pyphi.examples#

Example substrates and systems to go along with the documentation.

Functions

ac_2019_three_candidate_election_substrate()

The three-candidate, seven-voter election of Albantakis et al. (2019), Fig 11: voters A-G each in state 0, 1, or 2 (candidates "1", "2", "3"), and W in state 1, 2, or 3 for the candidate with a strict majority of votes, or 0 for a tie.

actual_causation_substrate()

The actual causation example substrate, consisting of an OR and AND gate with self-loops.

basic_noisy_selfloop_substrate()

Based on the basic_substrate, but with added selfloops and noisy edges.

basic_noisy_selfloop_system()

A system containing all the nodes of the basic_noisy_selfloop_substrate().

basic_state()

The state of nodes in basic_substrate().

basic_substrate([cm])

A 3-node substrate of logic gates.

basic_system()

A system containing all the nodes of the basic_substrate().

blackbox_substrate()

A micro-substrate to demonstrate blackboxing.

cond_depend_tpm()

A system of two general logic gates A and B such if they are in the same state they stay the same, but if they are in different states, they flip with probability 50%.

cond_independ_tpm()

A system of three general logic gates A, B and C such that: if A and B are in the same state then they stay the same; if they are in different states, they flip if C is ON and stay the same if C is OFF; and C is ON 50% of the time, independent of the previous state.

differentiation_macro_tpm(p, epsilon)

differentiation_micro_1_system()

differentiation_micro_tpm(p, epsilon)

disjunction_conjunction_substrate()

The disjunction-conjunction example from Actual Causation Figure 9.

fig10_substrate()

The substrate shown in Figures 4, 6, 8, 9 and 10 of the 2014 IIT 3.0 paper.

fig14_substrate()

The substrate shown in Figure 1A of the 2014 IIT 3.0 paper.

fig16_substrate()

The ABCDEFG portion of the substrate shown in Figure 16 of the 2014 IIT 3.0 paper.

fig1a_substrate()

The substrate shown in Figure 1A of the 2014 IIT 3.0 paper.

fig3a_substrate()

The substrate shown in Figure 3A of the 2014 IIT 3.0 paper.

fig3b_substrate()

The substrate shown in Figure 3B of the 2014 IIT 3.0 paper.

fig4_substrate()

The substrate shown in Figures 4, 6, 8, 9 and 10 of the 2014 IIT 3.0 paper.

fig4_system()

fig5a_substrate()

The substrate shown in Figure 5A of the 2014 IIT 3.0 paper.

fig5a_system()

fig5b_substrate()

The substrate shown in Figure 5B of the 2014 IIT 3.0 paper.

fig5b_system()

fig6_substrate()

The substrate shown in Figures 4, 6, 8, 9 and 10 of the 2014 IIT 3.0 paper.

fig8_substrate()

The substrate shown in Figures 4, 6, 8, 9 and 10 of the 2014 IIT 3.0 paper.

fig9_substrate()

The substrate shown in Figures 4, 6, 8, 9 and 10 of the 2014 IIT 3.0 paper.

frog_substrate([species])

The substrate of a frog from Grasso et al. (2021).

frog_transition([species])

The state transition analyzed for a frog from Grasso et al. (2021).

gomez_p53_mdm2_substrate()

The multi-valued p53-Mdm2 regulatory network from Gómez et al. (2020).

grid3_substrate()

3-node grid substrate.

grid3_system()

iit4_2023_fig1a_substrate()

The 3-unit logistic substrate of Fig 1A.

iit4_2023_fig1a_system()

iit4_2023_fig6a_substrate()

The 6-unit "bottleneck" architecture of Fig 6A.

iit4_2023_fig6a_system()

iit4_2023_fig6b_substrate()

The 6-unit "modular" architecture of Fig 6B.

iit4_2023_fig6b_system()

iit4_2023_fig6c_substrate()

The 6-unit "copy" architecture of Fig 6C.

iit4_2023_fig6c_system()

iit4_2023_fig6d_substrate([k])

The 6-unit "specialized" architecture of Fig 6D.

iit4_2023_fig6d_system()

iit4_2023_fig6e_substrate()

The 6-unit "structured" architecture of Fig 6E.

iit4_2023_fig6e_system()

iit4_2023_fig7_inactivated_substrate()

The Fig 7 network with unit E inactivated (Fig 7C).

iit4_2023_fig7_inactivated_system()

iit4_2023_fig7_substrate()

The 5-unit state-dependent network of Fig 7.

iit4_2023_fig7_system()

macro_substrate()

A substrate of micro elements which has greater integrated information after coarse graining to a macro scale.

macro_system()

A system containing all the nodes of macro_substrate().

marshall_2023_fig1_substrate([variant])

The four-unit systems of Marshall et al. (2023), Fig 1.

marshall_2023_fig2_substrate([panel])

The four-unit sigmoid systems of Marshall et al. (2023), Fig 2.

marshall_2023_fig3_substrate([moderate])

The eight-unit universe of Marshall et al. (2023), Fig 3.

mayner_2026_monad_substrate([p])

A single binary unit that keeps its state with probability p (Mayner, Marshall & Tononi 2026, Fig 2A-B): an imperfect COPY for p > 0.5.

pqr_substrate([cm])

A 3-node substrate of logic gates.

pqr_system()

A system containing all the nodes of the basic_substrate().

prevention_transition()

The Transition for the prevention example from Actual Causation Figure 7D.

propagation_delay_substrate()

A version of the primary example from the IIT 3.0 paper with deterministic COPY gates on each connection.

register_example(func)

Register an example function in EXAMPLES[category][name].

residue_substrate()

The substrate for the residue example.

residue_system()

The system containing all the nodes of the residue_substrate().

rule110_substrate()

A substrate of three elements which follows the logic of the Rule 110 cellular automaton with current and previous state (0, 0, 0).

rule110_system()

rule154_substrate()

A substrate of five elements which follows the logic of the Rule 154 cellular automaton.

rule154_system()

xor_substrate()

A fully connected system of three XOR gates.

xor_system()

The system containing all the nodes of the xor_substrate().