Python pymc3.Deterministic方法代码示例

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def fit(self, X, Y, n_samples=10000, tune_steps=1000, n_jobs=4):
        with pm.Model() as self.model:
            # Priors
            std = pm.Uniform("std", 0, self.sps, testval=X.std())
            beta = pm.StudentT("beta", mu=0, lam=self.sps, nu=self.nu)
            alpha = pm.StudentT("alpha", mu=0, lam=self.sps, nu=self.nu, testval=Y.mean())
            # Deterministic model
            mean = pm.Deterministic("mean", alpha + beta * X)
            # Posterior distribution
            obs = pm.Normal("obs", mu=mean, sd=std, observed=Y)
            ## Run MCMC
            # Find search start value with maximum a posterior estimation
            start = pm.find_MAP()
            # sample posterior distribution for latent variables
            trace = pm.sample(n_samples, njobs=n_jobs, tune=tune_steps, start=start)
            # Recover posterior samples
            self.burned_trace = trace[int(n_samples / 2):] 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def built_model(self):
        """
        Initialise :class:`pymc3.Model` depending on problem composites,
        geodetic and/or seismic data are included. Composites also determine
        the problem to be solved.
        """

        logger.info('... Building model ...\n')

        pc = self.config.problem_config

        with Model() as self.model:

            self.rvs, self.fixed_params = self.get_random_variables()

            self.init_hyperparams()

            total_llk = tt.zeros((1), tconfig.floatX)

            for datatype, composite in self.composites.items():
                if datatype in bconfig.modes_catalog[pc.mode].keys():
                    input_rvs = weed_input_rvs(
                        self.rvs, pc.mode, datatype=datatype)
                    fixed_rvs = weed_input_rvs(
                        self.fixed_params, pc.mode, datatype=datatype)

                else:
                    input_rvs = self.rvs
                    fixed_rvs = self.fixed_params

                total_llk += composite.get_formula(
                    input_rvs, fixed_rvs, self.hyperparams, pc)

            # deterministic RV to write out llks to file
            like = Deterministic('tmp', total_llk)

            # will overwrite deterministic name ...
            llk = Potential(self._like_name, like)
            logger.info('Model building was successful! \n') 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def built_hyper_model(self):
        """
        Initialise :class:`pymc3.Model` depending on configuration file,
        geodetic and/or seismic data are included. Estimates initial parameter
        bounds for hyperparameters.
        """

        logger.info('... Building Hyper model ...\n')

        pc = self.config.problem_config

        if len(self.hierarchicals) == 0:
            self.init_hierarchicals()

        point = self.get_random_point(include=['hierarchicals', 'priors'])

        if self.config.problem_config.mode == bconfig.geometry_mode_str:
            for param in pc.priors.values():
                point[param.name] = param.testvalue

        with Model() as self.model:

            self.init_hyperparams()

            total_llk = tt.zeros((1), tconfig.floatX)

            for composite in self.composites.values():
                if hasattr(composite, 'analyse_noise'):
                    composite.analyse_noise(point)
                    composite.init_weights()

                composite.update_llks(point)

                total_llk += composite.get_hyper_formula(self.hyperparams)

            like = Deterministic('tmp', total_llk)
            llk = Potential(self._like_name, like)
            logger.info('Hyper model building was successful!') 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def get_hyper_formula(self, hyperparams):
        """
        Get likelihood formula for the hyper model built. Has to be called
        within a with model context.

        problem_config : :class:`config.ProblemConfig`
        """

        hp_specific = self.config.dataset_specific_residual_noise_estimation
        logpts = hyper_normal(
            self.datasets, hyperparams, self._llks,
            hp_specific=hp_specific)
        llk = Deterministic(self._like_name, logpts)
        return llk.sum() 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def get_hyper_formula(self, hyperparams):
        """
        Get likelihood formula for the hyper model built. Has to be called
        within a with model context.
        """

        logpts = tt.zeros((self.n_t), tconfig.floatX)
        for k in range(self.n_t):
            logpt = self._eval_prior(
                hyperparams[bconfig.hyper_name_laplacian], self._llks[k])
            logpts = tt.set_subtensor(logpts[k:k + 1], logpt)

        llk = Deterministic(self._like_name, logpts)
        return llk.sum() 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def fit(self, X, y):
        """
        Fits a Gaussian Process regressor using MCMC.

        Parameters
        ----------
        X: np.ndarray, shape=(nsamples, nfeatures)
            Training instances to fit the GP.
        y: np.ndarray, shape=(nsamples,)
            Corresponding continuous target values to `X`.

        """
        self.X = X
        self.n = self.X.shape[0]
        self.y = y
        self.model = pm.Model()

        with self.model as model:
            l = pm.Uniform('l', 0, 10)

            log_s2_f = pm.Uniform('log_s2_f', lower=-7, upper=5)
            s2_f = pm.Deterministic('sigmaf', tt.exp(log_s2_f))

            log_s2_n = pm.Uniform('log_s2_n', lower=-7, upper=5)
            s2_n = pm.Deterministic('sigman', tt.exp(log_s2_n))

            f_cov = s2_f * covariance_equivalence[type(self.covfunc).__name__](1, l)
            Sigma = f_cov(self.X) + tt.eye(self.n) * s2_n ** 2
            y_obs = pm.MvNormal('y_obs', mu=np.zeros(self.n), cov=Sigma, observed=self.y)
        with self.model as model:
            if self.step is not None:
                self.trace = pm.sample(self.niter, step=self.step())[self.burnin:]
            else:
                self.trace = pm.sample(self.niter, init=self.init)[self.burnin:] 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def fit(self, X, y):
        """
        Fits a Student-t regressor using MCMC.

        Parameters
        ----------
        X: np.ndarray, shape=(nsamples, nfeatures)
            Training instances to fit the GP.
        y: np.ndarray, shape=(nsamples,)
            Corresponding continuous target values to `X`.

        """
        self.X = X
        self.n = self.X.shape[0]
        self.y = y
        self.model = pm.Model()

        with self.model as model:
            l = pm.Uniform('l', 0, 10)

            log_s2_f = pm.Uniform('log_s2_f', lower=-7, upper=5)
            s2_f = pm.Deterministic('sigmaf', tt.exp(log_s2_f))

            log_s2_n = pm.Uniform('log_s2_n', lower=-7, upper=5)
            s2_n = pm.Deterministic('sigman', tt.exp(log_s2_n))

            f_cov = s2_f * covariance_equivalence[type(self.covfunc).__name__](1, l)
            Sigma = f_cov(self.X) + tt.eye(self.n) * s2_n ** 2
            y_obs = pm.MvStudentT('y_obs', nu=self.nu, mu=np.zeros(self.n), Sigma=Sigma, observed=self.y)
        with self.model as model:
            if self.step is not None:
                self.trace = pm.sample(self.niter, step=self.step())[self.burnin:]
            else:
                self.trace = pm.sample(self.niter, init=self.init)[self.burnin:] 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def pymc3_noncentered_schools(data, draws, chains):
    """Non-centered eight schools implementation for pymc3."""
    import pymc3 as pm

    with pm.Model() as model:
        mu = pm.Normal("mu", mu=0, sd=5)
        tau = pm.HalfCauchy("tau", beta=5)
        eta = pm.Normal("eta", mu=0, sd=1, shape=data["J"])
        theta = pm.Deterministic("theta", mu + tau * eta)
        pm.Normal("obs", mu=theta, sd=data["sigma"], observed=data["y"])
        trace = pm.sample(draws, chains=chains)
    return model, trace 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def _build_dist(self, spec, label, dist, **kwargs):
        """Build and return a PyMC3 Distribution."""
        if isinstance(dist, str):
            if hasattr(pm, dist):
                dist = getattr(pm, dist)
            elif dist in self.dists:
                dist = self.dists[dist]
            else:
                raise ValueError(
                    f"The Distribution {dist} was not found in PyMC3 or the PyMC3BackEnd."
                )

        # Inspect all args in case we have hyperparameters
        def _expand_args(key, value, label):
            if isinstance(value, Prior):
                label = f"{label}_{key}"
                return self._build_dist(spec, label, value.name, **value.args)
            return value

        kwargs = {k: _expand_args(k, v, label) for (k, v) in kwargs.items()}

        # Non-centered parameterization for hyperpriors
        if (
            spec.noncentered
            and "sigma" in kwargs
            and "observed" not in kwargs
            and isinstance(kwargs["sigma"], pm.model.TransformedRV)
        ):
            old_sigma = kwargs["sigma"]
            _offset = pm.Normal(label + "_offset", mu=0, sigma=1, shape=kwargs["shape"])
            return pm.Deterministic(label, _offset * old_sigma)

        return dist(label, **kwargs) 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def _create_model(self):

		with pm.Model() as self.model:

			# getting the location primers
			for layer_index in range(self.num_layers):
				setattr(self, 'w%d' % layer_index, self.__get_weights(layer_index, self.weight_shapes[layer_index]))
				setattr(self, 'b%d' % layer_index, self.__get_biases(layer_index, self.bias_shapes[layer_index]))

				if layer_index == 0:
					fc = pm.Deterministic('fc%d' % layer_index, pm.math.tanh(pm.math.dot(self.network_input, self.weight(layer_index)) + self.bias(layer_index)))
					setattr(self, 'fc%d' % layer_index, fc)
				elif 0 < layer_index < self.num_layers - 1:
					fc = pm.Deterministic('fc%d' % layer_index, pm.math.tanh(pm.math.dot(getattr(self, 'fc%d' % (layer_index - 1)), self.weight(layer_index)) + self.bias(layer_index)))
					setattr(self, 'fc%d' % layer_index, fc)
				else:
					self._loc = pm.Deterministic('bnn_out', pm.math.sigmoid(pm.math.dot(getattr(self, 'fc%d' % (layer_index - 1)), self.weight(layer_index)) + self.bias(layer_index)) )	


			# getting the precision / standard deviation / variance
			self.tau_rescaling = np.zeros((self.num_obs, self.network_input.shape[1]))
			for obs_index in range(self.num_obs):
				self.tau_rescaling[obs_index] += self.var_e_ranges
			self.tau_rescaling = self.tau_rescaling**2

			tau        = pm.Gamma('tau', self.num_obs**2, 1., shape = (self.num_obs, self.network_input.shape[1]))
			self.tau   = tau / self.tau_rescaling
			self.scale = pm.Deterministic('scale', 1. / pm.math.sqrt(self.tau))


			# learn the floats
			self.loc        = pm.Deterministic('loc', (self.upper_rescalings - self.lower_rescalings) * self._loc + self.lower_rescalings)
			self.out_floats = pm.Normal('out_floats', self.loc[:, self.floats], tau = self.tau[:, self.floats], observed = self.network_output[:, self._floats])


			# learn the integers
			self.int_scale = pm.Deterministic('int_scale', 1. * self.scale)
			self.out_ints  = DiscreteLaplace('out_ints', loc = self.loc[:, self.ints], scale = self.int_scale[:, self.ints], observed = self.network_output[:, self._ints])


			# learn the categories
			dist_counter, cat_var_index = 0, 0
			
			self.alpha = pm.Deterministic('alpha', (self.loc + 1.) * self.scale)
			self.num_cats = 0
			for var_e_index, var_e_type in enumerate(self.var_e_types):
				if var_e_type == 'categorical' and self.var_e_begin[var_e_index] == var_e_index:
					begin, end  = self.var_e_begin[var_e_index], self.var_e_end[var_e_index]
					var_e_name  = self.var_e_names[var_e_index]
					param_index = np.argwhere(self.var_p_names == var_e_name)[0, 0]
					self.param_index = param_index

					out_dirichlet = pm.Dirichlet('dirich_%d' % dist_counter, a = self.alpha[:, begin : end], shape = (self.num_obs, int(end - begin)) )
					out_cats      = pm.Categorical('out_cats_%d' % dist_counter, p = out_dirichlet, observed = self.network_output[:, param_index])
					self.num_cats += 1
					dist_counter += 1 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def _create_model_old(self):
		self._get_rescalings()

		with pm.Model() as self.model:

			# getting the location
			for layer_index in range(self.num_layers):
				setattr(self, 'w%d' % layer_index, self.__get_weights(layer_index, self.weight_shapes[layer_index]))
				setattr(self, 'b%d' % layer_index, self.__get_biases(layer_index, self.bias_shapes[layer_index]))

				if layer_index == 0:
					fc = pm.Deterministic('fc%d' % layer_index, pm.math.tanh(pm.math.dot(self.network_input, self.weight(layer_index)) + self.bias(layer_index)))
					setattr(self, 'fc%d' % layer_index, fc)
				elif 0 < layer_index < self.num_layers - 1:
					fc = pm.Deterministic('fc%d' % layer_index, pm.math.tanh(pm.math.dot(getattr(self, 'fc%d' % (layer_index - 1)), self.weight(layer_index)) + self.bias(layer_index)))
					setattr(self, 'fc%d' % layer_index, fc)
				else:
					self.loc = pm.Deterministic('loc', (self.upper_rescalings - self.lower_rescalings) * pm.math.sigmoid(pm.math.dot(getattr(self, 'fc%d' % (layer_index - 1)), self.weight(layer_index)) + self.bias(layer_index)) + self.lower_rescalings)



			# getting the standard deviation (or rather precision)
			self.tau_rescaling = np.zeros((self.num_obs, self.observed_params.shape[1]))
			for obs_index in range(self.num_obs):
				self.tau_rescaling[obs_index] += self.domain_ranges
			self.tau_rescaling = self.tau_rescaling**2
			self.tau = pm.Gamma('tau', self.num_obs**2, 1., shape = (self.num_obs, self.observed_params.shape[1]))
			self.tau = self.tau / self.tau_rescaling
#			self.sd  = pm.Deterministic('sd', 0.05 + 1. / pm.math.sqrt(self.tau))
			self.scale  = pm.Deterministic('scale', 1. / pm.math.sqrt(self.tau))



			print(self.observed_params.shape)
			print(self._floats)
			print(self._integers)
			quit()

			# now that we got all locations and scales we can start getting the distributions


			# floats are easy, as we can take loc and scale as they are
			self.out = pm.Normal('out', self.loc, tau = self.tau, observed = self.observed_params)

			# integers are a bit more tricky and require the following transformation for the beta binomial
			alpha = ((n - mu) / sigma**2 - 1) / (n / mu - (n - mu) / sigma**2)
			beta  = (n / mu - 1) * alpha
			self.alpha = pm.Deterministic('alpha', alpha)
			self.beta  = pm.Deterministic('beta', beta) 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def get_formula(
            self, input_rvs, fixed_rvs, hyperparams, problem_config):
        """
        Get geodetic likelihood formula for the model built. Has to be called
        within a with model context.
        Part of the pymc3 model.

        Parameters
        ----------
        input_rvs : dict
            of :class:`pymc3.distribution.Distribution`
        fixed_rvs : dict
            of :class:`numpy.array`
        hyperparams : dict
            of :class:`pymc3.distribution.Distribution`
        problem_config : :class:`config.ProblemConfig`

        Returns
        -------
        posterior_llk : :class:`theano.tensor.Tensor`
        """
        hp_specific = self.config.dataset_specific_residual_noise_estimation

        self.input_rvs = input_rvs
        self.fixed_rvs = fixed_rvs

        logger.info(
            'Geodetic optimization on: \n '
            '%s' % ', '.join(self.input_rvs.keys()))

        self.input_rvs.update(fixed_rvs)

        t0 = time()
        disp = self.get_synths(self.input_rvs)
        t1 = time()
        logger.debug(
            'Geodetic forward model on test model takes: %f' %
            (t1 - t0))

        los_disp = (disp * self.slos_vectors).sum(axis=1)

        residuals = self.Bij.srmap(
            tt.cast((self.sdata - los_disp) * self.sodws, tconfig.floatX))

        self.init_hierarchicals(problem_config)
        if len(self.hierarchicals) > 0:
            residuals = self.remove_ramps(residuals)

        logpts = multivariate_normal_chol(
            self.datasets, self.weights, hyperparams, residuals,
            hp_specific=hp_specific)

        llk = Deterministic(self._like_name, logpts)
        return llk.sum() 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def impute(self, X):
        """Generate imputations using predictions from the fit bayesian model.

        The transform method returns the values for imputation. Missing values
        in a given dataset are replaced with the samples from the posterior
        predictive distribution of each missing data point.

        Args:
            X (pd.DataFrame): predictors to determine imputed values.

        Returns:
            np.array: imputed dataset.
        """
        # check if fitted then predict with least squares
        check_is_fitted(self, "statistics_")
        model = self.statistics_["param"]

        # add a Deterministic node for each missing value
        # sampling then pulls from the posterior predictive distribution
        # each missing data point. I.e. distribution for EACH missing
        with model:
            mu_pred = pm.Deterministic(
                "mu_pred", model["alpha"]+model["beta"].dot(X.T)
            )
            tr = pm.sample(
                self.sample,
                tune=self.tune,
                init=self.init,
                **self.sample_kwargs
            )
        self.trace_ = tr

        # decide how to impute. Use mean of posterior predictive or random draw
        # not supported yet, but eventually consider using the MAP
        if not self.fill_value or self.fill_value == "mean":
            imp = tr["mu_pred"].mean(0)
        elif self.fill_value == "random":
            imp = np.apply_along_axis(np.random.choice, 0, tr["mu_pred"])
        else:
            err = f"{self.fill_value} must be 'mean' or 'random'."
            raise ValueError(err)
        return imp 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def constant_data_to_xarray(self):
        """Convert constant data to xarray."""
        # For constant data, we are concerned only with deterministics and data.
        # The constant data vars must be either pm.Data (TensorSharedVariable) or pm.Deterministic
        constant_data_vars = {}  # type: Dict[str, Var]
        for var in self.model.deterministics:
            ancestors = self.theano.tensor.gof.graph.ancestors(var.owner.inputs)
            # no dependency on a random variable
            if not any((isinstance(a, self.pymc3.model.PyMC3Variable) for a in ancestors)):
                constant_data_vars[var.name] = var

        def is_data(name, var) -> bool:
            assert self.model is not None
            return (
                var not in self.model.deterministics
                and var not in self.model.observed_RVs
                and var not in self.model.free_RVs
                and var not in self.model.potentials
                and (self.observations is None or name not in self.observations)
            )

        # I don't know how to find pm.Data, except that they are named variables that aren't
        # observed or free RVs, nor are they deterministics, and then we eliminate observations.
        for name, var in self.model.named_vars.items():
            if is_data(name, var):
                constant_data_vars[name] = var

        if not constant_data_vars:
            return None
        if self.dims is None:
            dims = {}
        else:
            dims = self.dims
        constant_data = {}
        for name, vals in constant_data_vars.items():
            if hasattr(vals, "get_value"):
                vals = vals.get_value()
            # this might be a Deterministic, and must be evaluated
            elif hasattr(self.model[name], "eval"):
                vals = self.model[name].eval()
            vals = np.atleast_1d(vals)
            val_dims = dims.get(name)
            val_dims, coords = generate_dims_coords(
                vals.shape, name, dims=val_dims, coords=self.coords
            )
            # filter coords based on the dims
            coords = {key: xr.IndexVariable((key,), data=coords[key]) for key in val_dims}
            try:
                constant_data[name] = xr.DataArray(vals, dims=val_dims, coords=coords)
            except ValueError as e:  # pylint: disable=invalid-name
                raise ValueError("Error translating constant_data variable %s: %s" % (name, e))
        return xr.Dataset(data_vars=constant_data, attrs=make_attrs(library=self.pymc3)) 

# 需要导入模块: import pymc3 [as 别名]
# 或者: from pymc3 import Deterministic [as 别名]
def fit_cross_cov(self, n_exp=2, n_gauss=2, range_mu=None):
        """
        Fit an analytical covariance to the experimental data.
        Args:
            n_exp (int): number of exponential basic functions
            n_gauss (int): number of gaussian basic functions
            range_mu: prior mean of the range. Default mean of the lags

        Returns:
            pymc.Model: PyMC3 model to be sampled using MCMC
        """
        self.n_exp = n_exp
        self.n_gauss = n_gauss
        n_var = self.n_properties
        df = self.exp_var
        lags = self.lags

        # Prior standard deviation for the error of the regression
        prior_std_reg = df.std(0).max() * 10

        # Prior value for the mean of the ranges
        if not range_mu:
            range_mu = lags.mean()

        # pymc3 Model
        with pm.Model() as model:  # model specifications in PyMC3 are wrapped in a with-statement
            # Define priors
            sigma = pm.HalfCauchy('sigma', beta=prior_std_reg, testval=1., shape=n_var)

            psill = pm.Normal('sill', prior_std_reg, sd=.5 * prior_std_reg, shape=(n_exp + n_gauss))
            range_ = pm.Normal('range', range_mu, sd=range_mu * .3, shape=(n_exp + n_gauss))

            lambda_ = pm.Uniform('weights', 0, 1, shape=(n_var * (n_exp + n_gauss)))

            # Exponential covariance
            exp = pm.Deterministic('exp',
                                   # (lambda_[:n_exp*n_var]*
                                   psill[:n_exp] *
                                   (1. - T.exp(T.dot(-lags.values.reshape((len(lags), 1)),
                                                     (range_[:n_exp].reshape((1, n_exp)) / 3.) ** -1))))

            gauss = pm.Deterministic('gaus',
                                     psill[n_exp:] *
                                     (1. - T.exp(T.dot(-lags.values.reshape((len(lags), 1)) ** 2,
                                                       (range_[n_exp:].reshape((1, n_gauss)) * 4 / 7.) ** -2))))

            # We stack the basic functions in the same matrix and tile it to match the number of properties we have
            func = pm.Deterministic('func', T.tile(T.horizontal_stack(exp, gauss), (n_var, 1, 1)))

            # We weight each basic function and sum them
            func_w = pm.Deterministic("func_w", T.sum(func * lambda_.reshape((n_var, 1, (n_exp + n_gauss))), axis=2))

            for e, cross in enumerate(df.columns):
                # Likelihoods
                pm.Normal(cross + "_like", mu=func_w[e], sd=sigma[e], observed=df[cross].values)
        return model