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print(bestP) print('N estimators:', int(bestP['n_estimators'])) print('Learning rate:', bestP['learning_rate']) print('Subsample:', bestP['subsample']) print('Colsample bytree:', bestP['colsample_bytree']) print('Max depth:', int(bestP['max_depth'])) print('Num leaves:', int(bestP['num_leaves'])) print('Min child w...
train = train.drop(columns=['Name','Cabin','Ticket']) test = test.drop(columns=['Name','Cabin','Ticket'] )
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%%time model = lightgbm.LGBMRegressor( n_estimators = int(bestP['n_estimators']), learning_rate = bestP['learning_rate'], subsample = bestP['subsample'], colsample_bytree = bestP['colsample_bytree'], max_depth = int(bestP['max_depth']), num_leaves = int(bestP['num_leaves']), min_child_weight = int(bestP['min_child_wei...
train['Embarked_S'] =(train['Embarked'] == 'S' ).astype(int) train['Embarked_C'] =(train['Embarked'] == 'C' ).astype(int) train['Embarked_Q'] =(train['Embarked'] == 'Q' ).astype(int) train['Gender'] =(train['Sex'] == 'male' ).astype(int )
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joblib.dump(model, filename) del model, X_train, y_train, X_valid, y_valid gc.collect()<feature_engineering>
test['Embarked_S'] =(test['Embarked'] == 'S' ).astype(int) test['Embarked_C'] =(test['Embarked'] == 'C' ).astype(int) test['Embarked_Q'] =(test['Embarked'] == 'Q' ).astype(int) test['Gender'] =(test['Sex'] == 'male' ).astype(int )
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%%time validation = steval[['id']+['d_' + str(i)for i in range(1914,1942)]] validation['id']=pd.read_csv('/kaggle/input/m5-forecasting-accuracy/sales_train_validation.csv' ).id validation.columns=['id'] + ['F' + str(i + 1)for i in range(28)] test['sold'] = eval_prediction evaluation = test[['id','d','sold']] evaluation...
train = train.drop(columns = ['Sex']) test = test.drop(columns = ['Sex']) train = train.drop(columns = ['Embarked']) test = test.drop(columns = ['Embarked'] )
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gc.collect()<concatenate>
train.fillna(0, inplace=True) test.fillna(0, inplace=True )
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submit = pd.concat([validation,evaluation] ).reset_index(drop=True) submit.head()<save_to_csv>
X = train.drop(columns=['Survived']) y = train['Survived']
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print("Generating CSV file") submit.to_csv('submission.csv',index=False) print("Submission Successful" )<categorify>
X_train, X_test, y_train, y_test = train_test_split(X, y, random_state=42 )
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pretrain_dir = None one_fold = False run_test = False denoise = True ae_epochs = 20 ae_epochs_each = 5 ae_batch_size = 32 epochs_list = [30, 10, 3, 3, 5, 5] batch_size_list = [8, 16, 32, 64, 128, 256] if pretrain_dir is not None: for d in glob.glob(pretrain_dir + "*"): shutil.copy(d, ".") %matplotlib inline<load_from_...
model = LGBMClassifier(learning_rate=0.01, n_estimators=1000 )
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train = pd.read_json("/kaggle/input/stanford-covid-vaccine/train.json",lines=True) if denoise: train = train[train.signal_to_noise > 1].reset_index(drop = True) test = pd.read_json("/kaggle/input/stanford-covid-vaccine/test.json",lines=True) test_pub = test[test["seq_length"] == 107] test_pri = test[test["seq_length...
model.fit(X_train, y_train )
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targets = list(sub.columns[1:]) print(targets) y_train = [] seq_len = train["seq_length"].iloc[0] seq_len_target = train["seq_scored"].iloc[0] ignore = -10000 ignore_length = seq_len - seq_len_target for target in targets: y = np.vstack(train[target]) dummy = np.zeros([y.shape[0], ignore_length])+ ignore y = np.hsta...
model.fit(X_train, y_train )
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def get_structure_adj(train): Ss = [] for i in tqdm(range(len(train))): seq_length = train["seq_length"].iloc[i] structure = train["structure"].iloc[i] sequence = train["sequence"].iloc[i] cue = [] a_structures = { ("A", "U"): np.zeros([seq_length, seq_length]), ("C", "G"): np.zeros([seq_length, seq_length]), ("U", ...
pred = model.predict(X_test )
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def get_distance_matrix(As): idx = np.arange(As.shape[1]) Ds = [] for i in range(len(idx)) : d = np.abs(idx[i] - idx) Ds.append(d) Ds = np.array(Ds)+ 1 Ds = 1/Ds Ds = Ds[None, :,:] Ds = np.repeat(Ds, len(As), axis = 0) Dss = [] for i in [1, 2, 4]: Dss.append(Ds ** i) Ds = np.stack(Dss, axis = 3) print(Ds.shape) ...
print("R2-score: ",r2_score(pred, y_test)) print("Accuracy score: ",accuracy_score(pred, y_test)) print("F1-score: ",f1_score(pred, y_test))
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As = np.concatenate([As[:,:,:,None], Ss, Ds], axis = 3 ).astype(np.float32) As_pub = np.concatenate([As_pub[:,:,:,None], Ss_pub, Ds_pub], axis = 3 ).astype(np.float32) As_pri = np.concatenate([As_pri[:,:,:,None], Ss_pri, Ds_pri], axis = 3 ).astype(np.float32) del Ss, Ds, Ss_pub, Ds_pub, Ss_pri, Ds_pri As.shape, As_p...
actual_pred = model.predict(test )
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def return_ohe(n, i): tmp = [0] * n tmp[i] = 1 return tmp def get_input(train): mapping = {} vocab = ["A", "G", "C", "U"] for i, s in enumerate(vocab): mapping[s] = return_ohe(len(vocab), i) X_node = np.stack(train["sequence"].apply(lambda x : list(map(lambda y : mapping[y], list(x))))) mapping = {} vocab = ["S", "M"...
result = pd.DataFrame({'PassengerId':test['PassengerId'], 'Survived':actual_pred} )
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<train_model><EOS>
result.to_csv("submission.csv", index=False )
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<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<define_variables>
train = pd.read_csv('.. /input/train.csv') test = pd.read_csv('.. /input/test.csv' )
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kfold = KFold(5, shuffle = True, random_state = 42) scores = [] preds = np.zeros([len(X_node), X_node.shape[1], 5]) for i,(tr_idx, va_idx)in enumerate(kfold.split(X_node, As)) : print(f"------ fold {i} start -----") print(f"------ fold {i} start -----") print(f"------ fold {i} start -----") X_node_tr = X_node[tr_i...
def extract_title(name): name = name.split() for w in name: if '.' in w: return w return None all_titles = pd.concat([train, test], sort=False ).Name.apply(lambda name: extract_title(name)) all_titles.unique()
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p_pub = 0 p_pri = 0 for i in range(5): model.load_weights(f"./model{i}") p_pub += model.predict([X_node_pub, As_pub])/ 5 p_pri += model.predict([X_node_pri, As_pri])/ 5 if one_fold: p_pub *= 5 p_pri *= 5 break for i, target in enumerate(targets): test_pub[target] = [list(p_pub[k, :, i])for k in range(p_pub.shape[0])] ...
train['title'] = train.Name.apply(lambda name: extract_title(name)) test['title'] = test.Name.apply(lambda name: extract_title(name)) train.groupby('title' ).Survived.agg(['count', 'mean'] )
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preds_ls = [] for df, preds in [(test_pub, p_pub),(test_pri, p_pri)]: for i, uid in enumerate(df.id): single_pred = preds[i] single_df = pd.DataFrame(single_pred, columns=targets) single_df['id_seqpos'] = [f'{uid}_{x}' for x in range(single_df.shape[0])] preds_ls.append(single_df) preds_df = pd.concat(preds_ls) pred...
train.groupby('title' ).Survived.agg(['count', 'mean'] )
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%matplotlib inline warnings.filterwarnings('ignore' )<load_from_csv>
title_encoder = LabelEncoder().fit(train.title) train.title = title_encoder.transform(train.title) test.title = title_encoder.transform(test.title )
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train = pd.read_json(".. /input/stanford-covid-vaccine/train.json",lines=True) test = pd.read_json(".. /input/stanford-covid-vaccine/test.json",lines=True) sub = pd.read_csv(".. /input/stanford-covid-vaccine/sample_submission.csv") test_pub = test[test["seq_length"] == 107] test_pri = test[test["seq_length"] == 130]...
sex_encoder = LabelEncoder().fit(train.Sex) train.Sex = sex_encoder.transform(train.Sex) test.Sex = sex_encoder.transform(test.Sex )
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aug_df = pd.read_csv('.. /input/covid19-mrna-augmentation-data-and-features/aug_data1.csv') aug_df = aug_df.drop_duplicates(subset=['id', 'structure']) def aug_data(df): target_df = df.copy() new_df = aug_df[aug_df['id'].isin(target_df['id'])] del target_df['structure'] del target_df['predicted_loop_type'] new_df = n...
age_translator = pd.concat([train, test], sort=False ).groupby('title' ).Age.median().to_dict() train['completeAge'] = train.apply(lambda x: age_translator[x.title], axis=1) train.loc[train.Age.notnull() , 'completeAge'] = train.loc[train.Age.notnull() , 'Age'] test['completeAge'] = test.apply(lambda x: age_translator...
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As = [] for id in tqdm(train["id"]): a = np.load(f".. /input/stanford-covid-vaccine/bpps/{id}.npy" ).astype(np.float16) As.append(a) As = np.array(As) As_pub = [] for id in tqdm(test_pub["id"]): a = np.load(f".. /input/stanford-covid-vaccine/bpps/{id}.npy" ).astype(np.float16) As_pub.append(a) As_pub = np.array(As...
train['familysize'] = train.Parch + train.SibSp + 1 test['familysize'] = test.Parch + test.SibSp + 1 train.drop(['Parch', 'SibSp'], inplace=True, axis=1) train['hasfamily'] = 0 train.loc[train.familysize == 1, 'hasfamily'] = 1 test['hasfamily'] = 0 test.loc[test.familysize == 1, 'hasfamily'] = 1
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def get_structure_adj(train): Ss = [] for i in tqdm(range(len(train))): seq_length = train["seq_length"].iloc[i] structure = train["structure"].iloc[i] sequence = train["sequence"].iloc[i] cue = [] a_structures = { ("A", "U"): np.zeros([seq_length, seq_length]), ("C", "G"): np.zeros([seq_length, seq_length]), ("U", ...
train['ticketno'] = train.Ticket.apply(lambda x: x.split() [-1]) train.ticketno.replace('LINE', "0", inplace=True) train.ticketno = train['ticketno'].astype(np.int) test['ticketno'] = test.Ticket.apply(lambda x: x.split() [-1]) test.ticketno = test['ticketno'].astype(np.int )
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def get_distance_matrix(As): idx = np.arange(As.shape[1]) Ds = [] for i in range(len(idx)) : d = np.abs(idx[i] - idx) Ds.append(d) Ds = np.array(Ds)+ 1 Ds = Ds / Ds.shape[1] Ds = Ds[None, :,:] Ds = np.repeat(Ds, len(As), axis = 0) Dss = [] for i in [1]: Dss.append(Ds ** i) Ds = np.stack(Dss, axis = 3) return Ds.a...
train['decklevel'] = train.Cabin.dropna().apply(lambda x: str(x)[0]) test['decklevel'] = test.Cabin.dropna().apply(lambda x: str(x)[0]) decklevel_encoder = LabelEncoder().fit(train.decklevel.dropna()) train.loc[train.decklevel.notna() , 'decklevel'] = decklevel_encoder.transform(train.decklevel.dropna()) test.loc[t...
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As = np.concatenate([As[:,:,:,None], As_cf[:,:,:,None], As_rs[:,:,:,None], Ss, Ds], axis = 3 ).astype(np.float16) del Ss, Ds, As_cf, As_rs As_pub = np.concatenate([As_pub[:,:,:,None], As_pub_cf[:,:,:,None], As_pub_rs[:,:,:,None], Ss_pub, Ds_pub], axis = 3 ).astype(np.float16) del Ss_pub, Ds_pub, As_pub_cf, As_pub_rs ...
train.Embarked.fillna('S', inplace=True) embarked_encoder = LabelEncoder().fit(train.Embarked) train.Embarked = embarked_encoder.transform(train.Embarked) test.Embarked = embarked_encoder.transform(test.Embarked )
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f, ax = plt.subplots(1, 5, figsize=(15, 3)) for i in range(As.shape[-1]): ax[i].imshow(As[0, :, :, i].astype(np.float32)) plt.show()<load_pretrained>
test.loc[test.Fare.isna() , 'Fare'] = train.Fare.median()
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arnie_train_features = pickle.load(open('.. /input/covid19-mrna-augmentation-data-and-features/arnie/arnie/train_features.p', 'rb')) arnie_test_features = pickle.load(open('.. /input/covid19-mrna-augmentation-data-and-features/arnie/arnie/test_features.p', 'rb')) capr_train_features = pickle.load(open('.. /input/covid1...
featurelist = ['Pclass', 'Fare', 'title', 'Sex', 'Embarked', 'rich_small_families', 'completeAge', 'hasfamily']
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def return_ohe(n, i): tmp = [0] * n tmp[i] = 1 return tmp def get_input(train): mapping = {} vocab = ["A", "G", "C", "U"] for i, s in enumerate(vocab): mapping[s] = return_ohe(len(vocab), i) X_node = np.stack(train["sequence"].apply(lambda x : list(map(lambda y : mapping[y], list(x))))) mapping = {} vocab = ["S", "M"...
parameters = {'n_estimators': [40, 50, 60, 70], 'max_depth': [7, 10, 13], 'max_features': range(3, len(featurelist)) , 'min_samples_leaf': [1, 2, 3], 'min_samples_split': [7, 10, 12]} model = RandomForestClassifier(random_state=42) grid = GridSearchCV(model, param_grid=parameters, cv=5, n_jobs=-1, scoring='accuracy') ...
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del arnie_train_features, arnie_test_features, capr_train_features, capr_test_features<concatenate>
grid.best_params_
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targets = ['reactivity', 'deg_Mg_pH10', 'deg_pH10', 'deg_Mg_50C', 'deg_50C'] y_train = [] seq_len = train["seq_length"].iloc[0] seq_len_target = train["seq_scored"].iloc[0] ignore = -10000 ignore_length = seq_len - seq_len_target for target in targets: y = np.vstack(train[target]) dummy = np.zeros([y.shape[0], ignore_...
grid.best_score_
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N_NODE_FEATURES = X_node.shape[2] N_EDGE_FEATURES = As.shape[3]<import_modules>
print(classification_report(grid.predict(train[featurelist]), train['Survived']))
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import tensorflow as tf from tensorflow.keras import layers as L import tensorflow_addons as tfa from tensorflow.keras import backend as K from sklearn.utils import shuffle from sklearn.model_selection import GroupKFold<define_search_space>
result = test result.loc[:,'Survived'] = grid.predict(test[featurelist]) result.head()
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<compute_test_metric><EOS>
result[['PassengerId', 'Survived']].to_csv('submission.csv', header=True, index=False )
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<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<train_model>
init_notebook_mode()
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config = {} if ae_epochs > 0: base = get_base(config) ae_model = get_ae_model(base, config) for i in range(ae_epochs//ae_epochs_each): print(f"------ {i} ------") print("--- train ---") X_node_shuff, As_shuff = shuffle(X_node, As) ae_model.fit([X_node_shuff, As_shuff], [np.zeros(( len(X_node)))], epochs = ae_epoch...
features1 = ["Age","SibSp","Parch", "Pclass", "is_male", "is_female", "f_size", "Single", "SmallF", "MedF", "LargeF", "Title", "Embarked"] target = ["Survived"] print("Total number of features is {}".format(len(features1)) )
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del ae_model gc.collect()<save_model>
test_csv = prepare_data('.. /input/test.csv', True) test_data = test_csv[features1] test_csv.head(5 )
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np.save('X_node_pub.npy', X_node_pub) np.save('X_node_pri.npy', X_node_pri) np.save('As_pub.npy', As_pub) np.save('As_pri.npy', As_pri) del X_node_pub, X_node_pri, As_pub, As_pri, X_node_shuff, As_shuff, X_node_pub_shuff, As_pub_shuff, X_node_pri_shuff, As_pri_shuff<split>
train, valid = train_test_split(data, test_size=0.2) print("The Train Set Size is {} The Validation Set Size is {}".format(len(train), len(valid))) print("Test Set Size is {}".format(len(test_data)) )
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kfold = GroupKFold(5) config = {} scores = [] preds = np.zeros([len(X_node), X_node.shape[1], 5]) X_node, As, y, weights, groups_shuffled, SN_filter_mask = shuffle(X_node, As, y, train.signal_to_noise.values, train['id'],(train['SN_filter'] == 1 ).values) del train for i,(tr_idx, va_idx)in enumerate(kfold.split(X_no...
train_x , train_y = data[features1].as_matrix() , data[target].as_matrix() clf = DecisionTreeClassifier() clf.fit(train_x, train_y) print(( np.array(clf.predict(valid[features1].as_matrix())== valid[target].as_matrix().flatten() , dtype=np.int ).sum() * 100.) / len(valid)) result = pd.DataFrame(data={'PassengerId': te...
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preds_df = [] for p_ix, _id in zip(range(preds.shape[0]), groups_shuffled): for i in range(68): preds_df.append([f'{_id}_{i}', preds[p_ix, i, 0], preds[p_ix, i, 1], preds[p_ix, i, 3], y[p_ix, i, 0], y[p_ix, i, 1], y[p_ix, i, 3], SN_filter_mask[p_ix]]) preds_df = pd.DataFrame(preds_df, columns=['id_seqpos', 'reactivity...
class TitanicLoader(Dataset): def __init__(self,train,transforms=None): self.X = train.as_matrix(columns=features1) self.Y = train.as_matrix(columns=target ).flatten() self.count = len(self.X) self.transforms = transforms def __getitem__(self, index): nextItem = Variable(torch.tensor(self.X[index] ).type(torch.FloatT...
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del X_node, As<load_pretrained>
class DNN(nn.Module): def __init__(self, input_size, first_hidden_size, second_hidden_size, num_classes): super(DNN, self ).__init__() self.z1 = nn.Linear(input_size, first_hidden_size) self.relu = nn.ReLU() self.z2 = nn.Linear(first_hidden_size, second_hidden_size) self.z3 = nn.Linear(second_hidden_size, num_classes...
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X_node_pub = np.load('X_node_pub.npy') X_node_pri = np.load('X_node_pri.npy') As_pub = np.load('As_pub.npy') As_pri = np.load('As_pri.npy' )<load_pretrained>
def train_dnn(net, trainL, validL): count = 0 accuList = [] lossList = [] optimizer = torch.optim.Adam(net.parameters() ,lr=0.001) for epc in range(1,epochs + 1): print("Epoch vcount = 0 total_loss = 0 net.train() for data,target in trainL: optimizer.zero_grad() out = net(data) loss = F.nll_loss(out, target, size_ave...
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p_pub = 0 p_pri = 0 for i in range(5): config = {} base = get_base(config) if ae_epochs > 0: print("****** load ae model ******") base.load_weights("base_ae_lstm_lstm") model = get_model(base, config) model.load_weights(f"model{i}_lstm_lstm") p_pub += model.predict([X_node_pub, As_pub])/ 5 p_pri += model.predict([...
epochs = 12
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preds_ls = [] for df, preds in [(test_pub, p_pub),(test_pri, p_pri)]: for i, uid in enumerate(df.id): single_pred = preds[i] single_df = pd.DataFrame(single_pred, columns=targets) single_df['id_seqpos'] = [f'{uid}_{x}' for x in range(single_df.shape[0])] preds_ls.append(single_df) preds_df = pd.concat(preds_ls) pred...
titanic_train_DS = TitanicLoader(train) titanic_valid_DS = TitanicLoader(valid) train_loader = torch.utils.data.DataLoader(titanic_train_DS, batch_size=6, shuffle=False) valid_loader = torch.utils.data.DataLoader(titanic_valid_DS, batch_size=1, shuffle=False )
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import numpy as np import pandas as pd import os <import_modules>
myNet = DNN(len(features1), 23, 4, 2) accuList, lossList = train_dnn(myNet, train_loader, valid_loader )
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import json import tensorflow as tf from matplotlib import pyplot as plt<load_from_csv>
def get_preds(test, net): net.eval() preds = [] for data, target in test: out = net(data) pred = out.data.max(1, keepdim=True)[1] preds.append(pred.item()) return preds
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train_data = pd.read_json('/kaggle/input/stanford-covid-vaccine/train.json', lines = True) test_data = pd.read_json('/kaggle/input/stanford-covid-vaccine/test.json', lines = True) submission_format = pd.read_csv('/kaggle/input/stanford-covid-vaccine/sample_submission.csv', encoding = 'utf-8-sig' )<groupby>
test_data['Survived'] = -1 titanic_test_DS = TitanicLoader(test_data) test_loader = torch.utils.data.DataLoader(titanic_test_DS, batch_size=1, shuffle=False) result = pd.DataFrame(data={'PassengerId': test_csv['PassengerId'], 'Survived': get_preds(test_loader, myNet)}) result.to_csv(path_or_buf='neural_network_submi...
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train_data.groupby(['SN_filter'] ).size()<count_values>
neigh = KNeighborsClassifier(n_neighbors=5, weights='distance', p=1) neigh.fit(train[features1].as_matrix() , train[target].as_matrix().flatten()) print_acc(( np.array(neigh.predict(valid[features1].as_matrix())== valid[target].as_matrix().flatten() , dtype=np.int ).sum() * 100.) / len(valid), "K-NN") result = pd.Da...
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print('Training data: ',train_data['seq_scored'].value_counts()) print('Test data: ',test_data['seq_scored'].value_counts()) len(train_data['reactivity'].iloc[0] )<count_values>
gnb = GaussianNB() y_pred = gnb.fit(train[features1].as_matrix() , train[target].as_matrix().flatten() ).predict(valid[features1].as_matrix()) print_acc(float(np.array(y_pred == valid[target].as_matrix().flatten() , dtype=np.int ).sum() * 100)/ len(valid), "Naive Bayes") result = pd.DataFrame(data={'PassengerId': tes...
Titanic - Machine Learning from Disaster
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flag = False for i in range(0,len(train_data)) : if(( [x<0 for x in train_data['reactivity_error'].iloc[i]].count(True)> 0)| ([x<0 for x in train_data['deg_error_Mg_pH10'].iloc[i]].count(True)> 0)| ([x<0 for x in train_data['deg_error_pH10'].iloc[i]].count(True)> 0)| ([x<0 for x in train_data['deg_error_Mg_50C'].ilo...
clf1 = LogisticRegression(random_state=1) clf2 = RandomForestClassifier(n_estimators=25,random_state=1) clf3 = GaussianNB(var_smoothing=True) clf4 = LinearSVC(random_state=5) gbm = xgb.XGBClassifier(max_depth=5, n_estimators=300, learning_rate=0.05) eclf1 = VotingClassifier(estimators=[('lr', clf1),('rf', clf2),('...
Titanic - Machine Learning from Disaster
1,503,290
<feature_engineering><EOS>
gbm = xgb.XGBClassifier(max_depth=3, n_estimators=600, learning_rate=0.05) y_pred = gbm.fit(train[features1].as_matrix() , train[target].as_matrix().flatten() ).predict(valid[features1].as_matrix()) print_acc(float(np.array(y_pred == valid[target].as_matrix().flatten() , dtype=np.int ).sum() * 100)/ len(valid), "XGB"...
Titanic - Machine Learning from Disaster
434,514
<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<define_variables>
import numpy as np import pandas as pd import seaborn as sns import matplotlib.pyplot as plt from sklearn.ensemble import RandomForestClassifier
Titanic - Machine Learning from Disaster
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token2int = {x:i for i, x in enumerate('().ACGUBEHIMSX')} target_cols = ['reactivity', 'deg_Mg_pH10', 'deg_pH10', 'deg_Mg_50C', 'deg_50C']<load_pretrained>
train=pd.read_csv(".. /input/train.csv") test=pd.read_csv(".. /input/test.csv") def append_train_test(train,test): train["IsTrain"]=1 test["IsTrain"]=0 df=train.append(test) return df; full=append_train_test(train,test) train.info() print("------------------------") test.info() print("------------------------") f...
Titanic - Machine Learning from Disaster
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def read_bpps_sum(df): bpps_arr = [] for mol_id in df.id.to_list() : bpps_arr.append(np.load(f".. /input/stanford-covid-vaccine/bpps/{mol_id}.npy" ).sum(axis=1)) return bpps_arr def read_bpps_max(df): bpps_arr = [] for mol_id in df.id.to_list() : bpps_arr.append(np.load(f".. /input/stanford-covid-vaccine/bpps/{mol_id}....
full.loc[(full["Title"].isin(["Rev","Dr","Col","Capt","Major"])) &(full["Sex"]!="male")]
Titanic - Machine Learning from Disaster
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def get_bases(data): bases = [] for j in range(len(data)) : counts = dict(count(data.iloc[j]['sequence'])) bases.append(( counts['A'] / 107, counts['G'] / 107, counts['C'] / 107, counts['U'] / 107 )) bases = pd.DataFrame(bases, columns=['A_percent', 'G_percent', 'C_percent', 'U_percent']) return bases<create_datafram...
full.loc[(full["Title"].isin(["Rev","Capt","Major","Col","Jonkheer","Don","Sir","Dr"])) &(full["Sex"]=="male"),"Title"] = "Mr" full.loc[(full["Title"].isin(["Countess","Lady","Dona","Mme"])) ,"Title"]="Mrs" full.loc[(full["Title"].isin(["Mlle","Ms","Dr"])) &(full["Sex"]=="female"),"Title"]="Miss" full["Title"].value_co...
Titanic - Machine Learning from Disaster
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def get_pairs_rate(data): pairs_rate = [] for j in range(len(data)) : res = dict(count(data.iloc[j]['structure'])) pairs_rate.append(res['('] / 53.5) pairs_rate = pd.DataFrame(pairs_rate, columns=['pairs_rate']) return pairs_rate<define_variables>
full.isnull().sum()
Titanic - Machine Learning from Disaster
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def get_pairs(data): pairs = [] all_partners = [] for j in range(len(data)) : partners = [-1 for i in range(130)] pairs_dict = {} queue = [] for i in range(0, len(data.iloc[j]['structure'])) : if data.iloc[j]['structure'][i] == '(': queue.append(i) if data.iloc[j]['structure'][i] == ')': first = queue.pop() try: pairs...
full[full.Fare.isnull() ]
Titanic - Machine Learning from Disaster
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def get_loops(data): loops = [] for j in range(len(data)) : counts = dict(count(data.iloc[j]['predicted_loop_type'])) available = ['E', 'S', 'H', 'B', 'X', 'I', 'M'] row = [] for item in available: try: row.append(counts[item] / 107) except: row.append(0) loops.append(row) loops = pd.DataFrame(loops, columns=availab...
full.loc[(full.Fare.isnull()),"Fare"]=8.05
Titanic - Machine Learning from Disaster
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def get_structure_adj(train): Ss = [] for i in tqdm(range(len(train))): seq_length = train["seq_length"].iloc[i] structure = train["structure"].iloc[i] sequence = train["sequence"].iloc[i] cue = [] a_structures = { ("A", "U"): np.zeros([seq_length, seq_length]), ("C", "G"): np.zeros([seq_length, seq_length]), ("U", ...
full[full.Embarked.isnull() ]
Titanic - Machine Learning from Disaster
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As = [] data = train_data[train_data['signal_to_noise'] > 1].copy() for id in tqdm(data['id']): a = np.load(f"/kaggle/input/stanford-covid-vaccine/bpps/{id}.npy") As.append(a) As = np.array(As )<compute_test_metric>
full.loc[(full.Embarked.isnull()),"Embarked"]="C"
Titanic - Machine Learning from Disaster
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def get_distance_matrix(As): idx = np.arange(As.shape[1]) Ds = [] for i in range(len(idx)) : d = np.abs(idx[i] - idx) Ds.append(d) Ds = np.array(Ds)+ 1 Ds = 1/Ds Ds = Ds[None, :,:] Ds = np.repeat(Ds, len(As), axis = 0) Dss = [] for i in [1, 2, 4]: Dss.append(Ds ** i) Ds = np.stack(Dss, axis = 3) print(Ds.shape) ...
ImpAge=pd.DataFrame({'median' : data.groupby([ "Title", "Pclass"] ).Age.median() } ).reset_index() ImpAge.head(n=20 )
Titanic - Machine Learning from Disaster
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def preprocess_inputs(df, cols=['sequence', 'structure', 'predicted_loop_type'], seq_length = 107, flag = 'train'): base_fea = np.transpose( np.array( df[cols] .applymap(lambda seq: [token2int[x] for x in seq]) .values .tolist() ), (0, 2, 1) ) bpps_sum_fea = np.array(df['bpps_sum'].to_list())[:,:,np.newaxis] bpp...
def imputeAges(df): classes=[1,2,3] titles=["Mr","Mrs","Miss","Master"] for title in titles: for pclass in classes: x=ImpAge[(( ImpAge.Title==title)&(ImpAge.Pclass==pclass)) ]["median"].values[0] df.loc[(( df.Title==title)&(df.Pclass==pclass)&(df.Age.isnull())) ,"Age"]=x return df imputeAges(full) full.isnull().sum()
Titanic - Machine Learning from Disaster
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bases = get_bases(train_data) pairs = get_pairs(train_data) loops = get_loops(train_data) pairs_rate = get_pairs_rate(train_data) train_data = pd.concat([train_data, bases, pairs, loops, pairs_rate], axis=1) bases = get_bases(test_data) pairs = get_pairs(test_data) loops = get_loops(test_data) pairs_rate = get_...
features=["Age","Embarked","Fare","Parch","Pclass","Sex","SibSp","Title","FamilySize","FamilySizeBand"] target="Survived" full[features].head()
Titanic - Machine Learning from Disaster
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train_inputs = preprocess_inputs(train_data.loc[train_data['signal_to_noise'] > 1], seq_length = 107, flag = 'train') train_labels = np.array(train_data.loc[train_data['signal_to_noise'] > 1][target_cols].values.tolist() ).transpose(( 0, 2, 1))<compute_test_metric>
clf = RandomForestClassifier(n_jobs=2, random_state=0) clf = clf.fit(train_features, train_target) train_preds=clf.predict(train_features) print(clf) for i in range(0,10): print(features[i]," ",clf.feature_importances_[i] )
Titanic - Machine Learning from Disaster
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def root_mean_squared_error(y_true, y_pred): return tf.sqrt(mean_squared_error(y_true, y_pred)) def MCRMSE(y_true, y_pred): colwise_mse = tf.reduce_mean(tf.square(y_true - y_pred), axis=1) return tf.reduce_mean(tf.sqrt(colwise_mse), axis=1) def lstm_layer(hidden_dim, dropout): return tf.keras.layers.Bidirectional( t...
pd.crosstab(train_target, train_preds, rownames=['Actual Outcome'], colnames=['Predicted Outcome'] )
Titanic - Machine Learning from Disaster
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public_df = test_data.query("seq_length == 107" ).copy() private_df = test_data.query("seq_length == 130" ).copy()<load_pretrained>
test_preds=clf.predict(test_features ).astype(int) test_ids=full[891:]["PassengerId"] final = pd.DataFrame({ "PassengerId": test_ids, "Survived": test_preds }) final.info()
Titanic - Machine Learning from Disaster
434,514
<load_pretrained><EOS>
final.to_csv('submission2.csv', index=False )
Titanic - Machine Learning from Disaster
12,584,804
<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<load_pretrained>
!pip install seaborn==0.11.0
Titanic - Machine Learning from Disaster
12,584,804
model_LSTM_on_test_data_private = build_model(seq_len=130, pred_len=130, gru_flag = False) model_LSTM_on_test_data_private.load_weights('.. /input/openvaccine-covid-model-weights/LSTM model.h5') pred_test_data_private_LSTM = model_LSTM_on_test_data_private.predict(private_inputs) model_GRU_on_test_data_private = bui...
titanic = pd.read_csv('/kaggle/input/titanic/train.csv' )
Titanic - Machine Learning from Disaster
12,584,804
def format_predictions(public_preds, private_preds): preds = [] for df, preds_ in [(public_df, public_preds),(private_df, private_preds)]: for i, uid in enumerate(df.id): single_pred = preds_[i] single_df = pd.DataFrame(single_pred, columns=target_cols) single_df['id_seqpos'] = [f'{uid}_{x}' for x in range(single_df.s...
titanic.isnull().sum()
Titanic - Machine Learning from Disaster
12,584,804
lstm_preds = format_predictions(pred_test_data_public_LSTM, pred_test_data_private_LSTM) gru_preds = format_predictions(pred_test_data_public_GRU, pred_test_data_private_GRU )<merge>
titanic = titanic.drop({'Name', 'Ticket', 'Cabin'}, axis=1 )
Titanic - Machine Learning from Disaster
12,584,804
submission_LSTM = submission_format[['id_seqpos']].merge(lstm_preds, how = 'inner', on = 'id_seqpos') submission_GRU = submission_format[['id_seqpos']].merge(gru_preds, how = 'inner', on = 'id_seqpos' )<merge>
titanic['Embarked']= titanic['Embarked'].fillna(titanic['Embarked'].value_counts().index[0] )
Titanic - Machine Learning from Disaster
12,584,804
submission_lstm_gru_combined = submission_GRU.merge(submission_LSTM, how = 'inner', on = 'id_seqpos') gru_weight = 0.5 lstm_weight = 0.5 for i in range(len(target_cols)) : submission_lstm_gru_combined[target_cols[i]] = submission_lstm_gru_combined[target_cols[i]+'_x']*gru_weight + submission_lstm_gru_combined[target_c...
pd.pivot_table(titanic, values='Age', index=['Sex'], columns=['Pclass'], aggfunc=np.mean )
Titanic - Machine Learning from Disaster
12,584,804
submission_lstm_gru_combined = submission_lstm_gru_combined[['id_seqpos'] + target_cols]<save_to_csv>
for Pclass in titanic.Pclass.unique() : for Sex in titanic.Sex.unique() : titanic[(titanic['Pclass'] == Pclass)&(titanic['Sex'] == Sex)] = \ titanic[(titanic['Pclass'] == Pclass)&(titanic['Sex'] == Sex)] \ .fillna(np.rint(titanic[(titanic['Pclass'] == Pclass)&(titanic['Sex'] == Sex)].Age.mean()))
Titanic - Machine Learning from Disaster
12,584,804
os.chdir("/kaggle/working/") submission_LSTM.to_csv('submission_LSTM.csv', index = False) submission_GRU.to_csv('submission_GRU.csv', index = False) submission_lstm_gru_combined.to_csv('submission_lstm_gru_combined.csv', index = False )<define_variables>
titanic.isnull().sum()
Titanic - Machine Learning from Disaster
12,584,804
copyfile(src = ".. /usr/lib/modellib/modellib.py", dst = ".. /working/ModelLib.py" )<import_modules>
titanic['Sex'] = pd.get_dummies(titanic['Sex'], drop_first=True) titanic.rename({'Sex': 'Male'}, axis=1, inplace=True )
Titanic - Machine Learning from Disaster
12,584,804
import numpy as np import pandas as pd import torch from torch.utils.data import TensorDataset, Dataset, DataLoader from torch.utils.data.sampler import SubsetRandomSampler from sklearn.model_selection import KFold,StratifiedKFold from tqdm.auto import tqdm from ModelLib import Create_model,stratified_group_k_fold impo...
titanic['Embarked_fz'] = pd.factorize(titanic['Embarked'], sort=True)[0]
Titanic - Machine Learning from Disaster
12,584,804
random.seed(831) os.environ['PYTHONHASHSEED'] = str(721) np.random.seed(1111) torch.manual_seed(1117) torch.cuda.manual_seed(1001) torch.backends.cudnn.deterministic = True torch.backends.cudnn.benchmark = False device = 'cuda'<load_pretrained>
X = titanic.drop({'PassengerId', 'Survived', 'SibSp', 'Parch', 'Embarked'}, axis=1) y = titanic['Survived']
Titanic - Machine Learning from Disaster
12,584,804
train_x = np.load('.. /input/covid19fe/train_aug_x.npy') test_x = np.load('.. /input/covid19fe/test_aug_x.npy') train_bpps = np.load('.. /input/covid19fe/train_bpps.npy') test_bpps = np.load('.. /input/covid19fe/test_bpps.npy') train_viennarna_bpps = np.load('.. /input/covid19extrafeatures/train_viennarna_bpps.npy'...
X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.2, random_state=42 )
Titanic - Machine Learning from Disaster
12,584,804
train_bpps = np.concatenate([np.expand_dims(train_bpps,axis=1),np.expand_dims(train_viennarna_bpps,axis=1),np.expand_dims(train_mat,axis=1),np.expand_dims(train_aug_mat,axis=1)],axis=1) test_bpps = np.concatenate([np.expand_dims(test_bpps,axis=1),np.expand_dims(test_viennarna_bpps,axis=1),np.expand_dims(test_mat,axis=...
clf = RandomForestClassifier()
Titanic - Machine Learning from Disaster
12,584,804
train = pd.read_json('.. /input/stanford-covid-vaccine/train.json',lines=True ).drop('index',axis=1) test = pd.read_json('.. /input/stanford-covid-vaccine/test.json',lines=True ).drop('index',axis=1) train_length = train.seq_length.values test_length = test.seq_length.values train_scored = train.seq_scored.values tes...
parametrs = { 'n_estimators': range(10, 51, 10), 'max_depth': range(1,13, 2), 'min_samples_leaf': range(1,8), 'min_samples_split': range(2,10,2)}
Titanic - Machine Learning from Disaster
12,584,804
<data_type_conversions>
grid = GridSearchCV(clf, parametrs, cv=5) grid.fit(X_train, y_train )
Titanic - Machine Learning from Disaster
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class Covid19Dataset(Dataset): def __init__(self,X,bpps,mat,seq_length,scored_length,label=None,label_error=None,signal_to_noise=None,SN_filter_mask=None): self.X = X.astype(np.int) self.bpps = bpps.astype(np.float32) if label is not None: self.label = label.astype(np.float32) self.signal_to_noise = signal_to_noise....
grid.best_estimator_
Titanic - Machine Learning from Disaster
12,584,804
nepochs = 300 n_fold = 5 kf = StratifiedKFold(n_fold,shuffle=True,random_state=831) dataset = Covid19Dataset(train_x,train_bpps,train_mat,train_length,train_scored,label,label_error,signal_to_noise,SN_filter_mask) cv_score = [] loss_weights = torch.Tensor([1.2,1.2,1.2,0.7,0.7] ).reshape(1,5 ).to(device) oof = np.zer...
y_pred = grid.predict(X_test) y_proba = grid.predict_proba(X_test) y_proba = y_proba[:, 1]
Titanic - Machine Learning from Disaster
12,584,804
for i in range(n_fold): print(f"fold {i+1} score:",cv_score[i]) print() print("CV score:",np.mean(cv_score)) np.save('oof_{:5.5f}'.format(np.mean(cv_score)) ,oof )<create_dataframe>
confusion_matrix(y_test, y_pred )
Titanic - Machine Learning from Disaster
12,584,804
dataset = Covid19Dataset(test_x,test_bpps,test_mat,test_length,test_scored) args_loader = {'batch_size': 1, 'shuffle': False, 'num_workers': 0, 'pin_memory': True, 'drop_last': False} test_loader = DataLoader(dataset, **args_loader) test_predictions = np.zeros([len(test_x),130,5]) for j,col in enumerate(['reactivity...
precision_score(y_test, y_pred )
Titanic - Machine Learning from Disaster
12,584,804
ss = pd.read_csv(".. /input/stanford-covid-vaccine/sample_submission.csv",index_col=0 )<feature_engineering>
recall_score(y_test, y_pred )
Titanic - Machine Learning from Disaster
12,584,804
for n,row in tqdm(test.iterrows() ,total=len(test)) : test_id = row['id'] seq_len = row['seq_length'] for i in range(seq_len): for j,col in enumerate(['reactivity', 'deg_Mg_pH10', 'deg_Mg_50C']): ss.loc[test_id+'_'+str(i),col] = test_predictions[n,i,j]<save_to_csv>
f1_score(y_test, y_pred )
Titanic - Machine Learning from Disaster
12,584,804
ss.to_csv("submission_cnn_{:5.5f}.csv".format(np.mean(cv_score)) ,index=True )<install_modules>
titanic_test = pd.read_csv('/kaggle/input/titanic/test.csv') titanic_test['Embarked']= titanic_test['Embarked'].fillna(titanic_test['Embarked'].value_counts().index[0]) for Pclass in titanic_test.Pclass.unique() : for Sex in titanic_test.Sex.unique() : titanic_test[(titanic_test['Pclass'] == Pclass)&(titanic_test['Se...
Titanic - Machine Learning from Disaster
12,584,804
<import_modules><EOS>
submission = pd.DataFrame({'PassengerId':PassengerId,'Survived':y_test2}) submission.to_csv('submission.csv',index=False )
Titanic - Machine Learning from Disaster
1,007,734
<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<define_variables>
train = pd.read_csv('.. /input/train.csv') train.info()
Titanic - Machine Learning from Disaster
1,007,734
TARGETS = ['reactivity', 'deg_Mg_pH10', 'deg_pH10', 'deg_Mg_50C', 'deg_50C'] SCORED_TARGETS = [0, 1, 3] NUM_TARGETS = len(TARGETS) SEQ_SCORED_PUBLIC = 68 SEQ_SCORED_PRIVATE = 91 SEQ_LEN_PUBLIC = 107 SEQ_LEN_PRIVATE = 130<define_variables>
def prep_data(df): to_be_dropped = ['Name', 'Cabin', 'Ticket'] df['Embarked'] = df['Embarked'].fillna('S') df['Age'] = df['Age'].fillna(median_age) df['Fare'] = df['Fare'].fillna(median_fare) df['Companions'] = df['Parch'] + df['SibSp'] to_be_dropped.extend(['Parch', 'SibSp']) df.loc[ df['Age'] <= 16, 'Age'] = 0 df...
Titanic - Machine Learning from Disaster
1,007,734
BASE_PATH = ".. /input/stanford-covid-vaccine/" CP_PATH = "" PRETRAINED_PATH = ".. /input/covid-pretrained/pretrained_model.pt" DEVICE = torch.device('cuda') TODAY = str(datetime.date.today() )<load_from_disk>
y = train['Survived'] X = train.drop('Survived', axis = 1) X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.35, random_state=7 )
Titanic - Machine Learning from Disaster
1,007,734
train_df = pd.read_json(str(Path(BASE_PATH)/ 'train.json'), lines=True) test_df = pd.read_json(str(Path(BASE_PATH)/ 'test.json'), lines=True) public_df = test_df[test_df["seq_length"] == SEQ_LEN_PUBLIC].reset_index(drop=True) private_df = test_df[test_df["seq_length"] == SEQ_LEN_PRIVATE].reset_index(drop=True )<defi...
warnings.filterwarnings("ignore", category=DeprecationWarning) warnings.filterwarnings("ignore", category=UserWarning) lgbm = lgb.LGBMClassifier(nthread = 4, boosting_type = 'dart') param_grid = {'learning_rate': [0.08, 0.09, 0.1]} grid_search = GridSearchCV(lgbm, param_grid, scoring='roc_auc', cv=10) grid_result =...
Titanic - Machine Learning from Disaster
1,007,734
target_cols = ['reactivity', 'deg_Mg_pH10', 'deg_pH10', 'deg_Mg_50C', 'deg_50C'] input_cols = ['sequence', 'structure', 'predicted_loop_type'] error_cols = ['reactivity_error', 'deg_error_Mg_pH10', 'deg_error_Mg_50C', 'deg_error_pH10', 'deg_error_50C'] token_dicts = { "sequence": {x: i for i, x in enumerate("ACGU")}, "...
accuracy = accuracy_score(y_test, lgbm.predict(X_test)) print("Accuracy: %.2f%%" %(accuracy * 100.0))
Titanic - Machine Learning from Disaster
1,007,734
def set_seed(seed=42): random.seed(seed) np.random.seed(seed) os.environ["PYTHONHASHSEED"] = str(seed) torch.manual_seed(seed) torch.cuda.manual_seed(seed) torch.backends.cudnn.deterministic = True torch.backends.cudnn.benchmark = True SEED = 1234 set_seed(SEED )<categorify>
test = pd.read_csv('.. /input/test.csv') test.info()
Titanic - Machine Learning from Disaster
1,007,734
<train_model><EOS>
predictions = lgbm.predict(test) submission = pd.DataFrame({ "PassengerId": test.index, "Survived": predictions }) submission.to_csv('submission.csv', index=False )
Titanic - Machine Learning from Disaster
2,249,093
<SOS> metric: categorizationaccuracy Kaggle data source: titanic-machine-learning-from-disaster<load_from_csv>
print("Last updated:") print(datetime.datetime.now().strftime("%Y-%m-%d %H:%M"))
Titanic - Machine Learning from Disaster
2,249,093
aug_df = pd.read_csv('.. /input/covid-data/aug_data.csv' )<merge>
init_notebook_mode(connected=True)
Titanic - Machine Learning from Disaster
2,249,093
def augment_data(df, concat=True): df = df.copy() target_df = df.copy() new_df = aug_df[aug_df['id'].isin(target_df['id'])] del target_df['structure'] del target_df['predicted_loop_type'] new_df = new_df.merge(target_df, on=['id','sequence'], how='left' ).sort_values('index') df['cnt'] = df['id'].map(new_df[['id','cnt...
train_df=pd.read_csv(PATH+'train.csv') test_df=pd.read_csv(PATH+'test.csv' )
Titanic - Machine Learning from Disaster