def __init__(self, seed, neighbourhood_size, stopping_criterion):
self.seed = check_random_state(seed)
self.elite = None
self.random_state = check_random_state(seed)
self.neighborhood = list()
self.neighborhood_size = neighbourhood_size
self.stopping_criterion = stopping_criterion
self.current_generation = 0
def __init__(self, n_topics, alpha=0.1, beta=0.01, random_state=0):
self.n_topics = n_topics
self.alpha = alpha
self.beta = beta
self.random_state = random_state
rng = utils.check_random_state(random_state)
self._rands = rng.rand(1024**2 // 8)
def optimal_transport_two_gaussians(mu_1,
cov_1,
mu_2,
cov_2,
nsamples=1,
random_state=None):
"""
.. seealso::
Remark 2.31 of Peyré and Cuturi (2020)
http://arxiv.org/pdf/1803.00567.pdf
"""
rng = check_random_state(random_state)
dim = len(cov_1)
sqrt_cov_1 = la.sqrtm(cov_1)
inv_sqrt_cov_1 = la.inv(sqrt_cov_1)
scaling_matrix = la.sqrtm(sqrt_cov_1.dot(cov_2).dot(sqrt_cov_1))
scaling_matrix = inv_sqrt_cov_1.dot(scaling_matrix).dot(inv_sqrt_cov_1)
X = rng.randn(nsamples, dim)
X = X.dot(sqrt_cov_1) + mu_1
Y = mu_2 + (X - mu_1).dot(scaling_matrix)
return X, Y
def make_user_item_regression(random_state=123, n_user=20, n_item=20,
label_stdev=0.4, rank=2, bias=True,
first_order=True, stdev_w0=.2, stdev_w=0.3,
stdev_V=0.4, mean_w0=2, mean_w=5, mean_V=10):
n_features = n_user + n_item
n_samples = n_user * n_item
# create design matrix
user_cols = np.repeat(range(n_user), n_item)
item_cols = np.array(range(n_item) * n_user) + n_user
cols = np.hstack((user_cols, item_cols))
rows = np.hstack((np.arange(n_item*n_user), np.arange(n_item*n_user)))
X = sp.coo_matrix((np.ones_like(cols, dtype=np.float64), (rows, cols)))
X = sp.csc_matrix(X)
assert X.shape[0] == n_samples
assert X.shape[1] == n_features
# sample the model parameter
random_state = check_random_state(random_state)
w0 = random_state.normal(mean_w0, stdev_w0)
w = random_state.normal(mean_w, stdev_w, n_features)
V = random_state.normal(mean_V, stdev_V, (rank, n_features))
y = ffm_predict(w0, w, V, X)
if label_stdev > 0:
y = random_state.normal(y, label_stdev)
return X, y, (w0, w, V)
def __init__(
self,
params: Dict,
batch_size: int = 1,
n_sims: int = 1000,
distortion: Tuple[float, float] = None,
seed: int = None,
min_bin_length: int = 4,
normalize_samples: bool = False,
train: bool = True,
n_workers: int = 1,
) -> None:
self.params = params
self.batch_size = batch_size
self.rng = check_random_state(seed)
self.seed = seed
self.distortion = distortion
self.normalize_samples = normalize_samples
self.n_sims = n_sims
self.train = train
self.n_workers = n_workers
self.batch_seed_sequence = np.random.SeedSequence(seed)
self.seed = seed
def __iter__(self):
if not self.train:
self.batch_seed_sequence = np.random.SeedSequence(self.seed)
self.rng = check_random_state(self.seed)
with concurrent.futures.ProcessPoolExecutor(self.n_workers) as executor:
futures = [
executor.submit(
SimulationBatch(
distortion=self.distortion,
variable_binning=self.params["variable_binning"],
start=self.params["start"],
varying_start_value=self.params["varying_start_value"],
n_sims=self.batch_size,
n_agents=self.params["n_agents"],
timesteps=self.params["timesteps"],
seed=np.random.default_rng(rng),
compute_fiv=self.params["compute_fiv"],
normalize_samples=self.normalize_samples,
).next
)
for rng in self.batch_seed_sequence.spawn(self.n_sims // self.batch_size)
]
for future in concurrent.futures.as_completed(futures):
yield future.result()
def __init__(
self,
distortion: Tuple[float, float] = None,
variable_binning = False,
start: float = 0.5,
varying_start_value: bool = False,
n_sims: int = 1000,
n_agents: int = 1000,
timesteps: int = 200,
seed: int = None,
compute_fiv: bool = False,
normalize_samples: bool = False,
) -> None:
self.rng = check_random_state(seed)
self.distortion = distortion
if distortion is not None:
self.distortion = Distorter(*distortion, seed=self.rng)
if variable_binning and self.distortion is None:
raise ValueError("Variable binning requires distortion prior")
self.variable = variable_binning
self.n_sims = n_sims
self.start = start
self.varying_start_value = varying_start_value
self.n_agents = n_agents
self.timesteps = timesteps
self.compute_fiv = compute_fiv
self.normalize_samples = normalize_samples
self.seed = seed
self.n_samples = 0
self.set_priors()
def maximal_coupling_rejection(p, q, nsamples=1, random_state=None):
"""Rejection sampler to obtain pairs (X, Y) such that :math:`X \\sim p`, :math:`Y \\sim q` and the event :math:`\\{X=Y\\}` occurs with maximal probability.
:param p:
distribution of X
:param q:
distribution of Y
Both parameter distributions ``p, q`` must have the methods
- ``.rvs()`` to generate samples
- ``.logpdf()`` to evaluate the log probability density function
.. seealso::
`scipy.stats module <https://docs.scipy.org/doc/scipy/reference/stats.html>`_
"""
rng = check_random_state(random_state)
for _ in range(nsamples):
X = p.rvs(random_state=rng)
if np.log(rng.rand()) < (q.logpdf(X) - p.logpdf(X)):
return X, X
Y = q.rvs(random_state=rng)
while np.log(rng.rand()) < (p.logpdf(Y) - q.logpdf(Y)):
Y = q.rvs(random_state=rng)
return X, Y
def __init__(self,
n,
sig_init,
T_nov,
v_min=5.0,
sp_min=2.5,
random_state=check_random_state(0)):
"""Initialize igmm
Parameters:
n - dimension of data
sig_init - scale for initial covariance matrix
T_nov - novelty constant 0 < T_nov <= 1, defines distance that new data point must be from
any other components in order to create a new component. Bigger means that more components will be
created and T_nov = 1 means that every point will have a new component. The authors used 0.01
v_min - how many updates must pass before checking if a component should be removed
sp_min - minimum cumulative probability to keep a component
"""
self.n_dim = n
self.n_components = 0
self.sig_init = sig_init
self.T_nov = T_nov
self.v_min = v_min
self.sp_min = sp_min
self.random_state = random_state
def maximal_coupling_two_bernoullis(p, q, nsamples=1, random_state=None):
"""Rejection sampler to obtain pairs (X, Y) such that :math:`X \\sim p`, :math:`Y \\sim q` and the event :math:`\\{X=Y\\}` occurs with maximal probability.
.. seealso::
`scipy.stats module <https://docs.scipy.org/doc/scipy/reference/stats.html>`_
"""
rng = check_random_state(random_state)
if p == q:
X = rng.rand(nsamples) < p
return X, X
ber_p, ber_q = np.array((1 - p, p)), np.array((1 - q, q))
min_pq = np.minimum(ber_p, ber_q)
int_min_pq = np.sum(min_pq)
ber_p_tld = (ber_p - min_pq) / (1.0 - int_min_pq)
ber_q_tld = (ber_q - min_pq) / (1.0 - int_min_pq)
gam = np.diag(min_pq) + (1.0 - int_min_pq) * np.outer(ber_p_tld, ber_q_tld)
sample = rng.choice(4, size=nsamples, p=gam.ravel())
X = np.array([0, 0, 1, 1])
Y = np.array([0, 1, 0, 1])
return X[sample], Y[sample], gam
def simulate_xy(path: str,
T: int,
sigma2_v: float,
sigma2_w: float,
sigma2_x1: float,
random_state=None):
if os.path.exists(path):
with open(path, mode='rb') as f:
return pickle.load(f)
else:
random_state = check_random_state(random_state)
x = np.empty(shape=T, dtype=float)
y = np.empty(shape=T, dtype=float)
x_0 = random_state.normal(loc=0.0, scale=np.sqrt(sigma2_x1))
x_prev = x_0
for n in range(T):
v = random_state.normal(loc=0.0, scale=np.sqrt(sigma2_v))
x[n] = x_prev / 2 + 25 * (x_prev /
(1 + np.power(x_prev, 2))) + 8 * np.cos(
1.2 * (n + 1)) + v
x_prev = x[n]
w = random_state.normal(loc=0.0, scale=np.sqrt(sigma2_w))
y[n] = np.power(x[n], 2) / 20 + w
x = np.append(x_0, x)
# y = y[:, np.newaxis]
with open(path, mode='wb') as f:
pickle.dump((x, y), f)
return x, y
def __init__(self,
n_topic: int,
n_iter=2000,
alpha=0.1,
beta=0.01,
random_state=None,
refresh=10):
"""
:param n_topic: 主题数目
:param n_iter: 迭代次数
:param alpha: 文档主题分布超参数
:param beta: 主题单词分布超参数
:param random_state: 随机种子
:param refresh: 循环多少次输出当前日志
"""
self.n_topic = n_topic
self.n_iter = n_iter
self.alpha = alpha
self.beta = beta
# if random_state is None, check_random_state(None) does nothing
self.random_state = random_state
self.refresh = refresh
self.topic_word_ = None
self.doc_topic_ = None
self.nzt_ = None
if alpha <= 0 or beta <= 0:
raise ValueError('alpha and eta must be greater than zero')
# random number that are reused
rng = utils.check_random_state(random_state)
self._rands = rng.rand(1024**2 // 8) # 1MiB of random variates
def make_ldpc(n_code, d_v, d_c, systematic=False, sparse=True, seed=None):
"""Create an LDPC coding and decoding matrices H and G.
Parameters
----------
n_code: int, Length of the codewords.
d_v: int, Number of parity-check equations including a certain bit.
d_c: int, Number of bits in the same parity-check equation. d_c Must be
greater or equal to d_v and must divide n.
seed: int, seed of the random generator.
systematic: boolean, default False. if True, constructs a systematic
coding matrix G.
Returns:
--------
H: array (n_equations, n_code). Parity check matrix of an LDPC code with
code length `n_code` and `n_equations` number of equations.
G: (n_code, n_bits) array coding matrix.
"""
seed = utils.check_random_state(seed)
H = parity_check_matrix(n_code, d_v, d_c, seed=seed)
if systematic:
H, G = coding_matrix_systematic(H, sparse=sparse)
else:
G = coding_matrix(H, sparse=sparse)
return H, G
def __init__(self, n_topics, alpha=0.1, beta=0.01, random_state=0):
self.n_topics = n_topics
self.alpha = alpha
self.beta = beta
self.random_state = random_state
rng = utils.check_random_state(random_state)
self._rands = rng.rand(1024**2 // 8)
def fit(self, corpus):
"""
:param corpus: array-like, shape (n_samples, n_features)
Training data, where n_samples in the number of samples
and n_features is the number of features. Sparse matrix allowed.
:return:
"""
random_state = utils.check_random_state(self.random_state)
rands = self._rands.copy()
self._initialize(corpus) # 初始化所有有关信息
for n_iter in range(self.n_iter):
random_state.shuffle(rands)
if n_iter % self.refresh == 0:
pp = self.perplexity(corpus)
logger.info('<{}> log likelihood: {:.0f}'.format(n_iter, pp))
self._sample_topics(rands)
pp = self.perplexity(corpus)
logger.info('<{}> log likelihood: {:.0f}'.format(self.n_iter, pp))
# 计算文档主题分布和主题单词分布
self._count_distribution()
# 删除计算过程中的中间值，以节约空间
del self.TS
del self.DS
del self.ZS
del self.ndz_
return self
def fit(self):
"""
fit the model with X for one iteration
"""
random_state = utils.check_random_state(self.random_state)
rands = self._rands.copy()
self.update_potential()
_lda._sample_topics(self.WS, self.DS, self.ZS, self.nzw, self.ndz,
self.nz, self.alpha, self.beta, self.beta_sum, rands,
self.potential)
def fit(self):
"""
fit the model with X for one iteration
"""
random_state = utils.check_random_state(self.random_state)
rands = self._rands.copy()
self.update_potential()
_lda._sample_topics(self.WS, self.DS, self.ZS, self.nzw, self.ndz,
self.nz, self.alpha, self.beta, self.beta_sum,
rands, self.potential)
def wright_fisher(N, T, selection_strength, start=0.5, random_state=None):
rng = check_random_state(random_state)
series = np.zeros(T)
series[0] = int(start * N)
for i in range(1, T):
p_star = (
series[i - 1]
* (1 + selection_strength)
/ (series[i - 1] * selection_strength + N)
)
series[i] = rng.binomial(N, min(p_star, 1))
return series
def __init__(self, N, mu=0.001, b=0, burn_in=1000, timesteps=10, seed=None, verbose=False):
self.N = N
self.mu = mu
self.b = b
self.burn_in = burn_in
self.timesteps = timesteps
self.rng = check_random_state(seed)
self.verbose = verbose
self.n_traits = N
self.population = np.arange(self.N)
self.trait_fd = []
def __init__(self,
n_samples,
prior,
proposal,
supports,
theta_init=None,
random_state=None):
self.n_samples = n_samples
self.prior = prior
self.proposal = proposal
self.supports = supports
self.theta_init = theta_init
self.random_state = check_random_state(random_state)
def sample_gibbs_sweep(self, nb_sweeps=1, random_sate=None):
rng = check_random_state(random_sate)
n_rows, n_cols = self.shape
for _ in range(nb_sweeps):
for i in range(n_rows):
for j in range(n_cols):
sum_ngbr_01 = sum(self.state_matrix[self.neighbors(i, j)])
cond_proba = self.cond_proba[sum_ngbr_01]
self.state_matrix[i, j] = rng.rand() < cond_proba
return self.state_matrix, rng
def parity_check_matrix(n_code, d_v, d_c, seed=None):
"""
Build a regular Parity-Check Matrix H following Callager's algorithm.
Parameters
----------
n_code: int, Length of the codewords.
d_v: int, Number of parity-check equations including a certain bit.
Must be greater or equal to 2.
d_c: int, Number of bits in the same parity-check equation. d_c Must be
greater or equal to d_v and must divide n.
seed: int, seed of the random generator.
Returns
-------
H: array (n_equations, n_code). LDPC regular matrix H.
Where n_equations = d_v * n / d_c, the total number of parity-check
equations.
"""
rng = utils.check_random_state(seed)
if d_v <= 1:
raise ValueError("""d_v must be at least 2.""")
if d_c <= d_v:
raise ValueError("""d_c must be greater than d_v.""")
if n_code % d_c:
raise ValueError("""d_c must divide n for a regular LDPC matrix H.""")
n_equations = (n_code * d_v) // d_c
block = np.zeros((n_equations // d_v, n_code), dtype=int)
H = np.empty((n_equations, n_code))
block_size = n_equations // d_v
# Filling the first block with consecutive ones in each row of the block
for i in range(block_size):
for j in range(i * d_c, (i + 1) * d_c):
block[i, j] = 1
H[:block_size] = block
# reate remaining blocks by permutations of the first block's columns:
for i in range(1, d_v):
H[i * block_size:(i + 1) * block_size] = rng.permutation(block.T).T
H = H.astype(int)
return H
def __init__(self, n_topics, n_iter, alpha=0.1, eta=0.01, random_state=None,
refresh=10):
self.n_topics = n_topics
self.n_iter = n_iter
self.alpha = alpha
self.eta = eta
# if random_state is None, check_random_state(None) does nothing
# other than return the current numpy RandomState
self.random_state = random_state
self.refresh = refresh
if alpha <= 0 or eta <= 0:
raise ValueError("alpha and eta must be greater than zero")
# random numbers that are reused
rng = utils.check_random_state(random_state)
self._rands = rng.rand(1024**2 // 8) # 1MiB of random variates
def __init__(self, maze, num_advs=3, rewards={'*': 10}, terminal_markers='*', action_error_prob=0, random_state=None, directions="NSEWK"):
self.maze = Maze(maze) if not isinstance(maze, Maze) else maze
self.rewards = rewards
self.terminal_markers = terminal_markers
self.action_error_prob = action_error_prob
self.random_state = check_random_state(random_state)
self.num_advs = num_advs
self.area = np.product(self.maze.shape[-2:])
self.vol = np.product(self.maze.shape)
# find all available position
self.available_state = self.maze.flat_positions_containing('.')
# find all food court position
self.food_court = self.maze.flat_positions_containing('&')
# randomly choose position of adversary
self.adversaries_position = np.random.choice(self.available_state, replace=False, size=self.num_advs)
# randomly choose food court people
self.fooder = []
if self.food_court:
self.fooder = np.random.choice(self.food_court, replace=False, size=3)
# find stairs
self.stairs = self.maze.flat_positions_containing('%')
# dict to upstair or downstair
self.climb = {}
for st in self.stairs:
if st-self.area in self.stairs:
self.climb[st] = st-self.area
if st+self.area in self.stairs:
self.climb[st] = st+self.area
self.actions = [maze_actions[direction] for direction in directions]
self.num_actions = len(self.actions)
self.state = None
self.reset()
self.num_states = self.maze.shape[0] * self.maze.shape[1] * self.maze.shape[2]
self.current_situation = None
self.adversary_actions = None
self.total_hit = 0
def _fit(self, X):
random_state = utils.check_random_state(self.random_state)
rands = self._rands.copy()
self._initialize(X)
for it in range(self.n_iter):
random_state.shuffle(rands)
if it % self.refresh == 0:
ll = self.loglikelihood()
logger.info("<{}> log likelihood: {:.0f}".format(it, ll))
self.loglikelihoods_.append(ll)
self._sample_topics(rands)
ll = self.loglikelihood()
self.components_ = (self.nzw_ + self.eta).astype(float)
self.components_ /= np.sum(self.components_, axis=1)[:, np.newaxis]
self.topic_word_ = self.components_
self.doc_topic_ = (self.ndz_ + self.alpha).astype(float)
self.doc_topic_ /= np.sum(self.doc_topic_, axis=1)[:, np.newaxis]
# delete attributes no longer needed after fitting to save memory and reduce clutter
del self.WS
del self.DS
del self.ZS
return self,self.components_,self.doc_topic_,self.topic_word_
def __init__(self,
mutation_level,
is_input_node=False,
_computational_layer=None,
cl=True,
seed=None,
input_shape=None,
semantics=None,
input_data=None,
semantic_input=False,
semantic_input_node=None,
computational_layer=None,
semantics_computational_layer=None,
input_node=None,
depth=1):
self.mutation_level = mutation_level
self.input_node = input_node
self._computational_layer = _computational_layer
self.computational_layer = computational_layer
self.is_input_node = is_input_node
self.cl = cl
self.input_shape = input_shape
self.output_shape = None
self.out_connections = []
self.depth = depth # depending on computational_layer is = to previous or plus one
self.random_state = check_random_state(seed)
self.semantics = semantics
self.semantic_input = semantic_input
self.semantic_input_node = semantic_input_node
self.input_data = input_data
self.semantics_computational_layer = semantics_computational_layer
if self._computational_layer is None:
self._get_random_layer()
if semantics is None:
self.set_computational_layer()
self._input_node_output_shape()
def maximal_coupling_reflexion_two_gaussians(mu_1,
mu_2,
cov,
nsamples=1,
random_state=None):
rng = check_random_state(random_state)
L = la.cholesky(cov, lower=True)
z = la.solve_triangular(L, mu_1 - mu_2, lower=True, unit_diagonal=False)
e = z / la.norm(z)
dim = len(cov)
X = rng.randn(nsamples, dim)
Y = X.copy()
gauss = multivariate_normal(mean=np.zeros(dim)) # gaussian N(0, I)
accept = np.log(rng.rand(nsamples)) < gauss.logpdf(X + z) - gauss.logpdf(X)
Y[accept] += z
Y[~accept] -= np.outer(X[~accept].dot(e), 2.0 * e) # Householder reflexion
return X.dot(L.T) + mu_1, Y.dot(L.T) + mu_2
def common_random_number_coupling(p, q, nsamples=1, random_state=None):
"""
:param p:
distribution of X with methods
- ``.rvs()`` to generate samples from distribution :math:`p`
- ``.cdf()`` to evaluate the cumulative distribution function
:param q:
distribution of Y with method
- ``.ppf()`` to evaluate the inverse cumulative distribution function
.. seealso::
`scipy.stats module <https://docs.scipy.org/doc/scipy/reference/stats.html>`_
"""
rng = check_random_state(random_state)
X = p.rvs(size=nsamples, random_state=rng)
Y = q.ppf(p.cdf(X))
return X, Y
def fit(self, X):
n_samples = X.shape[0]
random_state = utils.check_random_state(self.random_state)
centroids = self.init_centroids(X, 'random', random_state)
new_centroids = centroids.copy()
clusters = np.zeros(n_samples)
for _ in range(self.max_ite):
for i in range(n_samples):
distances = np.sum((centroids - X[i])**2, axis=1)
clusters[i] = np.argsort(distances)[0]
for i in range(self.n_clusters):
new_centroids[i] = X[clusters == i].mean(axis=0)
if np.sum(new_centroids == centroids) == 4:
break
centroids = new_centroids
self.centroids = centroids
self.clusters = clusters
return self
def rvs(self, size=1, random_state=None):
rng = check_random_state(random_state)
unif = uniform.rvs(size=size, random_state=rng)
return self.ppf(unif)
nsamples = data.get('nsamples')
print('nsamples = {}'.format(nsamples))
p = data.get('p_distribution').get('class')
p_samples = data.get('p_distribution').get('samples')
q = data.get('q_distribution').get('class')
q_samples = data.get('q_distribution').get('samples')
except FileNotFoundError:
print('No previous samples were saved under {}'.format(file_name))
print('Generating samples may take a while')
p, q = p_distribution(), q_distribution()
nsamples = int(1e4)
seed = 0
rng = check_random_state(seed)
unif_01 = rng.rand(nsamples)
p_samples, q_samples = p.ppf(unif_01), q.ppf(unif_01)
data = {
'seed': seed,
'nsamples': nsamples,
'p_distribution': {
'class': p,
'samples': p_samples
},
'q_distribution': {
'class': q,
'samples': q_samples
}
}
def fit(self, X, y, sample_weight=None, check_input=True):
"""Build a decision tree from the training set (X, y).
Parameters
----------
X : array-like or sparse matrix, shape = [n_samples, n_features]
The training input samples. Internally, it will be converted to
``dtype=np.float32`` and if a sparse matrix is provided
to a sparse ``csc_matrix``.
y : array-like, shape = [n_samples] or [n_samples, n_outputs]
The target values (class labels in classification, real numbers in
regression). In the regression case, use ``dtype=np.float64`` and
``order='C'`` for maximum efficiency.
sample_weight : array-like, shape = [n_samples] or None
Sample weights. If None, then samples are equally weighted. Splits
that would create child nodes with net zero or negative weight are
ignored while searching for a split in each node. In the case of
classification, splits are also ignored if they would result in any
single class carrying a negative weight in either child node.
check_input : boolean, (default=True)
Allow to bypass several input checking.
Don't use this parameter unless you know what you do.
Returns
-------
self : object
Returns self.
"""
random_state = check_random_state(self.random_state)
if check_input:
X = check_array(X, dtype=DTYPE)
# Determine output settings
n_samples, self.n_features_ = X.shape
is_classification = isinstance(self, ClassifierMixin)
y = np.atleast_1d(y)
expanded_class_weight = None
if y.ndim == 1:
# reshape is necessary to preserve the data contiguity against vs
# [:, np.newaxis] that does not.
y = np.reshape(y, (-1, 1))
self.n_outputs_ = y.shape[1]
if is_classification:
y = np.copy(y)
self.classes_ = []
self.n_classes_ = []
if self.class_weight is not None:
y_original = np.copy(y)
for k in range(self.n_outputs_):
classes_k, y[:, k] = np.unique(y[:, k], return_inverse=True)
self.classes_.append(classes_k)
self.n_classes_.append(classes_k.shape[0])
if self.class_weight is not None:
expanded_class_weight = compute_sample_weight(
self.class_weight, y_original)
else:
self.classes_ = [None] * self.n_outputs_
self.n_classes_ = [1] * self.n_outputs_
self.n_classes_ = np.array(self.n_classes_, dtype=np.intp)
if getattr(y, "dtype", None) != DOUBLE or not y.flags.contiguous:
y = np.ascontiguousarray(y, dtype=DOUBLE)
# Check parameters
max_depth = ((2 ** 31) - 1 if self.max_depth is None
else self.max_depth)
max_leaf_nodes = (-1 if self.max_leaf_nodes is None
else self.max_leaf_nodes)
if isinstance(self.max_features, string_types):
if self.max_features == "auto":
if is_classification:
max_features = max(1, int(np.sqrt(self.n_features_)))
else:
max_features = self.n_features_
elif self.max_features == "sqrt":
max_features = max(1, int(np.sqrt(self.n_features_)))
elif self.max_features == "log2":
max_features = max(1, int(np.log2(self.n_features_)))
else:
raise ValueError(
'Invalid value for max_features. Allowed string '
'values are "auto", "sqrt" or "log2".')
elif self.max_features is None:
max_features = self.n_features_
elif isinstance(self.max_features, (numbers.Integral, np.integer)):
max_features = self.max_features
else: # float
if self.max_features > 0.0:
max_features = max(1, int(self.max_features * self.n_features_))
else:
max_features = 0
self.max_features_ = max_features
if len(y) != n_samples:
raise ValueError("Number of labels=%d does not match "
"number of samples=%d" % (len(y), n_samples))
if self.min_samples_split <= 0:
raise ValueError("min_samples_split must be greater than zero.")
if self.min_samples_leaf <= 0:
raise ValueError("min_samples_leaf must be greater than zero.")
if not 0 <= self.min_weight_fraction_leaf <= 0.5:
raise ValueError("min_weight_fraction_leaf must in [0, 0.5]")
if max_depth <= 0:
raise ValueError("max_depth must be greater than zero. ")
if not (0 < max_features <= self.n_features_):
raise ValueError("max_features must be in (0, n_features]")
if not isinstance(max_leaf_nodes, (numbers.Integral, np.integer)):
raise ValueError("max_leaf_nodes must be integral number but was "
"%r" % max_leaf_nodes)
if -1 < max_leaf_nodes < 2:
raise ValueError(("max_leaf_nodes {0} must be either smaller than "
"0 or larger than 1").format(max_leaf_nodes))
if sample_weight is not None:
if (getattr(sample_weight, "dtype", None) != DOUBLE or
not sample_weight.flags.contiguous):
sample_weight = np.ascontiguousarray(
sample_weight, dtype=DOUBLE)
if len(sample_weight.shape) > 1:
raise ValueError("Sample weights array has more "
"than one dimension: %d" %
len(sample_weight.shape))
if len(sample_weight) != n_samples:
raise ValueError("Number of weights=%d does not match "
"number of samples=%d" %
(len(sample_weight), n_samples))
if expanded_class_weight is not None:
if sample_weight is not None:
sample_weight = sample_weight * expanded_class_weight
else:
sample_weight = expanded_class_weight
# Set min_weight_leaf from min_weight_fraction_leaf
if self.min_weight_fraction_leaf != 0. and sample_weight is not None:
min_weight_leaf = (self.min_weight_fraction_leaf *
np.sum(sample_weight))
else:
min_weight_leaf = 0.
# Set min_samples_split sensibly
min_samples_split = max(self.min_samples_split,
2 * self.min_samples_leaf)
# Build tree
criterion = self.criterion
if not isinstance(criterion, Criterion):
if is_classification:
criterion = CRITERIA_CLF[self.criterion](self.n_outputs_,
self.n_classes_)
else:
criterion = CRITERIA_REG[self.criterion](self.n_outputs_)
SPLITTERS = DENSE_SPLITTERS
splitter = self.splitter
if not isinstance(self.splitter, Splitter):
splitter = SPLITTERS[self.splitter](criterion,
self.max_features_,
self.min_samples_leaf,
min_weight_leaf,
random_state)
self.tree_ = Tree(self.n_features_, self.n_classes_, self.n_outputs_)
# Use BestFirst if max_leaf_nodes given; use DepthFirst otherwise
if max_leaf_nodes < 0:
builder = DepthFirstTreeBuilder(splitter, min_samples_split,
self.min_samples_leaf,
min_weight_leaf,
max_depth)
else:
builder = BestFirstTreeBuilder(splitter, min_samples_split,
self.min_samples_leaf,
min_weight_leaf,
max_depth,
max_leaf_nodes)
builder.build(self.tree_, X, y, sample_weight)
if self.n_outputs_ == 1:
self.n_classes_ = self.n_classes_[0]
self.classes_ = self.classes_[0]
return self
def _random_init(X, n_components, random_state=None):
rs = check_random_state(random_state)
return [rs.rand(X.shape[i], n_components) for i in range(len(X.shape))]
def smacof(similarities, metric=True, n_components=2, init=None, n_init=8,
n_jobs=1, max_iter=300, verbose=0, eps=1e-3, random_state=None):
"""
Computes multidimensional scaling using SMACOF (Scaling by Majorizing a
Complicated Function) algorithm
The SMACOF algorithm is a multidimensional scaling algorithm: it minimizes
a objective function, the *stress*, using a majorization technique. The
Stress Majorization, also known as the Guttman Transform, guarantees a
monotone convergence of Stress, and is more powerful than traditional
techniques such as gradient descent.
The SMACOF algorithm for metric MDS can summarized by the following steps:
1. Set an initial start configuration, randomly or not.
2. Compute the stress
3. Compute the Guttman Transform
4. Iterate 2 and 3 until convergence.
The nonmetric algorithm adds a monotonic regression steps before computing
the stress.
Parameters
----------
similarities : symmetric ndarray, shape (n_samples, n_samples)
similarities between the points
metric : boolean, optional, default: True
compute metric or nonmetric SMACOF algorithm
n_components : int, optional, default: 2
number of dimension in which to immerse the similarities
overridden if initial array is provided.
init : {None or ndarray of shape (n_samples, n_components)}, optional
if None, randomly chooses the initial configuration
if ndarray, initialize the SMACOF algorithm with this array
n_init : int, optional, default: 8
Number of time the smacof algorithm will be run with different
initialisation. The final results will be the best output of the
n_init consecutive runs in terms of stress.
n_jobs : int, optional, default: 1
The number of jobs to use for the computation. This works by breaking
down the pairwise matrix into n_jobs even slices and computing them in
parallel.
If -1 all CPUs are used. If 1 is given, no parallel computing code is
used at all, which is useful for debugging. For n_jobs below -1,
(n_cpus + 1 + n_jobs) are used. Thus for n_jobs = -2, all CPUs but one
are used.
max_iter : int, optional, default: 300
Maximum number of iterations of the SMACOF algorithm for a single run
verbose : int, optional, default: 0
level of verbosity
eps : float, optional, default: 1e-6
relative tolerance w.r.t stress to declare converge
random_state : integer or numpy.RandomState, optional
The generator used to initialize the centers. If an integer is
given, it fixes the seed. Defaults to the global numpy random
number generator.
Returns
-------
X : ndarray (n_samples,n_components)
Coordinates of the n_samples points in a n_components-space
stress : float
The final value of the stress (sum of squared distance of the
disparities and the distances for all constrained points)
Notes
-----
"Modern Multidimensional Scaling - Theory and Applications" Borg, I.;
Groenen P. Springer Series in Statistics (1997)
"Nonmetric multidimensional scaling: a numerical method" Kruskal, J.
Psychometrika, 29 (1964)
"Multidimensional scaling by optimizing goodness of fit to a nonmetric
hypothesis" Kruskal, J. Psychometrika, 29, (1964)
"""
similarities, = check_arrays(similarities, sparse_format='dense')
random_state = check_random_state(random_state)
if hasattr(init, '__array__'):
init = np.asarray(init).copy()
if not n_init == 1:
warnings.warn(
'Explicit initial positions passed: '
'performing only one init of the MDS instead of %d'
% n_init)
n_init = 1
best_pos, best_stress = None, None
if n_jobs == 1:
for it in range(n_init):
pos, stress = _smacof_single(similarities, metric=metric,
n_components=n_components, init=init,
max_iter=max_iter, verbose=verbose,
eps=eps, random_state=random_state)
if best_stress is None or stress < best_stress:
best_stress = stress
best_pos = pos.copy()
else:
seeds = random_state.randint(np.iinfo(np.int32).max, size=n_init)
results = Parallel(n_jobs=n_jobs, verbose=max(verbose - 1, 0))(
delayed(_smacof_single)(
similarities, metric=metric, n_components=n_components,
init=init, max_iter=max_iter, verbose=verbose, eps=eps,
random_state=seed)
for seed in seeds)
positions, stress = zip(*results)
best = np.argmin(stress)
best_stress = stress[best]
best_pos = positions[best]
return best_pos, best_stress
def _smacof_single(similarities, metric=True, n_components=2, init=None,
max_iter=300, verbose=0, eps=1e-3, random_state=None):
"""
Computes multidimensional scaling using SMACOF algorithm
Parameters
----------
similarities: symmetric ndarray, shape [n * n]
similarities between the points
metric: boolean, optional, default: True
compute metric or nonmetric SMACOF algorithm
n_components: int, optional, default: 2
number of dimension in which to immerse the similarities
overwritten if initial array is provided.
init: {None or ndarray}, optional
if None, randomly chooses the initial configuration
if ndarray, initialize the SMACOF algorithm with this array
max_iter: int, optional, default: 300
Maximum number of iterations of the SMACOF algorithm for a single run
verbose: int, optional, default: 0
level of verbosity
eps: float, optional, default: 1e-6
relative tolerance w.r.t stress to declare converge
random_state: integer or numpy.RandomState, optional
The generator used to initialize the centers. If an integer is
given, it fixes the seed. Defaults to the global numpy random
number generator.
Returns
-------
X: ndarray (n_samples, n_components), float
coordinates of the n_samples points in a n_components-space
stress_: float
The final value of the stress (sum of squared distance of the
disparities and the distances for all constrained points)
"""
n_samples = similarities.shape[0]
random_state = check_random_state(random_state)
if similarities.shape[0] != similarities.shape[1]:
raise ValueError("similarities must be a square array (shape=%d)" %
n_samples)
if not np.allclose(similarities, similarities.T):
raise ValueError("similarities must be symmetric")
sim_flat = ((1 - np.tri(n_samples)) * similarities).ravel()
sim_flat_w = sim_flat[sim_flat != 0]
if init is None:
# Randomly choose initial configuration
X = random_state.rand(n_samples * n_components)
X = X.reshape((n_samples, n_components))
else:
# overrides the parameter p
n_components = init.shape[1]
if n_samples != init.shape[0]:
raise ValueError("init matrix should be of shape (%d, %d)" %
(n_samples, n_components))
X = init
old_stress = None
ir = IsotonicRegression()
for it in range(max_iter):
# Compute distance and monotonic regression
dis = euclidean_distances(X)
if metric:
disparities = similarities
else:
dis_flat = dis.ravel()
# similarities with 0 are considered as missing values
dis_flat_w = dis_flat[sim_flat != 0]
# Compute the disparities using a monotonic regression
disparities_flat = ir.fit_transform(sim_flat_w, dis_flat_w)
disparities = dis_flat.copy()
disparities[sim_flat != 0] = disparities_flat
disparities = disparities.reshape((n_samples, n_samples))
disparities *= np.sqrt((n_samples * (n_samples - 1) / 2) /
(disparities ** 2).sum())
# Compute stress
stress = ((dis.ravel() - disparities.ravel()) ** 2).sum() / 2
# Update X using the Guttman transform
dis[dis == 0] = 1e-5
ratio = disparities / dis
B = - ratio
B[np.arange(len(B)), np.arange(len(B))] += ratio.sum(axis=1)
X = 1. / n_samples * np.dot(B, X)
dis = np.sqrt((X ** 2).sum(axis=1)).sum()
if verbose >= 2:
print('it: %d, stress %s' % (it, stress))
if old_stress is not None:
if(old_stress - stress / dis) < eps:
if verbose:
print('breaking at iteration %d with stress %s' % (it,
stress))
break
old_stress = stress / dis
return X, stress
def main():
algorithm = args.algorithm
path = './auto_regulation_{}'.format(algorithm)
random_state = check_random_state(1)
if not os.path.exists(path):
os.makedirs(path)
t, y = load_data('./data/auto_regulation.pickle')
n_samples = args.n_samples
n_particles = args.n_particles
burn_in = args.burn_in
thinning = args.thinning
state_init = np.array([8, 8, 8, 5])
const = {
'k': 10,
'c5': 0.1,
'c6': 0.9,
'observation_std': 2.0,
'times': np.concatenate(([0.0], t))
}
prior = Prior([
# U(-7,2) as in the paper. However, in SciPy, the distribution is given as U(loc,loc+scale).
stats.uniform(-7, 9),
stats.uniform(-7, 9),
stats.uniform(-7, 9),
stats.uniform(-7, 9),
stats.uniform(-7, 9),
stats.uniform(-7, 9)
])
proposal = Proposal([
Distribution(stats.norm, scale=0.08),
Distribution(stats.norm, scale=0.08),
Distribution(stats.norm, scale=0.08),
Distribution(stats.norm, scale=0.08),
Distribution(stats.norm, scale=0.08),
Distribution(stats.norm, scale=0.08)
])
theta_init = stats.uniform.rvs(loc=-7, scale=9, size=6)
random_state = check_random_state(1)
if algorithm == 'abcmh':
alpha = args.alpha
hpr_p = args.hpr_p
kernel = args.kernel
mcmc = ABCAutoRegulation(n_samples=n_samples,
n_particles=n_particles,
alpha=alpha,
hpr_p=hpr_p,
state_init=state_init,
const=const,
kernel=kernel,
prior=prior,
proposal=proposal,
theta_init=theta_init,
random_state=random_state)
else:
mcmc = ParticleAutoRegulation(n_samples=n_samples,
n_particles=n_particles,
state_init=state_init,
const=const,
prior=prior,
proposal=proposal,
theta_init=theta_init,
random_state=random_state)
sampled_theta_path = os.path.join(path, 'sampled_theta.pickle')
if os.path.exists(sampled_theta_path):
with open(sampled_theta_path, 'rb') as f:
theta = pickle.load(f)
else:
theta = mcmc.do_inference(y)
with open(sampled_theta_path, 'wb') as f:
pickle.dump(theta, f)
theta_true = np.log(np.array([0.1, 0.7, 0.35, 0.2, 0.3, 0.1]))
theta = np.exp(theta)
theta = theta[burn_in::thinning]
truth = np.exp(theta_true)
pretty_names = [r'$c_1$', r'$c_2$', r'$c_3$', r'$c_4$', r'$c_7$', r'$c_8$']
for i in range(theta.shape[1]):
param_name = pretty_names[i]
param_values = theta[:, i]
fig, (ax1, ax2, ax3) = plt.subplots(3, 1, dpi=300)
plt.suptitle(param_name)
ax1.set_title('Trace plot')
ax1.plot(param_values, color='dimgrey')
ax1.axhline(truth[i], color='crimson', lw=2)
plot_acf(param_values, lags=100, ax=ax2, color='dimgrey')
ax3.set_title('Histogram')
ax3.hist(param_values, density=True, bins=30, color='dimgrey')
ax3.axvline(truth[i], color='crimson', lw=2)
plt.show()
def fit(self, X, y, sample_weight=None, check_input=True):
"""Build a decision tree from the training set (X, y).
Parameters
----------
X : array-like or sparse matrix, shape = [n_samples, n_features]
The training input samples. Internally, it will be converted to
``dtype=np.float32`` and if a sparse matrix is provided
to a sparse ``csc_matrix``.
y : array-like, shape = [n_samples] or [n_samples, n_outputs]
The target values (class labels in classification, real numbers in
regression). In the regression case, use ``dtype=np.float64`` and
``order='C'`` for maximum efficiency.
sample_weight : array-like, shape = [n_samples] or None
Sample weights. If None, then samples are equally weighted. Splits
that would create child nodes with net zero or negative weight are
ignored while searching for a split in each node. In the case of
classification, splits are also ignored if they would result in any
single class carrying a negative weight in either child node.
check_input : boolean, (default=True)
Allow to bypass several input checking.
Don't use this parameter unless you know what you do.
Returns
-------
self : object
Returns self.
"""
random_state = check_random_state(self.random_state)
if check_input:
X = check_array(X, dtype=DTYPE)
# Determine output settings
n_samples, self.n_features_ = X.shape
is_classification = isinstance(self, ClassifierMixin)
y = np.atleast_1d(y)
expanded_class_weight = None
if y.ndim == 1:
# reshape is necessary to preserve the data contiguity against vs
# [:, np.newaxis] that does not.
y = np.reshape(y, (-1, 1))
self.n_outputs_ = y.shape[1]
if is_classification:
y = np.copy(y)
self.classes_ = []
self.n_classes_ = []
if self.class_weight is not None:
y_original = np.copy(y)
for k in range(self.n_outputs_):
classes_k, y[:, k] = np.unique(y[:, k], return_inverse=True)
self.classes_.append(classes_k)
self.n_classes_.append(classes_k.shape[0])
if self.class_weight is not None:
expanded_class_weight = compute_sample_weight(
self.class_weight, y_original)
else:
self.classes_ = [None] * self.n_outputs_
self.n_classes_ = [1] * self.n_outputs_
self.n_classes_ = np.array(self.n_classes_, dtype=np.intp)
if getattr(y, "dtype", None) != DOUBLE or not y.flags.contiguous:
y = np.ascontiguousarray(y, dtype=DOUBLE)
# Check parameters
max_depth = ((2**31) - 1 if self.max_depth is None else self.max_depth)
max_leaf_nodes = (-1 if self.max_leaf_nodes is None else
self.max_leaf_nodes)
if isinstance(self.max_features, string_types):
if self.max_features == "auto":
if is_classification:
max_features = max(1, int(np.sqrt(self.n_features_)))
else:
max_features = self.n_features_
elif self.max_features == "sqrt":
max_features = max(1, int(np.sqrt(self.n_features_)))
elif self.max_features == "log2":
max_features = max(1, int(np.log2(self.n_features_)))
else:
raise ValueError(
'Invalid value for max_features. Allowed string '
'values are "auto", "sqrt" or "log2".')
elif self.max_features is None:
max_features = self.n_features_
elif isinstance(self.max_features, (numbers.Integral, np.integer)):
max_features = self.max_features
else: # float
if self.max_features > 0.0:
max_features = max(1,
int(self.max_features * self.n_features_))
else:
max_features = 0
self.max_features_ = max_features
if len(y) != n_samples:
raise ValueError("Number of labels=%d does not match "
"number of samples=%d" % (len(y), n_samples))
if self.min_samples_split <= 0:
raise ValueError("min_samples_split must be greater than zero.")
if self.min_samples_leaf <= 0:
raise ValueError("min_samples_leaf must be greater than zero.")
if not 0 <= self.min_weight_fraction_leaf <= 0.5:
raise ValueError("min_weight_fraction_leaf must in [0, 0.5]")
if max_depth <= 0:
raise ValueError("max_depth must be greater than zero. ")
if not (0 < max_features <= self.n_features_):
raise ValueError("max_features must be in (0, n_features]")
if not isinstance(max_leaf_nodes, (numbers.Integral, np.integer)):
raise ValueError("max_leaf_nodes must be integral number but was "
"%r" % max_leaf_nodes)
if -1 < max_leaf_nodes < 2:
raise ValueError(("max_leaf_nodes {0} must be either smaller than "
"0 or larger than 1").format(max_leaf_nodes))
if sample_weight is not None:
if (getattr(sample_weight, "dtype", None) != DOUBLE
or not sample_weight.flags.contiguous):
sample_weight = np.ascontiguousarray(sample_weight,
dtype=DOUBLE)
if len(sample_weight.shape) > 1:
raise ValueError("Sample weights array has more "
"than one dimension: %d" %
len(sample_weight.shape))
if len(sample_weight) != n_samples:
raise ValueError("Number of weights=%d does not match "
"number of samples=%d" %
(len(sample_weight), n_samples))
if expanded_class_weight is not None:
if sample_weight is not None:
sample_weight = sample_weight * expanded_class_weight
else:
sample_weight = expanded_class_weight
# Set min_weight_leaf from min_weight_fraction_leaf
if self.min_weight_fraction_leaf != 0. and sample_weight is not None:
min_weight_leaf = (self.min_weight_fraction_leaf *
np.sum(sample_weight))
else:
min_weight_leaf = 0.
# Set min_samples_split sensibly
min_samples_split = max(self.min_samples_split,
2 * self.min_samples_leaf)
# Build tree
criterion = self.criterion
if not isinstance(criterion, Criterion):
if is_classification:
criterion = CRITERIA_CLF[self.criterion](self.n_outputs_,
self.n_classes_)
else:
criterion = CRITERIA_REG[self.criterion](self.n_outputs_)
SPLITTERS = DENSE_SPLITTERS
splitter = self.splitter
if not isinstance(self.splitter, Splitter):
splitter = SPLITTERS[self.splitter](criterion, self.max_features_,
self.min_samples_leaf,
min_weight_leaf, random_state)
self.tree_ = Tree(self.n_features_, self.n_classes_, self.n_outputs_)
# Use BestFirst if max_leaf_nodes given; use DepthFirst otherwise
if max_leaf_nodes < 0:
builder = DepthFirstTreeBuilder(splitter, min_samples_split,
self.min_samples_leaf,
min_weight_leaf, max_depth)
else:
builder = BestFirstTreeBuilder(splitter, min_samples_split,
self.min_samples_leaf,
min_weight_leaf, max_depth,
max_leaf_nodes)
builder.build(self.tree_, X, y, sample_weight)
if self.n_outputs_ == 1:
self.n_classes_ = self.n_classes_[0]
self.classes_ = self.classes_[0]
return self