`subsystem`¶

Represents a candidate set for \(\varphi\) calculation.

class pyphi.subsystem.Subsystem(node_indices, network, cut=None, mice_cache=None, repertoire_cache=None, cache_info=None)¶

A set of nodes in a network.

Parameters:	nodes (tuple(int) – A sequence of indices of the nodes in this subsystem. network (Network) – The network the subsystem belongs to.

nodes¶: list(Node – A list of nodes in the subsystem.

node_indices¶: tuple(int – The indices of the nodes in the subsystem.

size¶: int – The number of nodes in the subsystem.

network¶: Network – The network the subsystem belongs to.

cut¶: Cut – The cut that has been applied to this subsystem.

connectivity_matrix¶: np.array – The connectivity matrix after applying the cut.

cut_matrix¶: np.array – A matrix of connections which have been severed by the cut.

perturb_vector¶: np.array – The vector of perturbation probabilities for each node.

null_cut¶: Cut – The cut object representing no cut.

past_tpm¶: np.array – The TPM conditioned on the past state of the external nodes (nodes outside the subsystem).

current_tpm¶: np.array – The TPM conditioned on the current state of the external nodes.

repertoire_cache_info()¶: Report repertoire cache statistics.

__eq__(other)¶

Return whether this subsystem is equal to the other object.

Two subsystems are equal if their sets of nodes, networks, and cuts are equal.

__bool__()¶: Return false if the subsystem has no nodes, true otherwise.

json_dict()¶

indices2nodes(indices)¶

cause_repertoire(mechanism, purview)¶

Return the cause repertoire of a mechanism over a purview.

Parameters:

mechanism (tuple(Node) – The mechanism for which to calculate the cause repertoire.
purview (tuple(Node) – The purview over which to calculate the cause repertoire.

Returns:

cause_repertoire –

The cause repertoire of the: mechanism over the purview.

Return type:

np.ndarray

effect_repertoire(mechanism, purview)¶

Return the effect repertoire of a mechanism over a purview.

Parameters:

mechanism (tuple(Node) – The mechanism for which to calculate the
repertoire. (effect) –
purview (tuple(Node) – The purview over which to calculate the
repertoire. –

Returns:

effect_repertoire –

The effect repertoire of the: mechanism over the purview.

Return type:

np.ndarray

unconstrained_cause_repertoire(purview)¶

Return the unconstrained cause repertoire for a purview.

This is just the cause repertoire in the absence of any mechanism.

unconstrained_effect_repertoire(purview)¶

Return the unconstrained effect repertoire for a purview.

This is just the effect repertoire in the absence of any mechanism.

expand_repertoire(direction, purview, repertoire, new_purview=None)¶: Return the unconstrained cause or effect repertoire based on a direction.

expand_cause_repertoire(purview, repertoire, new_purview=None)¶: Expand a partial cause repertoire over a purview to a distribution over the entire subsystem’s state space.

expand_effect_repertoire(purview, repertoire, new_purview=None)¶: Expand a partial effect repertoire over a purview to a distribution over the entire subsystem’s state space.

cause_info(mechanism, purview)¶: Return the cause information for a mechanism over a purview.

effect_info(mechanism, purview)¶: Return the effect information for a mechanism over a purview.

cause_effect_info(mechanism, purview)¶

Return the cause-effect information for a mechanism over a purview.

This is the minimum of the cause and effect information.

find_mip(direction, mechanism, purview)¶

Return the minimum information partition for a mechanism over a purview.

Parameters:

direction (str) – Either DIRECTIONS[PAST] or DIRECTIONS[FUTURE].
mechanism (tuple(Node) – The nodes in the mechanism.
purview (tuple(Node) – The nodes in the purview.

Returns:

mip –

The mininum-information partition in one temporal: direction.

Return type:

Mip

mip_past(mechanism, purview)¶

Return the past minimum information partition.

Alias for |find_mip| with direction set to DIRECTIONS[PAST].

mip_future(mechanism, purview)¶

Return the future minimum information partition.

Alias for |find_mip| with direction set to DIRECTIONS[FUTURE].

phi_mip_past(mechanism, purview)¶

Return the \(\varphi\) value of the past minimum information partition.

This is the distance between the unpartitioned cause repertoire and the MIP cause repertoire.

phi_mip_future(mechanism, purview)¶

Return the \(\varphi\) value of the future minimum information partition.

This is the distance between the unpartitioned effect repertoire and the MIP cause repertoire.

phi(mechanism, purview)¶: Return the \(\varphi\) value of a mechanism over a purview.

find_mice(direction, mechanism, purviews=False)¶

Return the maximally irreducible cause or effect for a mechanism.

Keyword Arguments:
Parameters:	direction (str) – The temporal direction, specifying cause or effect. mechanism (tuple(Node) – The mechanism to be tested for irreducibility.
	purviews (tuple(Node) – Optionally restrict the possible purviews to a subset of the subsystem. This may be useful for _e.g._ finding only concepts that are “about” a certain subset of nodes.
Returns:	mice – The maximally-irreducible cause or effect.
Return type:	`Mice`

Note

Strictly speaking, the MICE is a pair of repertoires: the core cause repertoire and core effect repertoire of a mechanism, which are maximally different than the unconstrained cause/effect repertoires (i.e., those that maximize \(\varphi\)). Here, we return only information corresponding to one direction, DIRECTIONS[PAST] or DIRECTIONS[FUTURE], i.e., we return a core cause or core effect, not the pair of them.

core_cause(mechanism, purviews=False)¶

Returns the core cause repertoire of a mechanism.

Alias for |find_mice| with direction set to DIRECTIONS[PAST].

core_effect(mechanism, purviews=False)¶

Returns the core effect repertoire of a mechanism.

Alias for |find_mice| with direction set to DIRECTIONS[PAST].

phi_max(mechanism)¶

Return the \(\varphi^{\textrm{max}}\) of a mechanism.

This is the maximum of \(\varphi\) taken over all possible purviews.

null_concept¶: Return the null concept of this subsystem, a point in concept space identified with the unconstrained cause and effect repertoire of this subsystem.

concept(mechanism)¶: Calculate a concept.

subsystem¶

`subsystem`¶