Kaggle competition: Histopathologic Cancer Detection
if use_ucf and use_sort:
train_df = train_df.sort_values('month')
 train_df = train_df.reset_index()<categorify>
from fastai.vision import *
from fastai.metrics import error_rate
df_group = train_df.groupby('building_id')['meter_reading_log1p']
building_median = df_group.median().astype(np.float16)
 train_df['building_median'] = train_df['building_id'].map(building_median)
 del df_group<count_missing_values>
path = Path('.. /input/histopathologic-cancer-detection');
path = Path('.');
path.ls()
weather_train_df.isna().sum()<groupby>
df = pd.read_csv(path/'.. /input/histopathologic-cancer-detection/train_labels.csv'); df.head()
weather_train_df.groupby('site_id' ).apply(lambda group: group.isna().sum() )<groupby>
img_path = path/'.. /input/histopathologic-cancer-detection/train'/df.iloc[0].id
img = img_path.with_suffix('.tif')
 open_image(img )
weather_train_df = weather_train_df.groupby('site_id' ).apply(lambda group: group.interpolate(limit_direction='both'))<groupby>
df_sample = df.copy()
df_sample = df.sample(n=10)
 for index, row in df_sample.iterrows() :
file = '.. /input/histopathologic-cancer-detection/train/'+row.id+'.tif'
image = Image.open(file)
 print(image.size )
weather_train_df.groupby('site_id' ).apply(lambda group: group.isna().sum() )<data_type_conversions>
src =(ImageItemList.from_csv(path/'.. /input/histopathologic-cancer-detection',csv_name='train_labels.csv', folder='train',suffix='.tif')
.random_split_by_pct(0.2, seed=42)
.label_from_df() 
.add_test_folder()
)
def add_lag_feature(weather_df, window=3):
group_df = weather_df.groupby('site_id')
 cols = ['air_temperature', 'cloud_coverage', 'dew_temperature', 'precip_depth_1_hr', 'sea_level_pressure', 'wind_direction', 'wind_speed']
rolled = group_df[cols].rolling(window=window, min_periods=0)
 lag_mean = rolled.mean().reset_index().astype(np.float16)
 lag_max = rolled.max().reset_index().astype(np.float16)
 lag_min = rolled.min().reset_index().astype(np.float16)
 lag_std = rolled.std().reset_index().astype(np.float16)
 for col in cols:
weather_df[f'{col}_mean_lag{window}'] = lag_mean[col]
weather_df[f'{col}_max_lag{window}'] = lag_max[col]
weather_df[f'{col}_min_lag{window}'] = lag_min[col]
weather_df[f'{col}_std_lag{window}'] = lag_std[col]<feature_engineering>
tfms = get_transforms()
data =(src.transform(tfms, size=48)
.databunch() 
.normalize(imagenet_stats))
set_localtime(weather_train_df )<categorify>
data.show_batch(rows=3 )
primary_use_list = building_meta_df['primary_use'].unique()
primary_use_dict = {key: value for value, key in enumerate(primary_use_list)}
print('primary_use_dict: ', primary_use_dict)
 building_meta_df['primary_use'] = building_meta_df['primary_use'].map(primary_use_dict)
 gc.collect()<feature_engineering>
def auc_score(y_pred,y_true,tens=True):
score = roc_auc_score(y_true,torch.sigmoid(y_pred)[:,1])
 if tens:
score = tensor(score)
 return score
learn = create_cnn(arch=models.resnet34, data=data, metrics=[error_rate,auc_score], model_dir='/tmp/.torch/models' )
train_df = reduce_mem_usage(train_df, use_float16=True)
 building_meta_df = reduce_mem_usage(building_meta_df, use_float16=True)
 weather_train_df = reduce_mem_usage(weather_train_df, use_float16=True )<define_variables>
lr=0.001
category_cols = ['building_id', 'site_id', 'primary_use']
feature_cols = ['square_feet', 'year_built'] + [
'hour', 'weekend',
'building_median'] + [
'air_temperature', 'cloud_coverage',
'dew_temperature', 'precip_depth_1_hr', 'sea_level_pressure',
'wind_direction', 'wind_speed' ]<prepare_x_and_y>
learn.fit_one_cycle(1, slice(lr))
def create_X_y(train_df, target_meter):
target_train_df = train_df[train_df['meter'] == target_meter]
target_train_df = target_train_df.merge(building_meta_df, on='building_id', how='left')
 target_train_df = target_train_df.merge(weather_train_df, on=['site_id', 'timestamp'], how='left')
 X_train = target_train_df[feature_cols + category_cols]
y_train = target_train_df['meter_reading_log1p'].values
del target_train_df
return X_train, y_train<train_model>
learn.save('stage1' )
def fit_lgbm(train, val, devices=(-1,), seed=None, cat_features=None, num_rounds=1500, lr=0.1, bf=0.1):

 X_train, y_train = train
X_valid, y_valid = val
metric = 'l2'
params = {'num_leaves': 31,
'objective': 'regression',
'learning_rate': lr,
"boosting": "gbdt",
"bagging_freq": 5,
"bagging_fraction": bf,
"feature_fraction": 0.9,
"metric": metric,
}
device = devices[0]
if device == -1:
pass
else:
print(f'using gpu device_id {device}...')
 params.update({'device': 'gpu', 'gpu_device_id': device})
 params['seed'] = seed
early_stop = 20
verbose_eval = 20
d_train = lgb.Dataset(X_train, label=y_train, categorical_feature=cat_features)
 d_valid = lgb.Dataset(X_valid, label=y_valid, categorical_feature=cat_features)
 watchlist = [d_train, d_valid]
print('training LGB:')
 model = lgb.train(params,
train_set=d_train,
num_boost_round=num_rounds,
valid_sets=watchlist,
verbose_eval=verbose_eval,
early_stopping_rounds=early_stop)
 y_pred_valid = model.predict(X_valid, num_iteration=model.best_iteration)
 print('best_score', model.best_score)
 log = {'train/mae': model.best_score['training']['l2'],
'valid/mae': model.best_score['valid_1']['l2']}
return model, y_pred_valid, log<choose_model_class>
learn.load("stage1")
 learn.unfreeze()
learn.lr_find()
learn.recorder.plot()
seed = 666
shuffle = False
kf = KFold(n_splits=folds, shuffle=shuffle, random_state=seed)
 oof_total = 0<split>
learn.fit_one_cycle(1, slice(1e-6, lr/5))
target_meter = 0
X_train, y_train = create_X_y(train_df, target_meter=target_meter)
 y_valid_pred_total = np.zeros(X_train.shape[0])
 gc.collect()
print('target_meter', target_meter, X_train.shape)
 cat_features = [X_train.columns.get_loc(cat_col)for cat_col in category_cols]
print('cat_features', cat_features)
 models0 = []
for train_idx, valid_idx in kf.split(X_train, y_train):
train_data = X_train.iloc[train_idx,:], y_train[train_idx]
valid_data = X_train.iloc[valid_idx,:], y_train[valid_idx]
print('train', len(train_idx), 'valid', len(valid_idx))
model, y_pred_valid, log = fit_lgbm(train_data, valid_data, cat_features=category_cols,
num_rounds=num_rounds, lr=0.05, bf=0.7)
 y_valid_pred_total[valid_idx] = y_pred_valid
models0.append(model)
 gc.collect()
if debug:
break
sns.distplot(y_train)
 sns.distplot(y_valid_pred_total)
 oof0 = mean_squared_error(y_train, y_valid_pred_total)
 oof_total += oof0 * len(y_train)
 del X_train, y_train
gc.collect()<split>
learn.fit_one_cycle(1, slice(1e-5, lr/5))
target_meter = 1
X_train, y_train = create_X_y(train_df, target_meter=target_meter)
 y_valid_pred_total = np.zeros(X_train.shape[0])
 gc.collect()
print('target_meter', target_meter, X_train.shape)
 cat_features = [X_train.columns.get_loc(cat_col)for cat_col in category_cols]
print('cat_features', cat_features)
 models1 = []
for train_idx, valid_idx in kf.split(X_train, y_train):
train_data = X_train.iloc[train_idx,:], y_train[train_idx]
valid_data = X_train.iloc[valid_idx,:], y_train[valid_idx]
print('train', len(train_idx), 'valid', len(valid_idx))
model, y_pred_valid, log = fit_lgbm(train_data, valid_data, cat_features=category_cols, num_rounds=num_rounds,
lr=0.05, bf=0.5)
 y_valid_pred_total[valid_idx] = y_pred_valid
models1.append(model)
 gc.collect()
if debug:
break
sns.distplot(y_train)
 sns.distplot(y_valid_pred_total)
 oof1 = mean_squared_error(y_train, y_valid_pred_total)
 oof_total += oof1 * len(y_train)
 del X_train, y_train
gc.collect()<split>
learn.save("stage3" )
target_meter = 2
X_train, y_train = create_X_y(train_df, target_meter=target_meter)
 y_valid_pred_total = np.zeros(X_train.shape[0])
 gc.collect()
print('target_meter', target_meter, X_train.shape)
 cat_features = [X_train.columns.get_loc(cat_col)for cat_col in category_cols]
print('cat_features', cat_features)
 models2 = []
for train_idx, valid_idx in kf.split(X_train, y_train):
train_data = X_train.iloc[train_idx,:], y_train[train_idx]
valid_data = X_train.iloc[valid_idx,:], y_train[valid_idx]
print('train', len(train_idx), 'valid', len(valid_idx))
model, y_pred_valid, log = fit_lgbm(train_data, valid_data, cat_features=category_cols,
num_rounds=num_rounds, lr=0.05, bf=0.8)
 y_valid_pred_total[valid_idx] = y_pred_valid
models2.append(model)
 gc.collect()
if debug:
break
sns.distplot(y_train)
 sns.distplot(y_valid_pred_total)
 oof2 = mean_squared_error(y_train, y_valid_pred_total)
 oof_total += oof2 * len(y_train)
 del X_train, y_train
gc.collect()<split>
learn.load("stage3")
 learn.unfreeze()
learn.lr_find()
learn.recorder.plot()
target_meter = 3
X_train, y_train = create_X_y(train_df, target_meter=target_meter)
 y_valid_pred_total = np.zeros(X_train.shape[0])
 gc.collect()
print('target_meter', target_meter, X_train.shape)
 cat_features = [X_train.columns.get_loc(cat_col)for cat_col in category_cols]
print('cat_features', cat_features)
 models3 = []
for train_idx, valid_idx in kf.split(X_train, y_train):
train_data = X_train.iloc[train_idx,:], y_train[train_idx]
valid_data = X_train.iloc[valid_idx,:], y_train[valid_idx]
print('train', len(train_idx), 'valid', len(valid_idx))
model, y_pred_valid, log = fit_lgbm(train_data, valid_data, cat_features=category_cols, num_rounds=num_rounds,
lr=0.03, bf=0.9)
 y_valid_pred_total[valid_idx] = y_pred_valid
models3.append(model)
 gc.collect()
if debug:
break
sns.distplot(y_train)
 sns.distplot(y_valid_pred_total)
 oof3 = mean_squared_error(y_train, y_valid_pred_total)
 oof_total += oof3 * len(y_train)
 del X_train, y_train
gc.collect()<compute_test_metric>
learn.fit_one_cycle(3, slice(1e-6, lr/5))
print('oof score meter0 =', np.sqrt(oof0))
print('oof score meter1 =', np.sqrt(oof1))
print('oof score meter2 =', np.sqrt(oof2))
print('oof score meter3 =', np.sqrt(oof3))
print('oof score total =', np.sqrt(oof_total / len(train_df)) )<drop_column>
learn.save("stage3-sm" )
del train_df, weather_train_df, building_meta_df
gc.collect()<feature_engineering>
learn.load("stage3-sm" )
print('loading...')
 test_df = pd.read_feather(root/'test.feather')
 weather_test_df = pd.read_feather(root/'weather_test.feather')
 building_meta_df = pd.read_feather(root/'building_metadata.feather')
 set_localtime(weather_test_df)
 print('preprocessing building...')
 test_df['date'] = test_df['timestamp'].dt.date
preprocess(test_df)
 test_df['building_median'] = test_df['building_id'].map(building_median)
 print('preprocessing weather...')
 weather_test_df = weather_test_df.groupby('site_id' ).apply(lambda group: group.interpolate(limit_direction='both'))
weather_test_df.groupby('site_id' ).apply(lambda group: group.isna().sum())
 print('reduce mem usage...')
 reduce_mem_usage(test_df, use_float16=True)
 reduce_mem_usage(weather_test_df, use_float16=True)
 gc.collect()<load_from_disk>
tfms = get_transforms()
data =(src.transform(tfms, size = 96)
.databunch().normalize(imagenet_stats))
learn.data = data
sample_submission = pd.read_feather(os.path.join(root, 'sample_submission.feather'))
reduce_mem_usage(sample_submission )<merge>
learn.fit_one_cycle(1, slice(1e-3))
def create_X(test_df, target_meter):
target_test_df = test_df[test_df['meter'] == target_meter]
target_test_df = target_test_df.merge(building_meta_df, on='building_id', how='left')
 target_test_df = target_test_df.merge(weather_test_df, on=['site_id', 'timestamp'], how='left')
 X_test = target_test_df[feature_cols + category_cols]
return X_test<predict_on_test>
learn.lr_find()
learn.recorder.plot()
def pred(X_test, models, batch_size=1000000):
iterations =(X_test.shape[0] + batch_size -1)// batch_size
print('iterations', iterations)
 y_test_pred_total = np.zeros(X_test.shape[0])
 for i, model in enumerate(models):
print(f'predicting {i}-th model')
 for k in tqdm(range(iterations)) :
y_pred_test = model.predict(X_test[k*batch_size:(k+1)*batch_size], num_iteration=model.best_iteration)
 y_test_pred_total[k*batch_size:(k+1)*batch_size] += y_pred_test
y_test_pred_total /= len(models)
 return y_test_pred_total 
<feature_engineering>
learn.unfreeze()
learn.fit_one_cycle(4, slice(1e-6))
sample_submission.loc[test_df['meter'] == 0, 'meter_reading'] = np.expm1(y_test0)
 sample_submission.loc[test_df['meter'] == 1, 'meter_reading'] = np.expm1(y_test1)
 sample_submission.loc[test_df['meter'] == 2, 'meter_reading'] = np.expm1(y_test2)
 sample_submission.loc[test_df['meter'] == 3, 'meter_reading'] = np.expm1(y_test3 )<save_to_csv>
learn.save('stage3-lg' )
if not debug:
sample_submission.to_csv('submission.csv', index=False, float_format='%.4f' )<feature_engineering>
leak_score0 = 0
leak_df = pd.read_pickle(ucf_root/'site0.pkl')
 leak_df['meter_reading'] = leak_df.meter_reading_scraped
leak_df.drop(['meter_reading_original','meter_reading_scraped'], axis=1, inplace=True)
 leak_df.fillna(0, inplace=True)
 leak_df = leak_df[leak_df.timestamp.dt.year > 2016]
leak_df.loc[leak_df.meter_reading < 0, 'meter_reading'] = 0
sample_submission.loc[sample_submission.meter_reading < 0, 'meter_reading'] = 0
for bid in leak_df.building_id.unique() :
temp_df = leak_df[(leak_df.building_id == bid)]
for m in temp_df.meter.unique() :
v0 = sample_submission.loc[(test_df.building_id == bid)&(test_df.meter==m), 'meter_reading'].values
v1 = temp_df[temp_df.meter==m].meter_reading.values
leak_score0 += mean_squared_error(np.log1p(v0), np.log1p(v1)) * len(v0)
 sample_submission.loc[(test_df.building_id == bid)&(test_df.meter==m), 'meter_reading'] = temp_df[temp_df.meter==m].meter_reading.values
leak_score0 /= len(leak_df )<feature_engineering>