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

2026-09-29 03:38:32 +08:00
commit 3981628ff8
682 changed files with 161475 additions and 0 deletions
@@ -0,0 +1,15 @@
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@@ -0,0 +1,109 @@
+phase: 4I
+name: MaleCNS-MB-mechanistic-validation-v1
+
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  model_root: /data/digital-drosophila/models/male-cns-lif
+  phase4i_model_root: /data/digital-drosophila/models/male-cns-lif/mb-mechanistic-v1
+  experiment_root: /data/digital-drosophila/experiments/phase4i-mb-mechanistic-validation
+  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
+
+expected_graph:
+  neurons: 166700
+  directed_edges: 25582938
+  synaptic_contact_weight_sum: 124177617
+  phase4h_plastic_candidate_edges: 14232
+
+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
+
+olfactory_audit:
+  seeds: [48101, 48102, 48103, 48104, 48105]
+  rate_hz: 50.0
+  duration_ms: 100.0
+  targets_per_identity: 64
+  temporal_bin_ms: 10.0
+  consensus_seed_count: 3
+  separability_gate:
+    maximum_mean_active_jaccard: 0.8
+    minimum_pair_cosine_distance: 0.01
+    majority_seeds: 3
+    between_exceeds_within_sigma: 2.0
+
+direct_kc:
+  ensemble_size: 64
+  target_compartment_verbatim: "y5B'2a"
+  matched_dan_type: PAM15
+  unrelated_compartment_verbatim: "y2a'1"
+  unrelated_dan_type: PPL103
+  pulse_times_ms: [10.0, 30.0, 50.0, 70.0, 90.0]
+  evaluation_duration_ms: 120.0
+  conditioning_trials: 3
+  train_seeds: [49001, 49002, 49003, 49004, 49005]
+  evaluation_seeds: [49101, 49102, 49103, 49104, 49105]
+
+plasticity:
+  overlay_equation: effective_weight = base_weight + plastic_delta
+  eta_effective_mv: 0.00275
+  eligibility_tau_ms: 1000.0
+  polarity: -1
+  max_fractional_depression_per_edge: 0.25
+  negative_delay_behavior_under_phase4h_rule: full_eligibility
+
+timing:
+  delta_t_ms: [-1000, -500, -250, -100, -50, 0, 50, 100, 250, 500, 1000]
+  common_kc_time_ms: 1000.0
+  trial_duration_ms: 2100.0
+  seed: 49201
+  far_to_coincident_nonspecific_ratio: 0.1
+
+controls:
+  conditions: [A-matched-DAN, A-D-zero, A-unrelated-DAN, B-matched-DAN, random-KC-DAN, frozen-no-plasticity]
+
+prohibitions:
+  modify_base_csr: false
+  modify_w_syn: false
+  modify_transmitter_sign: false
+  modify_lif_parameters: false
+  expand_plastic_mask: false
+  tune_eta_or_polarity: false
+  brain_backpropagation: false
+  reinforcement_learning: false
+  visual_or_game_integration: false
@@ -0,0 +1,118 @@
+{
+  "1_CS_A_CS_B_KC_separable": {
+    "answer": false,
+    "label": "FAIL-OLFACTORY-TO-KC-SEPARABILITY",
+    "reason": "Both conditions activated all 4,064 KCs in all five deterministic seeds."
+  },
+  "2_KC_active_set_overlap": {
+    "A_active": 4064,
+    "B_active": 4064,
+    "intersection": 4064,
+    "union": 4064,
+    "jaccard": 1.0,
+    "KC_A_specific": 0,
+    "KC_B_specific": 0,
+    "KC_shared": 4064,
+    "KC_inactive": 0
+  },
+  "3_plastic_edge_eligibility_overlap": {
+    "A_specific": 0,
+    "B_specific": 0,
+    "shared": 14232,
+    "inactive": 0,
+    "jaccard": 1.0,
+    "cosine_similarity": 0.9996244608183082,
+    "label": "PLASTIC-EDGE-REPRESENTATION-OVERLAP"
+  },
+  "4_direct_KC_memory_success": {
+    "answer": false,
+    "label": "FAIL-PLASTICITY-MECHANISM",
+    "baseline_A_B_distinct": true,
+    "A_specific_effect": false,
+    "B_preserved": false
+  },
+  "5_direct_KC_MBON_pre_post": {
+    "A": {
+      "MBON_spike_l1": 0,
+      "latency_change_ms": 0.0,
+      "final_g_max_abs_change": 1.2008056640625,
+      "final_g_mean_abs_change": 0.699432373046875,
+      "final_voltage_max_abs_change_mv": 0.133148193359375,
+      "downstream_spike_l1": 0
+    },
+    "B_after_A_conditioning": {
+      "MBON_spike_l1": 0,
+      "latency_change_ms": 0.0,
+      "final_g_max_abs_change": 120.6834716796875,
+      "final_g_mean_abs_change": 66.90739440917969,
+      "final_voltage_max_abs_change_mv": 0.614990234375,
+      "downstream_spike_l1": 2
+    }
+  },
+  "6_compartment_locality": {
+    "compartment_boundary_correct": true,
+    "target_compartment_updates": 200,
+    "off_compartment_updates": 0,
+    "inactive_edge_updates": 0,
+    "stimulus_source_locality_correct": false,
+    "A_injected_source_updates": 67,
+    "network_recruited_source_updates": 133,
+    "B_only_source_updates": 27,
+    "B_only_fraction_of_updates": 0.135
+  },
+  "7_eligibility_timing_curve": {
+    "status": "FAIL-ELIGIBILITY-TIMING",
+    "secondary_label": "ELIGIBILITY-TIMING-NONSPECIFIC",
+    "far_abs_dt_ge_500_to_zero_ratio": 0.7436025322625082,
+    "negative_delays_receive_full_eligibility": true,
+    "positive_delay_decay": "exp(-delta_t/1000ms)"
+  },
+  "8_maximum_plasticity_delta_t_ms": [-1000, -500, -250, -100, -50, 0],
+  "9_unit_tests": {
+    "passed": 8,
+    "total": 8,
+    "all_passed": true
+  },
+  "10_MBON_changed_metrics": {
+    "subthreshold_g": true,
+    "subthreshold_voltage": true,
+    "spike_count": false,
+    "first_spike_latency": false,
+    "population_separation_improved": false,
+    "effect_exceeds_1e-4_noise_floor": true
+  },
+  "11_causal_evidence": {
+    "actual_KC_to_MBON_to_downstream_paths_saved": 20,
+    "all_KC_MBON_edges_are_in_frozen_mask": true,
+    "structural_path_confirmed": true,
+    "A_specific_functional_spike_change_confirmed": false
+  },
+  "12_controls": {
+    "D_zero_changed_edges": 0,
+    "frozen_changed_edges": 0,
+    "unrelated_DAN_changed_edges": 202,
+    "B_matched_DAN_changed_edges": 177,
+    "random_KC_DAN_changed_edges": 2109,
+    "associative_specificity_pass": false
+  },
+  "13_five_seed_consistency": {
+    "A_subthreshold_change": "5/5",
+    "A_spike_change": "0/5",
+    "B_preserved": "0/5",
+    "direct_memory_pass": "0/5"
+  },
+  "14_mechanism_labels": [
+    "FAIL-OLFACTORY-KC-SEPARABILITY",
+    "PLASTIC-EDGE-REPRESENTATION-OVERLAP",
+    "FAIL-PLASTICITY-MECHANISM",
+    "FAIL-ELIGIBILITY-TIMING"
+  ],
+  "15_frozen_integrity": {
+    "phase_1_to_4H_checksums": "PASS",
+    "phase4C_reference_regression": "PASS",
+    "BrainIO_v1": "PASS",
+    "ActivityStream_v1": "PASS",
+    "base_CSR_unchanged": true
+  },
+  "stopped_before_phase4J": true
+}