulomb_test, on="id", how="left")
train = train.merge(bond_calc_train, on="id", how="left")
test = test.merge(bond_calc_test, on="id", how="left")
train = train.merge(tda_radius_df, on="molecule_name", how="left")
test = test.merge(tda_radius_df, on="molecule_name", how="left")
train = train.merge(tda_radius_df_03, on="molecule_name", how="left")
test = test.merge(tda_radius_df_03, on="molecule_name", how="left")
train = train.merge(pca_feat, on="molecule_name", how="left")
test = test.merge(pca_feat, on="molecule_name", how="left")
train = map_ob_charges(train, ob_charges, 0)
train = map_ob_charges(train, ob_charges, 1)
test = map_ob_charges(test, ob_charges, 0)
test = map_ob_charges(test, ob_charges, 1)
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
for f in ['atom_1', 'type_0', 'type']:
if f in use_cols.good_columns:
lbl = LabelEncoder()
lbl.fit(list(train[f].values) + list(test[f].values))
train[f] = lbl.transform(list(train[f].values))
test[f] = lbl.transform(list(test[f].values))
Path(save_path / f"{DATA_VERSION}_{TRIAL_NO}").mkdir(parents=True,
exist_ok=True)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/train_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
train)
to_pickle(
save_path /
f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl",
test)
else:
sample_loaded = False
prev_folder = f"../processed/{prev_data_version}/{prev_data_version}_{prev_trial_no}"
if DEBUG:
# v003_033
train_path = Path(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_basic_sampled.pkl"
)
test_path = Path(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_basic_sampled.pkl"
)
if train_path.exists() and test_path.exists():
print("sample loading")
train = unpickle(train_path)
test = unpickle(test_path)
sample_loaded = True
print("sample load finish")
if not sample_loaded:
print(f"loading previous dataest")
print("train loading")
train: pd.DataFrame = unpickle(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_basic.pkl",
)
assert "scalar_coupling_constant" in train.columns
print("test loading")
test: pd.DataFrame = unpickle(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_basic.pkl",
)
print(f"loading finished")
if DEBUG and not sample_loaded:
n_sample = 5000
print(f"sampling {n_sample} rows.")
train = train.sample(n=n_sample)
test = test.sample(n=n_sample)
Path(
f"../processed/{prev_data_version}/{prev_data_version}_{prev_trial_no}"
).mkdir(parents=True, exist_ok=True)
to_pickle(
f"{prev_folder}/train_concat_{prev_data_version}_{prev_trial_no}_basic_sampled.pkl",
train)
to_pickle(
f"{prev_folder}/test_concat_{prev_data_version}_{prev_trial_no}_basic_sampled.pkl",
test)
print("saved.")
###################################################################################################
# add additional feature for trying
# Path(save_path / f"{DATA_VERSION}_{TRIAL_NO}").mkdir(parents=True, exist_ok=True)
# to_pickle(save_path / f"{DATA_VERSION}_{TRIAL_NO}/train_concat_{DATA_VERSION}_{TRIAL_NO}.pkl", train)
# to_pickle(save_path / f"{DATA_VERSION}_{TRIAL_NO}/test_concat_{DATA_VERSION}_{TRIAL_NO}.pkl", test)
return train, test
angle_df_train, angle_df_test = angle_feature_conv()
train = train.merge(angle_df_train, on="id", how="left").merge(train_cos, on="id", how="left")
test = test.merge(angle_df_test, on="id", how="left").merge(test_cos, on="id", how="left")
train = reduce_mem_usage(train)
test = reduce_mem_usage(test)
for f in ['atom_1', 'type_0', 'type']:
if f in good_columns:
lbl = LabelEncoder()
lbl.fit(list(train[f].values) + list(test[f].values))
train[f] = lbl.transform(list(train[f].values))
test[f] = lbl.transform(list(test[f].values))
to_pickle(save_path/"train_v003.pkl", train)
to_pickle(save_path/"test_v003.pkl", test)
X = train[good_columns].copy()
y = train['scalar_coupling_constant']
y_fc = train['fc']
X_test = test[good_columns].copy()
# export colnames
pd.DataFrame({"columns": X.columns.tolist()}).to_csv(log_path/f"use_cols.csv")
####################################################################################################
# Model Fitting
n_fold = 5
folds = KFold(n_splits=n_fold, shuffle=True, random_state=11)