Kaggle competition: OSIC Pulmonary Fibrosis Progression
<SOS> metric: LaplaceLogLikelihood Kaggle data source: osic-pulmonary-fibrosis-progression<merge>
!pip install.. /input/kerasapplications/keras-team-keras-applications-3b180cb -f./ --no-index
!pip install.. /input/efficientnet/efficientnet-1.1.0/ -f./ --no-index
ts = time.time()
group = matrix.groupby(['date_block_num', 'shop_id', 'type_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = ['date_shop_type_avg_item_cnt']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'shop_id', 'type_code'], how='left')
 matrix['date_shop_type_avg_item_cnt'] = matrix['date_shop_type_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_shop_type_avg_item_cnt')
 matrix.drop(['date_shop_type_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<merge>
def seed_everything(seed=2020):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 tf.random.set_seed(seed)
 seed_everything(42 )
ts = time.time()
group = matrix.groupby(['date_block_num', 'shop_id', 'subtype_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = ['date_shop_subtype_avg_item_cnt']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'shop_id', 'subtype_code'], how='left')
 matrix['date_shop_subtype_avg_item_cnt'] = matrix['date_shop_subtype_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_shop_subtype_avg_item_cnt')
 matrix.drop(['date_shop_subtype_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<merge>
config = tf.compat.v1.ConfigProto()
config.gpu_options.allow_growth = True
session = tf.compat.v1.Session(config=config )
ts = time.time()
group = matrix.groupby(['date_block_num', 'city_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = [ 'date_city_avg_item_cnt' ]
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'city_code'], how='left')
 matrix['date_city_avg_item_cnt'] = matrix['date_city_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_city_avg_item_cnt')
 matrix.drop(['date_city_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<merge>
train = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/train.csv' )
ts = time.time()
group = matrix.groupby(['date_block_num', 'item_id', 'city_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = [ 'date_item_city_avg_item_cnt' ]
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'item_id', 'city_code'], how='left')
 matrix['date_item_city_avg_item_cnt'] = matrix['date_item_city_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_item_city_avg_item_cnt')
 matrix.drop(['date_item_city_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<merge>
def get_tab(df):
vector = [(df.Age.values[0] - 30)/ 30]
if df.Sex.values[0] == 'male':
vector.append(0)
 else:
vector.append(1)
 if df.SmokingStatus.values[0] == 'Never smoked':
vector.extend([0,0])
 elif df.SmokingStatus.values[0] == 'Ex-smoker':
vector.extend([1,1])
 elif df.SmokingStatus.values[0] == 'Currently smokes':
vector.extend([0,1])
 else:
vector.extend([1,0])
 return np.array(vector )
ts = time.time()
group = matrix.groupby(['date_block_num', 'type_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = [ 'date_type_avg_item_cnt' ]
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'type_code'], how='left')
 matrix['date_type_avg_item_cnt'] = matrix['date_type_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_type_avg_item_cnt')
 matrix.drop(['date_type_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<merge>
A = {}
TAB = {}
P = []
for i, p in tqdm(enumerate(train.Patient.unique())) :
sub = train.loc[train.Patient == p, :]
fvc = sub.FVC.values
weeks = sub.Weeks.values
c = np.vstack([weeks, np.ones(len(weeks)) ] ).T
a, b = np.linalg.lstsq(c, fvc)[0]
A[p] = a
TAB[p] = get_tab(sub)
 P.append(p )
ts = time.time()
group = matrix.groupby(['date_block_num', 'subtype_code'] ).agg({'item_cnt_month': ['mean']})
 group.columns = [ 'date_subtype_avg_item_cnt' ]
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num', 'subtype_code'], how='left')
 matrix['date_subtype_avg_item_cnt'] = matrix['date_subtype_avg_item_cnt'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'date_subtype_avg_item_cnt')
 matrix.drop(['date_subtype_avg_item_cnt'], axis=1, inplace=True)
 time.time() - ts<data_type_conversions>
class IGenerator(Sequence):
BAD_ID = ['ID00011637202177653955184', 'ID00052637202186188008618']
def __init__(self, keys, a, tab, batch_size=32):
self.keys = [k for k in keys if k not in self.BAD_ID]
self.a = a
self.tab = tab
self.batch_size = batch_size
self.train_data = {}
for p in train.Patient.values:
self.train_data[p] = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/')
 def __len__(self):
return 1000
def __getitem__(self, idx):
x = []
a, tab = [], []
keys = np.random.choice(self.keys, size = self.batch_size)
 for k in keys:
try:
i = np.random.choice(self.train_data[k], size=1)[0]
img = get_img(f'.. /input/osic-pulmonary-fibrosis-progression/train/{k}/{i}')
 x.append(img)
 a.append(self.a[k])
 tab.append(self.tab[k])
 except:
print(k, i)
 x,a,tab = np.array(x), np.array(a), np.array(tab)
 x = np.expand_dims(x, axis=-1)
 return [x, tab] , a
ts = time.time()
group = train.groupby(['item_id'] ).agg({'item_price': ['mean']})
 group.columns = ['item_avg_item_price']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['item_id'], how='left')
 matrix['item_avg_item_price'] = matrix['item_avg_item_price'].astype(np.float16)
 group = train.groupby(['date_block_num','item_id'] ).agg({'item_price': ['mean']})
 group.columns = ['date_item_avg_item_price']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num','item_id'], how='left')
 matrix['date_item_avg_item_price'] = matrix['date_item_avg_item_price'].astype(np.float16)
 lags = [1,2,3,4,5,6]
matrix = lag_feature(matrix, lags, 'date_item_avg_item_price')
 for i in lags:
matrix['delta_price_lag_'+str(i)] = \ 
(matrix['date_item_avg_item_price_lag_'+str(i)] - matrix['item_avg_item_price'])/ matrix['item_avg_item_price']
def select_trend(row):
for i in lags:
if row['delta_price_lag_'+str(i)]:
return row['delta_price_lag_'+str(i)]
return 0
matrix['delta_price_lag'] = matrix.apply(select_trend, axis=1)
 matrix['delta_price_lag'] = matrix['delta_price_lag'].astype(np.float16)
 matrix['delta_price_lag'].fillna(0, inplace=True)
 fetures_to_drop = ['item_avg_item_price', 'date_item_avg_item_price']
for i in lags:
fetures_to_drop += ['date_item_avg_item_price_lag_'+str(i)]
fetures_to_drop += ['delta_price_lag_'+str(i)]
matrix.drop(fetures_to_drop, axis=1, inplace=True)
 time.time() - ts<merge>
Dense, Dropout, Activation, Flatten, Input, BatchNormalization, GlobalAveragePooling2D, Add, Conv2D, AveragePooling2D,
LeakyReLU, Concatenate 
)
 def get_efficientnet(model, shape):
models_dict = {
'b0': efn.EfficientNetB0(input_shape=shape,weights=None,include_top=False),
'b1': efn.EfficientNetB1(input_shape=shape,weights=None,include_top=False),
'b2': efn.EfficientNetB2(input_shape=shape,weights=None,include_top=False),
'b3': efn.EfficientNetB3(input_shape=shape,weights=None,include_top=False),
'b4': efn.EfficientNetB4(input_shape=shape,weights=None,include_top=False),
'b5': efn.EfficientNetB5(input_shape=shape,weights=None,include_top=False),
'b6': efn.EfficientNetB6(input_shape=shape,weights=None,include_top=False),
'b7': efn.EfficientNetB7(input_shape=shape,weights=None,include_top=False)
 }
return models_dict[model]
def build_model(shape=(512, 512, 1), model_class=None):
inp = Input(shape=shape)
 base = get_efficientnet(model_class, shape)
 x = base(inp)
 x = GlobalAveragePooling2D()(x)
 inp2 = Input(shape=(4,))
x2 = tf.keras.layers.GaussianNoise(0.2 )(inp2)
 x = Concatenate()([x, x2])
 x = Dropout(0.4 )(x)
 x = Dense(1 )(x)
 model = Model([inp, inp2] , x)
 weights = [w for w in os.listdir('.. /input/osic-model-weights')if model_class in w][0]
model.load_weights('.. /input/osic-model-weights/' + weights)
 return model
model_classes = ['b5']
models = [build_model(shape=(512, 512, 1), model_class=m)for m in model_classes]
print('Number of models: ' + str(len(models)) )
ts = time.time()
group = train.groupby(['date_block_num','shop_id'] ).agg({'revenue': ['sum']})
 group.columns = ['date_shop_revenue']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['date_block_num','shop_id'], how='left')
 matrix['date_shop_revenue'] = matrix['date_shop_revenue'].astype(np.float32)
 group = group.groupby(['shop_id'] ).agg({'date_shop_revenue': ['mean']})
 group.columns = ['shop_avg_revenue']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=['shop_id'], how='left')
 matrix['shop_avg_revenue'] = matrix['shop_avg_revenue'].astype(np.float32)
 matrix['delta_revenue'] =(matrix['date_shop_revenue'] - matrix['shop_avg_revenue'])/ matrix['shop_avg_revenue']
matrix['delta_revenue'] = matrix['delta_revenue'].astype(np.float16)
 matrix = lag_feature(matrix, [1], 'delta_revenue')
 matrix.drop(['date_shop_revenue','shop_avg_revenue','delta_revenue'], axis=1, inplace=True)
 time.time() - ts<feature_engineering>
tr_p, vl_p = train_test_split(P,
shuffle=True,
train_size= 0.8 )
matrix['month'] = matrix['date_block_num'] % 12<categorify>
def score(fvc_true, fvc_pred, sigma):
sigma_clip = np.maximum(sigma, 70)
 delta = np.abs(fvc_true - fvc_pred)
 delta = np.minimum(delta, 1000)
 sq2 = np.sqrt(2)
 metric =(delta / sigma_clip)*sq2 + np.log(sigma_clip* sq2)
 return np.mean(metric )
days = pd.Series([31,28,31,30,31,30,31,31,30,31,30,31])
 matrix['days'] = matrix['month'].map(days ).astype(np.int8 )<data_type_conversions>
subs = []
for model in models:
metric = []
for q in tqdm(range(1, 10)) :
m = []
for p in vl_p:
x = []
tab = []
if p in ['ID00011637202177653955184', 'ID00052637202186188008618']:
continue
ldir = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/')
 for i in ldir:
if int(i[:-4])/ len(ldir)< 0.8 and int(i[:-4])/ len(ldir)> 0.15:
x.append(get_img(f'.. /input/osic-pulmonary-fibrosis-progression/train/{p}/{i}'))
tab.append(get_tab(train.loc[train.Patient == p, :]))
if len(x)< 1:
continue
tab = np.array(tab)
 x = np.expand_dims(x, axis=-1)
 _a = model.predict([x, tab])
 a = np.quantile(_a, q / 10)
 percent_true = train.Percent.values[train.Patient == p]
fvc_true = train.FVC.values[train.Patient == p]
weeks_true = train.Weeks.values[train.Patient == p]
fvc = a *(weeks_true - weeks_true[0])+ fvc_true[0]
percent = percent_true[0] - a * abs(weeks_true - weeks_true[0])
 m.append(score(fvc_true, fvc, percent))
print(np.mean(m))
metric.append(np.mean(m))
q =(np.argmin(metric)+ 1)/ 10
sub = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/sample_submission.csv')
 test = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 A_test, B_test, P_test,W, FVC= {}, {}, {},{},{}
STD, WEEK = {}, {}
for p in test.Patient.unique() :
x = []
tab = []
ldir = os.listdir(f'.. /input/osic-pulmonary-fibrosis-progression/test/{p}/')
 for i in ldir:
if int(i[:-4])/ len(ldir)< 0.8 and int(i[:-4])/ len(ldir)> 0.15:
x.append(get_img(f'.. /input/osic-pulmonary-fibrosis-progression/test/{p}/{i}'))
tab.append(get_tab(test.loc[test.Patient == p, :]))
if len(x)<= 1:
continue
tab = np.array(tab)
 x = np.expand_dims(x, axis=-1)
 _a = model.predict([x, tab])
 a = np.quantile(_a, q)
 A_test[p] = a
B_test[p] = test.FVC.values[test.Patient == p] - a*test.Weeks.values[test.Patient == p]
P_test[p] = test.Percent.values[test.Patient == p]
WEEK[p] = test.Weeks.values[test.Patient == p]
for k in sub.Patient_Week.values:
p, w = k.split('_')
 w = int(w)
 fvc = A_test[p] * w + B_test[p]
sub.loc[sub.Patient_Week == k, 'FVC'] = fvc
sub.loc[sub.Patient_Week == k, 'Confidence'] =(
 P_test[p] - A_test[p] * abs(WEEK[p] - w)
)
 _sub = sub[["Patient_Week","FVC","Confidence"]].copy()
subs.append(_sub )
ts = time.time()
cache = {}
matrix['item_shop_last_sale'] = -1
matrix['item_shop_last_sale'] = matrix['item_shop_last_sale'].astype(np.int8)
 for idx, row in matrix.iterrows() :
key = str(row.item_id)+' '+str(row.shop_id)
 if key not in cache:
if row.item_cnt_month!=0:
cache[key] = row.date_block_num
else:
last_date_block_num = cache[key]
matrix.at[idx, 'item_shop_last_sale'] = row.date_block_num - last_date_block_num
cache[key] = row.date_block_num
time.time() - ts<data_type_conversions>
N = len(subs)
 sub = subs[0].copy()
sub["FVC"] = 0
sub["Confidence"] = 0
for i in range(N):
sub["FVC"] += subs[0]["FVC"] *(1/N)
 sub["Confidence"] += subs[0]["Confidence"] *(1/N )
ts = time.time()
cache = {}
matrix['item_last_sale'] = -1
matrix['item_last_sale'] = matrix['item_last_sale'].astype(np.int8)
 for idx, row in matrix.iterrows() :
key = row.item_id
if key not in cache:
if row.item_cnt_month!=0:
cache[key] = row.date_block_num
else:
last_date_block_num = cache[key]
if row.date_block_num>last_date_block_num:
matrix.at[idx, 'item_last_sale'] = row.date_block_num - last_date_block_num
cache[key] = row.date_block_num
time.time() - ts<feature_engineering>
sub[["Patient_Week","FVC","Confidence"]].to_csv("submission_img.csv", index=False )
ts = time.time()
matrix['item_shop_first_sale'] = matrix['date_block_num'] - matrix.groupby(['item_id','shop_id'])['date_block_num'].transform('min')
 matrix['item_first_sale'] = matrix['date_block_num'] - matrix.groupby('item_id')['date_block_num'].transform('min')
 time.time() - ts<filter>
img_sub = sub[["Patient_Week","FVC","Confidence"]].copy()
ts = time.time()
matrix = matrix[matrix.date_block_num > 11]
time.time() - ts<correct_missing_values>
ROOT = ".. /input/osic-pulmonary-fibrosis-progression"
BATCH_SIZE=128
tr = pd.read_csv(f"{ROOT}/train.csv")
 tr.drop_duplicates(keep=False, inplace=True, subset=['Patient','Weeks'])
 chunk = pd.read_csv(f"{ROOT}/test.csv")
 print("add infos")
 sub = pd.read_csv(f"{ROOT}/sample_submission.csv")
 sub['Patient'] = sub['Patient_Week'].apply(lambda x:x.split('_')[0])
 sub['Weeks'] = sub['Patient_Week'].apply(lambda x: int(x.split('_')[-1]))
sub = sub[['Patient','Weeks','Confidence','Patient_Week']]
sub = sub.merge(chunk.drop('Weeks', axis=1), on="Patient" )
ts = time.time()
def fill_na(df):
for col in df.columns:
if('_lag_' in col)&(df[col].isnull().any()):
if('item_cnt' in col):
df[col].fillna(0, inplace=True)
 return df
matrix = fill_na(matrix)
 time.time() - ts<load_pretrained>
tr['WHERE'] = 'train'
chunk['WHERE'] = 'val'
sub['WHERE'] = 'test'
data = tr.append([chunk, sub] )
matrix.to_pickle('data.pkl')
 del matrix
del cache
del group
del items
del shops
del cats
del train
gc.collect() ;<load_pretrained>
print(tr.shape, chunk.shape, sub.shape, data.shape)
 print(tr.Patient.nunique() , chunk.Patient.nunique() , sub.Patient.nunique() ,
data.Patient.nunique())
data = pd.read_pickle('data.pkl' )<drop_column>
data['min_week'] = data['Weeks']
data.loc[data.WHERE=='test','min_week'] = np.nan
data['min_week'] = data.groupby('Patient')['min_week'].transform('min' )
data = data[[
'date_block_num',
'shop_id',
'item_id',
'item_cnt_month',
'city_code',
'item_category_id',
'type_code',
'subtype_code',
'item_cnt_month_lag_1',
'item_cnt_month_lag_2',
'item_cnt_month_lag_3',
'item_cnt_month_lag_6',
'item_cnt_month_lag_12',
'date_avg_item_cnt_lag_1',
'date_item_avg_item_cnt_lag_1',
'date_item_avg_item_cnt_lag_2',
'date_item_avg_item_cnt_lag_3',
'date_item_avg_item_cnt_lag_6',
'date_item_avg_item_cnt_lag_12',
'date_shop_avg_item_cnt_lag_1',
'date_shop_avg_item_cnt_lag_2',
'date_shop_avg_item_cnt_lag_3',
'date_shop_avg_item_cnt_lag_6',
'date_shop_avg_item_cnt_lag_12',
'date_cat_avg_item_cnt_lag_1',
'date_shop_cat_avg_item_cnt_lag_1',
'date_city_avg_item_cnt_lag_1',
'date_item_city_avg_item_cnt_lag_1',
'delta_price_lag',
'month',
'days',
'item_shop_last_sale',
'item_last_sale',
'item_shop_first_sale',
'item_first_sale',
]]<prepare_x_and_y>
base = data.loc[data.Weeks == data.min_week]
base = base[['Patient','FVC']].copy()
base.columns = ['Patient','min_FVC']
base['nb'] = 1
base['nb'] = base.groupby('Patient')['nb'].transform('cumsum')
 base = base[base.nb==1]
base.drop('nb', axis=1, inplace=True )
X_train = data[data.date_block_num < 33].drop(['item_cnt_month'], axis=1)
 Y_train = data[data.date_block_num < 33]['item_cnt_month']
X_valid = data[data.date_block_num == 33].drop(['item_cnt_month'], axis=1)
 Y_valid = data[data.date_block_num == 33]['item_cnt_month']
X_test = data[data.date_block_num == 34].drop(['item_cnt_month'], axis=1 )<set_options>
data = data.merge(base, on='Patient', how='left')
 data['base_week'] = data['Weeks'] - data['min_week']
del base
del data
gc.collect() ;<train_model>
COLS = ['Sex','SmokingStatus']
FE = []
for col in COLS:
for mod in data[col].unique() :
FE.append(mod)
 data[mod] =(data[col] == mod ).astype(int )
ts = time.time()
model = XGBRegressor(
 max_depth=8,
n_estimators=1000,
min_child_weight=300,
colsample_bytree=0.8,
subsample=0.8,
eta=0.3,
seed=42)
 model.fit(
 X_train,
Y_train,
eval_metric="rmse",
eval_set=[(X_train, Y_train),(X_valid, Y_valid)],
verbose=True,
early_stopping_rounds = 10)
 time.time() - ts<save_to_csv>
data['age'] =(data['Age'] - data['Age'].min())/(data['Age'].max() - data['Age'].min())
 data['BASE'] =(data['min_FVC'] - data['min_FVC'].min())/(data['min_FVC'].max() - data['min_FVC'].min())
 data['week'] =(data['base_week'] - data['base_week'].min())/(data['base_week'].max() - data['base_week'].min())
 data['percent'] =(data['Percent'] - data['Percent'].min())/(data['Percent'].max() - data['Percent'].min())
 FE += ['age','percent','week','BASE']
Y_pred = model.predict(X_valid ).clip(0, 20)
 Y_test = model.predict(X_test ).clip(0, 20)
 submission = pd.DataFrame({
"ID": test.index,
"item_cnt_month": Y_test
})
 submission.to_csv('xgb_submission.csv', index=False)
 pickle.dump(Y_pred, open('xgb_train.pickle', 'wb'))
pickle.dump(Y_test, open('xgb_test.pickle', 'wb'))<load_from_csv>
tr = data.loc[data.WHERE=='train']
chunk = data.loc[data.WHERE=='val']
sub = data.loc[data.WHERE=='test']
del data
items = pd.read_csv('.. /input/items.csv')
 shops = pd.read_csv('.. /input/shops.csv')
 cats = pd.read_csv('.. /input/item_categories.csv')
 train = pd.read_csv('.. /input/sales_train.csv')
 test = pd.read_csv('.. /input/test.csv' ).set_index('ID' )<filter>
C1, C2 = tf.constant(70, dtype='float32'), tf.constant(1000, dtype="float32")
 def score(y_true, y_pred):
tf.dtypes.cast(y_true, tf.float32)
 tf.dtypes.cast(y_pred, tf.float32)
 sigma = y_pred[:, 2] - y_pred[:, 0]
fvc_pred = y_pred[:, 1]
sigma_clip = tf.maximum(sigma, C1)
 delta = tf.abs(y_true[:, 0] - fvc_pred)
 delta = tf.minimum(delta, C2)
 sq2 = tf.sqrt(tf.dtypes.cast(2, dtype=tf.float32))
metric =(delta / sigma_clip)*sq2 + tf.math.log(sigma_clip* sq2)
 return K.mean(metric)
 def qloss(y_true, y_pred):
qs = [0.2, 0.50, 0.8]
q = tf.constant(np.array([qs]), dtype=tf.float32)
 e = y_true - y_pred
v = tf.maximum(q*e,(q-1)*e)
 return K.mean(v)
 def mloss(_lambda):
def loss(y_true, y_pred):
return _lambda * qloss(y_true, y_pred)+(1 - _lambda)*score(y_true, y_pred)
 return loss
def make_model(nh):
z = L.Input(( nh,), name="Patient")
 x = L.Dense(100, activation="relu", name="d1" )(z)
 x = L.Dense(100, activation="relu", name="d2" )(x)
 p1 = L.Dense(3, activation="linear", name="p1" )(x)
 p2 = L.Dense(3, activation="relu", name="p2" )(x)
 preds = L.Lambda(lambda x: x[0] + tf.cumsum(x[1], axis=1),
name="preds" )([p1, p2])
 model = M.Model(z, preds, name="CNN")
 model.compile(loss=mloss(0.8), optimizer=tf.keras.optimizers.Adam(lr=0.1, beta_1=0.9, beta_2=0.999, epsilon=None, decay=0.01, amsgrad=False), metrics=[score])
 return model
train = train[train.item_price<100000]
train = train[train.item_cnt_day<1001]<feature_engineering>
y = tr['FVC'].values
z = tr[FE].values
ze = sub[FE].values
nh = z.shape[1]
pe = np.zeros(( ze.shape[0], 3))
pred = np.zeros(( z.shape[0], 3))
median = train[(train.shop_id==32)&(train.item_id==2973)&(train.date_block_num==4)&(train.item_price>0)].item_price.median()
train.loc[train.item_price<0, 'item_price'] = median<feature_engineering>
NFOLD = 5
kf = KFold(n_splits=NFOLD )
train.loc[train.shop_id == 0, 'shop_id'] = 57
test.loc[test.shop_id == 0, 'shop_id'] = 57
train.loc[train.shop_id == 1, 'shop_id'] = 58
test.loc[test.shop_id == 1, 'shop_id'] = 58
train.loc[train.shop_id == 10, 'shop_id'] = 11
test.loc[test.shop_id == 10, 'shop_id'] = 11<categorify>
%%time
cnt = 0
EPOCHS = 800
for tr_idx, val_idx in kf.split(z):
cnt += 1
print(f"FOLD {cnt}")
 net = make_model(nh)
 net.fit(z[tr_idx], y[tr_idx], batch_size=BATCH_SIZE, epochs=EPOCHS,
validation_data=(z[val_idx], y[val_idx]), verbose=0)
 print("train", net.evaluate(z[tr_idx], y[tr_idx], verbose=0, batch_size=BATCH_SIZE))
print("val", net.evaluate(z[val_idx], y[val_idx], verbose=0, batch_size=BATCH_SIZE))
print("predict val...")
 pred[val_idx] = net.predict(z[val_idx], batch_size=BATCH_SIZE, verbose=0)
 print("predict test...")
 pe += net.predict(ze, batch_size=BATCH_SIZE, verbose=0)/ NFOLD
shops.loc[shops.shop_name == 'Сергиев Посад ТЦ "7Я"', 'shop_name'] = 'СергиевПосад ТЦ "7Я"'
shops['city'] = shops['shop_name'].str.split(' ' ).map(lambda x: x[0])
 shops.loc[shops.city == '!Якутск', 'city'] = 'Якутск'
shops['city_code'] = LabelEncoder().fit_transform(shops['city'])
 shops = shops[['shop_id','city_code']]
cats['split'] = cats['item_category_name'].str.split('-')
 cats['type'] = cats['split'].map(lambda x: x[0].strip())
 cats['type_code'] = LabelEncoder().fit_transform(cats['type'])
 cats['subtype'] = cats['split'].map(lambda x: x[1].strip() if len(x)> 1 else x[0].strip())
 cats['subtype_code'] = LabelEncoder().fit_transform(cats['subtype'])
 cats = cats[['item_category_id','type_code', 'subtype_code']]
items.drop(['item_name'], axis=1, inplace=True )<concatenate>
sigma_opt = mean_absolute_error(y, pred[:, 1])
 unc = pred[:,2] - pred[:, 0]
sigma_mean = np.mean(unc)
 print(sigma_opt, sigma_mean )
len(list(set(test.item_id)- set(test.item_id ).intersection(set(train.item_id)))) , len(list(set(test.item_id))), len(test )<data_type_conversions>
sub['FVC1'] = 1.*pe[:, 1]
sub['Confidence1'] = pe[:, 2] - pe[:, 0]
subm = sub[['Patient_Week','FVC','Confidence','FVC1','Confidence1']].copy()
subm.loc[~subm.FVC1.isnull() ].head(10 )
ts = time.time()
matrix = []
cols = ['date_block_num','shop_id','item_id']
for i in range(34):
sales = train[train.date_block_num==i]
matrix.append(np.array(list(product([i], sales.shop_id.unique() , sales.item_id.unique())) , dtype='int16'))
matrix = pd.DataFrame(np.vstack(matrix), columns=cols)
 matrix['date_block_num'] = matrix['date_block_num'].astype(np.int8)
 matrix['shop_id'] = matrix['shop_id'].astype(np.int8)
 matrix['item_id'] = matrix['item_id'].astype(np.int16)
 matrix.sort_values(cols,inplace=True)
 time.time() - ts<feature_engineering>
subm.loc[~subm.FVC1.isnull() ,'FVC'] = subm.loc[~subm.FVC1.isnull() ,'FVC1']
if sigma_mean<70:
subm['Confidence'] = sigma_opt
else:
subm.loc[~subm.FVC1.isnull() ,'Confidence'] = subm.loc[~subm.FVC1.isnull() ,'Confidence1']
train['revenue'] = train['item_price'] * train['item_cnt_day']<merge>
otest = pd.read_csv('.. /input/osic-pulmonary-fibrosis-progression/test.csv')
 for i in range(len(otest)) :
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'FVC'] = otest.FVC[i]
subm.loc[subm['Patient_Week']==otest.Patient[i]+'_'+str(otest.Weeks[i]), 'Confidence'] = 0.1
ts = time.time()
group = train.groupby(['date_block_num','shop_id','item_id'] ).agg({'item_cnt_day': ['sum']})
 group.columns = ['item_cnt_month']
group.reset_index(inplace=True)
 matrix = pd.merge(matrix, group, on=cols, how='left')
 matrix['item_cnt_month'] =(matrix['item_cnt_month'] 
.fillna(0)
.clip(0,20)
.astype(np.float16))
time.time() - ts<data_type_conversions>
subm[["Patient_Week","FVC","Confidence"]].to_csv("submission_regression.csv", index=False )
test['date_block_num'] = 34
test['date_block_num'] = test['date_block_num'].astype(np.int8)
 test['shop_id'] = test['shop_id'].astype(np.int8)
 test['item_id'] = test['item_id'].astype(np.int16 )<concatenate>
reg_sub = subm[["Patient_Week","FVC","Confidence"]].copy()
ts = time.time()
matrix = pd.concat([matrix, test], ignore_index=True, sort=False, keys=cols)
 matrix.fillna(0, inplace=True)
 time.time() - ts<data_type_conversions>
df1 = img_sub.sort_values(by=['Patient_Week'], ascending=True ).reset_index(drop=True)
 df2 = reg_sub.sort_values(by=['Patient_Week'], ascending=True ).reset_index(drop=True )
ts = time.time()
matrix = pd.merge(matrix, shops, on=['shop_id'], how='left')
 matrix = pd.merge(matrix, items, on=['item_id'], how='left')
 matrix = pd.merge(matrix, cats, on=['item_category_id'], how='left')
 matrix['city_code'] = matrix['city_code'].astype(np.int8)
 matrix['item_category_id'] = matrix['item_category_id'].astype(np.int8)
 matrix['type_code'] = matrix['type_code'].astype(np.int8)
 matrix['subtype_code'] = matrix['subtype_code'].astype(np.int8)
 time.time() - ts<merge>
df = df1[['Patient_Week']].copy()
df['FVC'] = 0.25*df1['FVC'] + 0.75*df2['FVC']
df['Confidence'] = 0.26*df1['Confidence'] + 0.74*df2['Confidence']
df.head()
<merge><EOS> 
df.to_csv('submission.csv', index=False )