def _bayesianridge(*, train, test, x_predict=None, metrics, n_iter=300, tol=0.001,
alpha_1=1e-06, alpha_2=1e-06, lambda_1=1e-06, lambda_2=1e-06, alpha_init=None,
lambda_init=None, compute_score=False, fit_intercept=True, normalize=False, copy_X=True,
verbose=False):
"""For more info visit :
https://scikit-learn.org/stable/modules/generated/sklearn.linear_model.BayesianRidge.html#sklearn.linear_model.BayesianRidge
"""
model = BayesianRidge(n_iter=n_iter, tol=tol, alpha_1=alpha_1, alpha_2=alpha_2, lambda_1=lambda_1,
lambda_2=lambda_2, alpha_init=alpha_init, lambda_init=lambda_init, compute_score=compute_score,
fit_intercept=fit_intercept, normalize=normalize, copy_X=copy_X, verbose=verbose)
model.fit(train[0], train[1])
model_name = 'Bayesian Ridge'
y_hat = model.predict(test[0])
if metrics == 'mse':
accuracy = _mse(test[1], y_hat)
if metrics == 'rmse':
accuracy = _rmse(test[1], y_hat)
if metrics == 'mae':
accuracy = _mae(test[1], y_hat)
if x_predict is None:
return (model_name, accuracy, None)
y_predict = model.predict(x_predict)
return (model_name, accuracy, y_predict)
def Basyen_stacking(oof_lgb,oof_xgb,predictions_lgb,predictions_xgb,sub,target):
res = sub.copy()
# 将lgb和xgb的结果进行stacking
train_stack = np.vstack([oof_lgb,oof_xgb]).transpose()
test_stack = np.vstack([predictions_lgb, predictions_xgb]).transpose()
folds_stack = RepeatedKFold(n_splits=5, n_repeats=2, random_state=4590)
oof_stack = np.zeros(train_stack.shape[0])
predictions = np.zeros(test_stack.shape[0])
for fold_, (trn_idx, val_idx) in enumerate(folds_stack.split(train_stack,target)):
print("fold {}".format(fold_))
trn_data, trn_y = train_stack[trn_idx], target[trn_idx]
val_data, val_y = train_stack[val_idx], target[val_idx]
clf_3 = BayesianRidge()
clf_3.fit(trn_data, trn_y)
oof_stack[val_idx] = clf_3.predict(val_data)
predictions += clf_3.predict(test_stack) / 10
cross_validation_loss = mean_squared_error(target, oof_stack)
print(cross_validation_loss)
res[1] = predictions
mean = res[1].mean()
print('mean:',mean)
res.to_csv("./Basyen_stacking.csv",index=False,header = None)
return cross_validation_loss
def fillna_knn_reg(df, base, target, fraction=1, threshold=10, n_neighbors=5):
assert isinstance(
base,
list) or isinstance(base, np.ndarray) and isinstance(target, str)
whole = [target] + base
print(threshold, "\n", fraction, "\n", n_neighbors)
miss = df[target].isnull()
notmiss = ~miss
X_target = df.loc[notmiss, whole]
Y = X_target[target]
X = X_target[base]
X_train, X_test, Y_train, Y_test = train_test_split(X,
Y,
test_size=0.2,
random_state=5)
print('fitting')
n_neighbors = n_neighbors
clf = BayesianRidge()
clf.fit(X, Y)
print('predicting')
print("Fit a model X_test and claculate Mean Squared Error with Y_test:")
print(np.mean((Y_test - clf.predict(X_test))**2))
Z = clf.predict(df.loc[miss, base])
print('writing result to df')
df.loc[miss, target] = Z
def train_BayesianRidge(self, data):
train, validacion = data
x_tr, y_tr = train
x_val, y_val = validacion
#print("El set de train tiene {} filas y {} columnas".format(x_tr.shape[0],x_tr.shape[1]))
#print("El set de validacion tiene {} filas y {} columnas".format(x_val.shape[0],x_val.shape[1]))
print('Start training BayesianRidge...')
start_time = self.timer()
bayesr = BayesianRidge(normalize=True, n_iter=1000)
bayesr.fit(x_tr, y_tr)
print("The R2 is: {}".format(bayesr.score(x_tr, y_tr)))
# print("The alpha choose by CV is:{}".format(bayesr.alpha_))
self.timer(start_time)
print("Making prediction on validation data")
y_val = np.expm1(y_val)
y_val_pred = np.expm1(bayesr.predict(x_val))
mae = mean_absolute_error(y_val, y_val_pred)
print("El mean absolute error de es {}".format(mae))
print('Saving model into a pickle')
try:
os.mkdir('pickles')
except:
pass
with open('pickles/bayesrCV.pkl', 'wb') as f:
pickle.dump(bayesr, f)
print('Making prediction and saving into a csv')
y_test = bayesr.predict(self.x_test)
return y_test
def modelResultMerge(predictions_lgb, predictions_xgb, train_lgb, train_xgb,
target):
train_stack = np.vstack([train_lgb, train_xgb]).transpose()
test_stack = np.vstack([predictions_lgb, predictions_xgb]).transpose()
folds_stack = RepeatedKFold(n_splits=5, n_repeats=2, random_state=2012)
oof_stack = np.zeros(train_stack.shape[0])
predictions = np.zeros(test_stack.shape[0])
for fold_, (trn_idx,
val_idx) in enumerate(folds_stack.split(train_stack, target)):
print("fold {}".format(fold_))
trn_data, trn_y = train_stack[trn_idx], target.iloc[trn_idx].values
val_data, val_y = train_stack[val_idx], target.iloc[val_idx].values
clf_3 = BayesianRidge()
clf_3.fit(trn_data, trn_y)
# clf_3 = linear_model.LinearRegression()
# clf_3.fit(trn_data, trn_y)
oof_stack[val_idx] = clf_3.predict(val_data)
predictions += clf_3.predict(test_stack) / 10
print(mean_squared_error(target.values, oof_stack))
return predictions
def stacking_predict(oof_lgb,
oof_xgb,
predictions_lgb,
predictions_xgb,
y_train,
verbose_eval=1):
# stacking
train_stack = np.vstack([oof_lgb, oof_xgb]).transpose()
test_stack = np.vstack([predictions_lgb, predictions_xgb]).transpose()
folds_stack = RepeatedKFold(n_splits=5, n_repeats=2, random_state=4590)
oof_stack = np.zeros(train_stack.shape[0])
predictions = np.zeros(test_stack.shape[0])
stack_models = []
for fold_, (trn_idx,
val_idx) in enumerate(folds_stack.split(train_stack, y_train)):
if verbose_eval:
print("fold {}".format(fold_))
trn_data, trn_y = train_stack[trn_idx], y_train[trn_idx]
val_data, val_y = train_stack[val_idx], y_train[val_idx]
clf_3 = BayesianRidge()
clf_3.fit(trn_data, trn_y)
stack_models.append(clf_3)
oof_stack[val_idx] = clf_3.predict(val_data)
predictions += clf_3.predict(test_stack) / 10
final_score = mean_squared_error(y_train, oof_stack)
if verbose_eval:
print(final_score)
return oof_stack, predictions, final_score, stack_models
class MixedRegressor(skl.base.BaseEstimator, skl.base.TransformerMixin):
"""docstring"""
def __init__(self, save_path=None):
super(MixedRegressor, self).__init__()
self.save_path = save_path
self.regressor = None
self.regressorlt40 = None
self.regressorgt60 = None
def fit(self, X, y, sample_weight=None):
X, y = check_X_y(X, y)
self.regressor = BayesianRidge()
self.regressorlt40 = BayesianRidge()
self.regressorgt60 = BayesianRidge()
self.regressor.fit(X, y)
lt40 = y < 40
gt60 = y > 60
Xlt40 = X[lt40]
Ylt40 = y[lt40]
Xgt60 = X[gt60]
Ygt60 = y[gt60]
self.regressorlt40.fit(Xlt40, Ylt40)
self.regressorgt60.fit(Xgt60, Ygt60)
return self
def predict(self, X):
check_is_fitted(self, ["regressor", "regressorlt40", "regressorgt60"])
X = check_array(X)
predictions = self.regressor.predict(X)
lt18 = predictions < 18
gt88 = predictions > 88
if (len(predictions[lt18]) > 0):
predlt18 = self.regressorlt40.predict(X[lt18])
predictions[lt18] = predlt18
if (len(predictions[gt88]) > 0):
predgt88 = self.regressorgt60.predict(X[gt88])
predictions[gt88] = predgt88
return predictions
def score(self, X, y, sample_weight=None):
scores = -(self.predict(X) - y)**2 / len(y)
score = np.sum(scores)
return score
def set_save_path(self, save_path):
self.save_path = save_path
def make_forward_model(data_ss, RDKit_FPs):
# forward model library from scikit-learn
from sklearn.linear_model import BayesianRidge
# xenonpy library for data splitting (cross-validation)
from xenonpy.datatools import Splitter
# property name will be used as a reference for calling models
prop = ['E', 'H**O-LUMO gap']
# prepare indices for cross-validation data sets
sp = Splitter(data_ss.shape[0], test_size=0, cv=5)
# initialize output variables
y_trues, y_preds = [[] for i in range(len(prop))], [[] for i in range(len(prop))]
y_trues_fit, y_preds_fit = [[] for i in range(len(prop))], [[] for i in range(len(prop))]
y_preds_std, y_preds_std_fit = [[] for i in range(len(prop))], [[] for i in range(len(prop))]
# cross-validation test
for iTr, iTe in sp.cv():
x_train = data_ss['SMILES'].iloc[iTr]
x_test = data_ss['SMILES'].iloc[iTe]
fps_train = RDKit_FPs.transform(x_train)
fps_test = RDKit_FPs.transform(x_test)
y_train = data_ss[prop].iloc[iTr]
y_test = data_ss[prop].iloc[iTe]
for i in range(len(prop)):
mdl = BayesianRidge(compute_score=True)
mdl.fit(fps_train, y_train.iloc[:, i])
prd_train, std_train = mdl.predict(fps_train, return_std=True)
prd_test, std_test = mdl.predict(fps_test, return_std=True)
y_trues[i].append(y_test.iloc[:, i].values)
y_trues_fit[i].append(y_train.iloc[:, i].values)
y_preds[i].append(prd_test)
y_preds_fit[i].append(prd_train)
y_preds_std[i].append(std_test)
y_preds_std_fit[i].append(std_train)
# write down list of property name(s) for forward models
prop = ['E', 'H**O-LUMO gap'] # match with data table for convenience
# calculate descriptor values for all SMILES in the data subset
fps_train = RDKit_FPs.transform(data_ss['SMILES'])
# initialize a dictionary for model storage
mdls = {}
# fill in and train the models
for x in prop:
mdls[x] = BayesianRidge()
mdls[x].fit(fps_train, data_ss[x])
# import descriptor calculator and forward model to iQSPR
prd_mdls = BayesianRidgeEstimator(descriptor=RDKit_FPs, **mdls)
return prd_mdls, mdls
def do_cv_pred(train, test, files, use_cols=10, verbose=False):
print("------- do preds --------")
ensemble_col = [
f[1] for i, f in enumerate(files) if (i % 20) <= use_cols
]
if use_cols == 2:
print(ensemble_col)
train_x = train[ensemble_col]
test_x = test[ensemble_col]
train_y = train["target"]
submission = pd.DataFrame()
submission["card_id"] = test["card_id"]
submission["target"] = 0
outliers = (train["target"] < -30).astype(int).values
split_num = 5
skf = model_selection.StratifiedKFold(n_splits=split_num,
shuffle=True,
random_state=4590)
train_preds = []
for idx, (train_index,
test_index) in enumerate(skf.split(train, outliers)):
X_train, X_test = train_x.iloc[train_index], train_x.iloc[
test_index]
y_train, y_test = train_y.iloc[train_index], train_y.iloc[
test_index]
reg = BayesianRidge().fit(X_train, y_train)
valid_set_pred = reg.predict(X_test)
score = evaluator.rmse(y_test, valid_set_pred)
if verbose:
print(reg.coef_)
print(score)
y_pred = reg.predict(test_x)
submission["target"] = submission["target"] + y_pred
train_id = train.iloc[test_index]
train_cv_prediction = pd.DataFrame()
train_cv_prediction["card_id"] = train_id["card_id"]
train_cv_prediction["cv_pred"] = valid_set_pred
train_preds.append(train_cv_prediction)
train_output = pd.concat(train_preds, axis=0)
submission["target"] = submission["target"] / split_num
submission.to_csv(path_const.OUTPUT_SUB, index=False)
train_output["cv_pred"] = np.clip(train_output["cv_pred"], -33.219281,
18.0)
train_output.to_csv(path_const.OUTPUT_OOF, index=False)
df_pred = pd.merge(train[["card_id", "target"]],
train_output,
on="card_id")
rmse_score = evaluator.rmse(df_pred["target"], df_pred["cv_pred"])
print(rmse_score)
def time_period_model_predict(train, test):
train_sr, test_sr = data_preprocessing(train, test)
train_time = train_sr.copy()
test_time = test_sr.copy()
X_train, X_test, y_train = time_model.feature_engineering(
train_time, test_time)
predictions_time, oof_stack_time = time_model.model_predict(
X_train, X_test, y_train)
#train_sr,test_sr = data_preprocessing(train,test)
train_period = train_sr.copy()
test_period = test_sr.copy()
X_train, X_test, y_train = period_model.feature_engineering(
train_period, test_period)
predictions_period, oof_stack_period = period_model.model_predict(
X_train, X_test, y_train)
y_train = train_sr['收率'].values
# 将时间点time和时间段period的结果进行stacking
train_stack = np.vstack(
[np.round(oof_stack_time, 3),
np.round(oof_stack_period, 3)]).transpose()
test_stack = np.vstack(
[np.round(predictions_time, 3),
np.round(predictions_period, 3)]).transpose()
folds_stack = RepeatedKFold(n_splits=5, n_repeats=2, random_state=4590)
oof_stack = np.zeros(train_stack.shape[0])
predictions = np.zeros(test_stack.shape[0])
for fold_, (trn_idx,
val_idx) in enumerate(folds_stack.split(train_stack, y_train)):
print("fold {}".format(fold_))
trn_data, trn_y = train_stack[trn_idx], y_train[trn_idx]
val_data, val_y = train_stack[val_idx], y_train[val_idx]
clf_3 = BayesianRidge()
clf_3.fit(trn_data, trn_y)
oof_stack[val_idx] = clf_3.predict(val_data)
predictions += clf_3.predict(test_stack) / 10
print("time_period_stacking score: {:<8.8f}".format(
mean_squared_error(y_train, oof_stack) / 2))
return predictions
def get_stacking(self, oof_list, prediction_list, labels):
'''
:param oof_list: out-of-fold predictions
:param prediction_list: test predictions
:param labels: true labels of the training data set
:return: stacking oof predictions of the training set and the testing set
'''
train_stack = np.vstack(oof_list).transpose() # vertical stack起来
test_stack = np.vstack(prediction_list).transpose()
repeats = len(oof_list) # 第一层做了多少个模型第二层就重复多少次CV 但也可以自己定啦
kfolder = RepeatedKFold(n_splits=self.n_fold,
n_repeats=repeats,
random_state=4590)
kfold = kfolder.split(train_stack, labels) # stacking的这些模型里面也要做CV的
preds_list = list() # predictions of the testing data's labels
stacking_oof = np.zeros(
train_stack.shape[0]
) # predictions of the oof training data's labels
for train_index, vali_index in kfold:
k_x_train = train_stack[train_index]
k_y_train = labels.loc[train_index]
k_x_vali = train_stack[vali_index]
assert self.stack_model in ['Ridge', 'Huber']
if self.stack_model == 'Ridge':
stacking_model = BayesianRidge() # BayesianRidge
if self.stack_model == 'Huber':
stacking_model = HuberRegressor()
stacking_model.fit(k_x_train, k_y_train)
k_pred = stacking_model.predict(k_x_vali)
stacking_oof[vali_index] = k_pred
preds = stacking_model.predict(test_stack)
preds_list.append(preds)
fold_mae_error = mean_absolute_error(labels, stacking_oof)
print(f'stacking fold mae training error is {fold_mae_error}')
fold_score = 1 / (1 + fold_mae_error)
print(f'fold score is {fold_score}')
preds_columns = [
'preds_{id}'.format(id=i) for i in range(self.n_fold * repeats)
]
preds_df = pd.DataFrame(data=preds_list)
preds_df = preds_df.T
preds_df.columns = preds_columns
stacking_prediction = list(preds_df.mean(axis=1))
return stacking_oof, stacking_prediction
def runBayesianRidgeRegressor(self):
lm = BayesianRidge(n_iter=300,
compute_score=True,
fit_intercept=True,
normalize=True)
print("Ridge Regression")
lm.fit(self.m_X_train, self.m_y_train)
predictY = lm.predict(self.m_X_test)
score = lm.score(self.m_X_test, self.m_y_test)
predictTraingY = lm.predict(self.m_X_train)
self.displayPredictPlot(predictY)
self.displayResidualPlot(predictY, predictTraingY)
self.dispalyModelResult(lm, predictY, score)
def update_model(nr_exp, budget):
global x_unlabeled, y_unlabeled, x_labeled, y_labeled, x_test, y_test, clf, server_buffer, errorHistoryUS
if clf is None:
clf = BayesianRidge()
clf.fit(x_labeled, y_labeled)
np.save('../outputs/model_size_' + str(x_unlabeled.shape[1]) + '.npy',
np.int32(asizeof.asizeof(pickle.dumps(clf))))
print(np.int32(asizeof.asizeof(pickle.dumps(clf))))
host = 'localhost'
port = 33333
my_socket = -1
while my_socket == -1:
my_socket = utilities.create_socket('normal', host, port)
print("Connection to edge for model sharing established")
my_socket.send(pickle.dumps(clf))
myfile = "../outputs/" + str(nr_exp) + "_budget_" + str(budget) + ".txt"
with open(myfile, "w") as f:
f.write("len_buffer_server\n")
while True:
time.sleep(budget)
len_buffer = len(server_buffer)
if len_buffer > 0:
buffer_data = server_buffer[:len_buffer]
del server_buffer[:len_buffer]
x = [bd[1] for bd in buffer_data]
idx = [bd[0] for bd in buffer_data]
x = np.array(x)
x = x.reshape((x.shape[0], x.shape[2]))
_, std = clf.predict(x, return_std=True)
most_uncertain_idx = np.argmax(std)
x_labeled = np.append(x_labeled,
x[most_uncertain_idx:most_uncertain_idx + 1],
axis=0)
y_labeled = np.append(y_labeled,
y_unlabeled[idx[most_uncertain_idx]])
clf = BayesianRidge()
clf.fit(x_labeled, y_labeled)
p = clf.predict(x_test)
errorHistoryUS.append(
np.sqrt(mean_squared_error(y_test.flatten(), p.flatten())))
with open(myfile, "a") as f:
f.write(str(len_buffer) + '\n')
try:
my_socket.send(pickle.dumps(clf))
except ConnectionResetError:
break
def stacking(train_df, test_df, save=True, verbose=True):
folds = KFold(n_splits=11, shuffle=True, random_state=326)
# Create arrays and dataframes to store results
oof_preds = np.zeros(train_df.shape[0])
sub_preds = np.zeros(test_df.shape[0])
feature_importance_df = pd.DataFrame()
feats = [f for f in train_df.columns if f not in ['target', 'card_id']]
# k-fold
for n_fold, (train_idx, valid_idx) in enumerate(folds.split(train_df[feats], train_df['target'])):
train_x, train_y = train_df[feats].iloc[train_idx], train_df['target'].iloc[train_idx]
valid_x, valid_y = train_df[feats].iloc[valid_idx], train_df['target'].iloc[valid_idx]
# clf = LinearRegression(n_jobs=-1)
clf = BayesianRidge()
# clf = Ridge()
# clf = Lasso()
# clf = ElasticNet()
# clf = SGDRegressor()
# clf = HuberRegressor()
clf.fit(train_x.values, train_y.values)
oof_preds[valid_idx] = clf.predict(valid_x.values)
sub_preds += clf.predict(test_df[feats].values) / folds.n_splits
if verbose:
print('Fold %2d RMSE : %.6f' % (n_fold + 1, rmse(valid_y, oof_preds[valid_idx])))
score = rmse(train_df['target'], oof_preds)
if verbose:
print(f'ALL RMSE: {score}')
if save:
out_dir = ("../data/output/stacking")
if not os.path.exists(out_dir):
os.makedirs(out_dir)
with open(os.path.join(out_dir, f"params_{score:.5f}.txt"), "w") as fp:
print(",".join(feats), file=fp)
oof_df = train_df.copy().reset_index()
oof_df['target'] = oof_preds
oof_df[['card_id', 'target']].to_csv(os.path.join(out_dir, f"oof_{score:.5f}.csv"), index=False)
submission = test_df.copy().reset_index()
submission['target'] = sub_preds
submission[['card_id', 'target']].to_csv(os.path.join(out_dir, f"stacking_{score:.5f}.csv"), index=False)
return score
class RegressionImputer(BaseEstimator, RegressorMixin):
"""Custom scikit-learn estimator for imputation with Bayesian regression"""
def __init__(self):
pass
def fit(self, X, y=None):
self.regr_ = BayesianRidge()
self.regr_.fit(X, y)
return self
def predict(self, X, y=None):
try:
getattr(self, "regr_")
except AttributeError:
raise RuntimeError("Imputer must be fitted before prediction.")
# predict measures
preds, stds = self.regr_.predict(X, return_std=True)
return (pd.DataFrame({
"pred_mean": preds,
"pred_std": stds
}).apply(lambda x: np.random.normal(x.pred_mean, x.pred_std),
axis=1).round())
def fnBayesianRidge(self, year, avgTemp, predictYear):
feature_train, feature_test, target_train, target_test = train_test_split(
year, avgTemp, test_size=0.1, random_state=42)
br = BayesianRidge(compute_score=True)
br.fit(feature_train[:, np.newaxis], target_train)
return (br.score(feature_test[:, np.newaxis],
target_test), br.predict(predictYear))
def bayes_ridge_reg(self):
br = BayesianRidge()
br.fit(self.x_data, self.y_data)
adjusted_result = br.predict(self.x_data)
print "bayes ridge params", br.coef_, br.intercept_
print "bayes ridge accuracy", get_accuracy(adjusted_result, self.y_data)
return map(int, list(adjusted_result))
def bayes(self):
clf = BayesianRidge(compute_score=True)
clf.fit(self.X_train, self.y_train)
y_pred = clf.predict(self.X_test)
dict = {}
set_metrics(y_pred, self.y_test, dict)
return dict
def ridreg(df, test):
clf = BayesianRidge()
target = df['count']
train = df[['time', 'temp']]
test = test2[['time', 'temp']]
clf.fit(train, target)
final = []
print(test.head(3))
for i, row in enumerate(test.values):
y = []
for x in row:
x = float(x)
y.append(x)
# print(x)
final.append(y)
predicted_probs = clf.predict(final)
# print(predicted_probs.shape)
# predicted_probs = pd.Series(predicted_probs)
# predicted_probs = predicted_probs.map(lambda x: int(x))
keep = pd.read_csv('data/test.csv')
keep = keep['datetime']
# #save to file
predicted_probs = pd.DataFrame(predicted_probs)
print(predicted_probs.head(3))
predicted_probs.to_csv('data/submission3.csv', index=False)
def impute_regression(data, target, n=1):
"""
Perform multiple imputation by drawing from posterior distribution of Bayesian ridge regression model.
Parameters
----------
data : DataFrame
Data to use for imputation.
target : str
Column to impute.
n : int
Number of multiple imputations to perform.
Returns
-------
out : DataFrame
One column per imputation, indices of original rows.
"""
# fit regression model without nas
y = data.dropna()[target]
X = data.dropna().drop(target, axis=1)
regr = BayesianRidge()
regr.fit(X, y)
# predict measures
preds, stds = regr.predict(data[data[target].isnull()].drop(target,
axis=1),
return_std=True)
# sample from distribution
return samplePredictions_df(preds, stds, n=n, name="imputation")
def train(self, X_train, y_train):
#X_train为矩阵，y_train为DataFrame()
folds_stack = RepeatedKFold(n_splits=5, n_repeats=2, random_state=4590)
oof_stack = np.zeros(X_train.shape[0])
for fold_, (trn_idx,
val_idx) in enumerate(folds_stack.split(X_train, y_train)):
print("fold {}".format(fold_))
trn_data, trn_y = X_train[trn_idx], y_train.iloc[trn_idx].values
val_data, val_y = X_train[val_idx], y_train.iloc[val_idx].values
clf = BayesianRidge()
clf.fit(trn_data, trn_y)
oof_stack[val_idx] = clf.predict(val_data)
#存储模型
joblib.dump(clf, 'stack_model' + str(fold_) + '.pkl')
print("stack score:{:<8.8f}".format(
mean_squared_error(y_train.values, oof_stack) / 2))
self.train_result = pd.DataFrame({
'real':
y_train.values,
'pred':
oof_stack,
'error': (y_train.values - oof_stack)**2
})
class BayesianRidgeRegression(skl.base.BaseEstimator,
skl.base.TransformerMixin):
def __init__(self, n_iter=300, save_path=None):
super(BayesianRidgeRegression, self).__init__()
self.save_path = save_path
self.n_iter = n_iter
self.model = None
def fit(self, X, y):
self.model = BayesianRidge(n_iter=self.n_iter, fit_intercept=True)
self.model.fit(X, y)
return self
def predict(self, X):
X = check_array(X)
prediction = self.model.predict(X)
print("BayesianRidge predicted")
return prediction
def score(self, X, y, sample_weight=None):
scores = (self.predict(X) - y)**2 / len(y)
score = np.sum(scores)
return -score
def set_save_path(self, save_path):
self.save_path = save_path
def ridreg(df,test):
clf = BayesianRidge()
target = df['count']
train = df[['time','temp']]
test = test2[['time','temp']]
clf.fit(train,target)
final = []
print(test.head(3))
for i, row in enumerate(test.values):
y=[]
for x in row:
x= float(x)
y.append(x)
# print(x)
final.append(y)
predicted_probs= clf.predict(final)
# print(predicted_probs.shape)
# predicted_probs = pd.Series(predicted_probs)
# predicted_probs = predicted_probs.map(lambda x: int(x))
keep = pd.read_csv('data/test.csv')
keep = keep['datetime']
# #save to file
predicted_probs= pd.DataFrame(predicted_probs)
print(predicted_probs.head(3))
predicted_probs.to_csv('data/submission3.csv',index=False)
def test_save_load():
clf = BayesianRidge(compute_score=True)
X, y = get_traininig_data()
clf.fit(X, y)
y_hat = clf.predict(X)
model = MyCustomModel(clf)
conda = {
"name": "test",
"channels": ["defaults"],
"dependencies": [{"pip": ["scipy", "sklearn"]}]
}
model_save_path = os.path.join(dirname(abspath(__file__)), "AzureMLModel")
local_dependencies = [dirname(abspath(__file__))]
save_generic_model(model, path=model_save_path, conda=conda, local_dependencies=local_dependencies)
df = pd.DataFrame(data=X)
df.columns = df.columns.astype(str)
loaded_generic_model = load_generic_model(model_save_path)
result_df = loaded_generic_model.predict(df)
assert (result_df.to_numpy() == y_hat.reshape(-1, 1)).all()
dfd_path = os.path.join(dirname((abspath(__file__))), "dfd")
os.makedirs(dfd_path, exist_ok=True)
data_save_path = os.path.join(dfd_path, "data.dataset.parquet")
df.to_parquet(data_save_path, engine="pyarrow")
meta_path = os.path.join(dfd_path, "_meta.yaml")
with open(meta_path, "w") as fp:
fp.write("type: DataFrameDirectory\nextension: {}\nformat: Parquet\ndata: data.dataset.parquet")
def test_return_std():
# Test return_std option for both Bayesian regressors
def f(X):
return np.dot(X, w) + b
def f_noise(X, noise_mult):
return f(X) + np.random.randn(X.shape[0]) * noise_mult
d = 5
n_train = 50
n_test = 10
w = np.array([1.0, 0.0, 1.0, -1.0, 0.0])
b = 1.0
X = np.random.random((n_train, d))
X_test = np.random.random((n_test, d))
for decimal, noise_mult in enumerate([1, 0.1, 0.01]):
y = f_noise(X, noise_mult)
m1 = BayesianRidge()
m1.fit(X, y)
y_mean1, y_std1 = m1.predict(X_test, return_std=True)
assert_array_almost_equal(y_std1, noise_mult, decimal=decimal)
m2 = ARDRegression()
m2.fit(X, y)
y_mean2, y_std2 = m2.predict(X_test, return_std=True)
assert_array_almost_equal(y_std2, noise_mult, decimal=decimal)
class BAYESIANRIDGE():
"""docstring for ClassName"""
def __init__(self, BayesianRidge, N):
self.cores_number = int(np.ceil(multiprocessing.cpu_count()/N))
self.model = BayesianRidge(
alpha_1=1e-06,
alpha_2=1e-06,
compute_score=False,
copy_X=True,
fit_intercept=True,
lambda_1=1e-06,
lambda_2=1e-06,
n_iter=300,
normalize=False,
tol=0.001,
verbose=False)
print("BayesianRidge Cores: ", np.nan)
def fit(self, X_train, y_train, X_test, y_test, error_type = "MAE"):
error_dict = {"MSE":"rmse", "R2":{"l1","l2"}, "MAE":"mae","LOGLOSS": "multi_logloss" }
error_metric = error_dict[error_type]
self.model.fit(X_train, y_train )
def predict(self, X_test):
prediction=self.model.predict(X_test)
return(prediction)
def BayesianRidgeRegression(data, label, pred_data, pred_last):
'''
效果很差
'''
data = np.array(data)
pred_data = np.array(pred_data)
label = np.array(label)
pred_last = np.array(pred_last)
from sklearn.linear_model import BayesianRidge, LinearRegression
clf = BayesianRidge(compute_score=True)
clf.fit(data, label)
print clf.score(data, label)
pred_result = clf.predict(pred_data)
print("Number of mislabeled points out of a total %d points : %d" %
(pred_data.shape[0], (pred_last != pred_result).sum()))
print clf.score(pred_data, pred_last)
ols = LinearRegression()
ols.fit(data, label)
print ols.score(data, label)
pred_result = ols.predict(pred_data)
print("Number of mislabeled points out of a total %d points : %d" %
(pred_data.shape[0], (pred_last != pred_result).sum()))
print ols.score(pred_data, pred_last)
return pred_result
def BayesianRidgeRegression(output, features, labels):
X = features.values #.reshape(-1,1) # features
y = labels.values #.reshape(-1,1) # labels
X_train, X_test, y_train, y_test = train_test_split(X,
y,
test_size=0.2,
random_state=0)
regressor = BayesianRidge()
regressor.fit(X_train, y_train) #training the algorithm
y_pred = regressor.predict(X_test) #predicting
# visualiation of 10 vessels (predicted vs actual value)
lr = np.round(
pd.DataFrame({
'Actual': y_test.flatten(),
'Predicted': y_pred.flatten()
}))
lr = lr.head(10)
lr.plot(kind='bar', figsize=(10, 6))
plt.grid(which='major', linestyle='-', linewidth='0.5', color='green')
plt.grid(which='minor', linestyle=':', linewidth='0.5', color='black')
plt.title(
'Actual vs Predicted {0} (10 vessels), \n BayesianRidge Regression'.
format(output),
fontsize=12)
plt.show()
#evaluation metrics
lrEvaluation = evaluation('BayesianRidge Regression {0}'.format(output),
y_pred, y_test)
return (lrEvaluation, lr)
def Model_stack(df_train_x, df_train_y, df_test):
# kernel has 'linear'/'poly'/'rbf'/'sigmoid'/'precomputed'/'callable' 如果没有给出，默认'rbf' callable 预先计算内核矩阵
svr_ = SVR(kernel='linear', degree=3, coef0=0.0, tol=0.001,
C=1.0, epsilon=0.1, shrinking=True, cache_size=20)
lgb_ = lgb.LGBMModel(boosting_type='gbdt', num_leaves=35,
max_depth=20, max_bin=255, learning_rate=0.03, n_estimator=10, subsample_for_bin=2000,
objective='regression', min_split_gain=0.0, min_child_weight=0.001, min_child_samples=20,
subsample=1.0, verbose=0, subsample_freq=1, colsample_bytree=1.0, reg_alpha=0.0,
reg_lambda=0.0, random_state=None, n_jobs=-1, silent=True)
RF_model = RandomForestRegressor(n_estimators=50, max_depth=25, min_samples_split=20, min_samples_leaf=10,
max_features='sqrt', oob_score=True, random_state=10)
# 贝叶斯岭回归
BR_model = BayesianRidge(alpha_1=1e-06, alpha_2=1e-06, compute_score=False, copy_X=True, fit_intercept=True,
lambda_1=1e-06, lambda_2=1e-06, n_iter=300, normalize=False, tol=0.0000001, verbose=False)
linear_model = LinearRegression()
ls = Lasso(alpha=0.00375)
x_train, x_test, y_train, y_test = train_test_split(df_train_x, df_train_y,
test_size=0.6)
rg = RidgeCV(cv=5)
stack = pd.DataFrame()
stack_test = pd.DataFrame()
ls.fit(x_train, y_train)
lgb_.fit(x_train, y_train)
RF_model.fit(x_train, y_train)
svr_.fit(x_train, y_train)
linear_model.fit(x_train, y_train)
BR_model.fit(x_train, y_train)
stack['rf'] = ls.predict(x_test)
stack['adaboost'] = lgb_.predict(x_test)
stack['gbdt'] = RF_model.predict(x_test)
stack['lightgbm'] = svr_.predict(x_test)
stack['linear_model'] = linear_model.predict(x_test)
stack['BR'] = BR_model.predict(x_test)
# print('stacking_model: ',Cross_validation(stack, y_test, rg))
rg.fit(stack, y_test)
stack_test['rf'] = ls.predict(df_test)
stack_test['adaboost'] = lgb_.predict(df_test)
stack_test['gbdt'] = RF_model.predict(df_test)
stack_test['lightgbm'] = svr_.predict(df_test)
stack_test['linear_model'] = linear_model.predict(df_test)
stack_test['BR'] = BR_model.predict(df_test)
final_ans = rg.predict(stack_test)
pd.DataFrame(final_ans).to_csv('predict_drop+3.txt', index=False, header=False)
def get_opti_temp(crop_list=["Onions", "Tomatoes"]):
clft = BayesianRidge()
clfo = BayesianRidge()
client = MongoClient(
) #//////////////////////////////////////////////////////////////////////
db = client.server_db
cursor_tomato = db.corpusoptitemp.find({"Datatype": "Tomatoes"})
cursor_onion = db.corpusoptitemp.find({"Datatype": "Onions"})
xt = []
yt = []
xo = []
yo = []
for docs in cursor_tomato:
item = []
item.append(docs["Temperature"])
item.append(docs["Humidity"])
xt.append(item)
yt.append(docs["Losses"])
for docs in cursor_onion:
item = []
item.append(docs["Temperature"])
item.append(docs["Humidity"])
xo.append(item)
yo.append(docs["Losses"])
clft.fit(xt, yt)
clfo.fit(xo, yo)
final = []
for temp in range(9, 40):
for hum in range(60, 100):
a = clft.predict([[temp, hum]])
b = clfo.predict([[temp, hum]])
item = []
item.append((a[0] + b[0]) / 2)
item.append(temp)
item.append(hum)
final.append(item)
#print final
final.sort(key=lambda x: x[0])
print "Store the produce at ", final[0][1], "C and at ", final[0][
2], "% relative humidity."
return final[0][1], final[0][2]
def bayesRegr(source, target):
# Binarize source
clf = BayesianRidge()
features = source.columns[:-1]
klass = source[source.columns[-1]]
clf.fit(source[features], klass)
preds = clf.predict(target[target.columns[:-1]])
return preds
def stacking_model(oof_list, prediction_list, labels, sample_ids):
train_stack = np.vstack(oof_list).transpose()
test_stack = np.vstack(prediction_list).transpose()
kfolder = RepeatedKFold(n_splits=5, n_repeats=2, random_state=666)
kfold = kfolder.split(train_stack, labels)
preds_list = list()
stacking_oof = np.zeros(train_stack.shape[0])
for train_index, vali_index in kfold:
k_x_train = train_stack[train_index]
k_y_train = labels.loc[train_index]
k_x_vali = train_stack[vali_index]
gbm = BayesianRidge(normalize=True)
gbm.fit(k_x_train, k_y_train)
k_pred = gbm.predict(k_x_vali)
stacking_oof[vali_index] = k_pred
preds = gbm.predict(test_stack)
preds_list.append(preds)
fold_mse_error = mean_squared_error(labels, stacking_oof)
print(f'stacking fold mse error is {fold_mse_error}')
mse = make_scorer(mean_squared_error)
gbm = BayesianRidge()
cv_mse_error = cross_val_score(gbm,
train_stack,
labels,
scoring=mse,
cv=5,
n_jobs=5)
cv_mse_error = np.mean(cv_mse_error)
print(f'stacking cv mse error is {cv_mse_error}')
preds_columns = ['preds_{id}'.format(id=i) for i in range(10)]
preds_df = pd.DataFrame(data=preds_list)
preds_df = preds_df.T
preds_df.columns = preds_columns
preds_list = list(preds_df.mean(axis=1))
sub_df = pd.DataFrame({'sample_id': sample_ids, 'rate': preds_list})
sub_df.to_csv('submittion_tree.csv', index=False, header=False)
def fit_polynomial_bayesian_skl(X, Y, degree,
lambda_shape=1.e-6, lambda_invscale=1.e-6,
padding=10, n=100,
X_unknown=None):
X_v = pol.polyvander(X, degree)
clf = BayesianRidge(lambda_1=lambda_shape, lambda_2=lambda_invscale)
clf.fit(X_v, Y)
coeff = np.copy(clf.coef_)
# there some weird intercept thing
# since the Vandermonde matrix has 1 at the beginning, just add this
# intercept to the first coeff
coeff[0] += clf.intercept_
ret_ = [coeff]
# generate the line
x = np.linspace(X.min()-padding, X.max()+padding, n)
x_v = pol.polyvander(x, degree)
# using the provided predict method
y_1 = clf.predict(x_v)
# using np.dot() with coeff
y_2 = np.dot(x_v, coeff)
ret_.append(((x, y_1), (x, y_2)))
if X_unknown is not None:
xu_v = pol.polyvander(X_unknown, degree)
# using the predict method
yu_1 = clf.predict(xu_v)
# using np.dot() with coeff
yu_2 = np.dot(xu_v, coeff)
ret_.append(((X_unknown, yu_1), (X_unknown, yu_2)))
return ret_
def fit_model_10(self,toWrite=False):
model = BayesianRidge(n_iter=5000)
for data in self.cv_data:
X_train, X_test, Y_train, Y_test = data
model.fit(X_train,Y_train)
pred = model.predict(X_test)
print("Model 10 score %f" % (logloss(Y_test,pred),))
if toWrite:
f2 = open('model10/model.pkl','w')
pickle.dump(model,f2)
f2.close()
def build_bayesian_rr(x_train, y_train, x_test, y_test, n_features):
"""
Constructing a Bayesian ridge regression model from input dataframe
:param x_train: features dataframe for model training
:param y_train: target dataframe for model training
:param x_test: features dataframe for model testing
:param y_test: target dataframe for model testing
:return: None
"""
clf = BayesianRidge()
clf.fit(x_train, y_train)
y_pred = clf.predict(x_test)
# Mean absolute error regression loss
mean_abs = sklearn.metrics.mean_absolute_error(y_test, y_pred)
# Mean squared error regression loss
mean_sq = sklearn.metrics.mean_squared_error(y_test, y_pred)
# Median absolute error regression loss
median_abs = sklearn.metrics.median_absolute_error(y_test, y_pred)
# R^2 (coefficient of determination) regression score function
r2 = sklearn.metrics.r2_score(y_test, y_pred)
# Explained variance regression score function
exp_var_score = sklearn.metrics.explained_variance_score(y_test, y_pred)
# Optimal ridge regression alpha value from CV
ridge_alpha = clf.alpha_
with open('../trained_networks/brr_%d_data.pkl' % n_features, 'wb') as results:
pickle.dump(clf, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(mean_abs, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(mean_sq, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(median_abs, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(r2, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(exp_var_score, results, pickle.HIGHEST_PROTOCOL)
pickle.dump(y_pred, results, pickle.HIGHEST_PROTOCOL)
return
def prediction_BayesianRidge (X_train, Y_train, X_test, Y_test,normalize):
# Print shapes of the training and testing data sets
#print ("Shapes of the training and testing data sets")
#print(X_train.shape, X_test.shape, Y_train.shape, Y_test.shape)
#Create our regression object
lreg = BayesianRidge(normalize=normalize)
#do a linear regression, except only on the training
lreg.fit(X_train,Y_train)
#print("The estimated intercept coefficient is %.2f " %lreg.intercept_)
#print("The number of coefficients used was %d " % len(lreg.coef_))
# Set a DataFrame from the Facts
coeff_df = DataFrame(X_train.columns)
coeff_df.columns = ["Fact"]
# Set a new column lining up the coefficients from the linear regression
coeff_df["Coefficient"] = pd.Series(lreg.coef_)
# Show
#coeff_df
#highest correlation between a fact and fraction votes
#print ("Highest correlation fact: %s is %.9f" % (cf_dict.loc[coeff_df.iloc[coeff_df["Coefficient"].idxmax()]["Fact"],"description"], coeff_df.iloc[coeff_df["Coefficient"].idxmax()]["Coefficient"]) )
#sns_plot = sns.jointplot(coeff_df.iloc[coeff_df["Coefficient"].idxmax()]["Fact"],"Fraction Votes",pd.merge(X_test,pd.DataFrame(Y_test), right_index=True, left_index=True),kind="scatter")
#Predictions on training and testing sets
pred_train = lreg.predict(X_train)
pred_test = lreg.predict(X_test)
# The mean square error
#print("MSE with X_train and Y_train: %.6f" % np.mean((Y_train - pred_train) ** 2))
#print("MSE with X_test and Y_test: %.6f" %np.mean((Y_test - pred_test) ** 2))
#Explained variance score: 1 is perfect prediction
#print("Variance score: %.2f" % lreg.score(X_test, Y_test))
result={}
result["method"]="BayesianRidge"
if normalize :
result["normalize"]="Y"
else:
result["normalize"]="N"
result["X_train_shape"]=X_train.shape
result["Y_train_shape"]=Y_train.shape
result["X_test_shape"]=X_test.shape
result["Y_test_shape"]=Y_test.shape
result["intercept"]=lreg.intercept_
result["num_coef"]=len(lreg.coef_)
result["max_fact"]=cf_dict.loc[coeff_df.iloc[coeff_df["Coefficient"].idxmax()]["Fact"],"description"]
result["max_fact_value"]=coeff_df.iloc[coeff_df["Coefficient"].idxmax()]["Coefficient"]
result["MSE_train"]=np.mean((Y_train - pred_train) ** 2)
result["MSE_test"]=np.mean((Y_test - pred_test) ** 2)
result["variance"]=lreg.score(X_test, Y_test)
return pred_test,coeff_df,pred_train,result
def sale(data):
data = int(data) + 1
return log(data)
dataset = pandas.read_csv("input/train2_.csv")
testset = pandas.read_csv("input/test2_.csv")
dataset['Sale'] = dataset['Sales'].apply(sale)
labelData = dataset['Sale'].values
myId = testset['Id'].values
testset.drop(['Id'], inplace=True, axis=1)
testData = testset.iloc[:, :].values
dataset.drop(['Sales', 'Sale'], inplace=True, axis=1)
dataData = dataset.iloc[:, :].values
BRModel = BayesianRidge(compute_score=True)
BRModel.fit(dataset.iloc[:, :].values, labelData)
preds = numpy.column_stack((myId, BRModel.predict(testData))).tolist()
preds = [[int(i[0])] + [exp(float(i[1])) - 1] for i in preds]
print BRModel.scores_
with open("result/sub_BayesRidge.csv", "w") as output:
writer = csv.writer(output, lineterminator='\n')
writer.writerow(["Id", "Sales"])
writer.writerows(preds)
def main():
usage = 'usage: %prog [options] <repr_hdf5> <data_hdf5> <target_index>'
parser = OptionParser(usage)
parser.add_option('-a', dest='add_only', default=False, action='store_true', help='Use additional features only; no sequence features')
parser.add_option('-b', dest='balance', default=False, action='store_true', help='Downsample the negative set to balance [Default: %default]')
parser.add_option('-o', dest='out_dir', default='postmodel', help='Output directory [Default: %default]')
parser.add_option('-r', dest='regression', default=False, action='store_true', help='Regression mode [Default: %default]')
parser.add_option('-s', dest='seq_only', default=False, action='store_true', help='Use sequence features only; no additional features [Default: %default]')
parser.add_option('--sample', dest='sample', default=None, type='int', help='Sample from the training set [Default: %default]')
parser.add_option('-t', dest='target_hdf5', default=None, help='Extract targets from this HDF5 rather than data_hdf5 argument')
parser.add_option('-x', dest='regex_add', default=None, help='Filter additional features using a comma-separated list of regular expressions')
(options,args) = parser.parse_args()
if len(args) != 3:
parser.error('Must provide full data HDF5, representation HDF5, and target index or filename')
else:
repr_hdf5_file = args[0]
data_hdf5_file = args[1]
target_i = args[2]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
random.seed(1)
#######################################################
# preprocessing
#######################################################
# load training targets
data_hdf5_in = h5py.File(data_hdf5_file, 'r')
if options.target_hdf5:
target_hdf5_in = h5py.File(options.target_hdf5, 'r')
else:
target_hdf5_in = data_hdf5_in
train_y = np.array(target_hdf5_in['train_out'])[:,target_i]
test_y = np.array(target_hdf5_in['test_out'])[:,target_i]
# load training representations
if not options.add_only:
repr_hdf5_in = h5py.File(repr_hdf5_file, 'r')
train_x = np.array(repr_hdf5_in['train_repr'])
test_x = np.array(repr_hdf5_in['test_repr'])
repr_hdf5_in.close()
if options.seq_only:
add_labels = []
else:
# load additional features
train_a = np.array(data_hdf5_in['train_add'])
test_a = np.array(data_hdf5_in['test_add'])
add_labels = np.array(data_hdf5_in['add_labels'])
if options.regex_add:
fi = filter_regex(options.regex_add, add_labels)
train_a, test_a, add_labels = train_a[:,fi], test_a[:,fi], add_labels[fi]
# append additional features
if options.add_only:
add_i = 0
train_x, test_x = train_a, test_a
else:
add_i = train_x.shape[1]
train_x = np.concatenate((train_x,train_a), axis=1)
test_x = np.concatenate((test_x,test_a), axis=1)
data_hdf5_in.close()
if options.target_hdf5:
target_hdf5_in.close()
# balance
if options.balance:
train_x, train_y = balance(train_x, train_y)
# sample
if options.sample is not None and options.sample < train_x.shape[0]:
sample_indexes = random.sample(range(train_x.shape[0]), options.sample)
train_x = train_x[sample_indexes]
train_y = train_y[sample_indexes]
#######################################################
# model
#######################################################
if options.regression:
# fit
model = BayesianRidge(fit_intercept=True)
model.fit(train_x, train_y)
# accuracy
acc_out = open('%s/r2.txt' % options.out_dir, 'w')
print >> acc_out, model.score(test_x, test_y)
acc_out.close()
test_preds = model.predict(test_x)
# plot a sample of predictions versus actual
plt.figure()
sns.jointplot(test_preds[:5000], test_y[:5000], joint_kws={'alpha':0.3})
plt.savefig('%s/scatter.pdf' % options.out_dir)
plt.close()
# plot the distribution of residuals
plt.figure()
sns.distplot(test_y-test_preds)
plt.savefig('%s/residuals.pdf' % options.out_dir)
plt.close()
else:
# fit
model = LogisticRegression(penalty='l2', C=1000)
model.fit(train_x, train_y)
# accuracy
test_preds = model.predict_proba(test_x)[:,1].flatten()
acc_out = open('%s/auc.txt' % options.out_dir, 'w')
print >> acc_out, roc_auc_score(test_y, test_preds)
acc_out.close()
# compute and print ROC curve
fpr, tpr, thresholds = roc_curve(test_y, test_preds)
roc_out = open('%s/roc.txt' % options.out_dir, 'w')
for i in range(len(fpr)):
print >> roc_out, '%f\t%f\t%f' % (fpr[i], tpr[i], thresholds[i])
roc_out.close()
# compute and print precision-recall curve
precision, recall, thresholds = precision_recall_curve(test_y, test_preds)
prc_out = open('%s/prc.txt' % options.out_dir, 'w')
for i in range(len(precision)):
print >> prc_out, '%f\t%f' % (precision[i], recall[i])
prc_out.close()
# save model
joblib.dump(model, '%s/model.pkl' % options.out_dir)
#######################################################
# analyze
#######################################################
# print coefficients table
coef_out = open('%s/add_coefs.txt' % options.out_dir, 'w')
for ai in range(len(add_labels)):
if options.regression:
coefi = model.coef_[add_i+ai]
else:
coefi = model.coef_[0,add_i+ai]
print >> coef_out, add_labels[ai], coefi
coef_out.close()
def do_validation(data_path, steps=10):
allfiles = initialize(data_path)
gbm = GradientBoostingRegressor(n_estimators=100, learning_rate=0.05, max_depth=6, min_samples_leaf=5, subsample=0.5)
ada = AdaBoostRegressor(n_estimators=200, learning_rate=1)
etree = ExtraTreesRegressor(n_estimators=200, n_jobs=-1, min_samples_leaf=5)
rf = RandomForestRegressor(n_estimators=200, max_features=4, min_samples_leaf=5)
kn = KNeighborsRegressor(n_neighbors=25)
logit = LogisticRegression(tol=0.05)
enet = ElasticNetCV(l1_ratio=0.75, max_iter=1000, tol=0.05)
svr = SVR(kernel="linear", probability=True)
ridge = Ridge(alpha=18)
bridge = BayesianRidge(n_iter=500)
gbm_metrics = 0.0
ada_metrics = 0.0
etree_metrics = 0.0
rf_metrics = 0.0
kn_metrics = 0.0
logit_metrics = 0.0
svr_metrics = 0.0
ridge_metrics = 0.0
bridge_metrics = 0.0
enet_metrics = 0.0
nnet_metrics = 0.0
logistic = LogisticRegression()
rbm = BernoulliRBM(random_state=0, verbose=True)
classifier = Pipeline(steps=[('rbm', rbm), ('logistic', logistic)])
for i in xrange(steps):
driver = allfiles[i]
df, Y = create_merged_dataset(driver)
df['label'] = Y
# Shuffle DF.
df = df.reindex(np.random.permutation(df.index))
train = df[:100]
label = train['label']
del train['label']
test = df[100:400]
Y = test['label']
del test['label']
#to_drop = ['driver', 'trip', 'speed1', 'speed2', 'speed3', 'speed4', 'speed5', 'speed6', 'speed7', 'speed8', 'speed9',
# 'speed10', 'speed11', 'speed12', 'speed13', 'speed14', 'speed15', 'speed16', 'speed17', 'speed18', 'speed19',
# 'speed20', 'speed21', 'speed22', 'speed23', 'speed24', 'speed25', 'speed26', 'speed27', 'speed28', 'speed29',
# 'speed30', 'speed31', 'speed32', 'speed33', 'speed34', 'speed35', 'speed36', 'speed37', 'speed38', 'speed39',
# 'speed40', 'speed41', 'speed42', 'speed43', 'speed44', 'speed45', 'speed46', 'speed47', 'speed48', 'speed49',
# 'speed50', 'speed51', 'speed52', 'speed53', 'speed54', 'speed55', 'speed56', 'speed57', 'speed58', 'speed59',
# 'speed60', 'speed61', 'speed62', 'speed63', 'speed64', 'speed65', 'speed66', 'speed67', 'speed68', 'speed69',
# 'speed70', 'speed71', 'speed72', 'speed73', 'speed74', 'speed75', 'speed76', 'speed77', 'speed78', 'speed79', 'speed80']
to_drop = ['driver', 'trip']
X_train = train.drop(to_drop, 1)
X_test = test.drop(to_drop, 1)
gbm.fit(X_train, label)
Y_hat = gbm.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
gbm_metrics += metrics.auc(fpr, tpr)
ada.fit(X_train, label)
Y_hat = ada.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
ada_metrics += metrics.auc(fpr, tpr)
etree.fit(X_train, label)
Y_hat = etree.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
etree_metrics += metrics.auc(fpr, tpr)
rf.fit(X_train, label)
Y_hat = rf.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
rf_metrics += metrics.auc(fpr, tpr)
kn.fit(X_train, label)
Y_hat = kn.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
kn_metrics += metrics.auc(fpr, tpr)
# Linear models.
to_drop = ['driver', 'trip', 'distance', 'sd_acceleration', 'final_angle', 'mean_acceleration', 'mean_avg_speed', 'sd_inst_speed',
'sd_avg_speed', 'mean_inst_speed', 'points']
X_train = train.drop(to_drop, 1)
X_test = test.drop(to_drop, 1)
logit.fit(X_train, label)
Y_hat = [i[1] for i in logit.predict_proba(X_test)]
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
logit_metrics += metrics.auc(fpr, tpr)
svr.fit(X_train, label)
Y_hat = svr.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
svr_metrics += metrics.auc(fpr, tpr)
ridge.fit(X_train, label)
Y_hat = ridge.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
ridge_metrics += metrics.auc(fpr, tpr)
bridge.fit(X_train, label)
Y_hat = bridge.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
bridge_metrics += metrics.auc(fpr, tpr)
enet.fit(X_train, label)
Y_hat = enet.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
enet_metrics += metrics.auc(fpr, tpr)
classifier.fit(X_train, label)
Y_hat = classifier.predict(X_test)
fpr, tpr, thresholds = metrics.roc_curve(Y, Y_hat)
nnet_metrics += metrics.auc(fpr, tpr)
print ""
print "GBM:", gbm_metrics/steps
print "AdaBoost:", ada_metrics/steps
print "Extra Trees:", etree_metrics/steps
print "RF:", rf_metrics/steps
print "KN:", kn_metrics/steps
print ""
print "Logit:", logit_metrics/steps
print "SVR:", svr_metrics/steps
print "Ridge:", ridge_metrics/steps
print "BayesianRidge:", bridge_metrics/steps
print "Elastic Net:", enet_metrics/steps
print "Neural Networks:", nnet_metrics/steps
print ""
trainingcounts = counts[100:] testcounts = counts[:100] trainingrates = countrates[100:] testrates = countrates[:100] trainingtimes = times[100:] testtimes = times[:100] # using trainingcounts and training hists use log linear #poisson_model = sm.GLM(trainingrates, # sm.tools.tools.add_constant(traininghists), # family =sm.families.Poisson(sm.genmod.families.links.log)) #results = poisson_model.fit() #print(results.summary()) #x = results.predict(sm.tools.tools.add_constant(testhists)) clf = BayesianRidge(compute_score=True) clf.fit(traininghists,trainingrates) x = clf.predict(testhists) answer = testrates plt.plot(bins,x) plt.plot(bins,answer) plt.show()
def bayes_ridge_reg(x_data,y_data):
br = BayesianRidge()
br.fit(x_data,y_data)
print 'br params',br.coef_,br.intercept_
adjusted_result = br.predict(x_data)
return map(int,list(adjusted_result))
# print("-----------------------------------------------")
# X_train, X_test = selectFeatures(X_train, X_test, y_train, k)
print("-----------------------------------------------")
print("SVM Classification of training set")
print("-----------------------------------------------")
class_weight = {0:5}
print("Class weight=", class_weight)
clf = BayesianRidge(compute_score=True).fit(X_train, y_train)
print("Test svm.SVC score=", clf.score(X_test, y_test))
print("Train svm.SVC score=", clf.score(X_train, y_train))
print("-----------------------------------------------")
print("Metrics on TEST SET")
print("-----------------------------------------------")
y_pred = clf.predict(X_test)
print(metrics.classification_report(y_test, y_pred, target_names=label_names))
print(metrics.confusion_matrix(y_test, y_pred))
print("-----------------------------------------------")
print("Metrics on TRAIN SET")
print("-----------------------------------------------")
y_predTrain = clf.predict(X_train)
print(metrics.classification_report(y_train, y_predTrain, target_names=label_names))
print(metrics.confusion_matrix(y_train, y_predTrain))
#met.crossValidationScores(clf, X_train, y_train)
# met.showRocAnalysis(X_bns, Y)
plt.plot(clf.scores_, color='navy', linewidth=lw)
plt.ylabel("Score")
plt.xlabel("Iterations")
# Plotting some predictions for polynomial regression
def f(x, noise_amount):
y = np.sqrt(x) * np.sin(x)
noise = np.random.normal(0, 1, len(x))
return y + noise_amount * noise
degree = 10
X = np.linspace(0, 10, 100)
y = f(X, noise_amount=0.1)
clf_poly = BayesianRidge()
clf_poly.fit(np.vander(X, degree), y)
X_plot = np.linspace(0, 11, 25)
y_plot = f(X_plot, noise_amount=0)
y_mean, y_std = clf_poly.predict(np.vander(X_plot, degree), return_std=True)
plt.figure(figsize=(6, 5))
plt.errorbar(X_plot, y_mean, y_std, color='navy',
label="Polynomial Bayesian Ridge Regression", linewidth=lw)
plt.plot(X_plot, y_plot, color='gold', linewidth=lw,
label="Ground Truth")
plt.ylabel("Output y")
plt.xlabel("Feature X")
plt.legend(loc="lower left")
plt.show()
X_train = np.vander(x_train, n_order + 1, increasing=True)
X_test = np.vander(x_test, n_order + 1, increasing=True)
# #############################################################################
# Plot the true and predicted curves with log marginal likelihood (L)
reg = BayesianRidge(tol=1e-6, fit_intercept=False, compute_score=True)
fig, axes = plt.subplots(1, 2, figsize=(8, 4))
for i, ax in enumerate(axes):
# Bayesian ridge regression with different initial value pairs
if i == 0:
init = [1 / np.var(y_train), 1.] # Default values
elif i == 1:
init = [1., 1e-3]
reg.set_params(alpha_init=init[0], lambda_init=init[1])
reg.fit(X_train, y_train)
ymean, ystd = reg.predict(X_test, return_std=True)
ax.plot(x_test, func(x_test), color="blue", label="sin($2\\pi x$)")
ax.scatter(x_train, y_train, s=50, alpha=0.5, label="observation")
ax.plot(x_test, ymean, color="red", label="predict mean")
ax.fill_between(x_test, ymean-ystd, ymean+ystd,
color="pink", alpha=0.5, label="predict std")
ax.set_ylim(-1.3, 1.3)
ax.legend()
title = "$\\alpha$_init$={:.2f},\\ \\lambda$_init$={}$".format(
init[0], init[1])
if i == 0:
title += " (Default)"
ax.set_title(title, fontsize=12)
text = "$\\alpha={:.1f}$\n$\\lambda={:.3f}$\n$L={:.1f}$".format(
reg.alpha_, reg.lambda_, reg.scores_[-1])
kr = KernelRidge(alpha=0.0001, coef0=1, degree=1, gamma=0.001, kernel='rbf',kernel_params=None) kr.fit(x_train_scaled, y_train) y3 = kr.predict(x_test_scaled) lasso = Lasso(alpha=1e-09) lasso.fit(x_train_scaled, y_train) y4 = lasso.predict(x_test_scaled) linear_ridge = Ridge(alpha=0.1) linear_ridge.fit(x_train_scaled,y_train) y5 = linear_ridge.predict(x_test_scaled) bayesian_ridge = BayesianRidge(alpha_1=1e-05, alpha_2=10, lambda_1=10, lambda_2=1e-05) bayesian_ridge.fit(x_train_scaled, y_train) y6 = bayesian_ridge.predict(x_test_scaled) sgd = SGDRegressor(alpha=0.1, epsilon=0.001, l1_ratio=0.2, loss='squared_loss', penalty='none', power_t=0.2) sgd.fit(x_train_scaled, y_train) y7 = sgd.predict(x_test_scaled) ########################################### print '########## TESTING ERRORS ##########' print "MAE for Linear Regression:", mean_absolute_error(y_test, y_predicted) print "MAE for SVR:", mean_absolute_error(y_test, y2) print "MAE for Kernel Ridge Regression:", mean_absolute_error(y_test, y3) print "MAE for Lasso Regression:", mean_absolute_error(y_test, y4) print "MAE for Linear Ridge Regression:", mean_absolute_error(y_test, y5) print "MAE for Bayesian Ridge Regression:", mean_absolute_error(y_test, y6) print "MAE for Stochastic Gradient Descent Regression:", mean_absolute_error(y_test, y7)
for _ in range(10):
train_latent_matrix = get_latent_matrix(x,y,x)
test_latent_matrix = get_latent_matrix(x,y,x_test)
# Clean out rows with NaN.
#mask = ~np.any(np.isnan(train_latent_matrix), axis=1)
#newx = train_latent_matrix[mask]
#newy = y[mask]
newx = np.nan_to_num(train_latent_matrix)
newy = y
#last_layer = SVR(kernel='rbf', C=1e3, gamma=0.1)
last_layer = BayesianRidge()
last_layer.fit(newx, newy)
output = last_layer.predict(test_latent_matrix)
assert len(output) == 8500
runs.append(output)
#for i in runs:
#print len(i)
fout = open('modelz.10.output', 'w')
for line in zip(*runs):
avg =sum(line)/len(line)
if avg > 5:
avg = 5.0
elif avg < 0:
avg = 0.0
fout.write(str(avg)[:6]+'\n')
io.imsave("/Users/qcaudron/Desktop/charo/2_smoothed.jpg", ski.img_as_uint(surf))
# <codecell>
z1 = np.mean(surf, axis=0)
z2 = np.mean(surf, axis=1)
#for i in range(surf.shape[1]) :
# plt.plot(surf[:, i], "k")
#plt.plot(z2)
r = [BayesianRidge().fit(np.vander(np.arange(surf.shape[i]), 2), np.mean(surf, axis = 1-i)) for i in [0, 1]]
r1 = BayesianRidge().fit(np.arange(len(z1)).reshape(len(z1),1), z1)
r2 = BayesianRidge().fit(np.arange(len(z2[500:-500])).reshape(len(z2[500:-500]),1), z2[500:-500])
#plt.plot(r1.predict(np.arange(len(z1)).reshape(len(z1),1)), linewidth=5)
plt.plot(r2.predict(np.arange(len(z2)).reshape(len(z2),1)), linewidth=5)
plt.plot(z2, linewidth=5)
#plt.axhline(b[np.argmax(h)], c="r", linewidth=3)
#plt.plot(r[0].predict(np.vander(np.arange(surf.shape[0]), 2)), linewidth=3)
#plt.plot(r[0].predict(np.arange(len(z1)).reshape(len(z1),1)), linewidth=3)
#plt.plot(r[0].predict(np.expand_dims(np.arange(surf.shape[0]), axis=1)), linewidth=5)
#plt.axhline(np.mean(z1 / r1.predict(np.arange(len(z1)).reshape(len(z1),1))))
# <codecell>
lz = np.log(z2)
r3 = BayesianRidge().fit(np.arange(len(lz[500:-500])).reshape(len(lz[500:-500]),1), lz[500:-500])
plt.plot(np.exp(lz))
plt.plot(np.exp(r3.predict(np.arange(len(lz)).reshape(len(lz),1))))
def main():
parser = argparse.ArgumentParser(description="""Creates embeddings predictions.""")
parser.add_argument('--train')
parser.add_argument('--test')
parser.add_argument('--embeddings')
parser.add_argument('--cv',default=False)
args = parser.parse_args()
stoplist = stopwords.words("english")
stoplist.extend("it's 've 's i'm he's she's you're we're they're i'll you'll he'll ".split(" "))
embeddings={}
for line in codecs.open(args.embeddings,encoding="utf-8").readlines():
line = line.strip()
if line:
a= line.split(" ")
embeddings[a[0]] = np.array([float(v) for v in a[1:]]) #cast to float, otherwise we cannot operate
train_indices = []
test_indices = []
train_scores = []
train_features = []
test_features = []
# if args.learner == "logisticregression":
# learner= LogisticRegression()
# learner_type = "classification"
# elif args.learner == "decisiontreeclassification":
# learner = tree.DecisionTreeClassifier()
# learner_type = "classification"
# elif args.learner == "decisiontreeregression":
# learner = tree.DecisionTreeRegressor()
# learner_type = "regression"
# elif args.learner == "bayesianridge":
# learner = BayesianRidge()
# learner_type = "regression"
# else:
learner = BayesianRidge()
learner_type = "regression"
le = preprocessing.LabelEncoder()
for line in open(args.train).readlines():
(index, score, tweet) = line.strip().split("\t")
train_indices.append(index)
train_scores.append(float(score))
tweet = tweet.split(" ")
train_features.append(embedfeats(tweet,embeddings,stoplist))
train_indices = np.array(train_indices)
train_scores = np.array(train_scores)
train_features = np.array(train_features)
train_scores_int = [roundup(v) for v in train_scores]
le.fit(train_scores_int)
train_scores_int_transformed = le.transform(train_scores_int)
if args.cv:
train_cv={}
cross=cross_validation.KFold(len(train_scores),n_folds=10)
acc=[]
for train_index, test_index in cross:
#if args.debug:
# print("TRAIN:", len(train_index), "TEST:", len(test_index))
X=train_features
y=train_scores
X_train, X_test = X[train_index], X[test_index]
y_train, y_test = y[train_index], y[test_index]
learner.fit(X_train,y_train)
y_pred= learner.predict(X_test)
assert(len(y_pred)==len(test_index))
tids=train_indices[test_index]
for twid,pred in zip(tids,y_pred):
train_cv[twid] = pred
acc.append(cosine_similarity(y_test,y_pred)[0][0])
print >>sys.stderr, "Cosine of 10-folds:", acc
print >>sys.stderr, "Macro average:", np.mean(np.array(acc)), np.std(np.array(acc))
for twid in train_indices:
print "{}\t{}".format(twid,train_cv[twid])
else:
for line in open(args.test).readlines():
(index, score, tweet) = line.strip().split("\t")
test_indices.append(index)
#scores.append(score)
tweet = tweet.split(" ")
test_features.append(embedfeats(tweet,embeddings,stoplist))
#print np.array(train_features).shape
# when features are generated, train and test
if learner_type == "regression":
learner.fit(train_features,train_scores)
else:
learner.fit(train_features,train_scores_int_transformed)
predicted_scores= learner.predict(test_features)
if learner_type != "regression":
predicted_scores = le.inverse_transform(predicted_scores)
for index, score in zip(test_indices,predicted_scores):
print index+"\t"+str(score)
import time import sys import numpy import vector from sklearn.linear_model import BayesianRidge, LinearRegression from sklearn.cross_validation import train_test_split usage = "filename features_file labels_file output_file" if __name__ == "__main__": if (len(sys.argv)!=5): print usage else: file_x = sys.argv[1] file_y = sys.argv[2] file_out = sys.argv[3] split_seed = sys.argv[4] X = numpy.genfromtxt(file_x, delimiter=' ') y = numpy.genfromtxt(file_y, delimiter=' ') # Split the data into training/testing sets X_train, X_test, y_train, y_test = train_test_split(X, y, test_size=0.33, random_state=split_seed) # Bayesian Ridge Regression clf = BayesianRidge(compute_score=True) clf.fit(X, y) y_predict=clf.predict(X_test) numpy.savetxt(file_out, y_predict)
def nickmain1():
train_all = pd.read_csv(trainloc)
target_all = pd.read_csv(trainloc)
test_all = pd.read_csv(testloc)
targets = ['Ca','P','pH','SOC','Sand']
train_cols_to_remove = ['PIDN']+targets
train_all["Depth"] = train_all["Depth"].replace(["Topsoil", "Subsoil"],[10,-10])
test_all["Depth"] = test_all["Depth"].replace(["Topsoil", "Subsoil"],[10,-10])
common_features = ['BSAN','BSAS','BSAV','CTI','ELEV','EVI','LSTD','LSTN','REF1','REF2','REF3','REF7','RELI','TMAP','TMFI']
feats_list = {}
colnames_nums = []
colnames = train_all.ix[:,'m7497.96':'m599.76'].columns.values
for x in colnames:
match = re.search(r'(?<=m)[0-9]*',x)
if match:
colnames_nums.append(int(match.group()))
print len(colnames)
print len(colnames_nums)
print len(train_all.ix[0,'m7497.96':'m599.76'].values)
for target in targets:
selector = SelectKBest(f_regression, k=200)
selector.fit_transform(train_all.ix[:,'m7497.96':'m599.76'], train_all[target])
selected = selector.get_support()
feats = [col for (col,sel) in zip(list(train_all.ix[:,'m7497.96':'m599.76'].columns.values), selected) if sel]
feats_list[target] = feats+common_features
#pickTest = ['PIDN', 'BSAN','BSAS','BSAV','CTI','ELEV','EVI','LSTD','LSTN','REF1','REF2','REF3','REF7','RELI','TMAP','TMFI','Depth']#ORIGINAL10
ids = np.genfromtxt(testloc, dtype=str, skip_header=1, delimiter=',', usecols=0)
df = pd.DataFrame({"PIDN": ids, "Ca": test_all['PIDN'], "P": test_all['PIDN'], "pH": test_all['PIDN'], "SOC": test_all['PIDN'], "Sand": test_all['PIDN']})
cv = cross_validation.KFold(len(train_all), n_folds=10, indices=False)
subresults = {}
results = []
if issub == False:
for train_sub, test_sub in cv:
for target in targets:
#clf = ensemble.GradientBoostingRegressor(n_estimators=6)
#clf = RandomForestRegressor(n_estimators = 40)
#clf = linear_model.Lasso(alpha=0.08)
#clf = svm.SVC()
#clf = tree.DecisionTreeRegressor(min_samples_leaf=20)
#clf = Ridge(alpha=1.0)
#clf = ElasticNet(alpha=0.1, l1_ratio=0.7)
clf = BayesianRidge(compute_score=True)
clf.fit(np.array(train_all[feats_list[target]])[train_sub], np.array(train_all[target])[train_sub])
pred = clf.predict(np.array(train_all[feats_list[target]])[test_sub])
subresults[target] = ev.rmse(np.array(train_all[target])[test_sub],np.array(pred))
#df[target] = pred
subtotal = 0
for x in subresults:
subtotal = subtotal + subresults[x]
print ("average for the run is ", subtotal/len(targets))
results.append(subtotal/len(targets))
print "Results: " + str( np.array(results).mean() )
else:
for target in targets:
#clf = ensemble.GradientBoostingRegressor(n_estimators=6)
#clf = RandomForestRegressor(n_estimators = 20)
#clf = linear_model.Lasso(alpha=0.08)
#clf = svm.SVC()
#clf = tree.DecisionTreeRegressor(min_samples_leaf=20)
#clf = Ridge(alpha=1.0)
#clf = ElasticNet(alpha=0.1, l1_ratio=0.7)
clf = BayesianRidge(compute_score=True)
clf.fit(np.array(train_all[feats_list[target]]), np.array(train_all[target]))
pred = clf.predict(np.array(test_all[feats_list[target]]))
df[target] = pred
df.to_csv(predloc, index=False, cols=["PIDN","Ca","P","pH","SOC","Sand"])
# Linear Regression print 'linear' lr = LinearRegression() #lr.fit(x[:, np.newaxis], y) #lr_sts_scores = lr.predict(xt[:, np.newaxis]) lr.fit(x, y) lr_sts_scores = lr.predict(xt) # Baysian Ridge Regression print 'baysian ridge' br = BayesianRidge(compute_score=True) #br.fit(x[:, np.newaxis], y) #br_sts_scores = br.predict(xt[:, np.newaxis]) br.fit(x, y) br_sts_scores = br.predict(xt) # Elastic Net print 'elastic net' enr = ElasticNet() #enr.fit(x[:, np.newaxis], y) #enr_sts_scores = enr.predict(xt[:, np.newaxis]) enr.fit(x, y) enr_sts_scores = enr.predict(xt) # Passive Aggressive Regression print 'passive aggressive' par = PassiveAggressiveRegressor() par.fit(x, y)
def main():
usage = "usage: %prog [options] <model_file>"
parser = OptionParser(usage)
parser.add_option(
"-c",
dest="center_dist",
default=10,
type="int",
help="Distance between the motifs and sequence center [Default: %default]",
)
parser.add_option(
"-d", dest="model_hdf5_file", default=None, help="Pre-computed model output as HDF5 [Default: %default]"
)
parser.add_option(
"-g", dest="cuda", default=False, action="store_true", help="Run on the GPGPU [Default: %default]"
)
parser.add_option("-l", dest="seq_length", default=600, type="int", help="Sequence length [Default: %default]")
parser.add_option("-o", dest="out_dir", default="heat", help="Output directory [Default: %default]")
parser.add_option(
"-t",
dest="targets",
default="0",
help="Comma-separated list of target indexes to plot (or -1 for all) [Default: %default]",
)
(options, args) = parser.parse_args()
if len(args) != 1:
parser.error("Must provide Basset model file")
else:
model_file = args[0]
out_targets = [int(ti) for ti in options.targets.split(",")]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
random.seed(1)
# torch options
cuda_str = ""
if options.cuda:
cuda_str = "-cuda"
#################################################################
# place filter consensus motifs
#################################################################
# determine filter consensus motifs
filter_consensus = get_filter_consensus(model_file, options.out_dir, cuda_str)
seqs_1hot = []
# num_filters = len(filter_consensus)
num_filters = 20
filter_len = filter_consensus[0].shape[1]
# position the motifs
left_i = options.seq_length / 2 - options.center_dist - filter_len
right_i = options.seq_length / 2 + options.center_dist
ns_1hot = np.zeros((4, options.seq_length)) + 0.25
# ns_1hot = np.zeros((4,options.seq_length))
# for i in range(options.seq_length):
# nt_i = random.randint(0,3)
# ns_1hot[nt_i,i] = 1
for i in range(num_filters):
for j in range(num_filters):
# copy the sequence of N's
motifs_seq = np.copy(ns_1hot)
# write them into the one hot coding
motifs_seq[:, left_i : left_i + filter_len] = filter_consensus[i]
motifs_seq[:, right_i : right_i + filter_len] = filter_consensus[j]
# save
seqs_1hot.append(motifs_seq)
# make a full array
seqs_1hot = np.array(seqs_1hot)
# reshape for spatial
seqs_1hot = seqs_1hot.reshape((seqs_1hot.shape[0], 4, 1, options.seq_length))
#################################################################
# place filter consensus motifs
#################################################################
# save to HDF5
seqs_file = "%s/motif_seqs.h5" % options.out_dir
h5f = h5py.File(seqs_file, "w")
h5f.create_dataset("test_in", data=seqs_1hot)
h5f.close()
# predict scores
scores_file = "%s/motif_seqs_scores.h5" % options.out_dir
torch_cmd = "th basset_place2_predict.lua %s %s %s %s" % (cuda_str, model_file, seqs_file, scores_file)
subprocess.call(torch_cmd, shell=True)
# load in scores
hdf5_in = h5py.File(scores_file, "r")
motif_seq_scores = np.array(hdf5_in["scores"])
hdf5_in.close()
#################################################################
# analyze
#################################################################
for ti in out_targets:
#################################################################
# compute pairwise expectations
#################################################################
# X = np.zeros((motif_seq_scores.shape[0],num_filters))
# xi = 0
# for i in range(num_filters):
# for j in range(num_filters):
# X[xi,i] += 1
# X[xi,j] += 1
# xi += 1
X = np.zeros((motif_seq_scores.shape[0], 2 * num_filters))
xi = 0
for i in range(num_filters):
for j in range(num_filters):
X[xi, i] += 1
X[xi, num_filters + j] += 1
xi += 1
# fit model
model = BayesianRidge()
model.fit(X, motif_seq_scores[:, ti])
# predict pairwise expectations
motif_seq_preds = model.predict(X)
print model.score(X, motif_seq_scores[:, ti])
# print filter coefficients
coef_out = open("%s/coefs_t%d.txt" % (options.out_dir, ti), "w")
for i in range(num_filters):
print >> coef_out, "%3d %6.2f" % (i, model.coef_[i])
coef_out.close()
#################################################################
# normalize pairwise predictions
#################################################################
filter_interaction = np.zeros((num_filters, num_filters))
table_out = open("%s/table_t%d.txt" % (options.out_dir, ti), "w")
si = 0
for i in range(num_filters):
for j in range(num_filters):
filter_interaction[i, j] = motif_seq_scores[si, ti] - motif_seq_preds[si]
cols = (i, j, motif_seq_scores[si, ti], motif_seq_preds[si], filter_interaction[i, j])
print >> table_out, "%3d %3d %6.3f %6.3f %6.3f" % cols
si += 1
table_out.close()
# plot heat map
plt.figure()
sns.heatmap(filter_interaction)
plt.savefig("%s/heat_t%d.pdf" % (options.out_dir, ti))
### Imputing DYAR
train = df[(df.DYAR.isnull() ==False) & (df.pct_team_tgts.isnull() == False)]
train.reset_index(inplace=True, drop=True)
test = df[(df.DYAR.isnull() == True) & (df.pct_team_tgts.isnull() == False)]
test.reset_index(inplace= True, drop=True)
features = ['targets', 'receptions', 'rec_tds', 'start_ratio', 'pct_team_tgts', 'pct_team_receptions', 'pct_team_touchdowns',
'rec_yards', 'dpi_yards', 'fumbles', 'first_down_ctchs', 'pct_of_team_passyards']
X = scale(train[features])
y = train.DYAR
# Our best model for predicting DYAR was a Bayesian Ridge Regressor
br = BayesianRidge()
br.fit(X,y)
dyar_predictions = pd.DataFrame(br.predict(scale(test[features])), columns = ['DYAR_predicts'])
test = test.join(dyar_predictions)
test['DYAR'] = test['DYAR_predicts']
test.drop('DYAR_predicts', inplace=True, axis=1)
frames = [train,test]
df = pd.concat(frames, axis=0, ignore_index=True)
### Imputing EYds
train = df[(df.EYds.isnull() ==False) & (df.pct_team_tgts.isnull() == False)]
train.reset_index(inplace=True, drop=True)
test = df[(df.EYds.isnull() == True) & (df.pct_team_tgts.isnull() == False)]
test.reset_index(inplace= True, drop=True)
# A Bayesian Ridge was also our best predictor for EYds. In general, we're able to most confidently predict EYds.
def main():
usage = 'usage: %prog [options] <model_file>'
parser = OptionParser(usage)
parser.add_option('-c', dest='center_dist', default=10, type='int', help='Distance between the motifs and sequence center [Default: %default]')
parser.add_option('-d', dest='model_hdf5_file', default=None, help='Pre-computed model output as HDF5 [Default: %default]')
parser.add_option('-g', dest='cuda', default=False, action='store_true', help='Run on the GPGPU [Default: %default]')
parser.add_option('-l', dest='seq_length', default=600, type='int', help='Sequence length [Default: %default]')
parser.add_option('-o', dest='out_dir', default='heat', help='Output directory [Default: %default]')
parser.add_option('-t', dest='targets', default='0', help='Comma-separated list of target indexes to plot (or -1 for all) [Default: %default]')
(options,args) = parser.parse_args()
if len(args) != 1:
parser.error('Must provide Basset model file')
else:
model_file = args[0]
out_targets = [int(ti) for ti in options.targets.split(',')]
if not os.path.isdir(options.out_dir):
os.mkdir(options.out_dir)
random.seed(1)
# torch options
cuda_str = ''
if options.cuda:
cuda_str = '-cuda'
#################################################################
# place filter consensus motifs
#################################################################
# determine filter consensus motifs
filter_consensus = get_filter_consensus(model_file, options.out_dir, cuda_str)
seqs_1hot = []
num_filters = len(filter_consensus)
# num_filters = 40
filter_len = filter_consensus[0].shape[1]
# position the motifs
left_i = options.seq_length/2 - options.center_dist - filter_len
right_i = options.seq_length/2 + options.center_dist
ns_1hot = np.zeros((4,options.seq_length)) + 0.25
# ns_1hot = np.zeros((4,options.seq_length))
# for i in range(options.seq_length):
# nt_i = random.randint(0,3)
# ns_1hot[nt_i,i] = 1
for i in range(num_filters):
for j in range(num_filters):
# copy the sequence of N's
motifs_seq = np.copy(ns_1hot)
# write them into the one hot coding
motifs_seq[:,left_i:left_i+filter_len] = filter_consensus[i]
motifs_seq[:,right_i:right_i+filter_len] = filter_consensus[j]
# save
seqs_1hot.append(motifs_seq)
# make a full array
seqs_1hot = np.array(seqs_1hot)
# reshape for spatial
seqs_1hot = seqs_1hot.reshape((seqs_1hot.shape[0],4,1,options.seq_length))
#################################################################
# place filter consensus motifs
#################################################################
# save to HDF5
seqs_file = '%s/motif_seqs.h5' % options.out_dir
h5f = h5py.File(seqs_file, 'w')
h5f.create_dataset('test_in', data=seqs_1hot)
h5f.close()
# predict scores
scores_file = '%s/motif_seqs_scores.h5' % options.out_dir
torch_cmd = 'th basset_place2_predict.lua %s %s %s %s' % (cuda_str, model_file, seqs_file, scores_file)
subprocess.call(torch_cmd, shell=True)
# load in scores
hdf5_in = h5py.File(scores_file, 'r')
motif_seq_scores = np.array(hdf5_in['scores'])
hdf5_in.close()
#################################################################
# analyze
#################################################################
for ti in out_targets:
#################################################################
# compute pairwise expectations
#################################################################
# X = np.zeros((motif_seq_scores.shape[0],num_filters))
# xi = 0
# for i in range(num_filters):
# for j in range(num_filters):
# X[xi,i] += 1
# X[xi,j] += 1
# xi += 1
X = np.zeros((motif_seq_scores.shape[0],2*num_filters))
xi = 0
for i in range(num_filters):
for j in range(num_filters):
X[xi,i] += 1
X[xi,num_filters+j] += 1
xi += 1
# fit model
model = BayesianRidge()
model.fit(X, motif_seq_scores[:,ti])
# predict pairwise expectations
motif_seq_preds = model.predict(X)
print model.score(X, motif_seq_scores[:,ti])
# print filter coefficients
coef_out = open('%s/coefs_t%d.txt' % (options.out_dir,ti), 'w')
for i in range(num_filters):
print >> coef_out, '%3d %6.2f' % (i,model.coef_[i])
coef_out.close()
#################################################################
# normalize pairwise predictions
#################################################################
filter_interaction = np.zeros((num_filters,num_filters))
table_out = open('%s/table_t%d.txt' % (options.out_dir,ti), 'w')
si = 0
for i in range(num_filters):
for j in range(num_filters):
filter_interaction[i,j] = motif_seq_scores[si,ti] - motif_seq_preds[si]
cols = (i, j, motif_seq_scores[si,ti], motif_seq_preds[si], filter_interaction[i,j])
print >> table_out, '%3d %3d %6.3f %6.3f %6.3f' % cols
si += 1
table_out.close()
scores_abs = abs(filter_interaction.flatten())
max_score = stats.quantile(scores_abs, .999)
print 'Limiting scores to +-%f' % max_score
filter_interaction_max = np.zeros((num_filters, num_filters))
for i in range(num_filters):
for j in range(num_filters):
filter_interaction_max[i,j] = np.min([filter_interaction[i,j], max_score])
filter_interaction_max[i,j] = np.max([filter_interaction_max[i,j], -max_score])
# plot heat map
plt.figure()
sns.heatmap(filter_interaction_max, xticklabels=False, yticklabels=False)
plt.savefig('%s/heat_t%d.pdf' % (options.out_dir,ti))
KNNmse = Model_two.predict(X_crosstest_scl)
print("KNN_RMSE:",np.sqrt(mean_squared_error(y_crosstest,KNNmse)))
print(datetime.now() - start)
start = datetime.now()
from sklearn import ensemble
Model_three = ensemble.RandomForestRegressor(n_estimators = 500,verbose=1,n_jobs=-1,random_state = 120,max_depth=16)
Model_three.fit(X_crosstrain_svd,y_crosstrain)
RFmse = Model_three.predict(X_crosstest_svd)
print("RandomForest_RMSE:",np.sqrt(mean_squared_error(y_crosstest,RFmse)))
print(datetime.now() - start)
start = datetime.now()
from sklearn.linear_model import BayesianRidge
BR = BayesianRidge(n_iter=500,tol= 0.001,normalize=True).fit(X_crosstrain_scl,y_crosstrain)
pred_BR = BR.predict(X_crosstest_scl)
print("BayesinRidge_RMSE:",np.sqrt(mean_squared_error(y_crosstest,pred_BR)))
print(datetime.now() - start)
start = datetime.now()
from sklearn.linear_model import LinearRegression
LR = LinearRegression(fit_intercept = True,normalize = True,n_jobs=-1).fit(X_crosstrain_svd,y_crosstrain)
pred_LR = LR.predict(X_crosstest_svd)
print("LinearRegression_RMSE:",np.sqrt(mean_squared_error(y_crosstest,pred_LR)))
print(datetime.now() - start)
#decision tree along with Adaboost
start = datetime.now()
from sklearn.tree import DecisionTreeRegressor
from sklearn.ensemble import AdaBoostRegressor