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Resonant Fractal Nature Theory — a mathematical framework for coherent patterns on graph-coupled networks.

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© 2026 TNFR project — MIT licensed.DOI 10.5281/zenodo.17602860
docs
grammar
PHYSICS_VERIFICATION.md
API_CONTRACTS.mdCANONICAL_OZ_SEQUENCES.mdEMPIRICAL_CONFRONTATION_EEG.mdREADME.mdSTRUCTURAL_FIELDS_TETRAD.mdSTRUCTURAL_INTERFACE_THEORY.md
theory
APPLIED_STRUCTURAL_ANALYSIS.mdCATALOG_TYPE_HYGIENE_PROGRAMME.mdDISSIPATIVE_AND_OPEN_SYSTEMS.mdEMERGENT_ONTOLOGY.mdEXTENDED_FIELDS_AND_DERIVED_QUANTITIES.mdFUNDAMENTAL_THEORY.mdGAUGE_SYMMETRY_AND_UNIFICATION.mdGLOSSARY.mdMATHEMATICAL_DYNAMICS_BASIS.mdMINIMAL_STRUCTURAL_DEGREES.mdNUCLEUS_A_PRIME_LADDER_ATLAS.mdNUCLEUS_B_EQUIVARIANCE_OBSTRUCTIONS.mdPHYSICAL_REGIME_CORRESPONDENCES.mdREADME.mdREMESH_INFINITY_DERIVATION.mdSTRUCTURAL_CONSERVATION_THEOREM.mdSTRUCTURAL_OPERATORS.mdSTRUCTURAL_STABILITY_AND_DYNAMICS.mdTNFR_BSD_RESEARCH_NOTES.mdTNFR_HODGE_RESEARCH_NOTES.mdTNFR_NAVIER_STOKES_RESEARCH_NOTES.mdTNFR_NUMBER_THEORY.mdTNFR_P_VS_NP_RESEARCH_NOTES.mdTNFR_RIEMANN_RESEARCH_NOTES.mdTNFR_VARIATIONAL_PRINCIPLE.mdTNFR_YANG_MILLS_RESEARCH_NOTES.mdTNFR.pdfUNIFIED_GRAMMAR_RULES.md
factorization-lab
analysis
analyze_patterns.pycertificate_manifest.py
benchmarks
benchmark_analysis.pybenchmark_expansion_suite.pyfull_spectrum_factorization.pypaley_gap_extended.pypaley_gap_smoke.pytest_benchmark_suite.py
demos
experiment_contexts
exp_0b1663cd19b7.jsonexp_0bf0054b7474.jsonexp_75a4c8ca616a.jsonexp_848ee0fd1857.jsonexp_f6fe00562193.jsonexp_fdf3da424e1e.json
failure_telemetry_batch.pyfeedback_integration_demo.pyintegration_demo_snapshots.dbseed_management_integration_demo.pysnapshot_integration_demo.pytrajectory_143.jsontrajectory_77.jsontrajectory_89.jsontrajectory_91.jsontrajectory_97.json
docs
FACTORING_PLAYBOOK.mdFALSE_POSITIVE_TEST_SUITE.mdOPERATOR_CERTIFICATES.mdROADMAP.mdSPECTRAL_ROUTE.md
experiment_contexts
exp_cebe1d9e7d8e.json
notebooks
spectral_history.ipynb
scripts
run_false_positive_tests.py
tests
run_false_positive_test_suite.pytest_cli.pytest_false_positive_methodology.pytest_false_positive_verifier.pytest_feedback_integration.pytest_partitioning.pytest_seed_management.pytest_self_opt_support.pytest_snapshot_system.pytest_spectral_paley.pytest_verification_robustness.py
tnfr_factorization
__init__.pyapi.pycli.pyfailure_telemetry.pyfeedback_adapter.pyfeedback_integration.pypartitioning.pyself_opt_support.pyspectral_paley.py
demo_snapshots.dbLICENSE_SNAPSHOT.mdPACKAGE_SUMMARY.mdREADME.mdseed_management.pysnapshot_system.pytest_certificate_hashing.pytest_installation.pyverification_trajectory_77.json
benchmarks
analyze_tetrad_universality.pyb0star_alpha_canonical_product_graphs.pybenchmark_optimization_tracks.pybenchmark_utils.pyboundary_vibration.pybridge_primes_riemann.pychiral_involution.pycli_utils.pycoherence_projector_sense_index.pycommutant_bridge.pycomposition_arithmetic.pyconfinement_zones_test.pyconservation_law_validation.pydirected_paley_bridge.pyemergent_arithmetic_pulse.pyemergent_atom_dynamics.pyemergent_atomic_shells.pyemergent_base_dimension.pyemergent_dimension_dynamics.pyemergent_fractal_pulse.pyemergent_fractal_simplex_dimension.pyemergent_integers_symmetry.pyemergent_musical_nfr.pyemergent_nfr_geometry.pyemergent_nfr_where.pyemergent_rationals.pyemergent_rhythm.pyemergent_screening.pyemergent_shell_cardinals.pyemergent_shell_ordering.pyemergent_simplex_dimension.pyemergent_substrate_symmetry.pyequivariance_wall.pyexternal_phase_gate_validation.pyfield_methods_battery.pygolden_residue_remesh_bridge.pyintegrated_force_regime_study.pyinverse_spectrum_to_symmetry.pyk_phi_safety_demo.pykuramoto_farey_bridge.pymissing_piece_bridge.pymultichannel_interface_benchmark.pynavier_stokes_recipe_bridge.pynodal_propagator_residue_bridge.pyns_moment_hierarchy_cascade.pyoperational_irreducibility.pypaley_bridge.pyphase_curvature_investigation.pyphase_wall.pyphi_s_confinement_investigation.pyprimes_as_consequence.pypulse_phase_coherence_budget.pyREADME.mdremesh_infinity_riemann_baseline.pyremesh_infinity_riemann_composed.pyremesh_infinity_riemann_modified_graph.pyremesh_infinity_riemann_operator.pyremesh_infinity_riemann_spectral_basis.pyremesh_infinity_riemann_spectral_robustness.pyremesh_infinity_riemann_spectral.pyresidue_phase_vs_riemann.pystructural_interface_benchmark.pytemporal_interface_benchmark.pytetrad_results_aggregate.pyu2_destabilization_irreversibility.pyuniversality_clusters.pyxi_c_fast_experiment.py
primality-test
benchmarks
comprehensive_benchmark.py
docs
ADVANCED_INTEGRATION.mdmathematical_foundation.mdperformance_analysis.md
examples
advanced_examples.pybasic_usage.py
tnfr_primality
__init__.py__main__.pyadvanced_cli.pyadvanced_core.pycli.pyconstants.pycore.pyoptimized.py
MANIFEST.inPACKAGE_SUMMARY.mdREADME.mdRELEASE_NOTES_v1.0.mdsetup.pytest_installation.py
tests
core_physics
__init__.pytest_conservation_laws.pytest_delta_nfr_computation_paths.pytest_delta_nfr.pytest_dispersion_coherence_sign_invariance.pytest_emergent_constants_guard.pytest_lyapunov_operators.pytest_nodal_equation.pytest_structural_triad.py
data
replay_manifests
sample_run
_manifest_summary.json_manifest.json_partition_files.txt.gz
self_opt_validation
seed_alpha
paley.json
seed_beta
integration.json
seed_gamma
unknown.json
self_optimization
test_run
partitioned
test_run
test_run_p0.jsontest_run_p1.json
_manifest_summary.json_manifest.json
engines
test_pattern_discovery_manifest.pytest_self_optimization_engine.py
mathematics
__init__.pytest_autodiff.pytest_backends.pytest_dissipative_dynamics.pytest_epi.pytest_factory_patterns.pytest_metrics.pytest_navier_stokes_refounded.pytest_number_theory_canonical.pytest_operators.pytest_residue_networks.pytest_riemann_nodal_pulse.pytest_riemann_pulse_coherence.pytest_spaces.pytest_transforms.pytest_validator.py
operators
test_canonical_operators_modern.pytest_grammar_canon.pytest_grammar_canonical_consistency.pytest_grammar_dynamics.pytest_operator_contracts.pytest_operator_strategies.py
parallel
test_fractal_partition_manifest.py
physics
test_conservation_gauge_unification.pytest_dissipative_conservation.pytest_emergent_chemistry.pytest_field_cache_invalidation.pytest_gauge.pytest_phase_transition.pytest_signatures.pytest_spectral_conservation.pytest_structural_diffusion.pytest_structural_integrity.pytest_symplectic_substrate.pytest_tetrad_bounds.pytest_variational.pytest_yang_mills_closure.pytest_yang_mills_derivability.pytest_yang_mills_scaling.pytest_yang_mills_structural_gap.pytest_yang_mills_u6_sweep.py
scripts
test_run_self_opt_validation.pytest_run_self_optimization.py
sdk
__init__.pytest_simple_advanced.py
__init__.pyconftest.pyREADME.mdtest_breast_cancer_phase_gate_demo.pytest_classical_mechanics.pytest_distributed_fft.pytest_external_phase_gate_validation.pytest_factorization_entrypoint.pytest_multichannel_interface.pytest_nodal_optimizer.pytest_phase_gate_api.pytest_replay_register_manifest.pytest_signal_confrontation.pytest_structural_interface_api.pytest_structural_interface_baselines.pytest_structural_interface_benchmark.pytest_temporal_interface.pytest_vectorized_coherence_length_regression.pytest_wine_quality_phase_gate_demo.pyutils.py
examples
01_foundations
01_hello_world.py02_musical_resonance.py03_network_formation.py04_operator_sequences.py05_coherence_evolution.py06_network_topologies.py07_phase_transitions.py08_emergent_phenomena.py09_visualization_suite.py10_simplified_sdk_showcase.py
02_physics_regimes
11_classical_limit_comparison.py115_operator_contract_audit.py12_classical_mechanics_demo.py13_quantum_mechanics_demo.py14_uncertainty_and_interference.py15_train_crossing_demo.py17_conservation_law_demo.py26_gauge_structure_demo.py27_variational_principle_demo.py28_dissipative_systems_demo.py29_lyapunov_stability_demo.py30_self_optimization_demo.py31_mathematical_constants_basis.py33_complex_field_unification.py34_conservation_protocol_suite.py35_tetrad_irreducibility.py36_grammar_violation_detector.py37_operator_tetrad_synergy.py38_grammar_energy_landscape.py39_nodal_equation_decomposition.py
03_riemann_zeta
157_nodal_pulse_phase_attack.py41_von_mangoldt_zeta_demo.py42_riemann_zeros_as_resonances.py43_prime_ladder_hamiltonian_demo.py44_weil_explicit_formula_demo.py45_li_keiper_demo.py46_weil_tnfr_positivity_demo.py47_alpha_sweep_demo.py48_admissible_family_sweep_demo.py49_nodeaware_gauge_sweep_demo.py50_uniform_coercivity_demo.py51_adaptive_coercivity_demo.py52_paley_gap_coercivity_demo.py53_lyapunov_spectral_positivity_demo.py54_hilbert_polya_demo.py55_structural_zero_density_demo.py56_spectral_emergence_demo.py57_admissible_rescaling_demo.py58_oscillatory_correction_demo.py
04_riemann_L_twisted
59_dirichlet_l_function_demo.py60_dirichlet_l_continuation_demo.py61_dirichlet_l_hamiltonian_demo.py62_dirichlet_weil_explicit_formula_demo.py63_dirichlet_li_keiper_demo.py64_twisted_weil_positivity_demo.py65_twisted_alpha_sweep_demo.py66_twisted_admissible_family_sweep_demo.py67_twisted_nodeaware_gauge_sweep_demo.py68_twisted_hermite_family_demo.py69_twisted_coercivity_uniform_demo.py70_twisted_paley_gap_coercivity_demo.py71_twisted_lyapunov_spectral_demo.py72_twisted_hilbert_polya_demo.py73_twisted_structural_zero_density_demo.py74_twisted_spectral_emergence_demo.py75_twisted_admissible_rescaling_demo.py76_twisted_oscillatory_correction_demo.py
05_type_hygiene
77_remesh_infinity_residue_split_demo.py78_nuf_type_signature_demo.py79_epi_type_signature_demo.py80_phi_type_signature_demo.py81_dnfr_type_signature_demo.py82_remesh_window_type_signature_demo.py83_delta_phi_max_type_signature_demo.py84_coupling_weights_type_signature_demo.py85_tetrad_closure_signature_demo.py86_currents_closure_signature_demo.py87_aggregates_closure_signature_demo.py88_urules_consistency_signature_demo.py89_operator_catalog_discipline_signature_demo.py
06_navier_stokes
158_navier_stokes_two_face_refounded.py
07_number_theory
100_prime_families_orbits.py101_numbers_as_coupled_network.py102_nodal_flow_primes_equilibria.py116_nuf_emergent_prime_visibility.py146_primality_grammatical_inertness.py147_numbers_as_free_monoid_words.py148_capacity_arm_carries_von_mangoldt.py149_p14_is_the_capacity_arm_operator.py153_structural_frequency_rank_cyclotomy.py40_arithmetic_number_theory.py94_generative_number_construction.py95_primes_from_spectral_waves.py96_spectral_vibration_of_coherence.py97_goldbach_additive_multiplicative.pyemergent_chemistry_particles_demo.py
08_emergent_geometry
103_emergent_substrate_meets_riemann.py106_per_node_polarization_geometry.py107_orthogonal_structure_emergent_geometry.py108_emergent_field_generating_structure.py112_structure_predicts_coherence_flow.py113_overdamped_projection_bridge.py114_substrate_conserved_quantities.py117_emergent_geometry_residue_graph.py118_emergent_vs_classical_operator.py119_phase_sector_directed_residue.py120_symmetry_wall_substrate_vs_spectrum.py121_canonical_symmetry_break_negative.py122_factorization_phase_sector.py123_symmetry_sector_decomposition.py124_emergent_metric_fractal_consistency.py125_node_is_the_emergent_substrate.py126_two_layers_base_fiber.py127_base_is_emergent_not_imposed.py128_base_substrate_coemergence.py129_spectral_gap_base_fiber_clock.py130_operators_break_substrate_charges.py131_coemergent_loop_convergence.py132_geometric_phase_holonomy.py133_psi_topological_defects.py134_spectral_dimension_heat_kernel.py135_arrow_of_time_h_theorem.py136_heat_kernel_coefficients.py137_synchronization_transition.py138_structure_frequency_synchronization.py139_grammar_formal_language.py140_grammar_automaton.py141_grammar_rule_decomposition.py142_grammar_operator_quotient.py143_glyphic_function_sublanguage.py144_branching_combinator.py145_syntactic_monoid_starfree.py150_emergent_grammatical_pattern_parry.py151_grammar_in_emergent_geometry.py152_operator_contract_tetrahedron.py154_conductor_annotated_qr_spectrum.py155_ontological_position_of_numbers.py156_emergence_directness_law.py98_emergent_symplectic_substrate.py99_structural_diffusion.pyunified_fields_showcase.py
09_millennium
109_p_vs_np_coherence_synthesis.py110_bsd_rank_structural_pressure.py111_hodge_discrete_and_honest_gap.py
10_applications
159_empirical_confrontation_pipeline.py90_phase_gate_monitor_demo.py91_breast_cancer_phase_gate_demo.py92_wine_quality_phase_gate_demo.py93_structural_interface_demo.pypytorch_cuda_demo.py
README.md
scripts
replay
__init__.pyregister_manifest.py
__init__.pyREADME.mdrebuild_failure_manifest.pyrun_reproducible_benchmarks.pyrun_self_opt_validation.pyrun_self_optimization.pytnfr_is_prime.pyvalidate_conservation_law.pyverify_internal_references.py
src
core
__init__.pyevaluation.py
tnfr
backends
__init__.pyjax_backend.pynumpy_backend.pyoptimized_numpy.pyREADME.mdtorch_backend.py
cli
__init__.py__init__.pyiarguments.pyarguments.pyiexecution.pyexecution.pyiinteractive_validator.pyREADME.mdutils.pyutils.pyi
compat
__init__.pydataclass.pyjsonschema_stub.pymatplotlib_stub.pynumpy_stub.pyREADME.md
config
__init__.py__init__.pyiconstants.pyconstants.pyidefaults_core.pydefaults_init.pydefaults_metric.pydefaults.pyfeature_flags.pyfeature_flags.pyiglyph_constants.pyoperator_names.pyoperator_names.pyiphysics_derivation.pyprecision_modes.pypresets.pypresets.pyiREADME.mdsecurity.pythresholds.pytnfr_config.py
constants
__init__.py__init__.pyialiases.pyaliases.pyicanonical.pymetric.pymetric.pyioperational.py
core
__init__.pycontainer.pydefault_implementations.pyexceptions.pyinterfaces.pyREADME.md
dynamics
__init__.py__init__.pyiadaptation.pyadaptation.pyiadaptive_sequences.pyadaptive_sequences.pyiadelic.pyadvanced_cache_optimizer.pyadvanced_fft_arithmetic.pyaliases.pyaliases.pyibifurcation.pycache_aware_fft_engine.pycanonical.pycanonical.pyicomputational_hub.pycoordination.pycoordination.pyidistributed_fft.pydnfr.pydnfr.pyidynamic_limits.pyemergent_centralization.pyemergent_integration_engine.pyfeedback.pyfeedback.pyifft_backend.pyfft_cache_coordinator.pyfft_dispatchers.pyfft_engine.pyfft_workers.pyfused_dnfr.pyhomeostasis.pyhomeostasis.pyiintegrators.pyintegrators.pyilearning.pylearning.pyimetabolism.pymulti_modal_cache.pynbody_tnfr.pynbody.pynodal_optimizer.pyoptimization_orchestrator.pypropagation.pyREADME.mdruntime.pyruntime.pyisampling.pysampling.pyiselectors.pyselectors.pyiself_optimizing_engine.pyspectral_structural_fusion.pystructural_cache.pystructural_clip.pysymplectic.pyunified_backend.pyunified_mathematical_cache_orchestrator.py
engines
computation
__init__.pyfft_engine.pyunified_fft_engine.pyunified_gpu_system.py
constants
__init__.pycanonical.pyoperational.py
integration
__init__.pyemergent_integration.py
pattern_discovery
__init__.pymathematical_patterns.pymulti_modal_cache.py
self_optimization
__init__.pyengine.py
__init__.pyREADME.md
errors
__init__.pycontextual.py
factorization
__init__.py
flatten
README.md
gamma
README.md
glyph_history
README.md
glyph_runtime
README.md
immutable
README.md
initialization
README.md
io
README.md
math
__init__.pyfields_symbolic.pygrammar_validators.pyoptimizer.pyREADME.mdsymbolic.py
mathematics
__init__.pybackend.pybackend.pyidynamics.pydynamics.pyiepi.pyepi.pyigenerators.pygenerators.pyiliouville.pymetrics.pymetrics.pyinumber_theory.pyoperators_factory.pyoperators_factory.pyioperators.pyoperators.pyioptimized_primality.pyprojection.pyprojection.pyiREADME.mdruntime.pyruntime.pyispaces.pyspaces.pyispectral.pytransforms.pytransforms.pyiunified_cache.pyunified_numerical.pyzeta.py
metrics
__init__.py__init__.pyibuffer_cache.pybuffer_cache.pyicache_utils.pycoherence.pycoherence.pyicommon.pycommon.pyicore.pycore.pyidiagnosis.pydiagnosis.pyiemergence.pyexport.pyexport.pyiglyph_timing.pyglyph_timing.pyilearning_metrics.pylearning_metrics.pyilocal_coherence.pyphase_coherence.pyphase_compatibility.pyREADME.mdreporting.pyreporting.pyisense_index.pysense_index.pyitelemetry.pytetrad.pytrig_cache.pytrig_cache.pyitrig.pytrig.pyi
multiscale
__init__.pyhierarchical.pyREADME.md
navier_stokes
__init__.pyconservative_face.pyoperator.py
node
README.md
observers
README.md
operators
network_analysis
__init__.pysource_detection.py
postconditions
__init__.pymutation.py
preconditions
__init__.pycoherence.pydissonance.pyemission.pymutation.pyreception.pyresonance.py
strategies
__init__.pydefaults.pygpu_strategies.pystrategy.py
__init__.py__init__.pyialgebra.pycanonical_patterns.pycascade.pycoherence.pycontraction.pycoupling.pycycle_detection.pydefinitions_base.pydefinitions.pydefinitions.pyidissonance.pyemission.pyexpansion.pygrammar_application.pygrammar_canon.pygrammar_context.pygrammar_core.pygrammar_dynamics.pygrammar_error_factory.pygrammar_memoization.pygrammar_patterns.pygrammar_telemetry.pygrammar_types.pygrammar_u6.pygrammar_validate.pygrammar.pygrammar.pyihamiltonian.pyhealth_analyzer.pyintrospection.pyjitter.pyjitter.pyilifecycle.pymetabolism.pymetrics_basic.pymetrics_core.pymetrics_network.pymetrics_structural.pymetrics_u6.pymetrics.pymutation.pynodal_equation.pyoperator_contracts.pypattern_detection.pypatterns.pyREADME.mdreception.pyrecursivity.pyregistry.pyregistry.pyiremesh.pyremesh.pyiresonance.pyself_organization.pysilence.pystructural_units.pytransition.py
parallel
__init__.pyauto_scaler.pydistributed.pyengine.pymonitoring.pypartitioner.pyREADME.md
performance
guardrails.py
physics
__init__.py_helpers.pycalibration.pycanonical.pycell.pyclassical_mechanics.pyconservation_gauge_unification.pyconservation.pydissipative_conservation.pyemergent_chemistry.pyemergent_particles.pyextended.pyfields.pygauge.pyintegrity.pyinteractions.pylife.pylyapunov.pypatterns.pyphase_transition.pyquantum_mechanics.pyREADME.mdsignatures.pyspectral_conservation.pyspectral_metrics.pystructural_diffusion.pysymplectic_substrate.pytelemetry.pyunified.pyvariational.pyvectorized_ops.py
primality
__init__.py
recipes
__init__.pycookbook.pyREADME.md
riemann
__init__.pyadmissible_family_sweep.pyadmissible_rescaling.pyaggregates_closure_signature.pyalpha_sweep.pyanalytic_continuation_dirichlet.pyanalytic_continuation.pycoercivity_uniform.pycoupling_weights_type_signature.pycurrents_closure_signature.pydelta_phi_max_type_signature.pydirichlet_l.pydnfr_type_signature.pyepi_type_signature.pyhilbert_polya.pyli_keiper.pylyapunov_spectral_positivity.pynodal_pulse.pynodeaware_gauge_sweep.pynuf_type_signature.pyoperator_catalog_discipline_signature.pyoperator.pyoscillatory_correction.pypaley_gap_coercivity.pyphi_type_signature.pyprime_ladder_hamiltonian.pypulse_coherence.pyremesh_infinity_residue_split.pyremesh_window_type_signature.pyspectral_emergence.pystructural_zero_density.pytelemetry.pytetrad_closure_signature.pytwisted_admissible_family_sweep.pytwisted_admissible_rescaling.pytwisted_alpha_sweep.pytwisted_coercivity_uniform.pytwisted_hermite_family.pytwisted_hilbert_polya.pytwisted_li_keiper.pytwisted_lyapunov_spectral_positivity.pytwisted_nodeaware_gauge_sweep.pytwisted_oscillatory_correction.pytwisted_paley_gap_coercivity.pytwisted_prime_ladder_hamiltonian.pytwisted_spectral_emergence.pytwisted_structural_zero_density.pytwisted_weil_explicit_formula.pytwisted_weil_positivity.pyurules_consistency_signature.pyvon_mangoldt.pyweil_explicit_formula.pyweil_positivity.py
schemas
__init__.pygrammar.jsonREADME.md
sdk
__init__.py__init__.pyiadaptive_system.pyadaptive_system.pyibuilders.pybuilders.pyifluent.pyfluent.pyiREADME.mdself_opt.pysimple.pytemplates.pytemplates.pyiutils.py
security
__init__.pycrypto.pydatabase.pyREADME.mdsubprocess.pyvalidation.py
sequencing
__init__.pypatterns.pyREADME.md
services
__init__.pyorchestrator.pyREADME.md
sparse
__init__.pyREADME.mdrepresentations.py
structural
README.md
telemetry
__init__.pycache_metrics.pycache_metrics.pyiconstants.pynu_f.pynu_f.pyiREADME.mdunified_telemetry_system.pyverbosity.pyverbosity.pyi
tools
__init__.pydomain_templates.pyREADME.mdsequence_generator.pytnfr_is_prime_cli_optimized.pytnfr_is_prime_cli.py
topology
__init__.pyasymmetry.pyREADME.md
utils
cache_layers.pycache.pycache.pyicallbacks.pycallbacks.pyichunks.pychunks.pyidata.pydata.pyifast_diameter.pygraph.pygraph.pyiinit.pyinit.pyiio.pyio.pyinumeric.pynumeric.pyiREADME.mdtopology.pyunified_cache.py
validation
__init__.py__init__.pyiaggregator.pybase.pycompatibility.pycompatibility.pyiconfig.pygraph.pygraph.pyihealth.pyinput_validation.pyinterface_baselines.pyinvariants.pymultichannel_interface.pyphase_gate.pyREADME.mdrules.pyrules.pyiruntime.pyruntime.pyisequence_validator.pysignal_confrontation.pysoft_filters.pysoft_filters.pyispectral.pyspectral.pyistructural_interface.pytemporal_interface.pyunified_validation_system.pyvalidator.pywindow.pywindow.pyi
visualization
__init__.pycascade_viz.pyhierarchy.pyREADME.mdsequence_plotter.py
yang_mills
__init__.pyclosure.pyderivability.pyscaling.pystructural_gap.pyu6_sweep.py
__init__.py__init__.pyi_compat.py_version.py_version.pyialias.pyalias.pyibackend_config.pycache.pycache.pyiexecution.pyexecution.pyiflatten.pyflatten.pyigamma.pygamma.pyiglyph_history.pyglyph_history.pyiglyph_runtime.pyglyph_runtime.pyiimmutable.pyimmutable.pyiinitialization.pyinitialization.pyiio.pyio.pyilocking.pylocking.pyinode.pynode.pyiobservers.pyobservers.pyiontosim.pyontosim.pyipy.typedrng.pyrng.pyisecure_config.pyselector.pyselector.pyisense.pysense.pyistructural.pystructural.pyitokens.pytokens.pyitrace.pytrace.pyitypes.pytypes.pyiunits.pyunits.pyi
tetrad_evaluator.py
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FILE: src/tnfr/validation/interface_baselines.py

interface_baselines.py

Classical graph-local baselines for structural-interface benchmarks.

This module is the fair-comparison layer for TNFR Structural Interface Theory. It provides classical, well-understood, graph-local node scores that any TNFR interface claim must be compared against. The closest classical analogue to the TNFR phase-gate stress is :func:local_disagreement; the remaining baselines (graph total variation, local class entropy, label-propagation residual, graph cut contribution, neighbour distance, degree, feature deviation, and constant/random controls) widen the comparison so that any reported TNFR advantage is measured against strong, not only weak, references.

Design rules

  • Pure-Python and deterministic. random_baseline uses a seeded :class:random.Random over a stable node order; everything else is exact.
  • Read-only: no graph attribute is mutated.
  • Each baseline returns a dict[node, float] so it can be ranked uniformly by :func:tnfr.validation.structural_interface.evaluate_interface_scores.
  • Formulas are documented per function (Milestone 2 acceptance criterion).

Honest note

For a binary label encoded as a phase (0 vs π), graph total variation on the phase signal is proportional to :func:local_disagreement. This is stated explicitly rather than hidden: the two baselines coincide up to a scale factor when the only per-node signal is the label itself.

References

  • docs/STRUCTURAL_INTERFACE_THEORY_PLAN.md §"Fair benchmark design"

Source Code

python
"""Classical graph-local baselines for structural-interface benchmarks.

This module is the *fair-comparison* layer for TNFR Structural Interface Theory.
It provides classical, well-understood, graph-local node scores that any TNFR
interface claim must be compared against.  The closest classical analogue to the
TNFR phase-gate stress is :func:`local_disagreement`; the remaining baselines
(graph total variation, local class entropy, label-propagation residual, graph
cut contribution, neighbour distance, degree, feature deviation, and
constant/random controls) widen the comparison so that any reported TNFR
advantage is measured against strong, not only weak, references.

Design rules
------------
- Pure-Python and deterministic.  ``random_baseline`` uses a seeded
  :class:`random.Random` over a stable node order; everything else is exact.
- Read-only: no graph attribute is mutated.
- Each baseline returns a ``dict[node, float]`` so it can be ranked uniformly by
  :func:`tnfr.validation.structural_interface.evaluate_interface_scores`.
- Formulas are documented per function (Milestone 2 acceptance criterion).

Honest note
-----------
For a *binary* label encoded as a phase (0 vs ``π``), graph total variation on
the phase signal is proportional to :func:`local_disagreement`.  This is stated
explicitly rather than hidden: the two baselines coincide up to a scale factor
when the only per-node signal is the label itself.

References
----------
- ``docs/STRUCTURAL_INTERFACE_THEORY_PLAN.md`` §"Fair benchmark design"
"""

from __future__ import annotations

import math
import random
from typing import Any, Mapping

try:
    import networkx as nx
except ImportError:  # pragma: no cover - optional dependency guard
    nx = None  # type: ignore[assignment]

__all__ = [
    "local_disagreement",
    "graph_total_variation",
    "local_class_entropy",
    "label_propagation_residual",
    "graph_cut_contribution",
    "mean_neighbour_distance",
    "degree_score",
    "feature_deviation",
    "constant_baseline",
    "random_baseline",
    "compute_all_baselines",
    "BASELINE_FORMULAS",
]

_DEFAULT_DISTANCE_KEY = "distance"

#: Short human-readable formula notes, surfaced in reports for transparency.
BASELINE_FORMULAS: Mapping[str, str] = {
    "local_disagreement": "count of neighbours whose state differs from the node",
    "graph_total_variation": "sum_j |v_i - v_j| over incident edges (v = numeric signal or label code)",
    "local_class_entropy": "Shannon entropy of class counts over the closed neighbourhood, normalized by log(#classes)",
    "label_propagation_residual": "1 - f_i[own_class] after clamped label propagation (alpha, iterations)",
    "graph_cut_contribution": "sum over cross-class incident edges of similarity weight 1/(1+distance)",
    "mean_neighbour_distance": "mean feature-space distance to neighbours (edge distance attribute)",
    "degree": "node degree",
    "feature_deviation": "|x_i - mean(x)| / std(x) for a chosen numeric feature",
    "constant": "constant 1.0 for every node (control)",
    "random": "uniform[0,1) per node from a seeded RNG (control)",
}


def _require_networkx() -> None:
    if nx is None:  # pragma: no cover - optional dependency guard
        raise RuntimeError("networkx is required for interface baselines")


def _stable_nodes(G: Any) -> list[Any]:
    """Return graph nodes in a deterministic order (by ``repr``)."""
    return sorted(G.nodes(), key=lambda node: repr(node))


def _has_numeric_attr(G: Any, key: str) -> bool:
    for node in G.nodes():
        value = G.nodes[node].get(key)
        if not isinstance(value, (int, float)) or isinstance(value, bool):
            return False
    return G.number_of_nodes() > 0


# ---------------------------------------------------------------------------
# Boundary-sensitive baselines
# ---------------------------------------------------------------------------


def local_disagreement(G: Any, *, state_key: str) -> dict[Any, float]:
    """Count, per node, the neighbours whose ``state_key`` differs.

    Formula: ``score_i = |{ j ~ i : state_j != state_i }|``.

    This is the closest classical analogue to TNFR phase-gate violations and is
    the primary reference baseline for any interface claim.
    """
    _require_networkx()
    scores: dict[Any, float] = {}
    for node in G.nodes():
        own = G.nodes[node].get(state_key)
        scores[node] = float(
            sum(
                1
                for neighbour in G.neighbors(node)
                if G.nodes[neighbour].get(state_key) != own
            )
        )
    return scores


def _state_codes(G: Any, state_key: str) -> dict[Any, int]:
    classes = sorted(
        {G.nodes[node].get(state_key) for node in G.nodes()}, key=lambda c: repr(c)
    )
    return {cls: code for code, cls in enumerate(classes)}


def graph_total_variation(
    G: Any,
    *,
    value_key: str | None = None,
    state_key: str | None = None,
) -> dict[Any, float]:
    """Per-node graph total variation of a numeric signal.

    Formula: ``score_i = sum_{j ~ i} |v_i - v_j|``.

    When ``value_key`` is given, ``v`` is that numeric node attribute.  Otherwise
    ``state_key`` must be given and categories are mapped to integer codes
    (``v`` = code).  For a binary label this is proportional to
    :func:`local_disagreement`.
    """
    _require_networkx()
    if value_key is None and state_key is None:
        raise ValueError("provide value_key or state_key")

    if value_key is not None:
        value = {node: float(G.nodes[node].get(value_key, 0.0)) for node in G.nodes()}
    else:
        codes = _state_codes(G, state_key)  # type: ignore[arg-type]
        value = {
            node: float(codes.get(G.nodes[node].get(state_key), 0))
            for node in G.nodes()
        }

    scores: dict[Any, float] = {}
    for node in G.nodes():
        own = value[node]
        scores[node] = float(
            sum(abs(own - value[neighbour]) for neighbour in G.neighbors(node))
        )
    return scores


def local_class_entropy(
    G: Any, *, state_key: str, normalize: bool = True
) -> dict[Any, float]:
    """Shannon entropy of class counts over each closed neighbourhood.

    The closed neighbourhood of ``i`` is ``{i} ∪ N(i)``.  Higher entropy means a
    more mixed neighbourhood, i.e. a stronger interface.  When ``normalize`` is
    True the entropy is divided by ``log(#global_classes)`` so scores lie in
    ``[0, 1]``.
    """
    _require_networkx()
    global_classes = {G.nodes[node].get(state_key) for node in G.nodes()}
    norm = math.log(len(global_classes)) if len(global_classes) > 1 else 0.0

    scores: dict[Any, float] = {}
    for node in G.nodes():
        counts: dict[Any, int] = {}
        members = [node, *G.neighbors(node)]
        for member in members:
            cls = G.nodes[member].get(state_key)
            counts[cls] = counts.get(cls, 0) + 1
        total = sum(counts.values())
        entropy = 0.0
        if total > 0:
            for count in counts.values():
                p = count / total
                entropy -= p * math.log(p)
        if normalize and norm > 0:
            scores[node] = float(entropy / norm)
        else:
            scores[node] = float(entropy)
    return scores


def label_propagation_residual(
    G: Any,
    *,
    state_key: str,
    alpha: float = 0.85,
    iterations: int = 30,
) -> dict[Any, float]:
    """Clamped label-propagation disagreement residual.

    Each node starts with a one-hot class vector.  At every iteration the soft
    label is updated as ``f_i <- (1 - alpha) * seed_i + alpha * mean_j f_j``.
    After ``iterations`` steps the residual is ``1 - f_i[own_class]`` (the soft
    probability mass that propagation moved away from the node's own class).
    Boundary nodes accumulate larger residuals.  Deterministic.
    """
    _require_networkx()
    nodes = list(G.nodes())
    classes = sorted(
        {G.nodes[node].get(state_key) for node in nodes}, key=lambda c: repr(c)
    )
    if len(classes) <= 1:
        return {node: 0.0 for node in nodes}
    index = {cls: i for i, cls in enumerate(classes)}
    k = len(classes)

    seed = {node: [0.0] * k for node in nodes}
    for node in nodes:
        seed[node][index[G.nodes[node].get(state_key)]] = 1.0
    f = {node: list(seed[node]) for node in nodes}

    for _ in range(max(1, int(iterations))):
        updated: dict[Any, list[float]] = {}
        for node in nodes:
            neighbours = list(G.neighbors(node))
            if neighbours:
                acc = [0.0] * k
                for neighbour in neighbours:
                    fj = f[neighbour]
                    for c in range(k):
                        acc[c] += fj[c]
                inv = 1.0 / len(neighbours)
                propagated = [value * inv for value in acc]
            else:
                propagated = list(seed[node])
            updated[node] = [
                (1.0 - alpha) * seed[node][c] + alpha * propagated[c] for c in range(k)
            ]
        f = updated

    residual: dict[Any, float] = {}
    for node in nodes:
        own = index[G.nodes[node].get(state_key)]
        total = sum(f[node]) or 1.0
        residual[node] = float(1.0 - f[node][own] / total)
    return residual


def graph_cut_contribution(
    G: Any,
    *,
    state_key: str,
    distance_key: str = _DEFAULT_DISTANCE_KEY,
) -> dict[Any, float]:
    """Per-node contribution to a similarity-weighted class cut.

    Formula: ``score_i = sum_{j ~ i, state_j != state_i} 1 / (1 + distance_ij)``.

    Unlike :func:`local_disagreement` (a raw count), this weights cross-class
    edges by feature-space proximity, so a node that is *close* to a
    differently-labelled neighbour scores higher than one whose cross-class
    neighbour is far.
    """
    _require_networkx()
    scores: dict[Any, float] = {}
    for node in G.nodes():
        own = G.nodes[node].get(state_key)
        total = 0.0
        for neighbour in G.neighbors(node):
            if G.nodes[neighbour].get(state_key) != own:
                distance = float(G.edges[node, neighbour].get(distance_key, 0.0))
                total += 1.0 / (1.0 + distance)
        scores[node] = float(total)
    return scores


# ---------------------------------------------------------------------------
# Topology / feature / control baselines
# ---------------------------------------------------------------------------


def mean_neighbour_distance(
    G: Any, *, distance_key: str = _DEFAULT_DISTANCE_KEY
) -> dict[Any, float]:
    """Mean feature-space distance to neighbours (edge ``distance_key``)."""
    _require_networkx()
    scores: dict[Any, float] = {}
    for node in G.nodes():
        distances = [
            float(G.edges[node, neighbour].get(distance_key, 0.0))
            for neighbour in G.neighbors(node)
        ]
        scores[node] = sum(distances) / len(distances) if distances else 0.0
    return scores


def degree_score(G: Any) -> dict[Any, float]:
    """Node degree (topology-only control)."""
    _require_networkx()
    return {node: float(G.degree[node]) for node in G.nodes()}


def feature_deviation(G: Any, *, value_key: str) -> dict[Any, float]:
    """Standardized absolute deviation of a numeric feature from its mean.

    Formula: ``score_i = |x_i - mean(x)| / std(x)`` (std clamped to 1 if zero).
    A simple, domain-agnostic feature baseline.
    """
    _require_networkx()
    values = {node: float(G.nodes[node].get(value_key, 0.0)) for node in G.nodes()}
    if not values:
        return {}
    mean = sum(values.values()) / len(values)
    variance = sum((v - mean) ** 2 for v in values.values()) / len(values)
    std = math.sqrt(variance) or 1.0
    return {node: abs(value - mean) / std for node, value in values.items()}


def constant_baseline(G: Any, *, value: float = 1.0) -> dict[Any, float]:
    """Constant score for every node (trivial control)."""
    _require_networkx()
    return {node: float(value) for node in G.nodes()}


def random_baseline(G: Any, *, seed: int = 0) -> dict[Any, float]:
    """Deterministic uniform[0,1) score per node from a seeded RNG."""
    _require_networkx()
    rng = random.Random(int(seed))
    return {node: rng.random() for node in _stable_nodes(G)}


# ---------------------------------------------------------------------------
# Aggregator
# ---------------------------------------------------------------------------


def compute_all_baselines(
    G: Any,
    *,
    state_key: str,
    distance_key: str = _DEFAULT_DISTANCE_KEY,
    phase_key: str = "phase",
    feature_key: str | None = None,
    seed: int = 0,
) -> dict[str, dict[Any, float]]:
    """Compute the full classical baseline suite as named node-score maps.

    The graph-total-variation baseline uses the numeric ``phase_key`` signal when
    every node carries it; otherwise it falls back to state-code total variation
    (documented to coincide with :func:`local_disagreement` up to scaling for
    binary labels).  ``feature_key`` adds :func:`feature_deviation` when supplied.
    """
    _require_networkx()
    use_phase = _has_numeric_attr(G, phase_key)
    maps: dict[str, dict[Any, float]] = {
        "local_disagreement": local_disagreement(G, state_key=state_key),
        "graph_total_variation": graph_total_variation(
            G,
            value_key=phase_key if use_phase else None,
            state_key=None if use_phase else state_key,
        ),
        "local_class_entropy": local_class_entropy(G, state_key=state_key),
        "label_propagation_residual": label_propagation_residual(
            G, state_key=state_key
        ),
        "graph_cut_contribution": graph_cut_contribution(
            G, state_key=state_key, distance_key=distance_key
        ),
        "mean_neighbour_distance": mean_neighbour_distance(
            G, distance_key=distance_key
        ),
        "degree": degree_score(G),
        "constant": constant_baseline(G),
        "random": random_baseline(G, seed=seed),
    }
    if feature_key is not None:
        maps["feature_deviation"] = feature_deviation(G, value_key=feature_key)
    return maps