phase: 4D
names:
  runtime: MaleCNS-LIF-runtime-v1
  io_api: MaleCNS-BrainIO-v1
  visual_adapter: MaleCNS-VisualAdapter-v1
  activity_stream: MaleCNS-ActivityStream-v1

paths:
  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
  model_root: /data/digital-drosophila/models/male-cns-lif
  runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
  phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
  experiment_root: /data/digital-drosophila/experiments/phase4d-io

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

input_batch:
  version: 1.0.0
  allowed_modes: [spike_injection, external_synaptic_drive]
  refractory_respecting_spike_injection: true
  external_drive_application: add to g after decay and delayed-connectome arrival, before membrane integration

visual_adapter:
  version: 1.0.0
  modes:
    reference-photoreceptor:
      hierarchy_population: visual_sensory
      input_mode: spike_injection
      biological_fidelity: reference_comparison_only
    engineering-first-order:
      hierarchy_population: first_order
      input_mode: external_synaptic_drive
      biological_fidelity: engineering_adapter
    engineering-second-order:
      hierarchy_population: second_order
      input_mode: external_synaptic_drive
      biological_fidelity: engineering_adapter
  synthetic_rate_hz: 50.0
  external_drive_mv: 8.0

readout:
  bins_ms: [1, 5, 10, 20, 50]
  output_populations: [descending, motor_related, ascending]

window_experiment:
  windows_ms: [5, 10, 20, 30, 50, 100]
  sources: [engineering-first-order, engineering-second-order, auditory, olfactory]
  seeds: [44001, 44002]

continuous_control:
  biological_duration_ms: 1000.0
  periods_ms: [10, 20, 50, 100]
  sequence: [sparse-A, sparse-B, dense, zero, sparse-A]
  seed: 44100

synthetic_patterns:
  sparse_fraction: 0.05
  dense_fraction: 0.25
  moving_fraction: 0.05
  deterministic_seed: 44200

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}

prohibitions:
  stable_retro: false
  rom_access: false
  controller_buttons: false
  training: false
  web_server: false
  connectome_or_sign_changes: false