def duplicate_exp(regs, n_cpus=None, n_bootstrap=30):
m = Mimic2(mode='total', duplicate=1)
ps = ParamSearch(m, n_cpus)
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for reg in regs:
for alpha in alphas:
name = reg.__name__ + '_dup_' + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(n_bootstrap)
def reg_exp(p):
m = Mimic2(mode='total', seed=p.seed)
ps = ParamSearch(m, p)
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for reg in p.regs:
for alpha in alphas:
name = reg.__name__ + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(p.n_bootstrap)
def expert_feature_only_exp(n_cpus=None, n_bootstrap=30):
m = Mimic2(mode='total', expert_feature_only=True)
ps = ParamSearch(m, n_cpus)
reg = ridge
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for alpha in alphas:
name = 'expert_only_ridge' + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(n_bootstrap)
def expert_feature_only_exp(p):
m = Mimic2(mode='total', expert_feature_only=True, seed=p.seed)
ps = ParamSearch(m, p)
reg = ridge
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for alpha in alphas:
name = 'expert_only_ridge' + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(p.n_bootstrap)
def duplicate_exp(p):
m = Mimic2(mode='total', duplicate=p.dup, noise=p.noise, seed=p.seed)
ps = ParamSearch(m, p)
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for reg in p.regs:
for alpha in alphas:
name = reg.__name__ + '_dup' + str(p.dup) + '_' + str(p.noise)\
+ '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(p.n_bootstrap)
def random_risk_exp(p): # p is argparser
m = Mimic2(mode='total', random_risk=True, seed=p.seed)
ps = ParamSearch(m, p)
reg = eye_loss
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for alpha in alphas:
name = 'random_risk_eye' + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(p.n_bootstrap)
def random_risk_exp(regs, n_cpus=None, n_bootstrap=30):
m = Mimic2(mode='total', random_risk=True)
ps = ParamSearch(m, n_cpus)
reg = eye_loss
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for reg in regs:
for alpha in alphas:
name = 'random_risk_' + reg.__name__ + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(n_bootstrap)
def two_stage_exp(threshold=0.90, n_cpus=None, n_bootstrap=30):
'''
remove features by setting a threshold on correlation,
then apply l2 regularization on the remaining features
'''
m = Mimic2(mode='total', two_stage=True, threshold=float(threshold))
ps = ParamSearch(m, n_cpus)
reg = ridge
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for alpha in alphas:
name = 'two_stage_ridge_' + str(threshold) + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(n_bootstrap)
def two_stage_exp(p):
'''
remove features by setting a threshold on correlation,
then apply l2 regularization on the remaining features
'''
m = Mimic2(mode='total',
two_stage=True,
threshold=p.threshold,
seed=p.seed)
ps = ParamSearch(m, p)
reg = ridge
alphas = [0.1, 0.01, 0.001, 0.0001, 0.00001]
for alpha in alphas:
name = 'two_stage_ridge_' + str(p.threshold) + '^' + str(alpha)
ps.add_param(name, reg, alpha)
ps.run(p.n_bootstrap)
def loadData(dataname,
get_test=False,
pin_memory=True,
batch_size=1000,
num_workers=0):
if dataname == 'mimic2':
m = Mimic2(mode='total')
ndim = m.xtrain.shape[1]
if get_test:
xtrain = np.vstack([m.xtrain, m.xval])
xval = m.xte
ytrain = np.hstack([m.ytrain, m.yval])
yval = m.yte
else:
xtrain = m.xtrain
xval = m.xval
ytrain = m.ytrain
yval = m.yval
# make y in {-1, 1}
ytrain = ytrain * 2 - 1
yval = yval * 2 - 1
d = m.r.size(0)
train_data = TensorDataset(*np2tensor(xtrain, ytrain))
data = DataLoader(train_data,
shuffle=True,
batch_size=batch_size,
num_workers=num_workers,
pin_memory=pin_memory)
valdata = TensorDataset(*np2tensor(xval, yval))
valdata = DataLoader(valdata,
batch_size=batch_size,
num_workers=num_workers,
pin_memory=pin_memory)
if get_test:
return valdata, None, ndim, None
else:
print('train shape:', xtrain.shape, 'n_islands:', None, 'ndim:',
ndim)
print('done loading data')
return data, valdata, None, None, ndim, None
# note: data are generated in heterogeneous groups ipython notebook
X, Y, Theta, \
Xval, Yval, val_theta,\
Xtest, Ytest, test_theta,\
ndim, n_islands = joblib.load('data/%s.pkl' % dataname)
if get_test:
xtest = torch.from_numpy(Xtest).float()
ytest = torch.from_numpy(Ytest).float()
test_data = TensorDataset(xtest, ytest)
test_data = DataLoader(test_data,
batch_size=batch_size,
num_workers=num_workers,
pin_memory=pin_memory)
return test_data, test_theta, ndim, n_islands
x = torch.from_numpy(X).float()
y = torch.from_numpy(Y).float()
train_data = TensorDataset(x, y)
train_data = DataLoader(train_data,
batch_size=batch_size,
shuffle=True,
num_workers=num_workers,
pin_memory=pin_memory)
xval = torch.from_numpy(Xval).float()
yval = torch.from_numpy(Yval).float()
val_data = TensorDataset(xval, yval)
val_data = DataLoader(val_data,
batch_size=batch_size,
num_workers=num_workers,
pin_memory=pin_memory)
print('train shape:', X.shape, 'n_islands:', n_islands, 'ndim:', ndim)
print('done loading data')
return train_data, val_data,\
Theta, val_theta,\
ndim, n_islands