phase: 4J
name: MaleCNS-MB-physiology-repair-v1

paths:
  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
  model_root: /data/digital-drosophila/models/male-cns-lif
  phase4j_model_root: /data/digital-drosophila/models/male-cns-lif/mb-physiology-v1
  experiment_root: /data/digital-drosophila/experiments/phase4j-mb-physiology-repair
  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

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

stimuli:
  targets_per_odor: 64
  rate_hz: 50.0
  duration_ms: 100.0
  calibration_odor_count: 4
  heldout_odor_count: 4
  evaluation_seeds: [50101, 50102, 50103, 50104, 50105]
  calibration_seed_base: 50000
  formal_CS_seeds: [48101, 48102, 48103, 48104, 48105]

apl_overlay:
  name: APL-Graded-Inhibition-v1
  interpretation: experimental physiology overlay supplementing missing graded/non-spiking APL behavior in point-LIF
  input_classes: [Kenyon_Cell, ALPN]
  replace_spiking_APL_output_in_memory_only: true
  calibration_reference_active_KC_fraction: [0.03, 0.09]
  target_fraction_for_scoring: 0.06
  tau_grid_ms: [20.0, 50.0, 100.0]
  gain_grid_mv_per_state_step: [0.00001, 0.00003, 0.0001, 0.0003, 0.001, 0.003, 0.01, 0.03]
  normalization_grid: [0.5, 1.0, 2.0]
  heldout_max_mean_jaccard: 0.8
  heldout_minimum_nonzero_fraction: 0.01

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
  delta_t_ms: [-1000, -500, -250, -100, -50, 0, 50, 100, 250, 500, 1000]
  pass_max_negative_LTD_fraction: 0.0
  pass_plus_1000_to_zero_ratio: 0.01
  provenance:
    - https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
    - https://pubmed.ncbi.nlm.nih.gov/26637800/

bidirectional_branch:
  name: order-sensitive-bidirectional-v1
  kc_before_dan_tau_ms: 100.0
  dan_before_kc_tau_ms: 100.0
  kc_before_dan_polarity: -1
  dan_before_kc_polarity: 1
  eta_effective_mv: 0.00275
  provenance:
    - https://pmc.ncbi.nlm.nih.gov/articles/PMC9012144/
  selection_policy: report_independently_never_select_by_memory_result

direct_kc:
  ensemble_size: 64
  target_compartment_verbatim: "y5B'2a"
  matched_dan_type: PAM15
  unrelated_compartment_verbatim: "y2a'1"
  unrelated_dan_type: PPL103
  pulse_times_ms: [10.0, 30.0, 50.0, 70.0, 90.0]
  dan_time_ms: 90.0
  duration_ms: 120.0
  conditioning_trials: 3
  train_seeds: [50201, 50202, 50203, 50204, 50205]
  evaluation_seeds: [50301, 50302, 50303, 50304, 50305]

gates:
  sparse_min_fraction: 0.03
  sparse_max_fraction: 0.09
  direct_seed_majority: 3
  subthreshold_noise_floor: 0.0001

prohibitions:
  modify_base_disk_artifacts: false
  expand_plastic_mask: false
  modify_global_or_KC_threshold: false
  winner_take_all_or_top_k: false
  tune_on_formal_CS: false
  tune_plasticity_polarity_or_eta: false
  modify_MBON_threshold_or_gain: false
  decoder_or_classifier: false
  game_visual_RL: false