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

2026-09-29 03:38:32 +08:00
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+phase: 4L
+name: MaleCNS-Olfactory-grounding-v1
+
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  dataset_root: /data/digital-drosophila/datasets/male-cns-v1.0
+  model_root: /data/digital-drosophila/models/male-cns-lif
+  phase4l_model_root: /data/digital-drosophila/models/male-cns-lif/olfactory-grounding-v1
+  experiment_root: /data/digital-drosophila/experiments/phase4l-olfactory-grounding
+  external_door_root: /data/digital-drosophila/experiments/phase4l-olfactory-grounding/external-resources/DoOR.data
+  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
+  phase4h_root: /data/digital-drosophila/experiments/phase4h-dopamine-plasticity
+  phase4h_model_root: /data/digital-drosophila/models/male-cns-lif/dopamine-plasticity-v1
+  phase4h_learned_root: /data/digital-drosophila/models/learned/phase4h
+  phase4i_root: /data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation
+  phase4i_model_root: /data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1
+  phase4j_root: /data/digital-drosophila/experiments/phase4j-mb-physiology-repair
+  phase4j_model_root: /data/digital-drosophila/models/male-cns-lif/mb-physiology-v1
+  phase4k_root: /data/digital-drosophila/experiments/phase4k-kc-recruitment-audit
+  phase4k_model_root: /data/digital-drosophila/models/male-cns-lif/kc-recruitment-audit-v1
+
+names:
+  reference: MaleCNS-LIF-reference-v1
+  runtime: MaleCNS-LIF-runtime-v1
+
+model:
+  dt_ms: 0.1
+  membrane_tau_ms: 20.0
+  synaptic_tau_ms: 5.0
+  refractory_ms: 2.2
+  resting_potential_mv: -52.0
+  reset_potential_mv: -52.0
+  threshold_mv: -45.0
+  synaptic_delay_ms: 1.8
+  w_syn_mv_per_anatomical_synapse: 0.275
+
+sign_policy:
+  neurotransmitter_sign: {acetylcholine: 1, gaba: -1, glutamate: -1, dopamine: 1, octopamine: 1, serotonin: 1, histamine: -1}
+  unknown_sign: 0
+  unclear_sign: 0
+
+readout:
+  bins_ms: [1, 5, 10, 20, 50, 100]
+
+device:
+  required_name_substring: RTX 4090
+  launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
+
+expected_graph:
+  neurons: 166700
+  directed_edges: 25582938
+  synaptic_contact_weight_sum: 124177617
+  phase4h_plastic_candidate_edges: 14232
+  plastic_mask_edges: 14232
+
+external_resource:
+  dataset: DoOR.data
+  version: 2.0.1
+  git_tag: v2.0.1
+  git_commit: eea72d64b42a4e91dafe822cf0b5204de33f8d34
+  source: https://github.com/ropensci/DoOR.data
+  license: CC BY-SA 4.0
+  response_scale: globally normalized consensus response [0,1]
+  receptor_naming: DoOR responding-unit/receptor column names
+  glomerulus_naming: DoOR door_mappings glomerulus field
+
+odor_encoder:
+  name: OlfactoryEncoder-v1
+  duration_ms: 100.0
+  max_total_rate_per_glomerulus_hz: 400.0
+  transform: total glomerular Poisson rate = 400 Hz * normalized DoOR response; distributed uniformly across exact-mapped MaleCNS ALPNs
+  calibration_odors: 6
+  heldout_odors: 6
+  strong_response_threshold: 0.2
+  minimum_mapped_strong_channels: 5
+  evaluation_seeds: [51101, 51102, 51103, 51104, 51105]
+  selection_policy: rank by mapped-signal fraction then mapped strong-channel count; split first 6 calibration and next 6 held-out; select held-out A/B by maximum external mapped-vector cosine distance before any KC simulation
+  modes: [physiological, matched_energy]
+  matched_energy_reference: median mapped response sum across the frozen 12-odor panel
+
+apl_overlay:
+  name: APL-Graded-Inhibition-v1
+  tau_ms: 20.0
+  gain: 0.01
+  normalization: 1.0
+  immutable_phase4j_parameters: true
+
+eligibility_v2:
+  name: causal-LTD-engineering-model
+  kc_trace_tau_ms: 100.0
+  trace_cap: 1.0
+  eta_effective_mv: 0.00275
+  polarity: -1
+  max_fractional_depression: 0.25
+  provenance:
+    - https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
+    - https://pubmed.ncbi.nlm.nih.gov/26637800/
+
+plasticity_accumulation:
+  name: PlasticityAccumulation-v1
+  rule: additive frozen TemporalEligibility-v2 per-pair update with per-edge floor at -25% base weight
+  recovery_between_short_pairings: none
+  pairing_counts: [1, 2, 5, 10, 20, 50, 100]
+  train_seeds: [51201, 51202, 51203, 51204, 51205]
+  evaluation_seeds: [51301, 51302, 51303, 51304, 51305]
+  target_compartment_verbatim: "y5B'2a"
+  matched_dan_type: PAM15
+  dan_time_ms: 90.0
+  duration_ms: 120.0
+  formal_conditioning_pairings: 50
+  explicit_engineering_assumption: repeated pair updates add linearly until the already-frozen 25-percent per-edge depression floor; no recovery is modeled over this short sweep
+
+gates:
+  sparse_min_fraction: 0.03
+  sparse_max_fraction: 0.09
+  minimum_separable_odor_pairs: 3
+  minimum_specific_kc: 1
+  minimum_specific_edges: 1
+  seed_majority: 3
+
+prohibitions:
+  modify_base_disk_artifacts: false
+  modify_eligibility_v2: false
+  tune_eta_from_phase4k_sensitivity: false
+  expand_plastic_mask: false
+  modify_W_syn_threshold_signs: false
+  force_top_k_or_manual_KC: false
+  decoder_classifier_game_visual_RL_web_3d: false