Archive MaleCNS research sources, provenance, bibliography and immutable data inventory

2026-09-29 03:38:32 +08:00
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+phase: 4H
+execution:
+  mode: two-stage
+  stage1_only_entrypoint: phase4h_audit.py
+  require_stage1_pass_before_conditioning: true
+
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
+  learned_root: /data/digital-drosophila/models/learned/phase4h
+  experiment_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
+  reference_root: /data/digital-drosophila/models/male-cns-lif/reference-v1
+  runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
+  io_root: /data/digital-drosophila/models/male-cns-lif/io-v1
+  phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
+  phase4d_root: /data/digital-drosophila/experiments/phase4d-io
+  phase4e_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
+  phase4f_root: /data/digital-drosophila/experiments/phase4f-retinotopic-vision
+  phase4f_model_root: /data/digital-drosophila/models/male-cns-lif/visual-encoder-v1
+  phase4g_root: /data/digital-drosophila/experiments/phase4g-frozen-interface
+  phase4g_model_root: /data/digital-drosophila/models/male-cns-lif/frozen-interface-v1
+  phase4g_learned_root: /data/digital-drosophila/models/learned/phase4g
+
+expected_graph:
+  neurons: 166700
+  directed_edges: 25582938
+  synaptic_contact_weight_sum: 124177617
+
+audit:
+  exact_class_values:
+    KC: Kenyon_Cell
+    MBON: MBON
+    DAN: DAN
+  pam_type_prefix: PAM
+  ppl1_type_prefix: PPL1
+  compartment_source_field: annotation_instance
+  compartment_parser: single_parenthesized_substring_verbatim
+  require_exact_compartment_string_match: true
+  candidate_requires_actual_kc_mbon_edge: true
+  candidate_requires_actual_dan_mbon_edge: true
+  candidate_requires_exact_dan_mbon_compartment_match: true
+  do_not_infer_missing_compartment_from_type: true
+
+plasticity:
+  base_connectome_mode: read_only
+  overlay_equation: effective_weight = base_weight + plastic_delta
+  rule: delta_w = polarity_compartment * eta * D_compartment(t) * eligibility_ij(t)
+  first_version_rule_family: compartment_specific_dopamine_gated_anti_hebbian_depression
+  default_confirmed_compartment_polarity: -1
+  unknown_compartment_policy: exclude_from_plastic_mask
+  pam_ppl1_cluster_valence_policy: prohibited
+  reward_interface_interpretation: artificial_unconditioned_signal_not_dopamine_concentration
+  polarity_provenance:
+    - https://pubmed.ncbi.nlm.nih.gov/26637800/
+    - https://pubmed.ncbi.nlm.nih.gov/25535793/
+    - https://www.nature.com/articles/s41586-024-07819-w
+
+prohibitions:
+  modify_phase1_to_phase4g: false
+  conditioning_during_stage1: false
+  weight_update_during_stage1: false
+  infer_unknown_mapping: false
+  train_base_brain: false
+