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

2026-09-29 03:38:32 +08:00
commit 3981628ff8
682 changed files with 161475 additions and 0 deletions
@@ -0,0 +1,115 @@
+phase: 4E
+names:
+  reference: MaleCNS-LIF-reference-v1
+  runtime: MaleCNS-LIF-runtime-v1
+  io_api: MaleCNS-BrainIO-v1
+  candidate: MaleCNS-VisualAdapter-v2-candidate
+
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  model_root: /data/digital-drosophila/models/male-cns-lif
+  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
+  experiment_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
+  candidate_root: /data/digital-drosophila/models/male-cns-lif/visual-interface-v2
+
+device:
+  required_name_substring: RTX 4090
+  launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
+
+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
+    histamine: -1
+    dopamine: 1
+    octopamine: 1
+    serotonin: 1
+  unknown_sign: 0
+  unclear_sign: 0
+
+visual_populations:
+  reference-photoreceptor: {source: hierarchy, value: visual_sensory, interface_kind: biological-reference, stimulation_mode: spike_injection}
+  engineering-first-order: {source: hierarchy, value: first_order, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
+  engineering-second-order: {source: hierarchy, value: second_order, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
+  engineering-higher-visual: {source: hierarchy, value: higher_visual, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
+  engineering-visual-projection: {source: metadata-expression, field: annotation_superclass, values: [visual_projection, visual_projection_tbc], interface_kind: engineering, stimulation_mode: external_synaptic_drive}
+
+calibration:
+  seed: 45000
+  trial_duration_ms: 100.0
+  chunk_ms: 10.0
+  fixed_rate_hz: 50.0
+  fixed_sparsity_percent: 5.0
+  amplitude_multiples: [0.25, 0.5, 1, 2, 4, 8, 16]
+  extended_amplitude_multiples: [32, 64]
+  rate_hz: [10, 25, 50, 100, 150, 200]
+  sparsity_percent: [0.1, 0.5, 1, 5, 10, 25, 50, 100]
+  latency_windows_ms: [5, 10, 20, 30, 50, 100, 200]
+  deterministic_repeats: 2
+  runaway:
+    active_fraction_gte: 0.80
+    mean_firing_rate_hz_gte: 100.0
+    peak_step_fraction_gte: 0.10
+  propagation_success:
+    require_output_active: true
+    require_non_target_active: true
+    minimum_graph_hops: 2
+
+patterns:
+  # Separability uses the selected propagating condition's sparsity. This is
+  # retained only as a fallback if that condition has no sparsity field.
+  sparse_percent: 5.0
+  dense_percent: 25.0
+  moving_segments: 5
+  trial_duration_ms: 100.0
+  seeds: [45101, 45102, 45103]
+
+continuous:
+  biological_duration_ms: 1000.0
+  periods_ms: [10, 20, 50, 100]
+  sequence: [sparse-A, sparse-B, sparse-A, moving, zero, dense]
+  seed: 45200
+
+readout:
+  bins_ms: [1, 5, 10, 20, 50]
+
+regression:
+  float_absolute_tolerance: 0.00390625
+  reference_trials:
+    - {name: auditory-10hz, population: auditory, rate_hz: 10, seed: 42001, duration_ms: 1000.0}
+    - {name: auditory-100hz, population: auditory, rate_hz: 100, seed: 42001, duration_ms: 1000.0}
+    - {name: olfactory-50hz, population: olfactory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
+    - {name: mechanosensory-50hz, population: mechanosensory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
+    - {name: gustatory-50hz, population: gustatory, rate_hz: 50, seed: 42003, duration_ms: 1000.0}
+
+candidate_selection:
+  rule: "gateway iff multi-hop propagation reaches descending or motor output and is non-runaway; rank by lowest amplitude multiple, then lowest min output hops, then hierarchy order. Formal adapter-v2 eligibility additionally requires deterministic nonzero output separability and matched-input-count validation"
+  hierarchy_order: [engineering-first-order, engineering-second-order, engineering-higher-visual, engineering-visual-projection]
+
+prohibitions:
+  connectome_changes: false
+  raw_weight_changes: false
+  lif_semantics_changes: false
+  transmitter_sign_changes: false
+  training: false
+  reinforcement_learning: false
+  game_integration: false
+  web_server: false
+  three_d_frontend: false
+  phase4f: false