def softmax(dist, return_numpy=True):
""" Computes the softmax function on a set of values
"""
if utils.is_distribution(dist):
if dist.IS_AOA:
output = []
for i in range(len(dist.values)):
output[i] = softmax(dist.values[i], return_numpy=True)
output = utils.to_categorical(np.array(output))
else:
dist = np.copy(dist.values)
output = dist - dist.max(axis=0)
output = np.exp(output)
output = output / np.sum(output, axis=0)
if return_numpy:
return output
else:
return utils.to_categorical(output)
def softmax(dist, return_numpy=True):
"""
Computes the softmax function on a set of values
"""
dist = utils.to_numpy(dist)
output = []
if utils.is_arr_of_arr(dist):
for i in range(len(dist.values)):
output.append(softmax(dist[i]), return_numpy=True)
output = dist - dist.max(axis=0)
output = np.exp(output)
output = output / np.sum(output, axis=0)
if return_numpy:
return output
else:
return utils.to_categorical(output)
def update_posterior_states(A,
obs,
prior=None,
return_numpy=True,
method=FPI,
**kwargs):
"""
Update marginal posterior over hidden states using variational inference
Can optionally set message passing algorithm used for inference
Parameters
----------
- 'A' [numpy nd.array (matrix or tensor or array-of-arrays) or Categorical]:
Observation likelihood of the generative model, mapping from hidden states to observations
Used to invert generative model to obtain marginal likelihood over hidden states,
given the observation
- 'obs' [numpy 1D array, array of arrays (with 1D numpy array entries), int or tuple]:
The observation (generated by the environment). If single modality, this can be a 1D array
(one-hot vector representation) or an int (observation index)
If multi-modality, this can be an array of arrays (whose entries are 1D one-hot vectors)
or a tuple (of observation indices)
- 'prior' [numpy 1D array, array of arrays (with 1D numpy array entries), Categorical, or None]:
Prior beliefs about hidden states, to be integrated with the marginal likelihood to obtain
a posterior distribution.
If None, prior is set to be equal to a flat categorical distribution (at the level of
the individual inference functions).
(optional)
- 'return_numpy' [bool]:
True/False flag to determine whether the posterior is returned as a numpy array or a Categorical
- 'method' [str]:
Algorithm used to perform the variational inference.
Options: 'FPI' - Fixed point iteration
- http://www.cs.cmu.edu/~guestrin/Class/10708/recitations/r9/VI-view.pdf,
slides 13- 18
- http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.137.221&rep=rep1&type=pdf,
slides 24 - 38
'VMP - Variational message passing (not implemented)
'MMP' - Marginal message passing (not implemented)
'BP' - Belief propagation (not implemented)
'EP' - Expectation propagation (not implemented)
'CV' - CLuster variation method (not implemented)
- **kwargs:
List of keyword/parameter arguments corresponding to parameter values for the respective
variational inference algorithm
Returns
----------
- 'qs' [numpy 1D array, array of arrays (with 1D numpy array entries), or Categorical]:
Marginal posterior beliefs over hidden states
"""
# safe convert to numpy
A = utils.to_numpy(A)
# collect model dimensions
if utils.is_arr_of_arr(A):
n_factors = A[0].ndim - 1
n_states = list(A[0].shape[1:])
n_modalities = len(A)
n_observations = []
for m in range(n_modalities):
n_observations.append(A[m].shape[0])
else:
n_factors = A.ndim - 1
n_states = list(A.shape[1:])
n_modalities = 1
n_observations = [A.shape[0]]
obs = process_observations(obs, n_modalities, n_observations)
if prior is not None:
prior = process_priors(prior, n_factors)
if method is FPI:
qs = run_fpi(A, obs, n_observations, n_states, prior, **kwargs)
elif method is VMP:
raise NotImplementedError(f"{VMP} is not implemented")
elif method is MMP:
raise NotImplementedError(f"{MMP} is not implemented")
elif method is BP:
raise NotImplementedError(f"{BP} is not implemented")
elif method is EP:
raise NotImplementedError(f"{EP} is not implemented")
elif method is CV:
raise NotImplementedError(f"{CV} is not implemented")
else:
raise ValueError(f"{method} is not implemented")
if return_numpy:
return qs
else:
return utils.to_categorical(qs)
def get_expected_obs(qs_pi, A, return_numpy=False):
"""
Given a posterior predictive density Qs_pi and an observation likelihood model A,
get the expected observations given the predictive posterior.
Parameters
----------
qs_pi [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array), Categorical
(either single-factor or AoA), or list]:
Posterior predictive density over hidden states. If a list, each entry of the list is the
posterior predictive for a given timepoint of an expected trajectory
A [numpy nd-array, array-of-arrays (where each entry is a numpy nd-array), or Categorical
(either single-factor of AoA)]:
Observation likelihood mapping from hidden states to observations, with different modalities
(if there are multiple) stored in different arrays
return_numpy [Boolean]:
True/False flag to determine whether output of function is a numpy array or a Categorical
Returns
-------
qo_pi [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array), Categorical
(either single-factor or AoA), or list]:
Expected observations under the given policy. If a list, a list of the expected observations
over the time horizon of policy evaluation, where
each entry is the expected observations at a given timestep.
"""
# initialise expected observations
qo_pi = []
A = utils.to_numpy(A)
if isinstance(qs_pi, list):
n_steps = len(qs_pi)
for t in range(n_steps):
qs_pi[t] = utils.to_numpy(qs_pi[t], flatten=True)
else:
n_steps = 1
qs_pi = [utils.to_numpy(qs_pi, flatten=True)]
if utils.is_arr_of_arr(A):
num_modalities = len(A)
for t in range(n_steps):
qo_pi_t = np.empty(num_modalities, dtype=object)
qo_pi.append(qo_pi_t)
# get expected observations over time
for t in range(n_steps):
for modality in range(num_modalities):
qo_pi[t][modality] = spm_dot(A[modality], qs_pi[t])
else:
# get expected observations over time
for t in range(n_steps):
qo_pi.append(spm_dot(A, qs_pi[t]))
if return_numpy:
if n_steps == 1:
return qo_pi[0]
else:
return qo_pi
else:
if n_steps == 1:
return utils.to_categorical(qo_pi[0])
else:
for t in range(n_steps):
qo_pi[t] = utils.to_categorical(qo_pi[t])
return qo_pi
def update_posterior_policies(
qs,
A,
B,
C,
policies,
use_utility=True,
use_states_info_gain=True,
use_param_info_gain=False,
pA=None,
pB=None,
gamma=16.0,
return_numpy=True,
):
""" Updates the posterior beliefs about policies based on expected free energy prior
@TODO: Needs to be amended for use with multi-step policies (where possible_policies is a
list of np.arrays (n_step x n_factor), not just a list of tuples as it is now)
Parameters
----------
- `qs` [1D numpy array, array-of-arrays, or Categorical (either single- or multi-factor)]:
Current marginal beliefs about hidden state factors
- `A` [numpy ndarray, array-of-arrays (in case of multiple modalities), or Categorical
(both single and multi-modality)]:
Observation likelihood model (beliefs about the likelihood mapping entertained by the agent)
- `B` [numpy ndarray, array-of-arrays (in case of multiple hidden state factors), or Categorical
(both single and multi-factor)]:
Transition likelihood model (beliefs about the likelihood mapping entertained by the agent)
- `C` [numpy 1D-array, array-of-arrays (in case of multiple modalities), or Categorical
(both single and multi-modality)]:
Prior beliefs about outcomes (prior preferences)
- `policies` [list of tuples]:
A list of all the possible policies, each expressed as a tuple of indices, where a given
index corresponds to an action on a particular hidden state factor e.g. policies[1][2] yields the
index of the action under policy 1 that affects hidden state factor 2
- `use_utility` [bool]:
Whether to calculate utility term, i.e how much expected observation confer with prior expectations
- `use_states_info_gain` [bool]:
Whether to calculate state information gain
- `use_param_info_gain` [bool]:
Whether to calculate parameter information gain @NOTE requires pA or pB to be specified
- `pA` [numpy ndarray, array-of-arrays (in case of multiple modalities), or Dirichlet
(both single and multi-modality)]:
Prior dirichlet parameters for A. Defaults to none, in which case info gain w.r.t. Dirichlet
parameters over A is skipped.
- `pB` [numpy ndarray, array-of-arrays (in case of multiple hidden state factors), or
Dirichlet (both single and multi-factor)]:
Prior dirichlet parameters for B. Defaults to none, in which case info gain w.r.t.
Dirichlet parameters over A is skipped.
- `gamma` [float, defaults to 16.0]:
Precision over policies, used as the inverse temperature parameter of a softmax transformation
of the expected free energies of each policy
- `return_numpy` [Boolean]:
True/False flag to determine whether output of function is a numpy array or a Categorical
Returns
--------
- `qp` [1D numpy array or Categorical]:
Posterior beliefs about policies, defined here as a softmax function of the
expected free energies of policies
- `efe` - [1D numpy array or Categorical]:
The expected free energies of policies
"""
n_policies = len(policies)
efe = np.zeros(n_policies)
q_pi = np.zeros((n_policies, 1))
for idx, policy in enumerate(policies):
qs_pi = get_expected_states(qs, B, policy)
qo_pi = get_expected_obs(qs_pi, A)
if use_utility:
efe[idx] += calc_expected_utility(qo_pi, C)
if use_states_info_gain:
efe[idx] += calc_states_info_gain(A, qs_pi)
if use_param_info_gain:
if pA is not None:
efe[idx] += calc_pA_info_gain(pA, qo_pi, qs_pi)
if pB is not None:
efe[idx] += calc_pB_info_gain(pB, qs_pi, qs, policy)
q_pi = softmax(efe * gamma)
if return_numpy:
q_pi = q_pi / q_pi.sum(axis=0) # type: ignore
else:
q_pi = utils.to_categorical(q_pi)
q_pi.normalize()
return q_pi, efe
def get_expected_states(qs, B, policy, return_numpy=False):
"""
Given a posterior density qs, a transition likelihood model B, and a policy,
get the state distribution expected under that policy's pursuit
Parameters
----------
- `qs` [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array), or
Categorical (either single-factor or AoA)]:
Current posterior beliefs about hidden states
- `B` [numpy nd-array, array-of-arrays (where each entry is a numpy nd-array), or Categorical
(either single-factor of AoA)]:
Transition likelihood mapping from states at t to states at t + 1, with different actions
(per factor) stored along the lagging dimension
- `policy` [np.arrays]:
np.array of size (policy_len x n_factors) where each value corrresponds to a control state
- `return_numpy` [Boolean]:
True/False flag to determine whether output of function is a numpy array or a Categorical
Returns
-------
- `qs_pi` [ list of np.arrays with len n_steps, where in case of multiple hidden state factors,
each np.array in the list is a 1 x n_factors array-of-arrays, otherwise a list of 1D numpy arrays]:
Expected states under the given policy - also known as the 'posterior predictive density'
"""
n_steps = policy.shape[0]
n_factors = policy.shape[1]
qs = utils.to_numpy(qs, flatten=True)
B = utils.to_numpy(B)
# initialise beliefs over expected states
qs_pi = []
if utils.is_arr_of_arr(B):
for t in range(n_steps):
qs_pi_t = np.empty(n_factors, dtype=object)
qs_pi.append(qs_pi_t)
# initialise expected states after first action using current posterior (t = 0)
for control_factor, control in enumerate(policy[0, :]):
qs_pi[0][control_factor] = spm_dot(B[control_factor][:, :, control], qs[control_factor])
# get expected states over time
if n_steps > 1:
for t in range(1, n_steps):
for control_factor, control in enumerate(policy[t, :]):
qs_pi[t][control_factor] = spm_dot(
B[control_factor][:, :, control], qs_pi[t - 1][control_factor]
)
else:
# initialise expected states after first action using current posterior (t = 0)
qs_pi.append(spm_dot(B[:, :, policy[0, 0]], qs))
# then loop over future timepoints
if n_steps > 1:
for t in range(1, n_steps):
qs_pi.append(spm_dot(B[:, :, policy[t, 0]], qs_pi[t - 1]))
if return_numpy:
if len(qs_pi) == 1:
return qs_pi[0]
else:
return qs_pi
else:
if len(qs_pi) == 1:
return utils.to_categorical(qs_pi[0])
else:
for t in range(n_steps):
qs_pi[t] = utils.to_categorical(qs_pi[t])
return qs_pi
def update_transition_dirichlet(pB,
B,
actions,
qs,
qs_prev,
lr=1.0,
factors="all",
return_numpy=True):
"""
Update Dirichlet parameters that parameterize the transition model of the generative model
(describing the probabilistic mapping between hidden states over time).
Parameters
-----------
- pB [numpy nd.array, array-of-arrays (with np.ndarray entries), or Dirichlet
(either single-modality or AoA)]:
The prior Dirichlet parameters of the generative model, parameterizing the agent's
beliefs about the transition likelihood.
- B [numpy nd.array, object-like array of arrays, or Categorical (either single-modality or AoA)]:
The transition likelihood of the generative model.
- actions [numpy 1D array]:
A 1D numpy array of shape (num_control_factors,) containing the action(s) performed at
a given timestep.
- qs [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array), or Categorical
(either single-factor or AoA)]:
Current marginal posterior beliefs about hidden state factors
- qs_prev [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array), or
Categorical (either single-factor or AoA)]:
Past marginal posterior beliefs about hidden state factors
- lr [float, optional]:
Learning rate.
- return_numpy [bool, optional]:
Logical flag to determine whether output is a numpy array or a Dirichlet
- factors [list, optional]:
Indices (in terms of range(Nf)) of the hidden state factors to include in learning.
Defaults to 'all', meaning that transition likelihood matrices for all hidden state factors
are updated as a function of transitions in the different control factors (i.e. actions)
"""
pB = utils.to_numpy(pB)
B = utils.to_numpy(B)
if utils.is_arr_of_arr(pB):
n_factors = len(pB)
else:
n_factors = 1
if return_numpy:
pB_updated = copy.deepcopy(pB)
else:
pB_updated = utils.to_dirichlet(copy.deepcopy(pB))
if not utils.is_distribution(qs):
qs = utils.to_categorical(qs)
if factors == "all":
if n_factors == 1:
dfdb = qs.cross(qs_prev, return_numpy=True)
dfdb = dfdb * (B[:, :, actions[0]] > 0).astype("float")
pB_updated[:, :,
actions[0]] = pB_updated[:, :, actions[0]] + (lr * dfdb)
elif n_factors > 1:
for factor in range(n_factors):
dfdb = qs[factor].cross(qs_prev[factor], return_numpy=True)
dfdb = dfdb * (B[factor][:, :, actions[factor]] >
0).astype("float")
pB_updated[factor][:, :, actions[factor]] = pB_updated[
factor][:, :, actions[factor]] + (lr * dfdb)
else:
for factor in factors:
dfdb = qs[factor].cross(qs_prev[factor], return_numpy=True)
dfdb = dfdb * (B[factor][:, :, actions[factor]] >
0).astype("float")
pB_updated[factor][:, :, actions[factor]] = pB_updated[
factor][:, :, actions[factor]] + (lr * dfdb)
return pB_updated
def update_likelihood_dirichlet(pA,
A,
obs,
qs,
lr=1.0,
modalities="all",
return_numpy=True):
""" Update Dirichlet parameters of the likelihood distribution
Parameters
-----------
- pA [numpy nd.array, array-of-arrays (with np.ndarray entries), or Dirichlet
(either single-modality or AoA)]:
The prior Dirichlet parameters of the generative model, parameterizing the
agent's beliefs about the observation likelihood.
- A [numpy nd.array, object-like array of arrays, or Categorical (either single-modality or AoA)]:
The observation likelihood of the generative model.
- obs [numpy 1D array, array-of-arrays (with 1D numpy array entries), int or tuple]:
A discrete observation (possible multi-modality) used in the update equation
- qs [numpy 1D array, array-of-arrays (where each entry is a numpy 1D array),
or Categorical (either single-factor or AoA)]:
Current marginal posterior beliefs about hidden state factors
- lr [float, optional]:
Learning rate.
- return_numpy [bool, optional]:
Logical flag to determine whether output is a numpy array or a Dirichlet
- modalities [list, optional]:
Indices (in terms of range(n_modalities)) of the observation modalities to include
in learning.Defaults to 'all', meaning that observation likelihood matrices
for all modalities are updated using their respective observations.
"""
pA = utils.to_numpy(pA)
A = utils.to_numpy(A)
if utils.is_arr_of_arr(pA):
n_modalities = len(pA)
n_observations = [
pA[modality].shape[0] for modality in range(n_modalities)
]
else:
n_modalities = 1
n_observations = [pA.shape[0]]
if return_numpy:
pA_updated = copy.deepcopy(pA)
else:
pA_updated = utils.to_dirichlet(copy.deepcopy(pA))
# observation index
if isinstance(obs, (int, np.integer)):
obs = np.eye(A.shape[0])[obs]
# observation indices
elif isinstance(obs, tuple):
obs = np.array(
[
np.eye(n_observations[modality])[obs[modality]]
for modality in range(n_modalities)
],
dtype=object,
)
# convert to Categorical to make the cross product easier
obs = utils.to_categorical(obs)
if modalities == "all":
if n_modalities == 1:
dfda = obs.cross(qs, return_numpy=True)
dfda = dfda * (A > 0).astype("float")
pA_updated = pA_updated + (lr * dfda)
elif n_modalities > 1:
for modality in range(n_modalities):
dfda = obs[modality].cross(qs, return_numpy=True)
dfda = dfda * (A[modality] > 0).astype("float")
pA_updated[modality] = pA_updated[modality] + (lr * dfda)
else:
for modality in modalities:
dfda = obs[modality].cross(qs, return_numpy=True)
dfda = dfda * (A[modality] > 0).astype("float")
pA_updated[modality] = pA_updated[modality] + (lr * dfda)
return pA_updated
def update_posterior_policies_mmp(
qs_seq_pi,
A,
B,
C,
policies,
use_utility=True,
use_states_info_gain=True,
use_param_info_gain=False,
prior=None,
pA=None,
pB=None,
F=None,
E=None,
gamma=16.0,
return_numpy=True,
):
"""
`qs_seq_pi`: numpy object array that stores posterior marginals beliefs over hidden states for each policy.
The structure is nested as policies --> timesteps --> hidden state factors. So qs_seq_pi[p_idx][t][f] is the belief about factor `f` at time `t`, under policy `p_idx`
`A`: numpy object array that stores likelihood mappings for each modality.
`B`: numpy object array that stores transition matrices (possibly action-conditioned) for each hidden state factor
`policies`: numpy object array that stores each (potentially-multifactorial) policy in `policies[p_idx]`. Shape of `policies[p_idx]` is `(num_timesteps, num_factors)`
`use_utility`: Boolean that determines whether expected utility should be incorporated into computation of EFE (default: `True`)
`use_states_info_gain`: Boolean that determines whether state epistemic value (info gain about hidden states) should be incorporated into computation of EFE (default: `True`)
`use_param_info_gain`: Boolean that determines whether parameter epistemic value (info gain about generative model parameters) should be incorporated into computation of EFE (default: `False`)
`prior`: numpy object array that stores priors over hidden states - this matters when computing the first value of the parameter info gain for the Dirichlet parameters over B
`pA`: numpy object array that stores Dirichlet priors over likelihood mappings (one per modality)
`pB`: numpy object array that stores Dirichlet priors over transition mappings (one per hidden state factor)
`F` : 1D numpy array that stores variational free energy of each policy
`E` : 1D numpy array that stores prior probability each policy (e.g. 'habits')
`gamma`: Float that encodes the precision over policies
`return_numpy`: Boolean that determines whether output should be a numpy array or an instance of the Categorical class (default: `True`)
"""
A = utils.to_numpy(A)
B = utils.to_numpy(B)
num_obs, num_states, num_modalities, num_factors = utils.get_model_dimensions(
A, B)
horizon = len(qs_seq_pi[0])
num_policies = len(qs_seq_pi)
# initialise`qo_seq` as object arrays to initially populate `qo_seq_pi`
qo_seq = utils.obj_array(horizon)
for t in range(horizon):
qo_seq[t] = utils.obj_array_zeros(num_obs)
# initialise expected observations
qo_seq_pi = utils.obj_array(num_policies)
for p_idx in range(num_policies):
# qo_seq_pi[p_idx] = copy.deepcopy(obs_over_time)
qo_seq_pi[p_idx] = qo_seq
efe = np.zeros(num_policies)
if F is None:
F = np.zeros(num_policies)
if E is None:
E = np.zeros(num_policies)
for p_idx, policy in enumerate(policies):
qs_seq_pi_i = qs_seq_pi[p_idx]
for t in range(horizon):
qo_pi_t = get_expected_obs(qs_seq_pi_i[t], A)
qo_seq_pi[p_idx][t] = qo_pi_t
if use_utility:
efe[p_idx] += calc_expected_utility(qo_seq_pi[p_idx][t], C)
if use_states_info_gain:
efe[p_idx] += calc_states_info_gain(A, qs_seq_pi_i[t])
if use_param_info_gain:
if pA is not None:
efe[p_idx] += calc_pA_info_gain(pA, qo_seq_pi[p_idx][t],
qs_seq_pi_i[t])
if pB is not None:
if t > 0:
efe[p_idx] += calc_pB_info_gain(
pB, qs_seq_pi_i[t], qs_seq_pi_i[t - 1], policy)
else:
if prior is not None:
efe[p_idx] += calc_pB_info_gain(
pB, qs_seq_pi_i[t], prior, policy)
q_pi = softmax(efe * gamma - F + E)
if return_numpy:
q_pi = q_pi / q_pi.sum(axis=0)
else:
q_pi = utils.to_categorical(q_pi)
q_pi.normalize()
return q_pi, efe