Sequential Monte Carlo¶
SMCUpdater
 SMCBased Particle Updater¶
Class Reference¶

class
qinfer.
SMCUpdater
(model, n_particles, prior, resample_a=None, resampler=None, resample_thresh=0.5, debug_resampling=False, track_resampling_divergence=False, zero_weight_policy=u'error', zero_weight_thresh=None, canonicalize=True)[source]¶ Bases:
qinfer.distributions.ParticleDistribution
Creates a new Sequential Monte carlo updater, using the algorithm of [GFWC12].
Parameters:  model (Model) – Model whose parameters are to be inferred.
 n_particles (int) – The number of particles to be used in the particle approximation.
 prior (Distribution) – A representation of the prior distribution.
 resampler (callable) – Specifies the resampling algorithm to be used. See Resampling Algorithms for more details.
 resample_thresh (float) – Specifies the threshold for \(N_{\text{ess}}\) to decide when to resample.
 debug_resampling (bool) – If
True
, debug information will be generated on resampling performance, and will be written to the standard Python logger.  track_resampling_divergence (bool) – If true, then the divergences
between the pre and postresampling distributions are tracked and
recorded in the
resampling_divergences
attribute.  zero_weight_policy (str) – Specifies the action to be taken when the
particle weights would all be set to zero by an update.
One of
["ignore", "skip", "warn", "error", "reset"]
.  zero_weight_thresh (float) – Value to be used when testing for the zeroweight condition.
 canonicalize (bool) – If
True
, particle locations will be updated to canonical locations as described by the model class after each prior sampling and resampling.

resample_count
¶ Returns the number of times that the updater has resampled the particle approximation.
Type: int

just_resampled
¶ True
if and only if there has been no data added since the last resampling, or if there has not yet been a resampling step.Type: bool

log_total_likelihood
¶ Returns the loglikelihood of all the data collected so far.
Equivalent to:
np.sum(np.log(updater.normalization_record))
Type: float

min_n_ess
¶ Returns the smallest effective sample size (ESS) observed in the history of this updater.
Type: float
Returns: The minimum of observed effective sample sizes as reported by n_ess
.

resampling_divergences
¶ List of KL divergences between the pre and postresampling distributions, if that is being tracked. Otherwise,
None
.Type: list
offloat
orNone

reset
(n_particles=None, only_params=None, reset_weights=True)[source]¶ Causes all particle locations and weights to be drawn fresh from the initial prior.
Parameters:

hypothetical_update
(outcomes, expparams, return_likelihood=False, return_normalization=False)[source]¶ Produces the particle weights for the posterior of a hypothetical experiment.
Parameters:  outcomes (int or an ndarray of dtype int.) – Integer index of the outcome of the hypothetical experiment.
 expparams (numpy.ndarray) – Experiments to be used for the hypothetical updates.
 weights (ndarray, shape (n_outcomes, n_expparams, n_particles)) – Weights assigned to each particle in the posterior distribution \(\Pr(\omega  d)\).

update
(outcome, expparams, check_for_resample=True)[source]¶ Given an experiment and an outcome of that experiment, updates the posterior distribution to reflect knowledge of that experiment.
After updating, resamples the posterior distribution if necessary.
Parameters:  outcome (int) – Label for the outcome that was observed, as defined
by the
Model
instance under study.  expparams (
ndarray
of dtype given by theexpparams_dtype
property of the underlying model) – Parameters describing the experiment that was performed.  check_for_resample (bool) – If
True
, after performing the update, the effective sample size condition will be checked and a resampling step may be performed.
 outcome (int) – Label for the outcome that was observed, as defined
by the

batch_update
(outcomes, expparams, resample_interval=5)[source]¶ Updates based on a batch of outcomes and experiments, rather than just one.
Parameters:  outcomes (numpy.ndarray) – An array of outcomes of the experiments that were performed.
 expparams (numpy.ndarray) – Either a scalar or record singleindex array of experiments that were performed.
 resample_interval (int) – Controls how often to check whether \(N_{\text{ess}}\) falls below the resample threshold.

bayes_risk
(expparams)[source]¶ Calculates the Bayes risk for a hypothetical experiment, assuming the quadratic loss function defined by the current model’s scale matrix (see
qinfer.abstract_model.Simulatable.Q
).Parameters: expparams ( ndarray
of dtype given by the current model’sexpparams_dtype
property, and of shape(1,)
) – The experiment at which to compute the Bayes risk.Return float: The Bayes risk for the current posterior distribution of the hypothetical experiment expparams
.

expected_information_gain
(expparams)[source]¶ Calculates the expected information gain for a hypothetical experiment.
Parameters: expparams ( ndarray
of dtype given by the current model’sexpparams_dtype
property, and of shape(1,)
) – The experiment at which to compute expected information gain.Return float: The Bayes risk for the current posterior distribution of the hypothetical experiment expparams
.

posterior_marginal
(idx_param=0, res=100, smoothing=0, range_min=None, range_max=None)[source]¶ Returns an estimate of the marginal distribution of a given model parameter, based on taking the derivative of the interpolated cdf.
Parameters:  idx_param (int) – Index of parameter to be marginalized.
 res1 (int) – Resolution of of the axis.
 smoothing (float) – Standard deviation of the Gaussian kernel used to smooth; same units as parameter.
 range_min (float) – Minimum range of the output axis.
 range_max (float) – Maximum range of the output axis.
See also

plot_posterior_marginal
(idx_param=0, res=100, smoothing=0, range_min=None, range_max=None, label_xaxis=True, other_plot_args={}, true_model=None)[source]¶ Plots a marginal of the requested parameter.
Parameters:  idx_param (int) – Index of parameter to be marginalized.
 res1 (int) – Resolution of of the axis.
 smoothing (float) – Standard deviation of the Gaussian kernel used to smooth; same units as parameter.
 range_min (float) – Minimum range of the output axis.
 range_max (float) – Maximum range of the output axis.
 label_xaxis (bool) – Labels the \(x\)axis with the model parameter name given by this updater’s model.
 other_plot_args (dict) – Keyword arguments to be passed to
matplotlib’s
plot
function.  true_model (np.ndarray) – Plots a given model parameter vector as the “true” model for comparison.
See also

plot_covariance
(corr=False, param_slice=None, tick_labels=None, tick_params=None)[source]¶ Plots the covariance matrix of the posterior as a Hinton diagram.
Note
This function requires that mpltools is installed.
Parameters:  corr (bool) – If
True
, the covariance matrix is first normalized by the outer product of the square root diagonal of the covariance matrix such that the correlation matrix is plotted instead.  param_slice (slice) – Slice of the modelparameters to be plotted.
 tick_labels (list) – List of tick labels for each component; by default, these are drawn from the model itself.
 corr (bool) – If

posterior_mesh
(idx_param1=0, idx_param2=1, res1=100, res2=100, smoothing=0.01)[source]¶ Returns a mesh, useful for plotting, of kernel density estimation of a 2D projection of the current posterior distribution.
Parameters:  idx_param1 (int) – Parameter to be treated as \(x\) when plotting.
 idx_param2 (int) – Parameter to be treated as \(y\) when plotting.
 res1 (int) – Resolution along the \(x\) direction.
 res2 (int) – Resolution along the \(y\) direction.
 smoothing (float) – Standard deviation of the Gaussian kernel used to smooth the particle approximation to the current posterior.
See also

plot_posterior_contour
(idx_param1=0, idx_param2=1, res1=100, res2=100, smoothing=0.01)[source]¶ Plots a contour of the kernel density estimation of a 2D projection of the current posterior distribution.
Parameters:  idx_param1 (int) – Parameter to be treated as \(x\) when plotting.
 idx_param2 (int) – Parameter to be treated as \(y\) when plotting.
 res1 (int) – Resolution along the \(x\) direction.
 res2 (int) – Resolution along the \(y\) direction.
 smoothing (float) – Standard deviation of the Gaussian kernel used to smooth the particle approximation to the current posterior.
See also