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Updated docstring for Potential function #6559

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87 changes: 83 additions & 4 deletions pymc/model.py
Original file line number Diff line number Diff line change
Expand Up @@ -2042,16 +2042,95 @@ def Deterministic(name, var, model=None, dims=None):


def Potential(name, var, model=None):
"""Add an arbitrary factor potential to the model likelihood
"""
Add an arbitrary factor potential to the model likelihood

The Potential function is used to add arbitrary factors (such as constraints or other likelihood components) to adjust the probability density of the model.

Warnings
--------
Potential functions only influence logp based sampling, like the one used by ``pm.sample``.
Potentials, modify the log-probability of the model by adding a contribution to the logp which is used by sampling algorithms which rely on the information about the observed data to generate posterior samples.
Potentials are not applicable in the context of forward sampling because they don't affect the prior distribution itself, only the computation of the logp.
Forward sampling algorithms generate sample points from the prior distribution of the model, without taking into account the likelihood function.
In other words, it does not use the information about the observed data.
Hence, Potentials do not affect forward sampling, which is used by ``sample_prior_predictive`` and ``sample_posterior_predictive``.
A warning saying "The effect of Potentials on other parameters is ignored during prior predictive sampling" is always emitted to alert user of this.

Parameters
----------
name: str
var: PyTensor variables
name : str
Name of the potential variable to be registered in the model.
var : tensor_like
Expression to be added to the model joint logp.
model : Model, optional
The model object to which the potential function is added.
If ``None`` is provided, the current model is used.

Returns
-------
var: var, with name attribute
var : tensor_like
The registered, named model variable.

Examples
--------
Have a look at the following example:

In this example, we define a constraint on ``x`` to be greater or equal to 0 via the ``pm.Potential`` function.
We pass ``-pm.math.log(pm.math.switch(constraint, 1, 0))`` as second argument which will return an expression depending on if the constraint is met or not and which will be added to the likelihood of the model.
The probablity density that this model produces agrees strongly with the constraint that ``x`` should be greater than or equal to 0. All the cases who do not satisfy the constraint are strictly not considered.

.. code:: python

with pm.Model() as model:
x = pm.Normal("x", mu=0, sigma=1)
y = pm.Normal("y", mu=x, sigma=1, observed=data)
constraint = x >= 0
potential = pm.Potential("x_constraint", pm.math.log(pm.math.switch(constraint, 1, 0.0)))

However, if we use ``-pm.math.log(pm.math.switch(constraint, 1, 0.5))`` the potential again penalizes the likelihood when constraint is not met but with some deviations allowed.
Here, Potential function is used to pass a soft constraint.
A soft constraint is a constraint that is only partially satisfied.
The effect of this is that the posterior probability for the parameters decreases as they move away from the constraint, but does not become exactly zero.
This allows the sampler to generate values that violate the constraint, but with lower probability.

.. code:: python

with pm.Model() as model:
x = pm.Normal("x", mu=0.1, sigma=1)
y = pm.Normal("y", mu=x, sigma=1, observed=data)
constraint = x >= 0
potential = pm.Potential("x_constraint", pm.math.log(pm.math.switch(constraint, 1, 0.5)))

In this example, Potential is used to obtain an arbitrary prior.
This prior distribution refers to the prior knowledge that the values of ``max_items`` are likely to be small rather than being large.
The prior probability of ``max_items`` is defined using a Potential object with the log of the inverse of ``max_items`` as its value.
This means that larger values of ``max_items`` have a lower prior probability density, while smaller values of ``max_items`` have a higher prior probability density.
When the model is sampled, the posterior distribution of ``max_items`` given the observed value of ``n_items`` will be influenced by the power-law prior defined in the Potential object

.. code:: python

with pm.Model():
# p(max_items) = 1 / max_items
max_items = pm.Uniform("max_items", lower=1, upper=100)
pm.Potential("power_prior", pm.math.log(1/max_items))

n_items = pm.Uniform("n_items", lower=1, upper=max_items, observed=60)

In the next example, the ``soft_sum_constraint`` potential encourages ``x`` and ``y`` to have a small sum, effectively adding a soft constraint on the relationship between the two variables.
This can be useful in cases where you want to ensure that the sum of multiple variables stays within a certain range, without enforcing an exact value.
In this case, the larger the deviation, larger will be the negative value (-((x + y)**2)) which the MCMC sampler will attempt to minimize.
However, the sampler might generate values for some small deviations but with lower probability hence this is a soft constraint.

.. code:: python

with pm.Model() as model:
x = pm.Normal("x", mu=0.1, sigma=1)
y = pm.Normal("y", mu=x, sigma=1, observed=data)
soft_sum_constraint = pm.Potential("soft_sum_constraint", -((x + y)**2))

The potential value is incorporated into the model log-probability, so it should be -inf (or very negative) when a constraint is violated, so that those draws are rejected. 0 won't have any effect and positive values will make the proposals more likely to be accepted.

"""
model = modelcontext(model)
var.name = model.name_for(name)
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