def test_kernels(self):
from GPy.kern import RBF,Linear,MLP,Bias,White
Q = self.Z.shape[1]
kernels = [RBF(Q,ARD=True), Linear(Q,ARD=True),MLP(Q,ARD=True), RBF(Q,ARD=True)+Linear(Q,ARD=True)+Bias(Q)+White(Q)
,RBF(Q,ARD=True)+Bias(Q)+White(Q), Linear(Q,ARD=True)+Bias(Q)+White(Q)]
for k in kernels:
k.randomize()
self._test_kernel_param(k)
self._test_Z(k)
self._test_qX(k)
self._test_kernel_param(k, psi2n=True)
self._test_Z(k, psi2n=True)
self._test_qX(k, psi2n=True)
def _create_kernel(self, V):
self._kerns = [RBF(1, ARD=True, active_dims=[i])
for i in range(self.n_dims)]
self._kernf = Fixed(self.n_dims, tdot(V))
self._kernb = Bias(self.n_dims)
self.kernel = np.sum(self._kerns) + self._kernf + self._kernb
class GP(BaseStrategy):
short_name = 'gp'
def __init__(self, acquisition=None, seed=None, seeds=1, max_feval=5E4, max_iter=1E5):
self.seed = seed
self.seeds = seeds
self.max_feval = max_feval
self.max_iter = max_iter
self.model = None
self.n_dims = None
self.kernel = None
self._kerns = None
self._kernf = None
self._kernb = None
if acquisition is None:
acquisition = {'name': 'osprey', 'params': {}}
self.acquisition_function = acquisition
self._acquisition_function = None
self._set_acquisition()
def _create_kernel(self, V):
self._kerns = [RBF(1, ARD=True, active_dims=[i])
for i in range(self.n_dims)]
self._kernf = Fixed(self.n_dims, tdot(V))
self._kernb = Bias(self.n_dims)
self.kernel = np.sum(self._kerns) + self._kernf + self._kernb
def _fit_model(self, X, Y):
model = GPRegression(X, Y, self.kernel)
model.optimize(messages=False, max_f_eval=self.max_feval)
self.model = model
def _get_random_point(self):
return np.array([np.random.uniform(low=0., high=1.)
for i in range(self.n_dims)])
def _is_var_positive(self, var):
if np.any(var < 0):
# RuntimeError may be overkill
raise RuntimeError('Negative variance predicted from regression model.')
else:
return True
def _ei(self, x, y_mean, y_var):
y_std = np.sqrt(y_var)
y_best = self.model.Y.max(axis=0)
z = (y_mean - y_best)/y_std
result = y_std*(z*norm.cdf(z) + norm.pdf(z))
return result
def _ucb(self, x, y_mean, y_var, kappa=1.0):
result = y_mean + kappa*np.sqrt(y_var)
return result
def _osprey(self, x, y_mean, y_var):
return (y_mean+y_var).flatten()
def _optimize(self, init=None):
# TODO start minimization from a range of points and take minimum
if not init:
init = self._get_random_point()
def z(x):
# TODO make spread of points around x and take mean value.
x = x.copy().reshape(-1, self.n_dims)
y_mean, y_var = self.model.predict(x, kern=(np.sum(self._kerns).copy() +
self._kernb.copy()))
# This code is for debug/testing phase only.
# Ideally we should test for negative variance regardless of the AF.
# However, we want to recover the original functionality of Osprey, hence the conditional block.
# TODO remove this.
if self.acquisition_function['name'] == 'osprey':
af = self._acquisition_function(x, y_mean=y_mean, y_var=y_var)
elif self.acquisition_function['name'] in ['ei', 'ucb']:
# y_var = np.abs(y_var)
if self._is_var_positive(y_var):
af = self._acquisition_function(x, y_mean=y_mean, y_var=y_var)
return (-1)*af
res = minimize(z, init, bounds=self.n_dims*[(0., 1.)],
options={'maxiter': self.max_iter, 'disp': 0})
return res.x
def _set_acquisition(self):
if isinstance(self.acquisition_function, list):
raise RuntimeError('Must specify only one acquisition function')
if sorted(self.acquisition_function.keys()) != ['name', 'params']:
raise RuntimeError('strategy/params/acquisition must contain keys '
'"name" and "params"')
if self.acquisition_function['name'] not in ['ei', 'ucb', 'osprey']:
raise RuntimeError('strategy/params/acquisition name must be one of '
'"ei", "ucb", "osprey"')
f = eval('self._'+self.acquisition_function['name'])
def g(x, y_mean, y_var):
return f(x, y_mean, y_var, **self.acquisition_function['params'])
self._acquisition_function = g
def _get_data(self, history, searchspace):
X = []
Y = []
V = []
ignore = []
for param_dict, scores, status in history:
# transform points into the GP domain. This invloves bringing
# int and enum variables to floating point, etc.
if status == 'FAILED':
# not sure how to deal with these yet
continue
point = searchspace.point_to_gp(param_dict)
if status == 'SUCCEEDED':
X.append(point)
Y.append(np.mean(scores))
V.append(np.var(scores))
elif status == 'PENDING':
ignore.append(point)
else:
raise RuntimeError('unrecognized status: %s' % status)
return (np.array(X).reshape(-1, self.n_dims),
np.array(Y).reshape(-1, 1),
np.array(V).reshape(-1, 1),
np.array(ignore).reshape(-1, self.n_dims))
def _from_gp(self, result, searchspace):
# Note that GP only deals with float-valued variables, so we have
# a transform step on either side, where int and enum valued variables
# are transformed before calling gp, and then the result suggested by
# GP needs to be reverse-transformed.
out = {}
for gpvalue, var in zip(result, searchspace):
out[var.name] = var.point_from_gp(float(gpvalue))
return out
def _is_within(self, point, X, tol=1E-2):
if True in (np.sqrt(((point - X)**2).sum(axis=0)) <= tol):
return True
return False
def suggest(self, history, searchspace, max_tries=5):
if not GPRegression:
raise ImportError('No module named GPy')
if not minimize:
raise ImportError('No module named SciPy')
if len(history) < self.seeds:
return RandomSearch().suggest(history, searchspace)
self.n_dims = searchspace.n_dims
X, Y, V, ignore = self._get_data(history, searchspace)
# TODO make _create_kernel accept optional args.
self._create_kernel(V)
self._fit_model(X, Y)
suggestion = self._optimize()
if suggestion in ignore or self._is_within(suggestion, X):
return RandomSearch().suggest(history, searchspace)
return self._from_gp(suggestion, searchspace)
class GP(BaseStrategy):
short_name = 'gp'
def __init__(self, seed=None, seeds=1, max_feval=5E4, max_iter=1E5):
self.seed = seed
self.seeds = seeds
self.max_feval = max_feval
self.max_iter = max_iter
self.model = None
self.n_dims = None
self.kernel = None
self._kerns = None
self._kernf = None
self._kernb = None
def _create_kernel(self, V):
self._kerns = [
RBF(1, ARD=True, active_dims=[i]) for i in range(self.n_dims)
]
self._kernf = Fixed(self.n_dims, tdot(V))
self._kernb = Bias(self.n_dims)
self.kernel = np.sum(self._kerns) + self._kernf + self._kernb
def _fit_model(self, X, Y):
model = GPRegression(X, Y, self.kernel)
model.optimize(messages=False, max_f_eval=self.max_feval)
self.model = model
def _get_random_point(self):
return np.array(
[np.random.uniform(low=0., high=1.) for i in range(self.n_dims)])
def _optimize(self, init=None):
if not init:
init = self._get_random_point()
def z(x):
y = x.copy().reshape(-1, self.n_dims)
s, v = self.model.predict(y,
kern=(np.sum(self._kerns).copy() +
self._kernb.copy()))
return -(s + v).flatten()
return minimize(z,
init,
bounds=self.n_dims * [(0., 1.)],
options={
'maxiter': self.max_iter,
'disp': 0
}).x
def _get_data(self, history, searchspace):
X = []
Y = []
V = []
ignore = []
for param_dict, scores, status in history:
# transform points into the GP domain. This invloves bringing
# int and enum variables to floating point, etc.
if status == 'FAILED':
# not sure how to deal with these yet
continue
point = searchspace.point_to_gp(param_dict)
if status == 'SUCCEEDED':
X.append(point)
Y.append(np.mean(scores))
V.append(np.var(scores))
elif status == 'PENDING':
ignore.append(point)
else:
raise RuntimeError('unrecognized status: %s' % status)
return (np.array(X).reshape(-1, self.n_dims),
np.array(Y).reshape(-1, 1), np.array(V).reshape(-1, 1),
np.array(ignore).reshape(-1, self.n_dims))
def _from_gp(self, result, searchspace):
# Note that GP only deals with float-valued variables, so we have
# a transform step on either side, where int and enum valued variables
# are transformed before calling gp, and then the result suggested by
# GP needs to be reverse-transformed.
out = {}
for gpvalue, var in zip(result, searchspace):
out[var.name] = var.point_from_gp(float(gpvalue))
return out
def _is_within(self, point, X, tol=1E-2):
if True in (np.sqrt(((point - X)**2).sum(axis=0)) <= tol):
return True
return False
def suggest(self, history, searchspace, max_tries=5):
if not GPRegression:
raise ImportError('No module named GPy')
if not minimize:
raise ImportError('No module named SciPy')
if len(history) < self.seeds:
return RandomSearch().suggest(history, searchspace)
self.n_dims = searchspace.n_dims
X, Y, V, ignore = self._get_data(history, searchspace)
self._create_kernel(V)
self._fit_model(X, Y)
suggestion = self._optimize()
if suggestion in ignore or self._is_within(suggestion, X):
return RandomSearch().suggest(history, searchspace)
return self._from_gp(suggestion, searchspace)
class GP(BaseStrategy):
short_name = 'gp'
def __init__(self,
acquisition=None,
seed=None,
seeds=1,
max_feval=5E4,
max_iter=1E5):
self.seed = seed
self.seeds = seeds
self.max_feval = max_feval
self.max_iter = max_iter
self.model = None
self.n_dims = None
self.kernel = None
self._kerns = None
self._kernf = None
self._kernb = None
if acquisition is None:
acquisition = {'name': 'osprey', 'params': {}}
self.acquisition_function = acquisition
self._acquisition_function = None
self._set_acquisition()
def _create_kernel(self, V):
self._kerns = [
RBF(1, ARD=True, active_dims=[i]) for i in range(self.n_dims)
]
self._kernf = Fixed(self.n_dims, tdot(V))
self._kernb = Bias(self.n_dims)
self.kernel = np.sum(self._kerns) + self._kernf + self._kernb
def _fit_model(self, X, Y):
model = GPRegression(X, Y, self.kernel)
model.optimize(messages=False, max_f_eval=self.max_feval)
self.model = model
def _get_random_point(self):
return np.array(
[np.random.uniform(low=0., high=1.) for i in range(self.n_dims)])
def _is_var_positive(self, var):
if np.any(var < 0):
# RuntimeError may be overkill
raise RuntimeError(
'Negative variance predicted from regression model.')
else:
return True
def _ei(self, x, y_mean, y_var):
y_std = np.sqrt(y_var)
y_best = self.model.Y.max(axis=0)
z = (y_mean - y_best) / y_std
result = y_std * (z * norm.cdf(z) + norm.pdf(z))
return result
def _ucb(self, x, y_mean, y_var, kappa=1.0):
result = y_mean + kappa * np.sqrt(y_var)
return result
def _osprey(self, x, y_mean, y_var):
return (y_mean + y_var).flatten()
def _optimize(self, init=None):
# TODO start minimization from a range of points and take minimum
if not init:
init = self._get_random_point()
def z(x):
# TODO make spread of points around x and take mean value.
x = x.copy().reshape(-1, self.n_dims)
y_mean, y_var = self.model.predict(
x, kern=(np.sum(self._kerns).copy() + self._kernb.copy()))
# This code is for debug/testing phase only.
# Ideally we should test for negative variance regardless of the AF.
# However, we want to recover the original functionality of Osprey, hence the conditional block.
# TODO remove this.
if self.acquisition_function['name'] == 'osprey':
af = self._acquisition_function(x, y_mean=y_mean, y_var=y_var)
elif self.acquisition_function['name'] in ['ei', 'ucb']:
# y_var = np.abs(y_var)
if self._is_var_positive(y_var):
af = self._acquisition_function(x,
y_mean=y_mean,
y_var=y_var)
return (-1) * af
res = minimize(z,
init,
bounds=self.n_dims * [(0., 1.)],
options={
'maxiter': self.max_iter,
'disp': 0
})
return res.x
def _set_acquisition(self):
if isinstance(self.acquisition_function, list):
raise RuntimeError('Must specify only one acquisition function')
if sorted(self.acquisition_function.keys()) != ['name', 'params']:
raise RuntimeError('strategy/params/acquisition must contain keys '
'"name" and "params"')
if self.acquisition_function['name'] not in ['ei', 'ucb', 'osprey']:
raise RuntimeError(
'strategy/params/acquisition name must be one of '
'"ei", "ucb", "osprey"')
f = eval('self._' + self.acquisition_function['name'])
def g(x, y_mean, y_var):
return f(x, y_mean, y_var, **self.acquisition_function['params'])
self._acquisition_function = g
def _get_data(self, history, searchspace):
X = []
Y = []
V = []
ignore = []
for param_dict, scores, status in history:
# transform points into the GP domain. This invloves bringing
# int and enum variables to floating point, etc.
if status == 'FAILED':
# not sure how to deal with these yet
continue
point = searchspace.point_to_gp(param_dict)
if status == 'SUCCEEDED':
X.append(point)
Y.append(np.mean(scores))
V.append(np.var(scores))
elif status == 'PENDING':
ignore.append(point)
else:
raise RuntimeError('unrecognized status: %s' % status)
return (np.array(X).reshape(-1, self.n_dims),
np.array(Y).reshape(-1, 1), np.array(V).reshape(-1, 1),
np.array(ignore).reshape(-1, self.n_dims))
def _from_gp(self, result, searchspace):
# Note that GP only deals with float-valued variables, so we have
# a transform step on either side, where int and enum valued variables
# are transformed before calling gp, and then the result suggested by
# GP needs to be reverse-transformed.
out = {}
for gpvalue, var in zip(result, searchspace):
out[var.name] = var.point_from_gp(float(gpvalue))
return out
def _is_within(self, point, X, tol=1E-2):
if True in (np.sqrt(((point - X)**2).sum(axis=0)) <= tol):
return True
return False
def suggest(self, history, searchspace, max_tries=5):
if not GPRegression:
raise ImportError('No module named GPy')
if not minimize:
raise ImportError('No module named SciPy')
if len(history) < self.seeds:
return RandomSearch().suggest(history, searchspace)
self.n_dims = searchspace.n_dims
X, Y, V, ignore = self._get_data(history, searchspace)
# TODO make _create_kernel accept optional args.
self._create_kernel(V)
self._fit_model(X, Y)
suggestion = self._optimize()
if suggestion in ignore or self._is_within(suggestion, X):
return RandomSearch().suggest(history, searchspace)
return self._from_gp(suggestion, searchspace)
class GP(BaseStrategy):
short_name = 'gp'
def __init__(self, seeds=1, max_feval=5E4, max_iter=1E5):
self.seeds = seeds
self.max_feval = max_feval
self.max_iter = max_iter
self.model = None
self.n_dims = None
self.kernel = None
self._kerns = None
self._kernf = None
self._kernb = None
def _create_kernel(self, V):
self._kerns = [RBF(1, ARD=True, active_dims=[i])
for i in range(self.n_dims)]
self._kernf = Fixed(self.n_dims, tdot(V))
self._kernb = Bias(self.n_dims)
self.kernel = np.sum(self._kerns) + self._kernf + self._kernb
def _fit_model(self, X, Y):
model = GPRegression(X, Y, self.kernel)
model.optimize(messages=False, max_f_eval=self.max_feval)
self.model = model
def _get_random_point(self):
return np.array([np.random.uniform(low=0., high=1.)
for i in range(self.n_dims)])
def _optimize(self, init=None):
if not init:
init = self._get_random_point()
def z(x):
y = x.copy().reshape(-1, self.n_dims)
s, v = self.model.predict(y, kern=(np.sum(self._kerns).copy() +
self._kernb.copy()))
return -(s+v).flatten()
return minimize(z, init, bounds=self.n_dims*[(0., 1.)],
options={'maxiter': self.max_iter, 'disp': 0}).x
def _get_data(self, history, searchspace):
X = []
Y = []
V = []
ignore = []
for param_dict, scores, status in history:
# transform points into the GP domain. This invloves bringing
# int and enum variables to floating point, etc.
if status == 'FAILED':
# not sure how to deal with these yet
continue
point = searchspace.point_to_gp(param_dict)
if status == 'SUCCEEDED':
X.append(point)
Y.append(np.mean(scores))
V.append(np.var(scores))
elif status == 'PENDING':
ignore.append(point)
else:
raise RuntimeError('unrecognized status: %s' % status)
return (np.array(X).reshape(-1, self.n_dims),
np.array(Y).reshape(-1, 1),
np.array(V).reshape(-1, 1),
np.array(ignore).reshape(-1, self.n_dims))
def _from_gp(self, result, searchspace):
# Note that GP only deals with float-valued variables, so we have
# a transform step on either side, where int and enum valued variables
# are transformed before calling gp, and then the result suggested by
# GP needs to be reverse-transformed.
out = {}
for gpvalue, var in zip(result, searchspace):
out[var.name] = var.point_from_gp(float(gpvalue))
return out
def _is_within(self, point, X, tol=1E-2):
if True in (np.sqrt(((point - X)**2).sum(axis=0)) <= tol):
return True
return False
def suggest(self, history, searchspace, max_tries=5):
if not GPRegression:
raise ImportError('No module named GPy')
if not minimize:
raise ImportError('No module named SciPy')
if len(history) < self.seeds:
return RandomSearch().suggest(history, searchspace)
self.n_dims = searchspace.n_dims
X, Y, V, ignore = self._get_data(history, searchspace)
self._create_kernel(V)
self._fit_model(X, Y)
suggestion = self._optimize()
if suggestion in ignore or self._is_within(suggestion, X):
return RandomSearch().suggest(history, searchspace)
return self._from_gp(suggestion, searchspace)
def gp_on_fold(feature_sets, train, test, y, y_all, learn_options):
sequences = np.array([str(x) for x in y_all.index.get_level_values(0).tolist()])
kern = WeightedDegree(
1, sequences, d=learn_options["kernel degree"], active_dims=[0]
)
X = np.arange(len(train))[:, None]
current_dim = 1
if "gc_count" in feature_sets:
kern += RBF(1, active_dims=[current_dim], name="GC_rbf")
X = np.concatenate((X, feature_sets["gc_count"].values), axis=1)
current_dim += 1
if X.shape[1] != current_dim:
raise AssertionError("incorrect number of columns")
if "drug" in feature_sets:
Q = feature_sets["drug"].values.shape[1]
kern += Linear(
Q, active_dims=range(current_dim, current_dim + Q), name="drug_lin"
)
X = np.concatenate((X, feature_sets["drug"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "gene effect" in feature_sets:
Q = feature_sets["gene effect"].values.shape[1]
kern += Linear(
Q, active_dims=range(current_dim, current_dim + Q), name="gene_lin"
)
X = np.concatenate((X, feature_sets["gene effect"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "Percent Peptide" in feature_sets:
Q = feature_sets["Percent Peptide"].values.shape[1]
kern += RBF(
Q, active_dims=range(current_dim, current_dim + Q), name="percent_pept"
)
X = np.concatenate((X, feature_sets["Percent Peptide"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "Nucleotide cut position" in feature_sets:
Q = feature_sets["Nucleotide cut position"].values.shape[1]
kern += RBF(
Q, active_dims=range(current_dim, current_dim + Q), name="nucleo_cut"
)
X = np.concatenate((X, feature_sets["Nucleotide cut position"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "Strand effect" in feature_sets:
Q = feature_sets["Strand effect"].values.shape[1]
kern += Linear(
Q, active_dims=range(current_dim, current_dim + Q), name="strand"
)
X = np.concatenate((X, feature_sets["Strand effect"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "NGGX" in feature_sets:
Q = feature_sets["NGGX"].values.shape[1]
kern += Linear(Q, active_dims=range(current_dim, current_dim + Q), name="NGGX")
X = np.concatenate((X, feature_sets["NGGX"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "TM" in feature_sets:
Q = feature_sets["TM"].values.shape[1]
kern += RBF(
Q, ARD=True, active_dims=range(current_dim, current_dim + Q), name="TM"
)
X = np.concatenate((X, feature_sets["TM"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
if "gene features" in feature_sets:
Q = feature_sets["gene features"].values.shape[1]
kern += Linear(
Q,
ARD=True,
active_dims=range(current_dim, current_dim + Q),
name="genefeat",
)
X = np.concatenate((X, feature_sets["gene features"].values), axis=1)
current_dim += Q
if X.shape[1] != current_dim:
raise AssertionError("incorrect number or columns")
kern += Bias(X.shape[1])
if learn_options["warpedGP"]:
m = WarpedGP(X[train], y[train], kernel=kern)
else:
m = GPRegression(X[train], y[train], kernel=kern)
m.optimize_restarts(3)
y_pred, _ = m.predict(X[test])
# TODO add offset such that low scores are around 0 (not -4 or so)
return y_pred, m[:]
