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: 4A
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  experiment_root: /data/digital-drosophila/experiments/phase4a-baseline
+
+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:
+  integrator: forward_euler
+  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
+  parameter_provenance: FlyWire-inspired 2024 LIF baseline; not MaleCNS measured single-cell parameters
+
+sign_policy:
+  neurotransmitter_sign:
+    acetylcholine: 1
+    gaba: -1
+    glutamate: -1
+    dopamine: 1
+    octopamine: 1
+    serotonin: 1
+    histamine: -1
+  histamine_policy_note: explicitly configured inhibitory baseline assumption; not silently inferred
+  unknown_sign: 0
+  unclear_sign: 0
+  unmapped_policy: error
+  unmapped_sign: 0
+
+weights:
+  transform: sqrt
+  supported_transforms: [linear, sqrt, log1p]
+  scale: 0.05
+  chunk_edges: 2000000
+  units: model synaptic-state increment per presynaptic spike
+  formula: effective_weight = presynaptic_sign * scale * f(raw_synapse_count)
+  preserve_raw_int64: true
+
+stimulations:
+  single_neuron:
+    kind: single_neuron_pulse
+    neuron_idx: 0
+    start_ms: 2.0
+    duration_ms: 1.0
+    amplitude_mv_equivalent: 400.0
+  known_type_AMMC005:
+    kind: known_type_pulse
+    type_name: AMMC005
+    max_neurons: 12
+    start_ms: 5.0
+    duration_ms: 1.0
+    amplitude_mv_equivalent: 400.0
+  sparse_poisson:
+    kind: sparse_poisson
+    target_fraction: 0.001
+    rate_hz: 20.0
+    event_amplitude_mv_equivalent: 1600.0
+
+smoke_tests:
+  - name: smoke-10ms-single-neuron
+    duration_ms: 10.0
+    stimulation: single_neuron
+    seed: 41001
+  - name: smoke-100ms-known-type
+    duration_ms: 100.0
+    stimulation: known_type_AMMC005
+    seed: 41002
+  - name: smoke-1s-sparse-poisson
+    duration_ms: 1000.0
+    stimulation: sparse_poisson
+    seed: 41003
+
+cpu_gpu_reference:
+  seed: 41100
+  subgraph_neurons: 512
+  steps: 100
+  pulse_start_step: 5
+  pulse_steps: 10
+  pulse_neurons: 4
+  pulse_amplitude_mv_equivalent: 400.0
+  absolute_tolerance: 1.0e-10
+
+validation:
+  finite_check_interval_steps: 100
+  explosive_step_fraction: 0.1
+  memory_growth_tolerance_bytes: 10485760
+
+output:
+  spike_representation: event_table_timestamp_ms_neuron_idx
+  dense_time_by_neuron_forbidden: true
+  rate_window_ms: 10.0
+
+reproducibility:
+  seed: 41000
+  deterministic_synthetic_inputs: true