Archive MaleCNS research sources, provenance, bibliography and immutable data inventory
This commit is contained in:
Digital Drosophila Archive
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+362
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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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|
||||
"reason_DoOR_not_imported": "Phase 4K mapping audit found no explicit MaleCNS glomerulus/receptor key for a non-guessing join",
|
||||
"unmatched_channels": "all until an explicit official receptor/glomerulus-to-MaleCNS mapping is supplied"
|
||||
},
|
||||
"phase": "4K",
|
||||
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|
||||
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|
||||
"recruitment": {
|
||||
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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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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"stopped_before_phase4l": true
|
||||
}
|
||||
@@ -0,0 +1,42 @@
|
||||
{
|
||||
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|
||||
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|
||||
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|
||||
"all_passed": true,
|
||||
"phase1_phase2_backup_sha256": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
},
|
||||
"phase3_sha256": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
},
|
||||
"phase3b_166700_sha256": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
},
|
||||
"phase3b_audit_sha256": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
},
|
||||
"raw_core_sha256": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
},
|
||||
"raw_skeleton_md5": {
|
||||
"passed": true,
|
||||
"returncode": 0,
|
||||
"stderr": ""
|
||||
}
|
||||
},
|
||||
"phase4c_reference_regression": true,
|
||||
"phase4c_to_4i_after": true,
|
||||
"phase4c_to_4i_before": true,
|
||||
"phase4j_after": true,
|
||||
"phase4j_before": true
|
||||
}
|
||||
@@ -0,0 +1,101 @@
|
||||
phase: 4K
|
||||
name: MaleCNS-KC-recruitment-MBON-causal-audit-v1
|
||||
|
||||
paths:
|
||||
connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
|
||||
dataset_root: /data/digital-drosophila/datasets/male-cns-v1.0
|
||||
model_root: /data/digital-drosophila/models/male-cns-lif
|
||||
phase4k_model_root: /data/digital-drosophila/models/male-cns-lif/kc-recruitment-audit-v1
|
||||
experiment_root: /data/digital-drosophila/experiments/phase4k-kc-recruitment-audit
|
||||
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
|
||||
phase4j_root: /data/digital-drosophila/experiments/phase4j-mb-physiology-repair
|
||||
phase4j_model_root: /data/digital-drosophila/models/male-cns-lif/mb-physiology-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
|
||||
|
||||
apl_overlay:
|
||||
name: APL-Graded-Inhibition-v1
|
||||
tau_ms: 20.0
|
||||
gain: 0.01
|
||||
normalization: 1.0
|
||||
immutable_phase4j_parameters: true
|
||||
|
||||
direct_kc:
|
||||
target_compartment_verbatim: "y5B'2a"
|
||||
matched_dan_type: PAM15
|
||||
pulse_times_ms: [10.0, 30.0, 50.0, 70.0, 90.0]
|
||||
dan_time_ms: 90.0
|
||||
duration_ms: 120.0
|
||||
trace_seed: 50201
|
||||
evaluation_seed: 50301
|
||||
|
||||
olfactory:
|
||||
rate_hz: 50.0
|
||||
duration_ms: 100.0
|
||||
seed: 50101
|
||||
targets_per_cs: 64
|
||||
|
||||
sensitivity:
|
||||
depression_fractions: [0.0, 0.01, 0.05, 0.10, 0.25, 0.50]
|
||||
evaluation_seeds: [50301, 50302, 50303, 50304, 50305]
|
||||
functional_change_definition: any_MBON_spike_count_or_first_latency_change
|
||||
|
||||
causal_attribution:
|
||||
rule: dominant_positive_synaptic_arrival_with_runtime_g_decay
|
||||
exact_delay_steps: 18
|
||||
shortest_static_path_forbidden: true
|
||||
|
||||
prohibitions:
|
||||
training: false
|
||||
modify_eta_or_eligibility_v2: false
|
||||
expand_plastic_mask: false
|
||||
modify_threshold_or_gain: false
|
||||
save_sensitivity_as_learned_model: false
|
||||
decoder_classifier_rl_game_visual: false
|
||||
+126
@@ -0,0 +1,126 @@
|
||||
{
|
||||
"APL_overlay_olfactory_CS": {
|
||||
"KC_cumulative_signed_drive": {
|
||||
"APL": -9769500.0,
|
||||
"DAN": 130319.75,
|
||||
"KC": 18975.0,
|
||||
"MBON": -53446.796875,
|
||||
"PN_olfactory": 2646478.0,
|
||||
"other": 299596.0625
|
||||
},
|
||||
"MBON_cumulative_positive_drive": {
|
||||
"DAN": 25172.94921875,
|
||||
"MBON": 11271.150390625,
|
||||
"feedback_neuron": 125852.3671875,
|
||||
"nonplastic_KC": 5210.97509765625,
|
||||
"other": 60751.6171875,
|
||||
"plastic_KC": 1531.1998291015625
|
||||
},
|
||||
"MBON_cumulative_signed_drive": {
|
||||
"DAN": 25172.94921875,
|
||||
"MBON": -82723.84375,
|
||||
"feedback_neuron": 80562.078125,
|
||||
"nonplastic_KC": 5210.97509765625,
|
||||
"other": -14471.3232421875,
|
||||
"plastic_KC": 1531.1998291015625
|
||||
},
|
||||
"shadow_validation": {
|
||||
"KC_final_g_max_abs_error": 0.0001983642578125,
|
||||
"MBON_final_g_max_abs_error": 0.000244140625
|
||||
},
|
||||
"wall_seconds": 3.5025182660028804
|
||||
},
|
||||
"direct_KC_SET_A": {
|
||||
"KC_cumulative_signed_drive": {
|
||||
"APL": -1347468.0,
|
||||
"DAN": 79602.609375,
|
||||
"KC": 141251.828125,
|
||||
"MBON": -33127.32421875,
|
||||
"PN_olfactory": 112.47500610351562,
|
||||
"other": 285788.625
|
||||
},
|
||||
"MBON_cumulative_positive_drive": {
|
||||
"DAN": 15265.2490234375,
|
||||
"MBON": 4620.5498046875,
|
||||
"feedback_neuron": 82093.2734375,
|
||||
"nonplastic_KC": 55235.40234375,
|
||||
"other": 33153.73046875,
|
||||
"plastic_KC": 8435.34765625
|
||||
},
|
||||
"MBON_cumulative_signed_drive": {
|
||||
"DAN": 15265.2490234375,
|
||||
"MBON": -72719.3515625,
|
||||
"feedback_neuron": 26264.41796875,
|
||||
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|
||||
"other": -6021.400390625,
|
||||
"plastic_KC": 8435.34765625
|
||||
},
|
||||
"shadow_validation": {
|
||||
"KC_final_g_max_abs_error": 7.62939453125e-05,
|
||||
"MBON_final_g_max_abs_error": 0.000274658203125
|
||||
},
|
||||
"wall_seconds": 3.5770981810055673
|
||||
},
|
||||
"direct_KC_SET_B": {
|
||||
"KC_cumulative_signed_drive": {
|
||||
"APL": -1294920.0,
|
||||
"DAN": 71042.125,
|
||||
"KC": 119059.59375,
|
||||
"MBON": -27526.67578125,
|
||||
"PN_olfactory": 125.125,
|
||||
"other": 241263.359375
|
||||
},
|
||||
"MBON_cumulative_positive_drive": {
|
||||
"DAN": 13631.75,
|
||||
"MBON": 3982.824951171875,
|
||||
"feedback_neuron": 72533.171875,
|
||||
"nonplastic_KC": 46404.87109375,
|
||||
"other": 30799.734375,
|
||||
"plastic_KC": 7160.451171875
|
||||
},
|
||||
"MBON_cumulative_signed_drive": {
|
||||
"DAN": 13631.75,
|
||||
"MBON": -63624.828125,
|
||||
"feedback_neuron": 20551.564453125,
|
||||
"nonplastic_KC": 46404.87109375,
|
||||
"other": -6260.3779296875,
|
||||
"plastic_KC": 7160.451171875
|
||||
},
|
||||
"shadow_validation": {
|
||||
"KC_final_g_max_abs_error": 0.0001068115234375,
|
||||
"MBON_final_g_max_abs_error": 0.00042724609375
|
||||
},
|
||||
"wall_seconds": 3.457104536006227
|
||||
},
|
||||
"original_olfactory_CS": {
|
||||
"KC_cumulative_signed_drive": {
|
||||
"APL": -2021202.125,
|
||||
"DAN": 275075.375,
|
||||
"KC": 7051682.0,
|
||||
"MBON": -73846.0234375,
|
||||
"PN_olfactory": 2615216.5,
|
||||
"other": 1504130.75
|
||||
},
|
||||
"MBON_cumulative_positive_drive": {
|
||||
"DAN": 54914.47265625,
|
||||
"MBON": 45657.4140625,
|
||||
"feedback_neuron": 335753.03125,
|
||||
"nonplastic_KC": 2211195.25,
|
||||
"other": 52991.68359375,
|
||||
"plastic_KC": 648042.625
|
||||
},
|
||||
"MBON_cumulative_signed_drive": {
|
||||
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|
||||
"MBON": -145908.4375,
|
||||
"feedback_neuron": 232603.78125,
|
||||
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|
||||
"other": -26807.833984375,
|
||||
"plastic_KC": 648042.625
|
||||
},
|
||||
"shadow_validation": {
|
||||
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|
||||
"MBON_final_g_max_abs_error": 0.00341796875
|
||||
},
|
||||
"wall_seconds": 4.3153701450064545
|
||||
}
|
||||
}
|
||||
+28
@@ -0,0 +1,28 @@
|
||||
{
|
||||
"PLASTICITY_TRANSFER_PASS": false,
|
||||
"WHOLE_BRAIN_RECRUITMENT_CONTAMINATION": false,
|
||||
"actual_changed_edges": 170,
|
||||
"effects": {
|
||||
"A": {
|
||||
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|
||||
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|
||||
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|
||||
"post_first_latency_ms": 12.4,
|
||||
"pre_first_latency_ms": 12.4,
|
||||
"spike_l1": 0
|
||||
},
|
||||
"B": {
|
||||
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|
||||
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|
||||
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|
||||
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|
||||
"pre_first_latency_ms": 12.4,
|
||||
"spike_l1": 0
|
||||
}
|
||||
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|
||||
"new_edges_added": false,
|
||||
"plasticity_label": "FAIL-PLASTICITY-TRANSFER",
|
||||
"spike_train_source": "deterministically regenerated from frozen Phase 4J protocol because exact Phase 4J event trains were not persisted",
|
||||
"target_MBON": 2,
|
||||
"weak_effect_label": "KC-MBON-PLASTICITY-EFFECT-TOO-WEAK"
|
||||
}
|
||||
+168
@@ -0,0 +1,168 @@
|
||||
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|
||||
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|
||||
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@@ -0,0 +1,42 @@
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+22
@@ -0,0 +1,22 @@
|
||||
{
|
||||
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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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|
||||
"reason_DoOR_not_imported": "Phase 4K mapping audit found no explicit MaleCNS glomerulus/receptor key for a non-guessing join",
|
||||
"unmatched_channels": "all until an explicit official receptor/glomerulus-to-MaleCNS mapping is supplied"
|
||||
}
|
||||
+23
@@ -0,0 +1,23 @@
|
||||
{
|
||||
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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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|
||||
}
|
||||
+33
@@ -0,0 +1,33 @@
|
||||
{
|
||||
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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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|
||||
}
|
||||
+64
@@ -0,0 +1,64 @@
|
||||
{
|
||||
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|
||||
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|
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|
||||
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|
||||
}
|
||||
Reference in New Issue
Block a user