Validate isolated author LIF semantics without changing frozen models

2026-09-30 07:23:09 +08:00
parent 5008cd85ca
commit 92241aea02
460 changed files with 46900 additions and 47 deletions
@@ -0,0 +1,26 @@
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@@ -0,0 +1,4 @@
+global_neuron_idx,local_index
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@@ -0,0 +1,102 @@
+{
+  "all_package_pins_match": true,
+  "author_platform": "Windows",
+  "author_python": "3.10.11",
+  "binary_identical_author_environment_claimed": false,
+  "packages": {
+    "brian2": {
+      "actual": "2.5.1",
+      "expected": "2.5.1",
+      "matches": true
+    },
+    "cython": {
+      "actual": "0.29.33",
+      "expected": "0.29.33",
+      "matches": true
+    },
+    "jinja2": {
+      "actual": "2.11.3",
+      "expected": "2.11.3",
+      "matches": true
+    },
+    "joblib": {
+      "actual": "1.2.0",
+      "expected": "1.2.0",
+      "matches": true
+    },
+    "markupsafe": {
+      "actual": "1.1.1",
+      "expected": "1.1.1",
+      "matches": true
+    },
+    "mpmath": {
+      "actual": "1.3.0",
+      "expected": "1.3.0",
+      "matches": true
+    },
+    "numpy": {
+      "actual": "1.22.3",
+      "expected": "1.22.3",
+      "matches": true
+    },
+    "packaging": {
+      "actual": "23.1",
+      "expected": "23.1",
+      "matches": true
+    },
+    "pandas": {
+      "actual": "1.4.3",
+      "expected": "1.4.3",
+      "matches": true
+    },
+    "pyarrow": {
+      "actual": "11.0.0",
+      "expected": "11.0.0",
+      "matches": true
+    },
+    "pyparsing": {
+      "actual": "3.0.9",
+      "expected": "3.0.9",
+      "matches": true
+    },
+    "python-dateutil": {
+      "actual": "2.8.2",
+      "expected": "2.8.2",
+      "matches": true
+    },
+    "pytz": {
+      "actual": "2023.3",
+      "expected": "2023.3",
+      "matches": true
+    },
+    "scipy": {
+      "actual": "1.8.1",
+      "expected": "1.8.1",
+      "matches": true
+    },
+    "setuptools": {
+      "actual": "67.8.0",
+      "expected": "67.8.0",
+      "matches": true
+    },
+    "six": {
+      "actual": "1.16.0",
+      "expected": "1.16.0",
+      "matches": true
+    },
+    "sympy": {
+      "actual": "1.12",
+      "expected": "1.12",
+      "matches": true
+    },
+    "wheel": {
+      "actual": "0.38.4",
+      "expected": "0.38.4",
+      "matches": true
+    }
+  },
+  "platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35",
+  "python": "3.10.12",
+  "python_executable": "/data/digital-drosophila/experiments/phase4ad-author-semantics/environment/.venv/bin/python",
+  "python_patch_matches": false
+}
@@ -0,0 +1,127 @@
+[
+  {
+    "active": true,
+    "code_objects": [],
+    "name": "default_neurons",
+    "order": 0,
+    "type": "NeuronGroup",
+    "when": "start"
+  },
+  {
+    "active": true,
+    "code_objects": [],
+    "name": "default_synapses",
+    "order": 0,
+    "type": "Synapses",
+    "when": "start"
+  },
+  {
+    "abstract_code": "not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n_g = g*exp(-dt*int(not_refractory)/tau)\n_v = g*tau*(-exp(dt*int(not_refractory)/t_mbr) + exp(dt*int(not_refractory)/tau))*exp(-dt*int(not_refractory)/t_mbr)*exp(-dt*int(not_refractory)/tau)/(t_mbr - tau) + v*exp(-dt*int(not_refractory)/t_mbr) + v_0 - v_0*exp(-dt*int(not_refractory)/t_mbr)\ng = _g\nv = _v",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # scalar code\n    _vectorisation_idx = 1\n    dt = _array_defaultclock_dt[0]\n    _lio_1 = (- dt) / tau\n    _lio_2 = exp(_lio_1)\n    _lio_3 = tau / (t_mbr - tau)\n    _lio_4 = dt / t_mbr\n    _lio_5 = dt / tau\n    _lio_6 = (- dt) / t_mbr\n    _lio_7 = v_0 - v_0\n    _lio_8 = v_0 - (v_0 * exp(_lio_6))\n    _lio_9 = ((_lio_3 * ((- exp(_lio_4)) + exp(_lio_5))) * exp(_lio_6)) * exp(_lio_1)\n    _lio_10 = exp(_lio_6)\n    # vector code\n    _vectorisation_idx = LazyArange(N)\n    g = _array_default_neurons_g.copy()\n    t = _array_defaultclock_t[0]\n    dt = _array_defaultclock_dt[0]\n    rfc = _array_default_neurons_rfc\n    v = _array_default_neurons_v.copy()\n    lastspike = _array_default_neurons_lastspike\n    not_refractory = _array_default_neurons_not_refractory.copy()\n    not_refractory = timestep(t - lastspike, dt) >= timestep(rfc, dt)\n    _g = _numpy.where(not_refractory, _lio_2 * g, g)\n    _v = _numpy.where(not_refractory, _lio_8 + ((_lio_9 * g) + (_lio_10 * v)), _lio_7 + v)\n    g[not_refractory] = _g[not_refractory]\n    v[not_refractory] = _v[not_refractory]\n    _array_default_neurons_g[:] = g\n    _array_default_neurons_v[:] = v\n    _array_default_neurons_not_refractory[:] = not_refractory\n",
+        "name": "default_neurons_stateupdater_codeobject",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "default_neurons_stateupdater",
+    "order": 0,
+    "type": "StateUpdater",
+    "user_code": "g = -g*int(not_refractory)/tau\nv = (g - v + v_0)*int(not_refractory)/t_mbr",
+    "when": "groups"
+  },
+  {
+    "active": true,
+    "code_objects": [],
+    "name": "oracle_seed_injection",
+    "order": 0,
+    "type": "NetworkOperation",
+    "when": "before_thresholds"
+  },
+  {
+    "abstract_code": "_cond = (v > v_th) and not_refractory",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    _array_default_neurons__spikespace[-1] = 0\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    numpy_True = _numpy.bool_(True)\n    numpy_False = _numpy.bool_(False)\n    # scalar code\n    _vectorisation_idx = 1\n    # vector code\n    _vectorisation_idx = LazyArange(N)\n    v = _array_default_neurons_v\n    not_refractory = _array_default_neurons_not_refractory\n    _cond = (v > v_th) & not_refractory\n    if _cond is True or _cond is numpy_True:\n        _events = _numpy.arange(N)\n    elif _cond is False or _cond is numpy_False:\n        _events = _numpy.array([])\n    else:\n        _events, = _cond.nonzero()\n    _array_default_neurons__spikespace[-1] = len(_events)\n    _array_default_neurons__spikespace[:len(_events)] = _events\n    # Set the neuron to refractory\n    _array_default_neurons_not_refractory[_events] = False\n    _array_default_neurons_lastspike[_events] = _array_defaultclock_t[0]\n",
+        "name": "default_neurons_spike_thresholder_codeobject_1",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "default_neurons_spike_thresholder",
+    "order": 0,
+    "type": "Thresholder",
+    "user_code": "_cond = v > v_th",
+    "when": "thresholds"
+  },
+  {
+    "abstract_code": "_to_record_i = _source_i\n_to_record_t = _source_t",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    _n_events = _array_default_neurons__spikespace[-1]\n    if _n_events > 0:\n        _events = _array_default_neurons__spikespace[:_n_events]\n        # Take subgroups into account\n        if _source_start != 0 or _source_stop != _source_N:\n            _events = _events[(_events >= _source_start) & (_events < _source_stop)]\n            _n_events = len(_events)\n        if _n_events > 0:\n            _vectorisation_idx = 1\n            _curlen = _array_spikemonitor_N[0]\n            _newlen = _curlen + _n_events\n            _owner.resize(_newlen)\n            _array_spikemonitor_N[0] = _newlen\n            _vectorisation_idx = _events\n            _idx = _events\n            _source_i = _array_default_neurons_i[_idx]\n            _source_t = _array_defaultclock_t[0]\n            _to_record_i = _source_i\n            _to_record_t = _source_t\n            _dynamic_array_spikemonitor_t[_curlen:_newlen] = _to_record_t\n            _dynamic_array_spikemonitor_i[_curlen:_newlen] = _to_record_i\n            _array_spikemonitor_count[_events - _source_start] += 1\n",
+        "name": "spikemonitor_codeobject",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "spikemonitor",
+    "order": 1,
+    "type": "SpikeMonitor",
+    "user_code": "None",
+    "when": "thresholds"
+  },
+  {
+    "abstract_code": "g += w\n",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    _owner.initialise_queue()\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    _owner.push_spikes()\n",
+        "name": "default_synapses_pre_push_spikes",
+        "type": "CallableProxyType"
+      },
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    _spiking_synapses = _queue.peek()\n    if len(_spiking_synapses):\n        # scalar code\n        # vector code\n        _idx = _spiking_synapses\n        _vectorisation_idx = _idx\n        #  Abstract code:  g += w\n        _postsynaptic_idx = _array_default_synapses__synaptic_post[_idx]\n        w = _array_default_synapses_w[_idx]\n        not_refractory = _array_default_neurons_not_refractory[_postsynaptic_idx]\n        _numpy.add.at(_array_default_neurons_g, _postsynaptic_idx[not_refractory], w[not_refractory])\n    # Advance the spike queue\n    _queue.advance()\n",
+        "name": "default_synapses_pre_codeobject_1",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "default_synapses_pre",
+    "order": -1,
+    "type": "SynapticPathway",
+    "user_code": "None",
+    "when": "synapses"
+  },
+  {
+    "abstract_code": "v = v_rst; w = 0; g = 0 * mV",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # scalar code\n    _vectorisation_idx = 1\n    w = 0\n    # vector code\n    _idx = _array_default_neurons__spikespace[:_array_default_neurons__spikespace[-1]]\n    _vectorisation_idx = _idx\n    v = v_rst\n    g = 0.0\n    _array_default_neurons_g[_idx] = g\n    _array_default_neurons_v[_idx] = v\n",
+        "name": "default_neurons_spike_resetter_codeobject_1",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "default_neurons_spike_resetter",
+    "order": 0,
+    "type": "Resetter",
+    "user_code": "None",
+    "when": "resets"
+  },
+  {
+    "abstract_code": "_to_record_v = _source_v\n_to_record_g = _source_g\n_to_record_lastspike = _source_lastspike\n_to_record_not_refractory = _source_not_refractory",
+    "active": true,
+    "code_objects": [
+      {
+        "generated_code": "after_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nbefore_run:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # EMPTY_CODE_BLOCK  -- overwrite in child template\nrun:\n    import numpy as _numpy\n    from brian2.codegen.runtime.numpy_rt.numpy_rt import LazyArange\n    # Resize dynamic arrays\n    _new_len = len(_dynamic_array_oracle_end_state_t) + 1\n    _owner.resize(_new_len)\n    # Store values\n    _dynamic_array_oracle_end_state_t[-1] = _array_defaultclock_t[0]\n    # scalar code\n    _vectorisation_idx = 1\n    # vector code\n    _vectorisation_idx = _array_oracle_end_state__indices\n    _idx = _array_oracle_end_state__indices\n    _source_not_refractory = _array_default_neurons_not_refractory[_idx]\n    _source_g = _array_default_neurons_g[_idx]\n    _source_v = _array_default_neurons_v[_idx]\n    _source_lastspike = _array_default_neurons_lastspike[_idx]\n    _to_record_v = _source_v\n    _to_record_g = _source_g\n    _to_record_lastspike = _source_lastspike\n    _to_record_not_refractory = _source_not_refractory\n    _dynamic_array_oracle_end_state_v[-1, :] = _to_record_v\n    _dynamic_array_oracle_end_state_g[-1, :] = _to_record_g\n    _dynamic_array_oracle_end_state_lastspike[-1, :] = _to_record_lastspike\n    _dynamic_array_oracle_end_state_not_refractory[-1, :] = _to_record_not_refractory\n",
+        "name": "oracle_end_state_codeobject",
+        "type": "CallableProxyType"
+      }
+    ],
+    "name": "oracle_end_state",
+    "order": 0,
+    "type": "StateMonitor",
+    "user_code": "None",
+    "when": "end"
+  }
+]
@@ -0,0 +1,123 @@
+{
+  "author_commit": "91bdd1e7dcf193f3e7ca5a8933497fcef63b7960",
+  "author_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e",
+  "config": {
+    "author_precisions": [
+      "float64",
+      "float32"
+    ],
+    "comparison": {
+      "exact_spike_events_required_for_oracle_validation": true,
+      "float32_state_max_abs_tolerance_mv": 0.001,
+      "float64_state_max_abs_tolerance_mv": 1e-08,
+      "precision_cross_comparison_may_diverge_but_must_be_reported": true
+    },
+    "component_policies": [
+      "frozen",
+      "reset_g_only",
+      "refractory_gate_only",
+      "reset_and_refractory"
+    ],
+    "dt_ms": 0.1,
+    "duration_ms": 1000.0,
+    "experiment": "experiments/phase4ad-author-semantics",
+    "human_authorization": "\u5141\u8bb8\u72ec\u7acb\u65b0\u6a21\u578b\u5206\u652f\u6d4b\u8bd5\u52a8\u529b\u5b66\u5047\u8bbe",
+    "late_start_ms": 500.0,
+    "model": {
+      "dt_ms": 0.1,
+      "membrane_tau_ms": 20.0,
+      "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
+    },
+    "model_directory": "models/male-cns-lif/author-semantics-lab-v1",
+    "motifs": [
+      "pair",
+      "trio",
+      "five",
+      "feedforward",
+      "no_input"
+    ],
+    "name": "author-semantics-lab-v1",
+    "no_training_or_candidate": true,
+    "phase": "4AD",
+    "prior_experiment": "experiments/phase4ac-lif-semantics",
+    "prior_model": "models/male-cns-lif/lif-semantics-audit-v1",
+    "root": "/data/digital-drosophila",
+    "seed_margin_mv": 1.0,
+    "seed_node": 1381
+  },
+  "delay_steps": 18,
+  "dt_ms": 0.1,
+  "edge_ids": [
+    1336648,
+    1336655,
+    1467340,
+    1467355,
+    1559765,
+    1559772
+  ],
+  "external_arrivals": {
+    "events": 0,
+    "ordering": "after default_synapses.pre"
+  },
+  "internal_voltage_unit": "volt",
+  "nodes": [
+    1197,
+    1381,
+    1511
+  ],
+  "parameter_checks": {
+    "membrane_tau_ms": {
+      "author": 20.0,
+      "config": 20.0
+    },
+    "refractory_ms": {
+      "author": 2.2,
+      "config": 2.2
+    },
+    "reset_potential_mv": {
+      "author": -52.0,
+      "config": -52.0
+    },
+    "resting_potential_mv": {
+      "author": -52.0,
+      "config": -52.0
+    },
+    "synaptic_delay_ms": {
+      "author": 1.8,
+      "config": 1.8
+    },
+    "synaptic_tau_ms": {
+      "author": 5.0,
+      "config": 5.0
+    },
+    "threshold_mv": {
+      "author": -45.0,
+      "config": -45.0
+    },
+    "w_syn_mv_per_anatomical_synapse": {
+      "author": 0.275,
+      "config": 0.275
+    }
+  },
+  "precision": "float64",
+  "preferences": {
+    "codegen.target": "numpy",
+    "core.default_float_dtype": "float64",
+    "legacy.refractory_timing": false
+  },
+  "refractory_steps": 22,
+  "returned_voltage_unit": "mV",
+  "seed": {
+    "injections": 0,
+    "margin_mv": 1.0,
+    "requested_global_node": 1381
+  },
+  "steps": 10000,
+  "weight_rule": "raw_count multiplied by unchanged author w_syn; no sign inference"
+}
@@ -0,0 +1,11 @@
+{
+  "schedule": [
+    "start",
+    "groups",
+    "thresholds",
+    "synapses",
+    "resets",
+    "end"
+  ],
+  "summary": "                    object                      |             part of             |       Clock dt       |       when        | order | active\n------------------------------------------------+---------------------------------+----------------------+-------------------+-------+-------\ndefault_neurons_stateupdater (StateUpdater)     | default_neurons (NeuronGroup)   | 100. us (every step) | groups            |     0 |  yes  \noracle_seed_injection (NetworkOperation)        | --                              | 100. us (every step) | before_thresholds |     0 |  yes  \ndefault_neurons_spike_thresholder (Thresholder) | default_neurons (NeuronGroup)   | 100. us (every step) | thresholds        |     0 |  yes  \nspikemonitor (SpikeMonitor)                     | spikemonitor (SpikeMonitor)     | 100. us (every step) | thresholds        |     1 |  yes  \ndefault_synapses_pre (SynapticPathway)          | default_synapses (Synapses)     | 100. us (every step) | synapses          |    -1 |  yes  \ndefault_neurons_spike_resetter (Resetter)       | default_neurons (NeuronGroup)   | 100. us (every step) | resets            |     0 |  yes  \noracle_end_state (StateMonitor)                 | oracle_end_state (StateMonitor) | 100. us (every step) | end               |     0 |  yes  "
+}
@@ -0,0 +1,7 @@
+{
+  "applied_mv": -44.0,
+  "injections": 1,
+  "margin_mv": 1.0,
+  "requested_global_node": 1381,
+  "spiked_at_zero": true
+}