Kaggle competition: Mechanisms of Action (MoA) Prediction
<SOS> metric: MeanColumnwiseLogLoss Kaggle data source: mechanisms-of-action-(moa)-prediction<compute_test_metric>
print(' MAE|',mean_absolute_error(y_test,y_pred_SGDC))
print(' MSE|',mean_squared_error(y_test,y_pred_SGDC))
print(' RMSE|',np.sqrt(mean_squared_error(y_test,y_pred_SGDC)) )<prepare_x_and_y>
sys.path.append('.. /input/iterativestratification')
 warnings.filterwarnings('ignore')
 os.listdir('.. /input/lish-moa')
 pd.set_option('max_columns', 2000 )
y_train = np.float64(y_train )<import_modules>
n_comp_GENES = 463
n_comp_CELLS = 60
VarianceThreshold_for_FS = 0.01
Dropout_Model = 0.25
print('n_comp_GENES', n_comp_GENES, 'n_comp_CELLS', n_comp_CELLS, 'total', n_comp_GENES + n_comp_CELLS )
from sklearn.ensemble import RandomForestClassifier<train_model>
commits_df = pd.DataFrame(columns = ['n_commit', 'n_comp_GENES', 'n_comp_CELLS', 'train_features','VarianceThreshold_for_FS', 'Dropout_Model', 'LB_score', 'CV_logloss'] )
RF = RandomForestClassifier(n_estimators=50,criterion='entropy',max_depth=10)
 RF.fit(X_train_std,y_train )<predict_on_test>
n=0
commits_df.loc[n, 'n_commit'] = 0
commits_df.loc[n, 'n_comp_GENES'] = 600
commits_df.loc[n, 'n_comp_CELLS'] = 50
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.8
commits_df.loc[n, 'train_features'] = 1245
commits_df.loc[n, 'Dropout_Model'] = 0.2619422201258426
commits_df.loc[n, 'CV_logloss'] = 0.01458269555140327
commits_df.loc[n, 'LB_score'] = 0.01839
y_pred_RF = RF.predict(X_test_std )<compute_test_metric>
n=1
commits_df.loc[n, 'n_commit'] = 4
commits_df.loc[n, 'n_comp_GENES'] = 610
commits_df.loc[n, 'n_comp_CELLS'] = 55
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.82
commits_df.loc[n, 'train_features'] = 1240
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.014584545081734047
commits_df.loc[n, 'LB_score'] = 0.01839
print(' Accuracy|',accuracy_score(y_test,y_pred_RF))
print('Precision|',precision_score(y_test,y_pred_RF,average='macro'))
print(' MAE|',mean_absolute_error(y_test,y_pred_RF))
print(' MSE|',mean_squared_error(y_test,y_pred_RF))
print(' RMSE|',np.sqrt(mean_squared_error(y_test,y_pred_RF)))
<train_model>
n=2
commits_df.loc[n, 'n_commit'] = 5
commits_df.loc[n, 'n_comp_GENES'] = 670
commits_df.loc[n, 'n_comp_CELLS'] = 67
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.67
commits_df.loc[n, 'train_features'] = 1298
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.014588561242139069
commits_df.loc[n, 'LB_score'] = 0.01840
RF2 = RandomForestClassifier(n_estimators=50,criterion='entropy',max_depth=10)
 RF2.fit(X_train_std,y_train )<import_modules>
n=3
commits_df.loc[n, 'n_commit'] = 6
commits_df.loc[n, 'n_comp_GENES'] = 450
commits_df.loc[n, 'n_comp_CELLS'] = 45
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.67
commits_df.loc[n, 'train_features'] = 1297
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.014586229676302227
commits_df.loc[n, 'LB_score'] = 0.01840
from keras.models import Sequential
from keras.layers import SimpleRNN, Embedding, Dense<choose_model_class>
n=4
commits_df.loc[n, 'n_commit'] = 9
commits_df.loc[n, 'n_comp_GENES'] = 463
commits_df.loc[n, 'n_comp_CELLS'] = 60
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.9
commits_df.loc[n, 'train_features'] = 1219
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.014572358066092783
commits_df.loc[n, 'LB_score'] = 0.01839
model = Sequential()<choose_model_class>
n=5
commits_df.loc[n, 'n_commit'] = 10
commits_df.loc[n, 'n_comp_GENES'] = 463
commits_df.loc[n, 'n_comp_CELLS'] = 80
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.92
commits_df.loc[n, 'train_features'] = 1214
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.014571552074579226
commits_df.loc[n, 'LB_score'] = 0.01841
model.add(Dense(26,input_dim=26, activation='relu'))
model.add(Dense(13,activation='relu'))
model.add(Dense(6,activation='relu'))
model.add(Dense(1,activation='relu'))<choose_model_class>
n=6
commits_df.loc[n, 'n_commit'] = 12
commits_df.loc[n, 'n_comp_GENES'] = 450
commits_df.loc[n, 'n_comp_CELLS'] = 65
commits_df.loc[n, 'VarianceThreshold_for_FS'] = 0.9
commits_df.loc[n, 'train_features'] = 1219
commits_df.loc[n, 'Dropout_Model'] = 0.25
commits_df.loc[n, 'CV_logloss'] = 0.01458043214513875
commits_df.loc[n, 'LB_score'] = 0.01840
model.compile(optimizer='sgd',loss='mse',metrics=['mae','acc'] )<import_modules>
commits_df['n_comp_total'] = commits_df['n_comp_GENES'] + commits_df['n_comp_CELLS']
commits_df['seed'] = 42
from keras.callbacks import EarlyStopping<choose_model_class>
commits_df['LB_score'] = pd.to_numeric(commits_df['LB_score'])
 commits_df = commits_df.sort_values(by=['LB_score', 'CV_logloss'], ascending = True ).reset_index(drop=True)
 commits_df['min'] = 0
commits_df.loc[0, 'min'] = 1
commits_df
callback_early = EarlyStopping(min_delta=0.01,patience=20 )<train_model>
commits_df.sort_values(by=['CV_logloss'], ascending = True )
history = model.fit(x=X_train_std,y=y_train, batch_size=10, epochs=50,validation_split=0.1,callbacks=[callback_early] )<compute_test_metric>
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' )
loss, mae, acc = model.evaluate(X_test_std,y_test)
 loss, mae, acc<predict_on_test>
GENES = [col for col in train_features.columns if col.startswith('g-')]
CELLS = [col for col in train_features.columns if col.startswith('c-')]
ypred_RN = model.predict(X_test_std )<compute_test_metric>
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]
print(' MAE|',mean_absolute_error(y_test,ypred_RN))
print(' MSE|',mean_squared_error(y_test,ypred_RN))
print(' RMSE|',np.sqrt(mean_squared_error(y_test,ypred_RN)) )<prepare_x_and_y>
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 )
X2 = df_train.drop('Category', axis=1 ).values
y2 = df_train['Category'].values<split>
data = pd.concat([pd.DataFrame(train_features[GENES]), pd.DataFrame(test_features[GENES])])
 data2 =(PCA(n_components=n_comp_GENES, 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_GENES)])
 test2 = pd.DataFrame(test2, columns=[f'pca_G-{i}' for i in range(n_comp_GENES)])
 train_features = pd.concat(( train_features, train2), axis=1)
 test_features = pd.concat(( test_features, test2), axis=1 )
X_train, X_test, y_train, y_test = train_test_split(X2, y2, test_size=0.15, random_state=42,stratify=y )<drop_column>
data = pd.concat([pd.DataFrame(train_features[CELLS]), pd.DataFrame(test_features[CELLS])])
 data2 =(PCA(n_components=n_comp_CELLS, 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_CELLS)])
 test2 = pd.DataFrame(test2, columns=[f'pca_C-{i}' for i in range(n_comp_CELLS)])
 train_features = pd.concat(( train_features, train2), axis=1)
 test_features = pd.concat(( test_features, test2), axis=1 )
test = df_test.drop('Id',axis=1)
<define_variables>
var_thresh = VarianceThreshold(VarianceThreshold_for_FS)
 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
test = test.values<normalization>
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]
std = StandardScaler()
X_train = std.fit_transform(X_train)
 X_test = std.transform(X_test )<normalization>
train = train.drop('cp_type', axis=1)
 test = test.drop('cp_type', axis=1 )
test = StandardScaler().fit_transform(test);<choose_model_class>
target_cols = target.drop('sig_id', axis=1 ).columns.values.tolist()
RF = RandomForestClassifier(n_estimators=50,criterion='entropy',max_depth=10 )<train_model>
folds = train.copy()
mskf = MultilabelStratifiedKFold(n_splits=7)
 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
RF.fit(X_train,y_train )<predict_on_test>
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
y_pred_RF = RF.predict(X_predict_std )<data_type_conversions>
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
Y = df_train['Category'].astype('category' )<count_unique_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
np.count_nonzero(Y.cat.categories.unique()), np.count_nonzero(np.unique(y_pred_RF))<prepare_output>
def process_data(data):
data = pd.get_dummies(data, columns=['cp_time','cp_dose'])
 return data
submit = pd.DataFrame({'Id': df_test.Id.tolist() })
 for category in Y.cat.categories:
submit[category] = np.where(y_pred_RF == category, 1, 0 )<save_to_csv>
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 )
submit.to_csv('San_Francisco_Crime_RF.csv', index = False )<load_from_csv>
DEVICE =('cuda' if torch.cuda.is_available() else 'cpu')
 EPOCHS = 25
BATCH_SIZE = 128
LEARNING_RATE = 1e-3
WEIGHT_DECAY = 1e-5
NFOLDS = 7
EARLY_STOPPING_STEPS = 10
EARLY_STOP = False
num_features=len(feature_cols)
 num_targets=len(target_cols)
 hidden_size=1500
train = pd.read_csv(".. /input/train.csv", parse_dates=["Dates"])
 test = pd.read_csv(".. /input/test.csv", parse_dates=["Dates"], index_col="Id" )<filter>
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(Dropout_Model)
 self.dense2 = nn.utils.weight_norm(nn.Linear(hidden_size, hidden_size))
self.batch_norm3 = nn.BatchNorm1d(hidden_size)
 self.dropout3 = nn.Dropout(Dropout_Model)
 self.dense3 = nn.utils.weight_norm(nn.Linear(hidden_size, num_targets))
def forward(self, x):
x = self.batch_norm1(x)
 x = F.leaky_relu(self.dense1(x))
x = self.batch_norm2(x)
 x = self.dropout2(x)
 x = F.leaky_relu(self.dense2(x))
x = self.batch_norm3(x)
 x = self.dropout3(x)
 x = self.dense3(x)
 return x
class LabelSmoothingLoss(nn.Module):
def __init__(self, classes, smoothing=0.0, dim=-1):
super(LabelSmoothingLoss, self ).__init__()
self.confidence = 1.0 - smoothing
self.smoothing = smoothing
self.cls = classes
self.dim = dim
def forward(self, pred, target):
pred = pred.log_softmax(dim=self.dim)
 with torch.no_grad() :
true_dist = torch.zeros_like(pred)
 true_dist.fill_(self.smoothing /(self.cls - 1))
true_dist.scatter_(1, target.data.unsqueeze(1), self.confidence)
 return torch.mean(torch.sum(-true_dist * pred, dim=self.dim))
train[train["X"] > -122.2]<filter>
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)
 valid_loss, valid_preds = valid_fn(model, loss_fn, validloader, DEVICE)
 print(f"FOLD: {fold}, EPOCH: {epoch}, train_loss: {train_loss}, 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[train["Y"] < 37.6]<filter>
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
train[train["Y"] > 38.0]<filter>
test_features = pd.read_csv('.. /input/lish-moa/test_features.csv')
 if test_features.shape[0] == 3982:
print("Running for ONE SEED...")
 SEED = [0]
else:
SEED = [0, 1, 2, 3, 4, 5, 6]
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
test[test["X"] < -122.6]<filter>
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 )
<filter><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 )