Basic Concepts in ZhuSuan


Distributions are basic functionalities for building probabilistic models. The Distribution class is the base class for various probabilistic distributions which support batch inputs, generating batches of samples and evaluate probabilities at batches of given values.

The list of all available distributions can be found on these pages:

We can create a univariate Normal distribution in ZhuSuan by:

>>> import zhusuan as zs
>>> a = zs.distributions.Normal(mean=0., logstd=0.)

The typical input shape for a Distribution is like batch_shape + input_shape, where input_shape represents the shape of a non-batch input parameter; batch_shape represents how many independent inputs are fed into the distribution. In general, distributions support broadcasting for inputs.

Samples can be generated by calling sample() method of distribution objects. The shape is ([n_samples] + )batch_shape + value_shape. The first additional axis is omitted only when passed n_samples is None (by default), in which case one sample is generated. value_shape is the non-batch value shape of the distribution. For a univariate distribution, its value_shape is [].

An example of univariate distributions (Normal):

>>> import tensorflow as tf
>>> _ = tf.InteractiveSession()

>>> b = zs.distributions.Normal([[-1., 1.], [0., -2.]], [0., 1.])

>>> b.batch_shape.eval()
array([2, 2], dtype=int32)

>>> b.value_shape.eval()
array([], dtype=int32)

>>> tf.shape(b.sample()).eval()
array([2, 2], dtype=int32)

>>> tf.shape(b.sample(1)).eval()
array([1, 2, 2], dtype=int32)

>>> tf.shape(b.sample(10)).eval()
array([10,  2,  2], dtype=int32)

and an example of multivariate distributions (OnehotCategorical):

>>> c = zs.distributions.OnehotCategorical([[0., 1., -1.],
...                                         [2., 3., 4.]])

>>> c.batch_shape.eval()
array([2], dtype=int32)

>>> c.value_shape.eval()
array([3], dtype=int32)

>>> tf.shape(c.sample()).eval()
array([2, 3], dtype=int32)

>>> tf.shape(c.sample(1)).eval()
array([1, 2, 3], dtype=int32)

>>> tf.shape(c.sample(10)).eval()
array([10,  2,  3], dtype=int32)

There are cases where a batch of random variables are grouped into a single event so that their probabilities can be computed together. This is achieved by setting group_ndims argument, which defaults to 0. The last group_ndims number of axes in batch_shape are grouped into a single event. For example, Normal(..., group_ndims=1) will set the last axis of its batch_shape to a single event, i.e., a multivariate Normal with identity covariance matrix.

The log probability density (mass) function can be evaluated by passing given values to log_prob() method of distribution objects. In that case, the given Tensor should be broadcastable to shape (... + )batch_shape + value_shape. The returned Tensor has shape (... + )batch_shape[:-group_ndims]. For example:

>>> d = zs.distributions.Normal([[-1., 1.], [0., -2.]], 0.,
...                             group_ndims=1)

>>> d.log_prob(0.).eval()
array([-2.83787704, -3.83787727], dtype=float32)

>>> e = zs.distributions.Normal(tf.zeros([2, 1, 3]), 0.,
...                             group_ndims=2)

>>> tf.shape(e.log_prob(tf.zeros([5, 1, 1, 3]))).eval()
array([5, 2], dtype=int32)


In ZhuSuan we support building probabilistic models as Bayesian networks, i.e., directed graphical models. Below we use a simple Bayesian linear regression example to illustrate this. The generative process of the model is

\[ \begin{align}\begin{aligned}w &\sim N(0, \alpha^2 I)\\y &\sim N(w^\top x, \beta^2)\end{aligned}\end{align} \]

where \(x\) denotes the input feature in the linear regression. We apply a Bayesian treatment and assume a Normal prior distribution of the regression weights \(w\). Suppose the input feature has 5 dimensions. For simplicity we define the input as a placeholder and fix the hyper-parameters:

x = tf.placeholder(tf.float32, shape=[5])
alpha = 1.
beta = 0.1

To define the model, the first step is to construct a BayesianNet instance:

bn = zs.BayesianNet()

A Bayesian network describes the dependency structure of the joint distribution over a set of random variables as directed graphs. To support this, a BayesianNet instance can keep two kinds of nodes:

  • Stochastic nodes. They are random variables in graphical models. The w node can be constructed as:

    w = bn.normal("w", tf.zeros([x.shape[-1]], std=alpha)

    Here w is a StochasticTensor that follows the Normal distribution:

    >>> print(w)
    < object at ...

    For any distribution available in zhusuan.distributions, we can find a method of BayesianNet for creating the corresponding stochastic node. The returned StochasticTensor instances are Tensor-like, which means that you can mix them with almost any Tensorflow primitives, for example, the predicted mean of the linear regression is an inner product between w and the input x:

    y_mean = tf.reduce_sum(w * x, axis=-1)
  • Deterministic nodes. As the above code shows, deterministic nodes can be constructed directly with Tensorflow operations, and in this way BayesianNet does not keep track of them. However, in some cases it’s convenient to enable the tracking by the deterministic() method:

    y_mean = bn.deterministic("y_mean", tf.reduce_sum(w * x, axis=-1))

    This allows you to fetch the y_mean Tensor from bn whenever you want it.

The full code of building a Bayesian linear regression model is like:

def bayesian_linear_regression(x, alpha, beta):
    bn = zs.BayesianNet()
    w = bn.normal("w", mean=0., std=alpha)
    y_mean = tf.reduce_sum(w * x, axis=-1)
    bn.normal("y", y_mean, std=beta)
    return bn

A unique feature of graphical models is that stochastic nodes are allowed to have undetermined behaviour (i.e., being latent), and we can observe them at any time (then they are fixed to the observations). In ZhuSuan, the BayesianNet can be initialized with a dictionary argument observed to assign observations to certain stochastic nodes, for example:

bn = zs.BayesianNet(observed={"w": w_obs})

will cause the random variable \(w\) to be observed as w_obs. The result is that in bn, y_mean is computed from the observed value of w (w_obs). For stochastic nodes that are not given observations, their samples will be used when the corresponding StochasticTensor is involved in computation with Tensors or fed into Tensorflow operations. In this example it means that if we don’t pass any observation to bn, the samples of w will be used to compute y_mean.

Although the above approach allows assigning observations to stochastic nodes, in most common cases, it is more convenient to first define the graphical model, and then pass observations whenever needed. Besides, the model should allow queries with different configurations of observations. To enable this workflow, we introduce a new class MetaBayesianNet. Conceptually we can view MetaBayesianNet instances as the original model and BayesianNet as the result of certain observations. As we shall see, BayesianNet instances can be lazily constructed from its meta class instance.

We made it very easy to define the model as a MetaBayesianNet. There is no change to the above code but just adding a decorator to the function:

def bayesian_linear_regression(x, alpha, beta):
    bn = zs.BayesianNet()
    w = bn.normal("w", mean=0., std=alpha)
    y_mean = tf.reduce_sum(w * x, axis=-1)
    bn.normal("y", y_mean, std=beta)
    return bn

The function decorated by zs.meta_bayesian_net() will return a MetaBayesianNet instead of the original BayesianNet instance:

>>> model = bayesian_linear_regression(x, alpha, beta)

>>> print(model)
<zhusuan.framework.meta_bn.MetaBayesianNet object at ...

As we have mentioned, MetaBayesianNet can allow different configurations of observations. This is achieved by its observe() method. We could pass observations as named arguments, and it will return a corresponding BayesianNet instance, for example:

bn = model.observe(w=w_obs)

will set w to be observed in the returned BayesianNet instance bn. Calling the above function with different named arguments instantiates the BayesianNet with different observations, which resembles the common behaviour of probabilistic graphical models.


The observation passed must have the same type and shape as the StochasticTensor.

If there are tensorflow Variables created in a model construction function, you may want to reuse them for BayesianNet instances with different observations. There is another decorator in ZhuSuan named reuse_variables() to make this convenient. You could add it to any function that creates Tensorflow variables:

def build_model(...):
    bn = zs.BayesianNet()
    return bn

or equivalently, switch on the reuse_variables option in the zs.meta_bayesian_net() decorator:

@zs.meta_bayesian_net(scope="model", reuse_variables=True)
def build_model(...):
    bn = zs.BayesianNet()
    return bn

Up to now we know how to construct a model and reuse it for different observations. After construction, BayesianNet supports queries about the current state of the network, such as:

# get named node(s)
w = bn["w"]
w, y = bn.get(["w", "y"])

# get log probabilities of stochastic nodes conditioned on the current
# value of other StochasticTensors.
log_pw, log_py = bn.cond_log_prob(["w", "y"])

# get log joint probability given the current values of all stochastic
# nodes
log_joint_value = bn.log_joint()

By default the log joint probability is computed by summing over conditional log probabilities at all stochastic nodes. This requires that the distribution batch shapes of all stochastic nodes are correctly aligned. If not, the returned value can be arbitrary. Most of the time you can adjust the group_ndims parameter of the stochastic nodes to fix this. If that’s not the case, we still allow customizing the log joint probability function by rewriting it in the MetaBayesianNet instance like:

meta_bn = build_linear_regression(x, alpha, beta)

def customized_log_joint(bn):
    return tf.reduce_sum(
        bn.cond_log_prob("w"), axis=-1) + bn.cond_log_prob("y")

meta_bn.log_joint = customized_log_joint

then all BayesianNet instances constructed from this meta_bn will use the provided customized function to compute the result of bn.log_joint().