Archive MaleCNS research sources, provenance, bibliography and immutable data inventory
This commit is contained in:
Digital Drosophila Archive
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Load Diff
+42
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||||
"peak_step_fraction": 5.99880023995201e-06,
|
||||
"propagation_depth_from_full_layer": 0,
|
||||
"rate_hz": 50.0,
|
||||
"requested_biological_ms": 100.0,
|
||||
"seed": 45004,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"sparsity_percent": 5.0,
|
||||
"sweep": "five-layer-comparison",
|
||||
"target_active": 3,
|
||||
"target_count": 460,
|
||||
"total_spikes": 3,
|
||||
"wall_seconds": 0.7689941450007609
|
||||
}
|
||||
],
|
||||
"phase4d_external_drive_multiple_w_syn": 29.09090909090909,
|
||||
"phase4d_external_drive_mv": 8.0,
|
||||
"trial_count": 61,
|
||||
"viable_condition_by_layer": {
|
||||
"engineering-visual-projection": {
|
||||
"aborted_runaway": false,
|
||||
"active_fraction": 0.008014397120575886,
|
||||
"active_neurons": 1336,
|
||||
"amplitude_multiple_w_syn": 32.0,
|
||||
"amplitude_mv": 8.8,
|
||||
"descending_active": 142,
|
||||
"descending_first_spike_latency_ms": 87.9,
|
||||
"descending_spikes": 248,
|
||||
"external_drive_events": 2334,
|
||||
"layer": "engineering-visual-projection",
|
||||
"mean_firing_rate_hz": 0.11271745650869826,
|
||||
"motor_active": 93,
|
||||
"motor_first_spike_latency_ms": 93.30000000000001,
|
||||
"motor_spikes": 121,
|
||||
"multi_hop_output_propagation": true,
|
||||
"non_target_active": 1324,
|
||||
"numerically_finite": true,
|
||||
"output_first_spike_latency_ms": 87.9,
|
||||
"peak_step_fraction": 0.0003299340131973605,
|
||||
"propagation_depth_from_full_layer": 2,
|
||||
"rate_hz": 50.0,
|
||||
"requested_biological_ms": 100.0,
|
||||
"seed": 60758,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"sparsity_percent": 5.0,
|
||||
"sweep": "amplitude-extended",
|
||||
"target_active": 12,
|
||||
"target_count": 460,
|
||||
"total_spikes": 1879,
|
||||
"wall_seconds": 0.8299968829960562
|
||||
}
|
||||
}
|
||||
}
|
||||
@@ -0,0 +1,115 @@
|
||||
phase: 4E
|
||||
names:
|
||||
reference: MaleCNS-LIF-reference-v1
|
||||
runtime: MaleCNS-LIF-runtime-v1
|
||||
io_api: MaleCNS-BrainIO-v1
|
||||
candidate: MaleCNS-VisualAdapter-v2-candidate
|
||||
|
||||
paths:
|
||||
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
|
||||
model_root: /data/digital-drosophila/models/male-cns-lif
|
||||
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
|
||||
experiment_root: /data/digital-drosophila/experiments/phase4e-visual-calibration
|
||||
candidate_root: /data/digital-drosophila/models/male-cns-lif/visual-interface-v2
|
||||
|
||||
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
|
||||
|
||||
visual_populations:
|
||||
reference-photoreceptor: {source: hierarchy, value: visual_sensory, interface_kind: biological-reference, stimulation_mode: spike_injection}
|
||||
engineering-first-order: {source: hierarchy, value: first_order, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
|
||||
engineering-second-order: {source: hierarchy, value: second_order, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
|
||||
engineering-higher-visual: {source: hierarchy, value: higher_visual, interface_kind: engineering, stimulation_mode: external_synaptic_drive}
|
||||
engineering-visual-projection: {source: metadata-expression, field: annotation_superclass, values: [visual_projection, visual_projection_tbc], interface_kind: engineering, stimulation_mode: external_synaptic_drive}
|
||||
|
||||
calibration:
|
||||
seed: 45000
|
||||
trial_duration_ms: 100.0
|
||||
chunk_ms: 10.0
|
||||
fixed_rate_hz: 50.0
|
||||
fixed_sparsity_percent: 5.0
|
||||
amplitude_multiples: [0.25, 0.5, 1, 2, 4, 8, 16]
|
||||
extended_amplitude_multiples: [32, 64]
|
||||
rate_hz: [10, 25, 50, 100, 150, 200]
|
||||
sparsity_percent: [0.1, 0.5, 1, 5, 10, 25, 50, 100]
|
||||
latency_windows_ms: [5, 10, 20, 30, 50, 100, 200]
|
||||
deterministic_repeats: 2
|
||||
runaway:
|
||||
active_fraction_gte: 0.80
|
||||
mean_firing_rate_hz_gte: 100.0
|
||||
peak_step_fraction_gte: 0.10
|
||||
propagation_success:
|
||||
require_output_active: true
|
||||
require_non_target_active: true
|
||||
minimum_graph_hops: 2
|
||||
|
||||
patterns:
|
||||
# Separability uses the selected propagating condition's sparsity. This is
|
||||
# retained only as a fallback if that condition has no sparsity field.
|
||||
sparse_percent: 5.0
|
||||
dense_percent: 25.0
|
||||
moving_segments: 5
|
||||
trial_duration_ms: 100.0
|
||||
seeds: [45101, 45102, 45103]
|
||||
|
||||
continuous:
|
||||
biological_duration_ms: 1000.0
|
||||
periods_ms: [10, 20, 50, 100]
|
||||
sequence: [sparse-A, sparse-B, sparse-A, moving, zero, dense]
|
||||
seed: 45200
|
||||
|
||||
readout:
|
||||
bins_ms: [1, 5, 10, 20, 50]
|
||||
|
||||
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}
|
||||
|
||||
candidate_selection:
|
||||
rule: "gateway iff multi-hop propagation reaches descending or motor output and is non-runaway; rank by lowest amplitude multiple, then lowest min output hops, then hierarchy order. Formal adapter-v2 eligibility additionally requires deterministic nonzero output separability and matched-input-count validation"
|
||||
hierarchy_order: [engineering-first-order, engineering-second-order, engineering-higher-visual, engineering-visual-projection]
|
||||
|
||||
prohibitions:
|
||||
connectome_changes: false
|
||||
raw_weight_changes: false
|
||||
lif_semantics_changes: false
|
||||
transmitter_sign_changes: false
|
||||
training: false
|
||||
reinforcement_learning: false
|
||||
game_integration: false
|
||||
web_server: false
|
||||
three_d_frontend: false
|
||||
phase4f: false
|
||||
+2198
File diff suppressed because it is too large
Load Diff
+42
@@ -0,0 +1,42 @@
|
||||
{
|
||||
"adapter_v2_eligible": false,
|
||||
"adapter_v2_gate_note": "gateway selection uses anatomy/path/propagation; formal adapter eligibility additionally requires deterministic separability",
|
||||
"condition": {
|
||||
"aborted_runaway": false,
|
||||
"active_fraction": 0.008014397120575886,
|
||||
"active_neurons": 1336,
|
||||
"amplitude_multiple_w_syn": 32.0,
|
||||
"amplitude_mv": 8.8,
|
||||
"descending_active": 142,
|
||||
"descending_first_spike_latency_ms": 87.9,
|
||||
"descending_spikes": 248,
|
||||
"external_drive_events": 2334,
|
||||
"layer": "engineering-visual-projection",
|
||||
"mean_firing_rate_hz": 0.11271745650869826,
|
||||
"motor_active": 93,
|
||||
"motor_first_spike_latency_ms": 93.30000000000001,
|
||||
"motor_spikes": 121,
|
||||
"multi_hop_output_propagation": true,
|
||||
"non_target_active": 1324,
|
||||
"numerically_finite": true,
|
||||
"output_first_spike_latency_ms": 87.9,
|
||||
"peak_step_fraction": 0.0003299340131973605,
|
||||
"propagation_depth_from_full_layer": 2,
|
||||
"rate_hz": 50.0,
|
||||
"requested_biological_ms": 100.0,
|
||||
"seed": 60758,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"sparsity_percent": 5.0,
|
||||
"sweep": "amplitude-extended",
|
||||
"target_active": 12,
|
||||
"target_count": 460,
|
||||
"total_spikes": 1879,
|
||||
"wall_seconds": 0.8299968829960562
|
||||
},
|
||||
"handpicked": false,
|
||||
"layer": "engineering-visual-projection",
|
||||
"minimum_output_hops": 1,
|
||||
"name": "visual_gateway_candidate",
|
||||
"rule": "gateway iff multi-hop propagation reaches descending or motor output and is non-runaway; rank by lowest amplitude multiple, then lowest min output hops, then hierarchy order. Formal adapter-v2 eligibility additionally requires deterministic nonzero output separability and matched-input-count validation",
|
||||
"selected": true
|
||||
}
|
||||
+883
@@ -0,0 +1,883 @@
|
||||
{
|
||||
"code": [
|
||||
{
|
||||
"path": "/data/digital-drosophila/models/male-cns-lif/visual-interface-v2/phase4e.py",
|
||||
"sha256": "a56fead8424e4e79be370dade0a86fec10438348968819481960b0b693411f73"
|
||||
},
|
||||
{
|
||||
"path": "/data/digital-drosophila/models/male-cns-lif/visual-interface-v2/phase4e.yaml",
|
||||
"sha256": "708b6bb75b82a967f8c1e65cce646f080a79f7b6048ca72e61de1dc184d9923a"
|
||||
}
|
||||
],
|
||||
"created_unix_time": 1789851581.1730437,
|
||||
"immutable_inputs": [
|
||||
{
|
||||
"path": "/data/digital-drosophila/models/male-cns-lif/reference-v1/checksums.sha256",
|
||||
"sha256": "bc49d61cc861fdcd2fb909bafdbb463376a1395877749c49a76855715256415e"
|
||||
},
|
||||
{
|
||||
"path": "/data/digital-drosophila/models/male-cns-lif/runtime-v1/checksums.sha256",
|
||||
"sha256": "c1230b3cd327323c7df8483ac1b6130defc84d03340372d37cd684fbaa03fb65"
|
||||
},
|
||||
{
|
||||
"path": "/data/digital-drosophila/models/male-cns-lif/io-v1/checksums.sha256",
|
||||
"sha256": "dd1f578447d445019598e78bd23a27a71b72a3470680d3a956aac6bf1efe26fe"
|
||||
},
|
||||
{
|
||||
"path": "/data/digital-drosophila/experiments/phase4c-runtime/manifests/checksums.sha256",
|
||||
"sha256": "ae60ab740804c1d5489139c9de2b65b06475d965ac001eecee7ba4d42ef42ba6"
|
||||
},
|
||||
{
|
||||
"path": "/data/digital-drosophila/experiments/phase4d-io/manifests/checksums.sha256",
|
||||
"sha256": "27fd9456b7f2e0c87dfd0f1725e48e11d836fbd4821623581e5f1cf8bd75da38"
|
||||
}
|
||||
],
|
||||
"outputs": [
|
||||
{
|
||||
"bytes": 1096,
|
||||
"path": "/data/digital-drosophila/experiments/phase4e-visual-calibration/activity-stream/activity-packet.schema.json",
|
||||
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|
||||
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|
||||
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|
||||
"bytes": 221,
|
||||
"path": "/data/digital-drosophila/experiments/phase4e-visual-calibration/activity-stream/replay-test.json",
|
||||
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|
||||
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|
||||
{
|
||||
"bytes": 881,
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"bytes": 897,
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"bytes": 892,
|
||||
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|
||||
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|
||||
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|
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|
||||
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|
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
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|
||||
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|
||||
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
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|
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|
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
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|
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|
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|
||||
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|
||||
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|
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|
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+12
@@ -0,0 +1,12 @@
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{
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@@ -0,0 +1,65 @@
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+398
@@ -0,0 +1,398 @@
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||||
"requested_biological_ms": 100.0,
|
||||
"seed": 45101,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"target_active": 2,
|
||||
"target_count": 2300,
|
||||
"total_spikes": 2,
|
||||
"wall_seconds": 0.7699391200039827
|
||||
},
|
||||
{
|
||||
"aborted_runaway": false,
|
||||
"active_fraction": 0.0,
|
||||
"active_neurons": 0,
|
||||
"descending_active": 0,
|
||||
"descending_first_spike_latency_ms": null,
|
||||
"descending_spikes": 0,
|
||||
"external_drive_events": 2347,
|
||||
"mean_firing_rate_hz": 0.0,
|
||||
"motor_active": 0,
|
||||
"motor_first_spike_latency_ms": null,
|
||||
"motor_spikes": 0,
|
||||
"multi_hop_output_propagation": false,
|
||||
"non_target_active": 0,
|
||||
"numerically_finite": true,
|
||||
"output_first_spike_latency_ms": null,
|
||||
"pattern": "moving",
|
||||
"peak_step_fraction": 0.0,
|
||||
"propagation_depth_from_full_layer": 0,
|
||||
"requested_biological_ms": 100.0,
|
||||
"seed": 45102,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"target_active": 0,
|
||||
"target_count": 2300,
|
||||
"total_spikes": 0,
|
||||
"wall_seconds": 0.7716315110083087
|
||||
},
|
||||
{
|
||||
"aborted_runaway": false,
|
||||
"active_fraction": 5.99880023995201e-06,
|
||||
"active_neurons": 1,
|
||||
"descending_active": 0,
|
||||
"descending_first_spike_latency_ms": null,
|
||||
"descending_spikes": 0,
|
||||
"external_drive_events": 2296,
|
||||
"mean_firing_rate_hz": 5.99880023995201e-05,
|
||||
"motor_active": 0,
|
||||
"motor_first_spike_latency_ms": null,
|
||||
"motor_spikes": 0,
|
||||
"multi_hop_output_propagation": false,
|
||||
"non_target_active": 0,
|
||||
"numerically_finite": true,
|
||||
"output_first_spike_latency_ms": null,
|
||||
"pattern": "moving",
|
||||
"peak_step_fraction": 5.99880023995201e-06,
|
||||
"propagation_depth_from_full_layer": 0,
|
||||
"requested_biological_ms": 100.0,
|
||||
"seed": 45103,
|
||||
"simulated_biological_ms": 100.0,
|
||||
"target_active": 1,
|
||||
"target_count": 2300,
|
||||
"total_spikes": 1,
|
||||
"wall_seconds": 0.769372779999685
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
Reference in New Issue
Block a user