Kaggle competition: Mechanisms of Action (MoA) Prediction
print('Correcting predictions')
 df_submit['prediction_mod'] = -1.0
matchId = df_submit['matchId'].unique()
for match in matchId:
df_match = df_submit[df_submit['matchId']==match]
df_max = df_match.groupby(['groupId'] ).max()
pred_sort = sorted(df_max['prediction'])
 for i in df_max.index:
groupPlace = pred_sort.index(df_max.loc[i]['prediction'])
 if len(pred_sort)> 1:
df_max.at[i,'prediction_mod'] = groupPlace/(len(pred_sort)-1)
 else:
df_max.at[i,'prediction_mod'] = 1.0
for i in df_match.index:
df_submit.at[i, 'prediction_mod'] = df_max['prediction_mod'].loc[df_match['groupId'].loc[i]]
y_submit_cor = df_submit['prediction_mod']
print('Submission scores corrected')
 df_submit.head()<save_to_csv>
warnings.filterwarnings('ignore' )
df_test = pd.read_csv('.. /input/sample_submission.csv')
 df_test['winPlacePerc'] = df_submit['prediction_mod'].copy()
df_test.to_csv('submission_rfr.csv', index=False)
 print('Random Forest submission file made
' )<set_options>
from sklearn.preprocessing import QuantileTransformer
%matplotlib inline
%pylab inline
warnings.filterwarnings(action='ignore')
<set_options>
train_features = pd.read_csv('.. /input/lish-moa/train_features.csv')
 train_targets_scored = pd.read_csv('.. /input/lish-moa/train_targets_scored.csv')
 train_targets_nonscored = pd.read_csv('.. /input/lish-moa/train_targets_nonscored.csv')
 test_features = pd.read_csv('.. /input/lish-moa/test_features.csv')
 sample_submission = pd.read_csv('.. /input/lish-moa/sample_submission.csv' )
plt.figure(figsize =(20, 20))<load_from_csv>
GENES = [col for col in train_features.columns if col.startswith('g-')]
CELLS = [col for col in train_features.columns if col.startswith('c-')]
df = pd.read_csv('.. /input/train_V2.csv' )<drop_column>
for col in(GENES + CELLS):
transformer = QuantileTransformer(n_quantiles=100,random_state=0, output_distribution="normal")
 vec_len = len(train_features[col].values)
 vec_len_test = len(test_features[col].values)
 raw_vec = train_features[col].values.reshape(vec_len, 1)
 transformer.fit(raw_vec)
 train_features[col] = transformer.transform(raw_vec ).reshape(1, vec_len)[0]
test_features[col] = transformer.transform(test_features[col].values.reshape(vec_len_test, 1)).reshape(1, vec_len_test)[0]
del df<load_from_csv>
def seed_everything(seed=42):
random.seed(seed)
 os.environ['PYTHONHASHSEED'] = str(seed)
 np.random.seed(seed)
 torch.manual_seed(seed)
 torch.cuda.manual_seed(seed)
 torch.backends.cudnn.deterministic = True
seed_everything(seed=42 )
train_df = pd.read_csv(".. /input/train_V2.csv")
 test_df = pd.read_csv(".. /input/test_V2.csv" )<categorify>
n_comp = 600
data = pd.concat([pd.DataFrame(train_features[GENES]), pd.DataFrame(test_features[GENES])])
 data2 =(PCA(n_components=n_comp, random_state=42 ).fit_transform(data[GENES]))
train2 = data2[:train_features.shape[0]]; test2 = data2[-test_features.shape[0]:]
train2 = pd.DataFrame(train2, columns=[f'pca_G-{i}' for i in range(n_comp)])
 test2 = pd.DataFrame(test2, columns=[f'pca_G-{i}' for i in range(n_comp)])
 train_features = pd.concat(( train_features, train2), axis=1)
 test_features = pd.concat(( test_features, test2), axis=1 )
matchTyp = ['squad-fpp', 'duo', 'solo-fpp', 'squad', 'duo-fpp', 'solo',
'normal-squad-fpp', 'crashfpp', 'flaretpp', 'normal-solo-fpp',
'flarefpp', 'normal-duo-fpp', 'normal-duo', 'normal-squad',
'crashtpp', 'normal-solo']
mapping = {}
for i, j in enumerate(matchTyp):
mapping[i] = j
train_df["matchTypeMap"] = train_df["matchType"].apply(lambda x: ''.join(str(i)for i, j in mapping.items() if x == j)).map(int64)
 test_df["matchTypeMap"] = test_df["matchType"].apply(lambda x: ''.join(str(i)for i, j in mapping.items() if x == j)).map(int64 )<drop_column>
n_comp = 50
data = pd.concat([pd.DataFrame(train_features[CELLS]), pd.DataFrame(test_features[CELLS])])
 data2 =(PCA(n_components=n_comp, random_state=42 ).fit_transform(data[CELLS]))
train2 = data2[:train_features.shape[0]]; test2 = data2[-test_features.shape[0]:]
train2 = pd.DataFrame(train2, columns=[f'pca_C-{i}' for i in range(n_comp)])
 test2 = pd.DataFrame(test2, columns=[f'pca_C-{i}' for i in range(n_comp)])
 train_features = pd.concat(( train_features, train2), axis=1)
 test_features = pd.concat(( test_features, test2), axis=1 )
train_df.drop(["matchType"], axis =1, inplace=True)
 test_df.drop(["matchType"], axis =1, inplace=True )<count_missing_values>
var_thresh = VarianceThreshold(0.8)
 data = train_features.append(test_features)
 data_transformed = var_thresh.fit_transform(data.iloc[:, 4:])
 train_features_transformed = data_transformed[ : train_features.shape[0]]
test_features_transformed = data_transformed[-test_features.shape[0] : ]
train_features = pd.DataFrame(train_features[['sig_id','cp_type','cp_time','cp_dose']].values.reshape(-1, 4),\
columns=['sig_id','cp_type','cp_time','cp_dose'])
 train_features = pd.concat([train_features, pd.DataFrame(train_features_transformed)], axis=1)
 test_features = pd.DataFrame(test_features[['sig_id','cp_type','cp_time','cp_dose']].values.reshape(-1, 4),\
columns=['sig_id','cp_type','cp_time','cp_dose'])
 test_features = pd.concat([test_features, pd.DataFrame(test_features_transformed)], axis=1)
 train_features.shape
train_df.dropna(inplace = True)
 train_df.isnull().any().any()<prepare_x_and_y>
def fe_cluster(train, test, n_clusters_g = 35, n_clusters_c = 5, SEED = 123):
features_g = list(train.columns[4:776])
 features_c = list(train.columns[776:876])
 def create_cluster(train, test, features, kind = 'g', n_clusters = n_clusters_g):
train_ = train[features].copy()
test_ = test[features].copy()
data = pd.concat([train_, test_], axis = 0)
 kmeans = KMeans(n_clusters = n_clusters, random_state = SEED ).fit(data)
 train[f'clusters_{kind}'] = kmeans.labels_[:train.shape[0]]
test[f'clusters_{kind}'] = kmeans.labels_[train.shape[0]:]
train = pd.get_dummies(train, columns = [f'clusters_{kind}'])
 test = pd.get_dummies(test, columns = [f'clusters_{kind}'])
 return train, test
train, test = create_cluster(train, test, features_g, kind = 'g', n_clusters = n_clusters_g)
 train, test = create_cluster(train, test, features_c, kind = 'c', n_clusters = n_clusters_c)
 return train, test
train_features ,test_features=fe_cluster(train_features,test_features )
X = train_df.drop(["Id", "groupId", "matchId", "winPlacePerc"], axis = 1)
 y = train_df["winPlacePerc"]
test = test_df.drop(["Id", "groupId", "matchId"], axis = 1 )<drop_column>
def fe_stats(train, test):
features_g = list(train.columns[4:776])
 features_c = list(train.columns[776:876])
 for df in train, test:
df['g_sum'] = df[features_g].sum(axis = 1)
 df['g_mean'] = df[features_g].mean(axis = 1)
 df['g_std'] = df[features_g].std(axis = 1)
 df['g_kurt'] = df[features_g].kurtosis(axis = 1)
 df['g_skew'] = df[features_g].skew(axis = 1)
 df['c_sum'] = df[features_c].sum(axis = 1)
 df['c_mean'] = df[features_c].mean(axis = 1)
 df['c_std'] = df[features_c].std(axis = 1)
 df['c_kurt'] = df[features_c].kurtosis(axis = 1)
 df['c_skew'] = df[features_c].skew(axis = 1)
 df['gc_sum'] = df[features_g + features_c].sum(axis = 1)
 df['gc_mean'] = df[features_g + features_c].mean(axis = 1)
 df['gc_std'] = df[features_g + features_c].std(axis = 1)
 df['gc_kurt'] = df[features_g + features_c].kurtosis(axis = 1)
 df['gc_skew'] = df[features_g + features_c].skew(axis = 1)
 return train, test
train_features,test_features=fe_stats(train_features,test_features )
del train_df<train_model>
train = train_features.merge(train_targets_scored, on='sig_id')
 train = train[train['cp_type']!='ctl_vehicle'].reset_index(drop=True)
 test = test_features[test_features['cp_type']!='ctl_vehicle'].reset_index(drop=True)
 target = train[train_targets_scored.columns]
model = xgboost.XGBRegressor(max_depth=17, gamma=0.3, learning_rate= 0.1)
 model.fit(X,y)
 del X
del y<predict_on_test>
train = train.drop('cp_type', axis=1)
 test = test.drop('cp_type', axis=1 )
pred = model.predict(test )<save_to_csv>
target_cols = target.drop('sig_id', axis=1 ).columns.values.tolist()
test_id = test_df["Id"]
submit_xg = pd.DataFrame({'Id': test_id, "winPlacePerc": pred} , columns=['Id', 'winPlacePerc'])
 print(submit_xg.head())
 submit_xg.to_csv("submission.csv", index = False )<set_options>
folds = train.copy()
mskf = MultilabelStratifiedKFold(n_splits=5)
 for f,(t_idx, v_idx)in enumerate(mskf.split(X=train, y=target)) :
folds.loc[v_idx, 'kfold'] = int(f)
 folds['kfold'] = folds['kfold'].astype(int)
 folds
warnings.filterwarnings(action='ignore')
 plt.style.use('fivethirtyeight')
 gc.enable()<load_from_csv>
class MoADataset:
def __init__(self, features, targets):
self.features = features
self.targets = targets
def __len__(self):
return(self.features.shape[0])
 def __getitem__(self, idx):
dct = {
'x' : torch.tensor(self.features[idx, :], dtype=torch.float),
'y' : torch.tensor(self.targets[idx, :], dtype=torch.float)
 }
return dct
class TestDataset:
def __init__(self, features):
self.features = features
def __len__(self):
return(self.features.shape[0])
 def __getitem__(self, idx):
dct = {
'x' : torch.tensor(self.features[idx, :], dtype=torch.float)
 }
return dct
%time
train_d=dd.read_csv('.. /input/train_V2.csv',blocksize=25e6)
<load_from_csv>
def train_fn(model, optimizer, scheduler, loss_fn, dataloader, device):
model.train()
final_loss = 0
for data in dataloader:
optimizer.zero_grad()
inputs, targets = data['x'].to(device), data['y'].to(device)
 outputs = model(inputs)
 loss = loss_fn(outputs, targets)
 loss.backward()
optimizer.step()
scheduler.step()
final_loss += loss.item()
final_loss /= len(dataloader)
 return final_loss
def valid_fn(model, loss_fn, dataloader, device):
model.eval()
final_loss = 0
valid_preds = []
for data in dataloader:
inputs, targets = data['x'].to(device), data['y'].to(device)
 outputs = model(inputs)
 loss = loss_fn(outputs, targets)
 final_loss += loss.item()
valid_preds.append(outputs.sigmoid().detach().cpu().numpy())
 final_loss /= len(dataloader)
 valid_preds = np.concatenate(valid_preds)
 return final_loss, valid_preds
def inference_fn(model, dataloader, device):
model.eval()
preds = []
for data in dataloader:
inputs = data['x'].to(device)
 with torch.no_grad() :
outputs = model(inputs)
 preds.append(outputs.sigmoid().detach().cpu().numpy())
 preds = np.concatenate(preds)
 return preds
train=pd.read_csv('.. /input/train_V2.csv',nrows=100000)
 test=pd.read_csv(".. /input/test_V2.csv",)
 test_id=test['Id']<count_missing_values>
class SmoothBCEwLogits(_WeightedLoss):
def __init__(self, weight=None, reduction='mean', smoothing=0.0):
super().__init__(weight=weight, reduction=reduction)
 self.smoothing = smoothing
self.weight = weight
self.reduction = reduction
@staticmethod
def _smooth(targets:torch.Tensor, n_labels:int, smoothing=0.0):
assert 0 <= smoothing < 1
with torch.no_grad() :
targets = targets *(1.0 - smoothing)+ 0.5 * smoothing
return targets
def forward(self, inputs, targets):
targets = SmoothBCEwLogits._smooth(targets, inputs.size(-1),
self.smoothing)
 loss = F.binary_cross_entropy_with_logits(inputs, targets,self.weight)
 if self.reduction == 'sum':
loss = loss.sum()
elif self.reduction == 'mean':
loss = loss.mean()
return loss
train.isnull().sum()<count_missing_values>
class Model(nn.Module):
def __init__(self, num_features, num_targets, hidden_size):
super(Model, self ).__init__()
self.batch_norm1 = nn.BatchNorm1d(num_features)
 self.dense1 = nn.utils.weight_norm(nn.Linear(num_features, hidden_size))
self.batch_norm2 = nn.BatchNorm1d(hidden_size)
 self.dropout2 = nn.Dropout(0.4)
 self.dense2 = nn.utils.weight_norm(nn.Linear(hidden_size, hidden_size))
self.batch_norm3 = nn.BatchNorm1d(hidden_size)
 self.dropout3 = nn.Dropout(0.4)
 self.dense3 = nn.utils.weight_norm(nn.Linear(hidden_size, num_targets))
def forward(self, x):
x = self.batch_norm1(x)
 x = F.relu(self.dense1(x))
x = self.batch_norm2(x)
 x = self.dropout2(x)
 x = F.relu(self.dense2(x))
x = self.batch_norm3(x)
 x = self.dropout3(x)
 x = self.dense3(x)
 return x
train.isnull().sum()<groupby>
def process_data(data):
data = pd.get_dummies(data, columns=['cp_time','cp_dose'])
 return data
train_group=train.groupby('groupId',as_index=False)['winPlacePerc'].agg('mean' )<filter>
feature_cols = [c for c in process_data(folds ).columns if c not in target_cols]
feature_cols = [c for c in feature_cols if c not in ['kfold','sig_id']]
len(feature_cols )
train[train['groupId']==2]['winPlacePerc']<drop_column>
DEVICE =('cuda' if torch.cuda.is_available() else 'cpu')
 EPOCHS = 25
BATCH_SIZE = 128
LEARNING_RATE = 1e-3
WEIGHT_DECAY = 1e-5
NFOLDS = 5
EARLY_STOPPING_STEPS = 10
EARLY_STOP = False
num_features=len(feature_cols)
 num_targets=len(target_cols)
 hidden_size=2048
train_corr=train.drop(columns=['Id',"matchId","groupId"])
<feature_engineering>
def run_training(fold, seed):
seed_everything(seed)
 train = process_data(folds)
 test_ = process_data(test)
 trn_idx = train[train['kfold'] != fold].index
val_idx = train[train['kfold'] == fold].index
train_df = train[train['kfold'] != fold].reset_index(drop=True)
 valid_df = train[train['kfold'] == fold].reset_index(drop=True)
 x_train, y_train = train_df[feature_cols].values, train_df[target_cols].values
x_valid, y_valid = valid_df[feature_cols].values, valid_df[target_cols].values
train_dataset = MoADataset(x_train, y_train)
 valid_dataset = MoADataset(x_valid, y_valid)
 trainloader = torch.utils.data.DataLoader(train_dataset, batch_size=BATCH_SIZE, shuffle=True)
 validloader = torch.utils.data.DataLoader(valid_dataset, batch_size=BATCH_SIZE, shuffle=False)
 model = Model(
 num_features=num_features,
num_targets=num_targets,
hidden_size=hidden_size, 
)
 model.to(DEVICE)
 optimizer = torch.optim.Adam(model.parameters() , lr=LEARNING_RATE, weight_decay=WEIGHT_DECAY)
 scheduler = optim.lr_scheduler.OneCycleLR(optimizer=optimizer, pct_start=0.1, div_factor=1e3,
max_lr=1e-2, epochs=EPOCHS, steps_per_epoch=len(trainloader))
loss_fn = nn.BCEWithLogitsLoss()
loss_tr = SmoothBCEwLogits(smoothing =0.001)
 early_stopping_steps = EARLY_STOPPING_STEPS
early_step = 0
oof = np.zeros(( len(train), target.iloc[:, 1:].shape[1]))
best_loss = np.inf
for epoch in range(EPOCHS):
train_loss = train_fn(model, optimizer,scheduler, loss_tr, trainloader, DEVICE)
 print(f"SEED: {seed}, FOLD: {fold}, EPOCH: {epoch}, train_loss: {train_loss}")
 valid_loss, valid_preds = valid_fn(model, loss_fn, validloader, DEVICE)
 print(f"SEED: {seed} ,FOLD: {fold}, EPOCH: {epoch}, valid_loss: {valid_loss}")
 if valid_loss < best_loss:
best_loss = valid_loss
oof[val_idx] = valid_preds
torch.save(model.state_dict() , f"FOLD{fold}_.pth")
 elif(EARLY_STOP == True):
early_step += 1
if(early_step >= early_stopping_steps):
break
x_test = test_[feature_cols].values
testdataset = TestDataset(x_test)
 testloader = torch.utils.data.DataLoader(testdataset, batch_size=BATCH_SIZE, shuffle=False)
 model = Model(
 num_features=num_features,
num_targets=num_targets,
hidden_size=hidden_size, 
)
 model.load_state_dict(torch.load(f"FOLD{fold}_.pth"))
model.to(DEVICE)
 predictions = np.zeros(( len(test_), target.iloc[:, 1:].shape[1]))
predictions = inference_fn(model, testloader, DEVICE)
 return oof, predictions
train_dbno=pd.DataFrame(train['DBNOs'].value_counts() ,columns=['DBNOs'])
 dbno=train_dbno.iloc[:9,:]
dbno.iloc[8]['DBNOs']=train_dbno.iloc[8:,:].sum() ['DBNOs'] 
<define_variables>
def run_k_fold(NFOLDS, seed):
oof = np.zeros(( len(train), len(target_cols)))
 predictions = np.zeros(( len(test), len(target_cols)))
 for fold in range(NFOLDS):
oof_, pred_ = run_training(fold, seed)
 predictions += pred_ / NFOLDS
oof += oof_
return oof, predictions
set1=set(i for i in train[(train['kills']>40)&(train['heals']==0)].index.tolist() )<define_variables>
SEED = [0, 1, 2]
oof = np.zeros(( len(train), len(target_cols)))
 predictions = np.zeros(( len(test), len(target_cols)))
 for seed in SEED:
oof_, predictions_ = run_k_fold(NFOLDS, seed)
 oof += oof_ / len(SEED)
 predictions += predictions_ / len(SEED)
 train[target_cols] = oof
test[target_cols] = predictions
set2=set(i for i in train[(train['move']==0)&(train['kills']>20)].index.tolist() )<define_variables>
valid_results = train_targets_scored.drop(columns=target_cols ).merge(train[['sig_id']+target_cols], on='sig_id', how='left' ).fillna(0)
 y_true = train_targets_scored[target_cols].values
y_pred = valid_results[target_cols].values
score = 0
for i in range(len(target_cols)) :
score_ = log_loss(y_true[:, i], y_pred[:, i])
 score += score_ / target.shape[1]
print("CV log_loss: ", score)
<define_variables><EOS> 
sub = sample_submission.drop(columns=target_cols ).merge(test[['sig_id']+target_cols], on='sig_id', how='left' ).fillna(0)
 sub.to_csv('submission.csv', index=False )