qishizhe/digital-drosophila
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Browse Source
This commit is contained in:
Digital Drosophila Archive
2026-09-29 03:38:32 +08:00
commit 3981628ff8
682 changed files with 161475 additions and 0 deletions
Download Patch File Download Diff File Expand all files Collapse all files
registry/catalog-20260929/evidence/phase4k-kc-recruitment-audit/audit/base-sha256.json
+14
View File
@@ -0,0 +1,14 @@
{
"after": {
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indices.int32.npy": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indptr.int64.npy": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-weights.int64.npy": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/unified-metadata.parquet": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63"
},
"before": {
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indices.int32.npy": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indptr.int64.npy": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-weights.int64.npy": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b",
"/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/unified-metadata.parquet": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63"
}
}
registry/catalog-20260929/evidence/phase4k-kc-recruitment-audit/audit/final-summary.json
+362
View File
@@ -0,0 +1,362 @@
{
"MBON_decomposition": {
"A": {
"actual_delta_cumulative_drive": -11.144619941711426,
"actual_delta_final_g_sum": -1.2728946208953857,
"actual_delta_over_total_excitatory_drive": -5.606159788465977e-05,
"actual_delta_over_total_signed_drive": -0.00042137033698697127,
"effect": {
"MBON_delta_g_max_abs": 1.149932861328125,
"MBON_delta_v_max_abs": 0.1024169921875,
"MBON_first_latency_delta_ms": 0.0,
"MBON_spike_count_delta": 0,
"MBON_spike_l1": 0,
"downstream_first_latency_delta_ms": 0.0,
"downstream_spike_count_delta": 0
},
"final_total_g_sum": 7165.68310546875,
"plastic_KC_excitatory_drive": 8424.2060546875,
"plastic_KC_fraction_of_total_excitatory_drive": 0.042376900675437645,
"total_cumulative_signed_drive": 26448.515625,
"total_excitatory_drive": 198792.40625
},
"B": {
"actual_delta_cumulative_drive": -7.901164531707764,
"actual_delta_final_g_sum": -1.205099105834961,
"actual_delta_over_total_excitatory_drive": -4.5299095695043064e-05,
"actual_delta_over_total_signed_drive": -0.0004618457177948536,
"effect": {
"MBON_delta_g_max_abs": 163.25543212890625,
"MBON_delta_v_max_abs": 0.607940673828125,
"MBON_first_latency_delta_ms": 0.0,
"MBON_spike_count_delta": 0,
"MBON_spike_l1": 0,
"downstream_first_latency_delta_ms": 0.0,
"downstream_spike_count_delta": 2
},
"final_total_g_sum": 4702.4765625,
"plastic_KC_excitatory_drive": 7139.62353515625,
"plastic_KC_fraction_of_total_excitatory_drive": 0.0409330154368676,
"total_cumulative_signed_drive": 17107.80078125,
"total_excitatory_drive": 174422.125
}
},
"base_modified": false,
"drive_decomposition": {
"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,
"nonplastic_KC": 55235.40234375,
"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": {
"DAN": 54914.47265625,
"MBON": -145908.4375,
"feedback_neuron": 232603.78125,
"nonplastic_KC": 2211195.25,
"other": -26807.833984375,
"plastic_KC": 648042.625
},
"shadow_validation": {
"KC_final_g_max_abs_error": 0.0001983642578125,
"MBON_final_g_max_abs_error": 0.00341796875
},
"wall_seconds": 4.3153701450064545
}
},
"eligibility_v2_modified": false,
"integrity": {
"all_passed": true,
"base_CSR_unchanged": true,
"dataset_phase1_to_3b": {
"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
},
"isolated_replay": {
"PLASTICITY_TRANSFER_PASS": false,
"WHOLE_BRAIN_RECRUITMENT_CONTAMINATION": false,
"actual_changed_edges": 170,
"effects": {
"A": {
"delta_g_max_abs": 1.15008544921875,
"delta_v_max_abs": 0.0,
"latency_delta_ms": 0.0,
"post_first_latency_ms": 12.4,
"pre_first_latency_ms": 12.4,
"spike_l1": 0
},
"B": {
"delta_g_max_abs": 1.1561279296875,
"delta_v_max_abs": 0.12083816528320312,
"latency_delta_ms": 0.0,
"post_first_latency_ms": 12.4,
"pre_first_latency_ms": 12.4,
"spike_l1": 0
}
},
"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"
},
"labels": {
"KC_recruitment": "KC-RECRUITMENT-SOURCE-IDENTIFIED",
"MBON_readout_insensitive": false,
"odor_input": "ODOR-INPUT-NOT-GLOMERULUS-GROUNDED",
"plasticity_transfer": "FAIL-PLASTICITY-TRANSFER",
"whole_brain_recruitment_contamination": false
},
"olfactory_provenance": {
"ALPN_count": 686,
"ALPN_to_KC_edges": 22586,
"ALPN_to_KC_synapse_weight": 390928,
"DoOR_imported": false,
"current_CS_definition": "first 64 and next 64 neuron_idx after sorting the broad olfactory population",
"current_CS_glomerulus_grounded": false,
"current_CS_neurons": 128,
"current_CS_selection_used_explicit_identity": false,
"explicit_glomerulus_or_receptor_columns": [
"annotation_receptorType"
],
"explicit_identity_nonempty_counts_in_current_CS": {
"annotation_receptorType": 0
},
"label": "ODOR-INPUT-NOT-GLOMERULUS-GROUNDED",
"olfactory_population_count": 2639,
"olfactory_population_definition": "annotation_class == olfactory",
"prepared_next_input_scheme": "odor response vector -> explicit receptor/glomerulus mapping -> matched MaleCNS PN identities -> real ALPN-to-KC edges",
"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",
"plastic_mask_expanded": false,
"recommendation": "repair upstream odor/glomerulus-grounded encoding and KC recruitment before changing MBON plasticity/readout",
"recruitment": {
"B_set_KC_active": 27,
"B_source_changed_edges": 23,
"B_source_path_classes": {
"APL-related": 1,
"MBON/DAN feedback": 22
},
"active_non_A_KC": 136,
"causal_paths_found": 136,
"causal_rule": "dominant_positive_synaptic_arrival_with_runtime_g_decay",
"classification": {
"APL-related": 1,
"MBON/DAN feedback": 123,
"PN/olfactory feedback": 9,
"direct recurrent": 3
},
"injected_A_KC": 64,
"interpretation_limit": "dominant positive arrival under exact runtime timing is an attribution path, not an intervention-based proof",
"label": "KC-RECRUITMENT-SOURCE-IDENTIFIED",
"static_shortest_path_used": false,
"traced_recruited_KC": 136,
"unique_B_source_KC_with_changed_edges": 23
},
"sensitivity": {
"MBON_READOUT_INSENSITIVE": false,
"changed_real_edges": 170,
"criterion": "any_MBON_spike_count_or_first_latency_change",
"curve": [
{
"MBON_delta_g_max_abs_mean": 0.0,
"MBON_delta_v_max_abs_mean": 0.0,
"MBON_spike_l1_mean": 0.0,
"depression_fraction": 0.0,
"downstream_spike_abs_delta_mean": 0.0,
"functional_seed_count": 0,
"seeds": 5
},
{
"MBON_delta_g_max_abs_mean": 44.438987731933594,
"MBON_delta_v_max_abs_mean": 1.202423095703125,
"MBON_spike_l1_mean": 0.0,
"depression_fraction": 0.01,
"downstream_spike_abs_delta_mean": 15.0,
"functional_seed_count": 0,
"seeds": 5
},
{
"MBON_delta_g_max_abs_mean": 45.279144287109375,
"MBON_delta_v_max_abs_mean": 6.0185089111328125,
"MBON_spike_l1_mean": 1.0,
"depression_fraction": 0.05,
"downstream_spike_abs_delta_mean": 33.0,
"functional_seed_count": 5,
"seeds": 5
},
{
"MBON_delta_g_max_abs_mean": 124.070068359375,
"MBON_delta_v_max_abs_mean": 15.75347900390625,
"MBON_spike_l1_mean": 5.0,
"depression_fraction": 0.1,
"downstream_spike_abs_delta_mean": 88.0,
"functional_seed_count": 5,
"seeds": 5
},
{
"MBON_delta_g_max_abs_mean": 262.3074645996094,
"MBON_delta_v_max_abs_mean": 37.597146606445314,
"MBON_spike_l1_mean": 14.0,
"depression_fraction": 0.25,
"downstream_spike_abs_delta_mean": 80.0,
"functional_seed_count": 5,
"seeds": 5
},
{
"MBON_delta_g_max_abs_mean": 347.9573974609375,
"MBON_delta_v_max_abs_mean": 54.33984375,
"MBON_spike_l1_mean": 13.0,
"depression_fraction": 0.5,
"downstream_spike_abs_delta_mean": 163.0,
"functional_seed_count": 5,
"seeds": 5
}
],
"diagnostic_only_not_saved_as_learned_model": true,
"first_fraction_with_any_functional_MBON_change": 0.05,
"label": "MBON-READOUT-SENSITIVE-WITHIN-TESTED-RANGE"
},
"stopped_before_phase4l": true
}
registry/catalog-20260929/evidence/phase4k-kc-recruitment-audit/audit/integrity.json
+42
View File
@@ -0,0 +1,42 @@
{
"all_passed": true,
"base_CSR_unchanged": true,
"dataset_phase1_to_3b": {
"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
}
registry/catalog-20260929/evidence/phase4k-kc-recruitment-audit/audit/phase4k.yaml
+101
View File
@@ -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