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.. currentmodule:: qinfer

Sequential Monte Carlo

Introduction

Arguably the core of QInfer, the :mod:`qinfer.smc` module implements the sequential Monte Carlo algorithm in a flexible and robust manner. At its most basic, using QInfer's SMC implementation consists of specifying a model, a prior, and a number of SMC particles to use.

The main component of QInfer's SMC support is the :class:`SMCUpdater` class, which performs Bayesian updates on a given prior in response to new data. In doing so, :class:`SMCUpdater` will also ensure that the posterior particles are properly resampled. For more details on the SMC algorithm as implemented by QInfer, please see [GFWC12]_.

Using :class:`SMCUpdater`

Creating and Configuring Updaters

The most straightfoward way of creating an :class:`SMCUpdater` instance is to provide a model, a number of SMC particles and a prior distribution to choose those particles from. Using the example of a :class:`SimplePrecessionModel`, and a uniform prior \omega \sim \text{Uni}(0, 1):

>>> from qinfer import SMCUpdater, UniformDistribution, SimplePrecessionModel
>>> model = SimplePrecessionModel()
>>> prior = UniformDistribution([0, 1])
>>> updater = SMCUpdater(model, 1000, prior)

Updating from Data

Once an updater has been created, one can then use it to update the prior distribution to a posterior conditioned on experimental data. For example,

>>> true_model = prior.sample()
>>> experiment = np.array([12.1], dtype=model.expparams_dtype)
>>> outcome = model.simulate_experiment(true_model, experiment)
>>> updater.update(outcome, experiment)

Drawing Posterior Samples and Estimates

Since :class:`SMCUpdater` inherits from :class:`Distribution`, it can be sampled in the same way described in :ref:`distributions_guide`.

>>> posterior_samples = updater.sample(n=100)
>>> posterior_samples.shape == (100, 1)
True

More commonly, however, one will want to calculate estimates such as \hat{\vec{x}} = \mathbb{E}_{\vec{x}|\text{data}}[\vec{x}]. These estimates are given methods such as :meth:`~SMCUpdater.est_mean` and :meth:`~SMCUpdater.est_covariance_mtx`.

>>> est = updater.est_mean()
>>> print(est)# doctest: +SKIP
[ 0.53147953]

Plotting Posterior Distributions

The :class:`SMCUpdater` also provides tools for producing plots to describe the updated posterior. For instance, the :meth:`~SMCUpdater.plot_posterior_marginal` method uses kernel density estimation to plot the marginal over all but a single parameter over the posterior.

.. plot::

    prior = UniformDistribution([0, 1])
    model = SimplePrecessionModel()
    updater = SMCUpdater(model, 2000, prior)

    # Plot according to the initial prior.
    updater.plot_posterior_marginal()

    # Simulate 50 different measurements and use
    # them to update.
    true = prior.sample()
    heuristic = ExpSparseHeuristic(updater)

    for idx_exp in range(25):
        expparams = heuristic()
        datum = model.simulate_experiment(true, expparams)
        updater.update(datum, expparams)

    # Plot the posterior.
    updater.plot_posterior_marginal()

    # Add a legend and show the final plot.
    plt.legend(['Prior', 'Posterior'])
    plt.show()

For multi-parameter models, the :meth:`~SMCUpdater.plot_covariance` method plots the covariance matrix for the current posterior as a Hinton diagram. That is, positive elements are shown as white squares, while negative elements are shown as black squares. The relative sizes of each square indicate the magnitude, making it easy to quickly identify correlations that impact estimator performance. In the example below, we use the :ref:`simple_est_guide` to quickly analyze :ref:`rb_guide` data and show the resulting correlation between the p, A and B parameters. For more detail, please see the randomized benchmarking example.

.. plot::

    p = 0.995
    A = 0.5
    B = 0.5

    ms = np.linspace(1, 800, 201).astype(int)
    signal = A * p ** ms + B

    n_shots = 25
    counts = np.random.binomial(p=signal, n=n_shots)

    data = np.column_stack([counts, ms, n_shots * np.ones_like(counts)])
    mean, cov, extra = simple_est_rb(data, return_all=True, n_particles=12000, p_min=0.8)
    extra['updater'].plot_covariance()

    plt.show()



Advanced Usage

Custom Resamplers

By default, :class:`SMCUpdater` uses the Liu and West resampling algorithm [LW01]_ with a = 0.98. The resampling behavior can be controlled, however, by passing resampler objects to :class:`SMCUpdater`. For instance, if one wants to create an updater with a = 0.9 as was suggested by [WGFC13a]_:

>>> from qinfer import LiuWestResampler
>>> updater = SMCUpdater(model, 1000, prior, resampler=LiuWestResampler(0.9))

This causes the resampling procedure to more aggressively approximate the posterior as a Gaussian distribution, and can allow for a much smaller number of particles to be used when the Gaussian approximation is accurate. For multimodal problems, it can make sense to relax the requirement that the resampler preserve the mean and covariance, and to instead allow the resampler to increase the uncertianty. For instance, the modified Liu-West resampler a = 1 and h = 0.005 can accurately find exactly degenrate peaks in precession models [Gra15]_.

Posterior Credible Regions

Posterior credible regions can be found by using the :meth:`~SMCUpdater.est_credible_region` method. This method returns a set of points \{\vec{x}_i'\} such that the sum \sum_i w_i' of the corresponding weights \{w_i'\} is at least a specified ratio of the total weight.

This does not admit a very compact description, however, such that it is useful to find region estimators \hat{X} containing all of the particles describing a credible region, as above.

The :meth:`~SMCUpdater.region_est_hull` method does this by finding a convex hull of the credible particles, while :meth:`~SMCUpdater.region_est_ellipsoid` finds the minimum-volume enclosing ellipse (MVEE) of the convex hull region estimator.

The derivation of these estimators, as well as a detailed discussion of their performances, can be found in [GFWC12]_ and [Fer14]_.

Online Bayesian Cramer-Rao Bound Estimation

TODO

Model Selection with Bayes Factors

When considering which of two models A or B best explains a data record D, the normalizations of SMC updates of the posterior conditoned on each provide the probabilities \Pr(D | A) and \Pr(D | B). The normalization records can be obtained from the :attr:`~SMCUpdater.normalization_record` properties of each. As the probabilities of any individual data record quickly reach zero, however, it becomes numerically unstable to consider these probabilities directly. Instead, the property :attr:`~SMCUpdater.log_total_likelihood` records the quantity

\ell(D | M) = \sum_i \log \Pr(d_i | M)

for M \in \{A, B\}. This is related to the Bayes factor f by

f = \exp(\ell(D | A) - \ell(D | B)).

As discussed in [WGFC13b]_, the Bayes factor tells which of the two models under consideration is to be preferred as an explanation for the observed data.