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

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Digital Drosophila Archive
2026-09-29 03:38:32 +08:00
commit 3981628ff8
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registry/catalog-20260929/evidence/phase4c-runtime/benchmarks/summary.json
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registry/catalog-20260929/evidence/phase4c-runtime/configs/phase4c.yaml
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phase: 4C
names:
reference: MaleCNS-LIF-reference-v1
runtime: MaleCNS-LIF-runtime-v1
description: Shiu-like LIF dynamics adapted to MaleCNS v1.0
paths:
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
phase4b_root: /data/digital-drosophila/experiments/phase4b-dynamics
model_root: /data/digital-drosophila/models/male-cns-lif
experiment_root: /data/digital-drosophila/experiments/phase4c-runtime
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 exact delayed events while v is clamped at V_reset
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'
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}
visual_dynamics:
duration_ms: 100.0
rate_hz: 50
seed: 43100
tonic_histamine_baseline_hz: 50
modulation_rate_hz: 10
modulation_start_ms: 50.0
benchmark:
population: auditory
rate_hz: 10
seed: 43200
durations_ms: [10.0, 100.0, 1000.0, 10000.0]
gpu_sample_interval_seconds: 0.1
backends: [eager, hybrid-exact, compile-default, compile-reduce-overhead, cudagraph-custom-state, custom-cuda]
warmup_ms: 10.0
regression:
require_exact_spike_events: true
float_absolute_tolerance: 1.0e-5
reject_on_spike_divergence: true
reproducibility:
global_seed: 43000
local_repository_commit: d826733f1c620a2ad0b096c846b9b8e9eb3ac0fa
deterministic_forced_inputs: true
source_phase: Phase 4B PASS
prohibitions:
alter_connectome: false
alter_raw_synapse_counts: false
alter_transmitter_signs: false
train_weights: false
game_rl_web_3d: false
registry/catalog-20260929/evidence/phase4c-runtime/manifests/manifest.json
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registry/catalog-20260929/evidence/phase4c-runtime/visual-audit/dynamics-summary.json
+281
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@@ -0,0 +1,281 @@
{
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}
registry/catalog-20260929/evidence/phase4c-runtime/visual-audit/summary.json
+96
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@@ -0,0 +1,96 @@
{
"all_histaminergic": true,
"all_ol_sensory": true,
"anatomical_membership_counts": {
"lamina": 14929,
"lobula": 1655,
"lobula_plate": 14340,
"medulla": 50994,
"optic_lobe_interneurons": 89403,
"optic_lobe_interneurons_unassigned_to_named_region": 7485,
"photoreceptor": 6091,
"retinal_sensory": 6091,
"visual_projection_neurons": 9203
},
"anatomical_rule_provenance": {
"named_optic_regions": "explicit annotation_type prefix/set rules, preserved in this audit; no body_id was guessed",
"optic_lobe_interneurons": "annotation_superclass=ol_intrinsic",
"photoreceptor_retinal_sensory": "annotation_class=visual AND annotation_superclass=ol_sensory; observed types recorded verbatim",
"visual_projection_neurons": "annotation_superclass in {visual_projection, visual_projection_tbc}"
},
"conclusion": "The 6091 annotation_class=visual bodies are photoreceptor/retinal sensory input neurons, not the whole visual processing network.",
"edge_statistics_file": "/data/digital-drosophila/experiments/phase4c-runtime/visual-audit/hierarchy-edge-statistics.json",
"field_breakdown": {
"annotation_class": {
"visual": 6091
},
"annotation_instance": {
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"R7d_L": 40,
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"R8_unclear_L": 188,
"R8_unclear_R": 254,
"R8d_L": 35,
"R8d_R": 41,
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"R8p_R": 158,
"R8y_L": 230,
"R8y_R": 251
},
"annotation_subclass": {
"<null>": 6091
},
"annotation_superclass": {
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},
"annotation_type": {
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"R7R8_unclear": 85,
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"R7d": 82,
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},
"neurotransmitter": {
"histamine": 6091
},
"side": {
"<null>": 6062,
"L": 19,
"R": 10
}
},
"hierarchy_counts": {
"central_brain": 50717,
"first_order": 23707,
"higher_visual": 4407,
"second_order": 81483,
"visual_sensory": 6091
},
"hierarchy_definition": "exclusive shortest directed connectome distance from the 6091 sensory neurons: depth 0 sensory, depth 1 first-order, depth 2 second-order, depth >=3 split into optic/visual-superclass higher_visual versus non-optic downstream central_brain; unreachable bodies are excluded",
"phase4b_visual_count": 6091,
"raw_visual_types": [
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"R7R8_unclear",
"R7_unclear",
"R7d",
"R7p",
"R7y",
"R8_unclear",
"R8d",
"R8p",
"R8y"
]
}