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 +1,91 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "external_drive_is_connectome_transmission": false,
+  "properties": {
+    "batch_id": {
+      "type": "string"
+    },
+    "events": {
+      "items": {
+        "properties": {
+          "amplitude_mv": {
+            "type": "number"
+          },
+          "channel_id": {
+            "type": "string"
+          },
+          "duration_ms": {
+            "exclusiveMinimum": 0,
+            "type": "number"
+          },
+          "source_id": {
+            "type": "string"
+          },
+          "start_ms": {
+            "minimum": 0,
+            "type": "number"
+          },
+          "stimulation_mode": {
+            "enum": [
+              "spike_injection",
+              "external_synaptic_drive"
+            ]
+          },
+          "target_neuron_idx": {
+            "items": {
+              "maximum": 166699,
+              "minimum": 0,
+              "type": "integer"
+            },
+            "type": "array"
+          },
+          "value": {
+            "oneOf": [
+              {
+                "type": "number"
+              },
+              {
+                "items": {
+                  "type": "number"
+                },
+                "type": "array"
+              }
+            ]
+          },
+          "value_kind": {
+            "enum": [
+              "binary",
+              "scalar_intensity",
+              "poisson_rate_hz",
+              "signed_modulation"
+            ]
+          }
+        },
+        "required": [
+          "target_neuron_idx",
+          "stimulation_mode",
+          "value_kind",
+          "value",
+          "start_ms",
+          "duration_ms",
+          "source_id",
+          "channel_id"
+        ],
+        "type": "object"
+      },
+      "type": "array"
+    },
+    "version": {
+      "const": "1.0.0"
+    }
+  },
+  "required": [
+    "version",
+    "batch_id",
+    "events"
+  ],
+  "timestamp_unit": "biological ms",
+  "title": "MaleCNS InputBatch",
+  "type": "object",
+  "version": "1.0.0"
+}
@@ -0,0 +1,102 @@
+phase: 4D
+names:
+  runtime: MaleCNS-LIF-runtime-v1
+  io_api: MaleCNS-BrainIO-v1
+  visual_adapter: MaleCNS-VisualAdapter-v1
+  activity_stream: MaleCNS-ActivityStream-v1
+
+paths:
+  connectome_root: /data/digital-drosophila/datasets/male-cns-v1.0/processed/neuron-only
+  model_root: /data/digital-drosophila/models/male-cns-lif
+  runtime_root: /data/digital-drosophila/models/male-cns-lif/runtime-v1
+  phase4c_root: /data/digital-drosophila/experiments/phase4c-runtime
+  experiment_root: /data/digital-drosophila/experiments/phase4d-io
+
+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
+
+input_batch:
+  version: 1.0.0
+  allowed_modes: [spike_injection, external_synaptic_drive]
+  refractory_respecting_spike_injection: true
+  external_drive_application: add to g after decay and delayed-connectome arrival, before membrane integration
+
+visual_adapter:
+  version: 1.0.0
+  modes:
+    reference-photoreceptor:
+      hierarchy_population: visual_sensory
+      input_mode: spike_injection
+      biological_fidelity: reference_comparison_only
+    engineering-first-order:
+      hierarchy_population: first_order
+      input_mode: external_synaptic_drive
+      biological_fidelity: engineering_adapter
+    engineering-second-order:
+      hierarchy_population: second_order
+      input_mode: external_synaptic_drive
+      biological_fidelity: engineering_adapter
+  synthetic_rate_hz: 50.0
+  external_drive_mv: 8.0
+
+readout:
+  bins_ms: [1, 5, 10, 20, 50]
+  output_populations: [descending, motor_related, ascending]
+
+window_experiment:
+  windows_ms: [5, 10, 20, 30, 50, 100]
+  sources: [engineering-first-order, engineering-second-order, auditory, olfactory]
+  seeds: [44001, 44002]
+
+continuous_control:
+  biological_duration_ms: 1000.0
+  periods_ms: [10, 20, 50, 100]
+  sequence: [sparse-A, sparse-B, dense, zero, sparse-A]
+  seed: 44100
+
+synthetic_patterns:
+  sparse_fraction: 0.05
+  dense_fraction: 0.25
+  moving_fraction: 0.05
+  deterministic_seed: 44200
+
+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}
+
+prohibitions:
+  stable_retro: false
+  rom_access: false
+  controller_buttons: false
+  training: false
+  web_server: false
+  connectome_or_sign_changes: false