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

2026-09-29 03:38:32 +08:00
commit 3981628ff8
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+phase: 4B
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  experiment_root: /data/digital-drosophila/experiments/phase4b-dynamics
+
+expected_graph:
+  neurons: 166700
+  directed_edges: 25582938
+  synaptic_contact_weight_sum: 124177617
+  isolated_neurons: 217
+  self_loops: 101
+
+device:
+  required_name_substring: RTX 4090
+  launcher_visible_gpu_uuid: GPU-79f3a85d-adce-7833-7003-6488140ca596
+  mixed_multi_gpu: false
+
+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
+  integration: forward_euler
+  refractory_g_policy: g continues to decay and receive delayed events while v is clamped at V_reset
+  provenance: Shiu-2024-compatible baseline supplied by user; not MaleCNS measured single-cell parameters
+
+sign_policy:
+  neurotransmitter_sign:
+    acetylcholine: 1
+    gaba: -1
+    glutamate: -1
+    histamine: -1
+    dopamine: 1
+    octopamine: 1
+    serotonin: 1
+  unknown_sign: 0
+  unclear_sign: 0
+  unmapped_policy: error
+
+sensory_populations:
+  visual:
+    expression: annotation_class == 'visual'
+  mechanosensory:
+    expression: annotation_class in {'mechanosensory','mechanosensory_tactile','mechanosensory_proprioceptive'} and annotation_subclass != 'auditory'
+  olfactory:
+    expression: annotation_class == 'olfactory'
+  gustatory:
+    expression: annotation_class == 'gustatory'
+  auditory:
+    expression: annotation_subclass == 'auditory'
+
+baseline_sweep:
+  rates_hz: [10, 25, 50, 100, 150, 200]
+  seeds: [42001, 42002, 42003]
+  duration_ms: 1000.0
+  event_logging: false
+
+weight_sweep:
+  population: auditory
+  rate_hz: 100
+  seed: 42100
+  duration_ms: 1000.0
+  values_mv: [0.1375, 0.20625, 0.275, 0.34375, 0.55]
+
+stimulation:
+  mode: refractory-respecting forced sensory-neuron Poisson spikes
+  note: no arbitrary current amplitude is introduced; accepted events become presynaptic spikes
+
+classification:
+  supercritical_peak_step_fraction: 0.10
+  supercritical_active_fraction: 0.80
+  supercritical_mean_rate_hz: 100.0
+  propagating_min_depth: 2
+  abort_supercritical: true
+  check_interval_steps: 50
+
+performance:
+  population: auditory
+  rate_hz: 10
+  seed: 42200
+  duration_ms: 1000.0
+  gpu_sample_interval_seconds: 0.2
+  compare_logging_disabled_and_full: true
+
+profiler:
+  population: auditory
+  rate_hz: 10
+  seed: 42201
+  duration_ms: 1000.0
+  synchronized_category_timing: true
+
+causal_validation:
+  requested_chains: 100
+  requested_inhibitory_transmissions: 100
+  seed: 42300
+  max_edges_examined: 5000000
+
+cpu_gpu_reference:
+  seed: 42400
+  subgraph_neurons: 512
+  steps: 100
+  absolute_tolerance: 1.0e-10
+
+audit:
+  finite_check_interval_steps: 100
+  memory_growth_tolerance_bytes: 10485760
+  preserve_source_data: true
+
+reproducibility:
+  global_seed: 42000
+  deterministic_inputs: true