Kaggle competition: COVID19 Global Forecasting (Week 3)
<SOS> metric: MCRMSLE Kaggle data source: covid19-global-forecasting-week-3<count_values>
pd.options.display.max_rows = 500
pd.options.display.max_columns = 500
%matplotlib inline
def rmse(yt, yp):
return np.sqrt(np.mean(( yt-yp)**2))
class CovidModel:
def __init__(self):
pass
def predict_first_day(self, date):
return None
def predict_next_day(self, yesterday_pred_df):
return None
class CovidModelAhmet(CovidModel):
def preprocess(self, df, meta_df):
df["Date"] = pd.to_datetime(df['Date'])
 df = df.merge(meta_df, on=self.loc_group, how="left")
 df["lat"] =(df["lat"] // 30 ).astype(np.float32 ).fillna(0)
 df["lon"] =(df["lon"] // 60 ).astype(np.float32 ).fillna(0)
 df["population"] = np.log1p(df["population"] ).fillna(-1)
 df["area"] = np.log1p(df["area"] ).fillna(-1)
 for col in self.loc_group:
df[col].fillna("", inplace=True)
 df['day'] = df.Date.dt.dayofyear
df['geo'] = ['_'.join(x)for x in zip(df['Country_Region'], df['Province_State'])]
return df
def get_model(self):
def nn_block(input_layer, size, dropout_rate, activation):
out_layer = KL.Dense(size, activation=None )(input_layer)
 out_layer = KL.Activation(activation )(out_layer)
 out_layer = KL.Dropout(dropout_rate )(out_layer)
 return out_layer
ts_inp = KL.Input(shape=(len(self.ts_features),))
global_inp = KL.Input(shape=(len(self.global_features),))
inp = KL.concatenate([global_inp, ts_inp])
 hidden_layer = nn_block(inp, 64, 0.0, "relu")
 gate_layer = nn_block(hidden_layer, 32, 0.0, "sigmoid")
 hidden_layer = nn_block(hidden_layer, 32, 0.0, "relu")
 hidden_layer = KL.multiply([hidden_layer, gate_layer])
 out = KL.Dense(len(self.TARGETS), activation="linear" )(hidden_layer)
 model = tf.keras.models.Model(inputs=[global_inp, ts_inp], outputs=out)
 return model
def get_input(self, df):
return [df[self.global_features], df[self.ts_features]]
def train_models(self, df, num_models=20, save=False):
def custom_loss(y_true, y_pred):
return K.sum(K.sqrt(K.sum(K.square(y_true - y_pred), axis=0, keepdims=True)))/len(self.TARGETS)
 models = []
for i in range(num_models):
model = self.get_model()
model.compile(loss=custom_loss, optimizer=Nadam(lr=1e-4))
hist = model.fit(self.get_input(df), df[self.TARGETS],
batch_size=2048, epochs=200, verbose=0, shuffle=True)
 if save:
model.save_weights("model{}.h5".format(i))
models.append(model)
 return models
def predict_one(self, df):
pred = np.zeros(( df.shape[0], 2))
for model in self.models:
pred += model.predict(self.get_input(df)) /len(self.models)
 pred = np.maximum(pred, df[self.prev_targets].values)
 pred[:, 0] = np.log1p(np.expm1(pred[:, 0])+ 0.1)
 pred[:, 1] = np.log1p(np.expm1(pred[:, 1])+ 0.01)
 return np.clip(pred, None, 15)
 def __init__(self):
df = pd.read_csv(".. /input/covid19-global-forecasting-week-3/train.csv")
 sub_df = pd.read_csv(".. /input/covid19-global-forecasting-week-3/test.csv")
 meta_df = pd.read_csv(".. /input/covid19-forecasting-metadata/region_metadata.csv")
 self.loc_group = ["Province_State", "Country_Region"]
df = self.preprocess(df, meta_df)
 sub_df = self.preprocess(sub_df, meta_df)
 df = df.merge(sub_df[["ForecastId", "Date", "geo"]], how="left", on=["Date", "geo"])
 df = df.append(sub_df[sub_df["Date"] > df["Date"].max() ], sort=False)
 df["day"] = df["day"] - df["day"].min()
self.TARGETS = ["ConfirmedCases", "Fatalities"]
self.prev_targets = ['prev_ConfirmedCases_1', 'prev_Fatalities_1']
for col in self.TARGETS:
df[col] = np.log1p(df[col])
 self.NUM_SHIFT = 7
self.global_features = ["lat", "lon", "population", "area"]
self.ts_features = []
for s in range(1, self.NUM_SHIFT+1):
for col in self.TARGETS:
df["prev_{}_{}".format(col, s)] = df.groupby(self.loc_group)[col].shift(s)
 self.ts_features.append("prev_{}_{}".format(col, s))
self.df = df[df["Date"] >= df["Date"].min() + timedelta(days=self.NUM_SHIFT)].copy()
def predict_first_day(self, day):
self.models = self.train_models(self.df[self.df["day"] < day])
 temp_df = self.df.loc[self.df["day"] == day].copy()
y_pred = self.predict_one(temp_df)
 self.y_prevs = [None]*self.NUM_SHIFT
for i in range(1, self.NUM_SHIFT):
self.y_prevs[i] = temp_df[['prev_ConfirmedCases_{}'.format(i), 'prev_Fatalities_{}'.format(i)]].values
temp_df[self.TARGETS] = y_pred
self.day = day
return temp_df[["geo", "day"] + self.TARGETS]
def predict_next_day(self, yesterday_pred_df):
self.day = self.day + 1
temp_df = self.df.loc[self.df["day"] == self.day].copy()
yesterday_pred_df = temp_df[["geo"]].merge(yesterday_pred_df[["geo"] + self.TARGETS], on="geo", how="left")
 temp_df[self.prev_targets] = yesterday_pred_df[self.TARGETS].values
for i in range(2, self.NUM_SHIFT+1):
temp_df[['prev_ConfirmedCases_{}'.format(i), 'prev_Fatalities_{}'.format(i)]] = self.y_prevs[i-1]
y_pred, self.y_prevs = self.predict_one(temp_df), [None, temp_df[self.prev_targets].values] + self.y_prevs[1:-1]
temp_df[self.TARGETS] = y_pred
return temp_df[["geo", "day"] + self.TARGETS]
test_data['Nationality'].value_counts()<data_type_conversions>
class CovidModelCPMP(CovidModel):
def __init__(self):
train = pd.read_csv('.. /input/covid19-global-forecasting-week-3/train.csv')
 train['Province_State'].fillna('', inplace=True)
 train['Date'] = pd.to_datetime(train['Date'])
 train['day'] = train.Date.dt.dayofyear
train['geo'] = ['_'.join(x)for x in zip(train['Country_Region'], train['Province_State'])]
test = pd.read_csv('.. /input/covid19-global-forecasting-week-3/test.csv')
 test['Province_State'].fillna('', inplace=True)
 test['Date'] = pd.to_datetime(test['Date'])
 test['day'] = test.Date.dt.dayofyear
test['geo'] = ['_'.join(x)for x in zip(test['Country_Region'], test['Province_State'])]
day_min = train['day'].min()
train['day'] -= day_min
test['day'] -= day_min
self.min_test_val_day = test.day.min()
self.max_test_val_day = train.day.max()
self.max_test_day = test.day.max()
train['ForecastId'] = -1
test['Id'] = -1
test['ConfirmedCases'] = 0
test['Fatalities'] = 0
data = pd.concat([train,
test[test.day > self.max_test_val_day][train.columns]
] ).reset_index(drop=True)
 self.data = data
self.train = train
self.test = test
self.dates = data[data['geo'] == 'France_'].Date.values
region_meta = pd.read_csv('.. /input/covid19-forecasting-metadata/region_metadata.csv')
 region_meta['Province_State'].fillna('', inplace=True)
 region_meta['geo'] = ['_'.join(x)for x in zip(region_meta['Country_Region'], region_meta['Province_State'],)]
population = data[['geo']].merge(region_meta, how='left', on='geo' ).fillna(0)
 population = population.groupby('geo')[['population']].first()
population['population'] = np.log1p(population['population'])
 self.population = population[['population']].values
continents = region_meta['continent']
continents = pd.factorize(continents)[0]
continents_ids_base = continents.reshape(( -1, 1))
ohe = OneHotEncoder(sparse=False)
 self.continents_ids_base = ohe.fit_transform(continents_ids_base)
 self.geo_data = data.pivot(index='geo', columns='day', values='ForecastId')
 self.num_geo = self.geo_data.shape[0]
self.ConfirmedCases = data.pivot(index='geo', columns='day', values='ConfirmedCases')
 self.Fatalities = data.pivot(index='geo', columns='day', values='Fatalities')
 self.cases = np.log1p(self.ConfirmedCases.values)
 self.deaths = np.log1p(self.Fatalities.values)
 self.case_threshold = 30
self.c_case = 10
self.t_case = 100
self.c_death = 10
self.t_death = 5
time_cases = self.c_case *(self.cases >= np.log1p(self.t_case))
time_cases = np.cumsum(time_cases, axis=1)
 self.time_cases = 1 * np.log1p(time_cases)
 time_deaths = self.c_death *(self.deaths >= np.log1p(self.t_death))
time_deaths = np.cumsum(time_deaths, axis=1)
 self.time_deaths = 1 *np.log1p(time_deaths)
 countries = [g.split('_')[0] for g in self.geo_data.index]
countries = pd.factorize(countries)[0]
country_ids_base = countries.reshape(( -1, 1))
ohe = OneHotEncoder(sparse=False)
 self.country_ids_base = 0.2 * ohe.fit_transform(country_ids_base)
 self.start_lag_death = 13
self.end_lag_death = 5
self.num_train = 5
self.num_lag_case = 14
self.lag_period = max(self.start_lag_death, self.num_lag_case)
 self.df = train[['geo', 'day', 'ConfirmedCases', 'Fatalities']].copy()
self.df.ConfirmedCases = np.log1p(self.df.ConfirmedCases)
 self.df.Fatalities = np.log1p(self.df.Fatalities)
 def get_country_ids(self):
countries = [g.split('_')[0] for g in self.geo_data.index]
countries = pd.factorize(countries)[0]
countries[self.cases[:, :self.last_train+1].max(axis=1)< np.log1p(self.case_threshold)] = -1
countries = pd.factorize(countries)[0]
country_ids_base = countries.reshape(( -1, 1))
ohe = OneHotEncoder(sparse=False)
 country_ids_base = 0.2 * ohe.fit_transform(country_ids_base)
 return country_ids_base
def val_score(self, true, pred):
return np.sqrt(mean_squared_error(true.ravel() , pred.ravel()))
def get_dataset(self, start_pred, num_train):
days = np.arange(start_pred - num_train + 1, start_pred + 1)
 lag_cases = np.vstack([self.cases[:, d - self.lag_period : d] for d in days])
 lag_deaths = np.vstack([self.deaths[:, d - self.lag_period : d] for d in days])
 target_cases = np.vstack([self.cases[:, d : d + 1] for d in days])
 target_deaths = np.vstack([self.deaths[:, d : d + 1] for d in days])
 continents_ids = np.vstack([self.continents_ids_base for d in days])
 country_ids = np.vstack([self.country_ids_base for d in days])
 population = np.vstack([self.population for d in days])
 time_case = np.vstack([self.time_cases[:, d - 1: d ] for d in days])
 time_death = np.vstack([self.time_deaths[:, d - 1 : d ] for d in days])
 return(lag_cases, lag_deaths, target_cases, target_deaths,
continents_ids, country_ids, population, time_case, time_death, days)
 def update_time(self, time_death, time_case, pred_death, pred_case):
new_time_death = np.expm1(time_death)+ self.c_death *(pred_death >= np.log1p(self.t_death))
new_time_death = 1 *np.log1p(new_time_death)
 new_time_case = np.expm1(time_case)+ self.c_case *(pred_case >= np.log1p(self.t_case))
new_time_case = 1 *np.log1p(new_time_case)
 return new_time_death, new_time_case
def update_valid_dataset(self, dataset, pred_death, pred_case, pred_day): 
(lag_cases, lag_deaths, target_cases, target_deaths,
continents_ids, country_ids, population, time_case, time_death, days)= dataset
if pred_day != days[-1]:
print('error', pred_day, days[-1])
 return None
day = days[-1] + 1
new_lag_cases = np.hstack([lag_cases[:, 1:], pred_case])
 new_lag_deaths = np.hstack([lag_deaths[:, 1:], pred_death])
 new_target_cases = self.cases[:, day:day+1]
new_target_deaths = self.deaths[:, day:day+1]
new_continents_ids = continents_ids
new_country_ids = country_ids
new_population = population
new_time_death, new_time_case = self.update_time(time_death, time_case, pred_death, pred_case)
 new_days = 1 + days
return(new_lag_cases, new_lag_deaths, new_target_cases, new_target_deaths,
new_continents_ids, new_country_ids, new_population,
new_time_case, new_time_death, new_days)
 def fit_eval(self, dataset, fit): 
(lag_cases, lag_deaths, target_cases, target_deaths,
continents_ids, country_ids, population,
time_case, time_death, days)= dataset
X_death = np.hstack([lag_cases[:, -self.start_lag_death:-self.end_lag_death],
lag_deaths[:, -self.num_lag_case:],
country_ids,
continents_ids,
population,
time_case,
time_death,
])
 y_death = target_deaths
y_death_prev = lag_deaths[:, -1:]
if fit:
self.lr_death.fit(X_death, y_death)
 y_pred_death = self.lr_death.predict(X_death)
 y_pred_death = np.maximum(y_pred_death, y_death_prev)
 X_case = np.hstack([lag_cases[:, -self.num_lag_case:],
country_ids,
continents_ids,
population,
time_case,
])
 y_case = target_cases
y_case_prev = lag_cases[:, -1:]
if fit:
self.lr_case.fit(X_case, y_case)
 y_pred_case = self.lr_case.predict(X_case)
 y_pred_case = np.maximum(y_pred_case, y_case_prev)
 return y_pred_death, y_pred_case
def get_pred_df(self, val_death_preds, val_case_preds,):
pred_deaths = self.Fatalities.iloc[:, self.start_val:self.start_val+self.num_val].copy()
pred_deaths.iloc[:, :] = val_death_preds
pred_deaths = pred_deaths.stack().reset_index()
pred_deaths.columns = ['geo', 'day', 'Fatalities']
pred_deaths
pred_cases = self.ConfirmedCases.iloc[:, self.start_val:self.start_val+self.num_val].copy()
pred_cases.iloc[:, :] = val_case_preds
pred_cases = pred_cases.stack().reset_index()
pred_cases.columns = ['geo', 'day', 'ConfirmedCases']
pred_cases
sub = self.data[['geo', 'day']]
sub = sub[sub.day == self.start_val]
sub = sub.merge(pred_cases, how='left', on=['geo', 'day'])
 sub = sub.merge(pred_deaths, how='left', on=['geo', 'day'])
 sub = sub[(sub.day >= self.start_val)&(sub.day <= self.end_val)]
return sub
def predict_first_day(self, day):
self.start_val = day
self.end_val = day + 1
self.num_val = self.end_val - self.start_val + 1
score = True
self.last_train = self.start_val - 1
print(self.dates[self.last_train], self.start_val, self.num_val)
 self.country_ids_base = self.get_country_ids()
train_data = self.get_dataset(self.last_train, self.num_train)
 alpha = 3
self.lr_death = Ridge(alpha=alpha, fit_intercept=True)
 self.lr_case = Ridge(alpha=alpha, fit_intercept=True)
 _ = self.fit_eval(train_data, fit=True)
 self.valid_data = self.get_dataset(self.start_val, 1)
 val_death_preds, val_case_preds = self.fit_eval(self.valid_data, fit=False)
 df = self.get_pred_df(val_death_preds, val_case_preds)
 return df
def predict_next_day(self, yesterday_pred_df):
yesterday_pred_df = yesterday_pred_df.sort_values(by='geo' ).reset_index(drop=True)
 if yesterday_pred_df.day.nunique() != 1:
print('error', yesterday_pred_df.day.unique())
 return None
pred_death = yesterday_pred_df[['Fatalities']].values
pred_case = yesterday_pred_df[['ConfirmedCases']].values
pred_day = yesterday_pred_df.day.unique() [0]
new_valid_data = self.update_valid_dataset(self.valid_data,
pred_death, pred_case, pred_day)
 if len(new_valid_data)> 0:
self.valid_data = new_valid_data
self.start_val = pred_day + 1
self.end_val = pred_day + 2
val_death_preds, val_case_preds = self.fit_eval(self.valid_data, fit=False)
 df = self.get_pred_df(val_death_preds, val_case_preds)
 return df
train_data['Nationality'].fillna(value='Nationality_unk',inplace=True)
 test_data['Nationality'].fillna(value='Nationality_unk',inplace=True )<count_values>
class CovidModelGIBA(CovidModel):
def __init__(self, lag=1, seed=1):
self.lag = lag
self.seed = seed
print('Lag:', lag, 'Seed:', seed)
 train = pd.read_csv('.. /input/covid19-global-forecasting-week-3/train.csv')
 train['Date'] = pd.to_datetime(train['Date'])
 self.maxdate = str(train['Date'].max())[:10]
self.testdate = str(train['Date'].max() + pd.Timedelta(days=1)) [:10]
print('Last Date in Train:',self.maxdate, 'Test first Date:',self.testdate)
 train['Province_State'].fillna('', inplace=True)
 train['day'] = train.Date.dt.dayofyear
self.day_min = train['day'].min()
train['day'] -= self.day_min
train['geo'] = ['_'.join(x)for x in zip(train['Country_Region'], train['Province_State'])]
test = pd.read_csv('.. /input/covid19-global-forecasting-week-3/test.csv')
 test['Date'] = pd.to_datetime(test['Date'])
 test['Province_State'].fillna('', inplace=True)
 test['day'] = test.Date.dt.dayofyear
test['day'] -= self.day_min
test['geo'] = ['_'.join(x)for x in zip(test['Country_Region'], test['Province_State'])]
test['Id'] = -1
test['ConfirmedCases'] = 0
test['Fatalities'] = 0
self.trainmaxday = train['day'].max()
self.testday1 = train['day'].max() + 1
self.testdayN = test['day'].max()
publictest = test.loc[ test.Date > train.Date.max() ].copy()
train = pd.concat(( train, publictest), sort=False)
 train.sort_values(['Country_Region','Province_State','Date'], inplace=True)
 train = train.reset_index(drop=True)
 train['ForecastId'] = pd.merge(train, test, on=['Country_Region','Province_State','Date'], how='left')['ForecastId_y'].values
train['cid'] = train['Country_Region'] + '_' + train['Province_State']
train['log0'] = np.log1p(train['ConfirmedCases'])
 train['log1'] = np.log1p(train['Fatalities'])
 train = train.loc[(train.log0 > 0)|(train.ForecastId.notnull())|(train.Date >= '2020-03-17')].copy()
train = train.reset_index(drop=True)
 train['days_since_1case'] = train.groupby('cid')['Id'].cumcount()
dt = pd.read_csv('.. /input/covid19-lockdown-dates-by-country/countryLockdowndates.csv')
 dt.columns = ['Country_Region','Province_State','Date','Type','Reference']
dt = dt.loc[ dt.Date == dt.Date ]
dt['Province_State'] = dt['Province_State'].fillna('')
 dt['Date'] = pd.to_datetime(dt['Date'])
 dt['Date'] = dt['Date'] + pd.Timedelta(days=8)
 dt['Type'] = pd.factorize(dt['Type'])[0]
dt['cid'] = dt['Country_Region'] + '_' + dt['Province_State']
del dt['Reference'], dt['Country_Region'], dt['Province_State']
train = pd.merge(train, dt, on=['cid','Date'], how='left')
 train['Type'] = train.groupby('cid')['Type'].fillna(method='ffill')
 train['target0'] = np.log1p(train['ConfirmedCases'])
 train['target1'] = np.log1p(train['Fatalities'])
 self.train = train.copy()
def create_features(self, df, valid_day):
df['lag0_1'] = df.groupby('cid')['target0'].shift(self.lag)
 df['lag1_1'] = df.groupby('cid')['target1'].shift(self.lag)
 df['lag0_1'] = df.groupby('cid')['lag0_1'].fillna(method='bfill')
 df['lag1_1'] = df.groupby('cid')['lag1_1'].fillna(method='bfill')
 df['m0'] = df.groupby('cid')['lag0_1'].rolling(2 ).mean().values
df['m1'] = df.groupby('cid')['lag0_1'].rolling(3 ).mean().values
df['m2'] = df.groupby('cid')['lag0_1'].rolling(4 ).mean().values
df['m3'] = df.groupby('cid')['lag0_1'].rolling(5 ).mean().values
df['m4'] = df.groupby('cid')['lag0_1'].rolling(7 ).mean().values
df['m5'] = df.groupby('cid')['lag0_1'].rolling(10 ).mean().values
df['m6'] = df.groupby('cid')['lag0_1'].rolling(12 ).mean().values
df['m7'] = df.groupby('cid')['lag0_1'].rolling(16 ).mean().values
df['m8'] = df.groupby('cid')['lag0_1'].rolling(20 ).mean().values
df['n0'] = df.groupby('cid')['lag1_1'].rolling(2 ).mean().values
df['n1'] = df.groupby('cid')['lag1_1'].rolling(3 ).mean().values
df['n2'] = df.groupby('cid')['lag1_1'].rolling(4 ).mean().values
df['n3'] = df.groupby('cid')['lag1_1'].rolling(5 ).mean().values
df['n4'] = df.groupby('cid')['lag1_1'].rolling(7 ).mean().values
df['n5'] = df.groupby('cid')['lag1_1'].rolling(10 ).mean().values
df['n6'] = df.groupby('cid')['lag1_1'].rolling(12 ).mean().values
df['n7'] = df.groupby('cid')['lag1_1'].rolling(16 ).mean().values
df['n8'] = df.groupby('cid')['lag1_1'].rolling(20 ).mean().values
df['m0'] = df.groupby('cid')['m0'].fillna(method='bfill')
 df['m1'] = df.groupby('cid')['m1'].fillna(method='bfill')
 df['m2'] = df.groupby('cid')['m2'].fillna(method='bfill')
 df['m3'] = df.groupby('cid')['m3'].fillna(method='bfill')
 df['m4'] = df.groupby('cid')['m4'].fillna(method='bfill')
 df['m5'] = df.groupby('cid')['m5'].fillna(method='bfill')
 df['m6'] = df.groupby('cid')['m6'].fillna(method='bfill')
 df['m7'] = df.groupby('cid')['m7'].fillna(method='bfill')
 df['m8'] = df.groupby('cid')['m8'].fillna(method='bfill')
 df['n0'] = df.groupby('cid')['n0'].fillna(method='bfill')
 df['n1'] = df.groupby('cid')['n1'].fillna(method='bfill')
 df['n2'] = df.groupby('cid')['n2'].fillna(method='bfill')
 df['n3'] = df.groupby('cid')['n3'].fillna(method='bfill')
 df['n4'] = df.groupby('cid')['n4'].fillna(method='bfill')
 df['n5'] = df.groupby('cid')['n5'].fillna(method='bfill')
 df['n6'] = df.groupby('cid')['n6'].fillna(method='bfill')
 df['n7'] = df.groupby('cid')['n7'].fillna(method='bfill')
 df['n8'] = df.groupby('cid')['n8'].fillna(method='bfill')
 df['flag_China'] = 1*(df['Country_Region'] == 'China')
 df['flag_US'] = 1*(df['Country_Region'] == 'US')
 df['flag_Kosovo_'] = 1*(df['cid'] == 'Kosovo_')
 df['flag_Korea'] = 1*(df['cid'] == 'Korea, South_')
 df['flag_Nepal_'] = 1*(df['cid'] == 'Nepal_')
 df['flag_Holy See_'] = 1*(df['cid'] == 'Holy See_')
 df['flag_Suriname_'] = 1*(df['cid'] == 'Suriname_')
 df['flag_Ghana_'] = 1*(df['cid'] == 'Ghana_')
 df['flag_Togo_'] = 1*(df['cid'] == 'Togo_')
 df['flag_Malaysia_'] = 1*(df['cid'] == 'Malaysia_')
 df['flag_US_Rhode'] = 1*(df['cid'] == 'US_Rhode Island')
 df['flag_Bolivia_'] = 1*(df['cid'] == 'Bolivia_')
 df['flag_China_Tib'] = 1*(df['cid'] == 'China_Tibet')
 df['flag_Bahrain_'] = 1*(df['cid'] == 'Bahrain_')
 df['flag_Honduras_'] = 1*(df['cid'] == 'Honduras_')
 df['flag_Bangladesh']= 1*(df['cid'] == 'Bangladesh_')
 df['flag_Paraguay_'] = 1*(df['cid'] == 'Paraguay_')
 tr = df.loc[ df.day < valid_day ].copy()
vl = df.loc[ df.day == valid_day ].copy()
tr = tr.loc[ tr.lag0_1 > 0 ].copy()
maptarget0 = tr.groupby('cid')['target0'].agg(log0_max='max' ).reset_index()
maptarget1 = tr.groupby('cid')['target1'].agg(log1_max='max' ).reset_index()
vl['log0_max'] = pd.merge(vl, maptarget0, on='cid' , how='left')['log0_max'].values
vl['log1_max'] = pd.merge(vl, maptarget1, on='cid' , how='left')['log1_max'].values
vl['log0_max'] = vl['log0_max'].fillna(0)
 vl['log1_max'] = vl['log1_max'].fillna(0)
 return tr, vl
def train_models(self, valid_day = 10):
train = self.train.copy()
train.loc[(train.cid=='China_Guizhou')&(train.Date=='2020-03-17'), 'target0' ] = np.log1p(146)
 train.loc[(train.cid=='Guyana_')&(train.Date>='2020-03-22')&(train.Date<='2020-03-30'), 'target0' ] = np.log1p(12)
 train.loc[(train.cid=='US_Virgin Islands')&(train.Date>='2020-03-29')&(train.Date<='2020-03-29'), 'target0' ] = np.log1p(24)
 train.loc[(train.cid=='US_Virgin Islands')&(train.Date>='2020-03-30')&(train.Date<='2020-03-30'), 'target0' ] = np.log1p(27)
 train.loc[(train.cid=='Iceland_')&(train.Date>='2020-03-15')&(train.Date<='2020-03-15'), 'target1' ] = np.log1p(0)
 train.loc[(train.cid=='Kazakhstan_')&(train.Date>='2020-03-20')&(train.Date<='2020-03-20'), 'target1' ] = np.log1p(0)
 train.loc[(train.cid=='Serbia_')&(train.Date>='2020-03-26')&(train.Date<='2020-03-26'), 'target1' ] = np.log1p(5)
 train.loc[(train.cid=='Serbia_')&(train.Date>='2020-03-27')&(train.Date<='2020-03-27'), 'target1' ] = np.log1p(6)
 train.loc[(train.cid=='Slovakia_')&(train.Date>='2020-03-22')&(train.Date<='2020-03-31'), 'target1' ] = np.log1p(1)
 train.loc[(train.cid=='US_Hawaii')&(train.Date>='2020-03-25')&(train.Date<='2020-03-31'), 'target1' ] = np.log1p(1)
 param = {
'subsample': 0.9850,
'colsample_bytree': 0.850,
'max_depth': 6,
'gamma': 0.000,
'learning_rate': 0.010,
'min_child_weight': 5.00,
'reg_alpha': 0.000,
'reg_lambda': 0.400,
'silent':1,
'objective':'reg:squarederror',
'nthread': 12,
'seed': self.seed
}
tr, vl = self.create_features(train.copy() , valid_day)
 features = [f for f in tr.columns if f not in [
'Id','ConfirmedCases','Fatalities','log0','log1','target0','target1','ypred0','ypred1','Province_State','Country_Region','Date','ForecastId','cid','geo','day',
'GDP_region','TRUE POPULATION','pct_in_largest_city',' TFR ',' Avg_age ','latitude','longitude','abs_latitude','temperature', 'humidity',
'Personality_pdi','Personality_idv','Personality_mas','Personality_uai','Personality_ltowvs','Personality_assertive','personality_perform','personality_agreeableness',
'murder','High_rises','max_high_rises','AIR_CITIES','AIR_AVG','continent_gdp_pc','continent_happiness','continent_generosity','continent_corruption','continent_Life_expectancy'
] ]
self.features = features
nrounds0 = 630
nrounds1 = 630
dtrain = xgb.DMatrix(tr[features], tr['target0'])
 param['seed'] = self.seed
self.model0 = xgb.train(param, dtrain, nrounds0, verbose_eval=0)
 param['seed'] = self.seed+1
self.model1 = xgb.train(param, dtrain, nrounds0, verbose_eval=0)
 dtrain = xgb.DMatrix(tr[features], tr['target1'])
 param['seed'] = self.seed
self.model2 = xgb.train(param, dtrain, nrounds1, verbose_eval=0)
 param['seed'] = self.seed+1
self.model3 = xgb.train(param, dtrain, nrounds1, verbose_eval=0)
 self.vl = vl
return 1
def predict_first_day(self, day):
self.day = day
self.train_models(day)
 dvalid = xgb.DMatrix(self.vl[self.features])
 ypred0 =(self.model0.predict(dvalid)+ self.model1.predict(dvalid)) / 2
ypred1 =(self.model2.predict(dvalid)+ self.model3.predict(dvalid)) / 2
self.vl['ypred0'] = ypred0
self.vl['ypred1'] = ypred1
self.vl.loc[ self.vl.ypred0<self.vl.log0_max, 'ypred0'] = self.vl.loc[ self.vl.ypred0<self.vl.log0_max, 'log0_max']
self.vl.loc[ self.vl.ypred1<self.vl.log1_max, 'ypred1'] = self.vl.loc[ self.vl.ypred1<self.vl.log1_max, 'log1_max']
VALID = self.vl[["geo", "day", 'ypred0', 'ypred1']].copy()
VALID.columns = ["geo", "day", 'ConfirmedCases', 'Fatalities']
return VALID.reset_index(drop=True)
 def predict_next_day(self, yesterday):
self.day += 1
feats = ['geo','day']
self.train[ 'ypred0' ] = pd.merge(self.train[feats], yesterday[feats+['ConfirmedCases']], on=feats, how='left')['ConfirmedCases'].values
self.train.loc[ self.train.ypred0.notnull() , 'target0'] = self.train.loc[ self.train.ypred0.notnull() , 'ypred0']
self.train[ 'ypred1' ] = pd.merge(self.train[feats], yesterday[feats+['Fatalities']], on=feats, how='left')['Fatalities'].values
self.train.loc[ self.train.ypred1.notnull() , 'target1'] = self.train.loc[ self.train.ypred1.notnull() , 'ypred1']
del self.train['ypred0'], self.train['ypred1']
tr, vl = self.create_features(self.train.copy() , self.day)
 dvalid = xgb.DMatrix(vl[self.features])
 ypred0 =(self.model0.predict(dvalid)+ self.model1.predict(dvalid)) /2
ypred1 =(self.model2.predict(dvalid)+ self.model3.predict(dvalid)) /2
vl['ypred0'] = ypred0
vl['ypred1'] = ypred1
vl.loc[ vl.ypred0<vl.log0_max, 'ypred0'] = vl.loc[ vl.ypred0<vl.log0_max, 'log0_max']
vl.loc[ vl.ypred1<vl.log1_max, 'ypred1'] = vl.loc[ vl.ypred1<vl.log1_max, 'log1_max']
self.vl = vl
VALID = vl[["geo", "day", 'ypred0', 'ypred1']].copy()
VALID.columns = ["geo", "day", 'ConfirmedCases', 'Fatalities']
return VALID.reset_index(drop=True )
train_data['Size'].value_counts()<count_values>
TARGETS = ["ConfirmedCases", "Fatalities"]
def rmse(y_true, y_pred):
return np.sqrt(mean_squared_error(y_true, y_pred))
df = pd.read_csv(".. /input/covid19-global-forecasting-week-3/train.csv")
 df[TARGETS] = np.log1p(df[TARGETS].values)
 sub_df = pd.read_csv(".. /input/covid19-global-forecasting-week-3/test.csv")
 def preprocess(df):
for col in ["Country_Region", "Province_State"]:
df[col].fillna("", inplace=True)
 df["Date"] = pd.to_datetime(df['Date'])
 df['day'] = df.Date.dt.dayofyear
df['geo'] = ['_'.join(x)for x in zip(df['Country_Region'], df['Province_State'])]
return df
df = preprocess(df)
 sub_df = preprocess(sub_df)
 sub_df["day"] -= df["day"].min()
df["day"] -= df["day"].min()
test_data['Size'].value_counts()<data_type_conversions>
TEST_FIRST = sub_df[sub_df["Date"] > df["Date"].max() ]["Date"].min()
print(TEST_FIRST)
 TEST_DAYS =(sub_df["Date"].max() - TEST_FIRST ).days + 1
TEST_FIRST =(TEST_FIRST - df["Date"].min() ).days
print(TEST_FIRST, TEST_DAYS)
 def get_blend(pred_dfs, weights, verbose=True):
if verbose:
for n1, n2 in [("cpmp", "giba"),("cpmp", "ahmet"),("giba", "ahmet")]:
for t in TARGETS:
print(n1, n2, t, np.round(rmse(pred_dfs[n1][t], pred_dfs[n2][t]), 4))
blend_df = pred_dfs["cpmp"].copy()
blend_df[TARGETS] = 0
for name, pred_df in pred_dfs.items() :
blend_df[TARGETS] += weights[name]*pred_df[TARGETS].values
return blend_df
cov_models = {"ahmet": CovidModelAhmet() , "cpmp": CovidModelCPMP() , 'giba': CovidModelGIBA() }
weights = {"ahmet": 0.35, "cpmp": 0.30, "giba": 0.35}
pred_dfs = {name: cm.predict_first_day(TEST_FIRST ).sort_values("geo")for name, cm in cov_models.items() }
blend_df = get_blend(pred_dfs, weights)
 eval_df = blend_df.copy()
for d in range(1, TEST_DAYS):
pred_dfs = {name: cm.predict_next_day(blend_df ).sort_values("geo")for name, cm in cov_models.items() }
blend_df = get_blend(pred_dfs, weights)
 eval_df = eval_df.append(blend_df)
 print(d, eval_df.shape, flush=True )
train_data['Size'].fillna(value='Size_unk',inplace=True)
 test_data['Size'].fillna(value="Size_unk",inplace=True )<count_values>
print(sub_df.shape)
 sub_df = sub_df.merge(df.append(eval_df, sort=False), on=["geo", "day"], how="left")
 print(sub_df.shape)
 print(sub_df[TARGETS].isnull().mean() )
<count_values><EOS> 
sub_df[TARGETS] = np.expm1(sub_df[TARGETS].values)
 sub_df.to_csv("submission.csv", index=False, columns=["ForecastId"] + TARGETS)
 sub_df.head()