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
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+{
+  "artifact": "reference-v1",
+  "created_unix_time": 1789847798.9948018,
+  "files": [
+    {
+      "bytes": 3371,
+      "path": "VERSION.json",
+      "sha256": "b094472c713fb48be6d35ab2b4cad4d5ce8afb070afd9c6e16de47a120a3f14a"
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+    {
+      "bytes": 2949,
+      "path": "config.yaml",
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+    {
+      "bytes": 64615,
+      "path": "model.py",
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+  "immutable_mode": "0444"
+}
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+{
+  "code": {
+    "config.yaml": {
+      "path": "/data/digital-drosophila/models/male-cns-lif/reference-v1/config.yaml",
+      "sha256": "3c8651a903302845020917e8c7fee5caa39b6d2bef167a8a448c1a7560689414"
+    },
+    "model.py": {
+      "path": "/data/digital-drosophila/models/male-cns-lif/reference-v1/model.py",
+      "sha256": "693468685a7ff3db1d09a088e0bbdaa78c595d64086b27e9cc18abceb4c7d174"
+    }
+  },
+  "description": "Shiu-like LIF dynamics adapted to MaleCNS v1.0",
+  "graph": {
+    "directed_edges": 25582938,
+    "isolated_neurons": 217,
+    "neurons": 166700,
+    "self_loops": 101,
+    "synaptic_contact_weight_sum": 124177617
+  },
+  "inputs": {
+    "csr_metadata": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-metadata.json",
+      "sha256": "3786a0c79fc25bdc4d11f67d4de1f9f6a88da750431e96508bf72bbfa42bb6f8"
+    },
+    "indices": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indices.int32.npy",
+      "sha256": "ce20f7433f78442c717ad2a7b5394cf4a3b109d990b4be0788040b7b0f4ed150"
+    },
+    "indptr": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-indptr.int64.npy",
+      "sha256": "fe43420f11e6242a11f8199ae7f097cab4b8a6db181d36f2a46b9e46670acbb4"
+    },
+    "mapping": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/body-id-neuron-idx.parquet",
+      "sha256": "2b615c00d290e34fbe7792a5050eee4ce086446cd54ec89c96d7b1bc4a8e6009"
+    },
+    "metadata": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/neuron-index/unified-metadata.parquet",
+      "sha256": "922af16846a065c3dbfca7c11146b83ca217fcbd7392edc745f444a04eae8c63"
+    },
+    "raw_weights": {
+      "path": "/data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only/gpu/csr-weights.int64.npy",
+      "sha256": "c7ae101451dd19c47fd976bcfacbc52d67193a68ffa04c5b4d2e911cfd52d99b"
+    }
+  },
+  "local_repository_commit": "d826733f1c620a2ad0b096c846b9b8e9eb3ac0fa",
+  "name": "MaleCNS-LIF-reference-v1",
+  "not_claimed": "strict Shiu 2024 original-model reproduction",
+  "parameters": {
+    "dt_ms": 0.1,
+    "integration": "forward_euler",
+    "membrane_tau_ms": 20.0,
+    "refractory_g_policy": "g continues to decay and receive exact delayed events while v is clamped at V_reset",
+    "refractory_ms": 2.2,
+    "reset_potential_mv": -52.0,
+    "resting_potential_mv": -52.0,
+    "synaptic_delay_ms": 1.8,
+    "synaptic_tau_ms": 5.0,
+    "threshold_mv": -45.0,
+    "w_syn_mv_per_anatomical_synapse": 0.275
+  },
+  "phase4b_checksum_verification": "PASS",
+  "phase4b_checksums_sha256": "8f09b27d60fdde213d4038176169127bbca16d4da5bbc85d3bf1ea1755a9de76",
+  "phase4b_manifest_sha256": "d930b92524d494937e11bd2dbfe50ac31d924daf8140d80ccd17fb2ad2d0b09a",
+  "reason": "MaleCNS v1.0 transmitter inventory includes histamine and differs from the original dataset/inventory",
+  "remote_model_directory_is_git_repository": false,
+  "sign_policy": {
+    "neurotransmitter_sign": {
+      "acetylcholine": 1,
+      "dopamine": 1,
+      "gaba": -1,
+      "glutamate": -1,
+      "histamine": -1,
+      "octopamine": 1,
+      "serotonin": 1
+    },
+    "unclear_sign": 0,
+    "unknown_sign": 0,
+    "unmapped_policy": "error"
+  },
+  "source_phase": "Phase 4B PASS"
+}
@@ -0,0 +1,4 @@
+b094472c713fb48be6d35ab2b4cad4d5ce8afb070afd9c6e16de47a120a3f14a  VERSION.json
+3c8651a903302845020917e8c7fee5caa39b6d2bef167a8a448c1a7560689414  config.yaml
+693468685a7ff3db1d09a088e0bbdaa78c595d64086b27e9cc18abceb4c7d174  model.py
+994d31222a1728feb4ea747d9fd16d0b36fe53321a55ef7b7e39f0905de629e4  MANIFEST.json
@@ -0,0 +1,116 @@
+phase: 4B
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  experiment_root: /data/digital-drosophila/experiments/phase4b-dynamics
+
+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 delayed events while v is clamped at V_reset
+  provenance: Shiu-2024-compatible baseline supplied by user; not MaleCNS measured single-cell parameters
+
+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'
+
+baseline_sweep:
+  rates_hz: [10, 25, 50, 100, 150, 200]
+  seeds: [42001, 42002, 42003]
+  duration_ms: 1000.0
+  event_logging: false
+
+weight_sweep:
+  population: auditory
+  rate_hz: 100
+  seed: 42100
+  duration_ms: 1000.0
+  values_mv: [0.1375, 0.20625, 0.275, 0.34375, 0.55]
+
+stimulation:
+  mode: refractory-respecting forced sensory-neuron Poisson spikes
+  note: no arbitrary current amplitude is introduced; accepted events become presynaptic spikes
+
+classification:
+  supercritical_peak_step_fraction: 0.10
+  supercritical_active_fraction: 0.80
+  supercritical_mean_rate_hz: 100.0
+  propagating_min_depth: 2
+  abort_supercritical: true
+  check_interval_steps: 50
+
+performance:
+  population: auditory
+  rate_hz: 10
+  seed: 42200
+  duration_ms: 1000.0
+  gpu_sample_interval_seconds: 0.2
+  compare_logging_disabled_and_full: true
+
+profiler:
+  population: auditory
+  rate_hz: 10
+  seed: 42201
+  duration_ms: 1000.0
+  synchronized_category_timing: true
+
+causal_validation:
+  requested_chains: 100
+  requested_inhibitory_transmissions: 100
+  seed: 42300
+  max_edges_examined: 5000000
+
+cpu_gpu_reference:
+  seed: 42400
+  subgraph_neurons: 512
+  steps: 100
+  absolute_tolerance: 1.0e-10
+
+audit:
+  finite_check_interval_steps: 100
+  memory_growth_tolerance_bytes: 10485760
+  preserve_source_data: true
+
+reproducibility:
+  global_seed: 42000
+  deterministic_inputs: true