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Validate isolated author LIF semantics without changing frozen models

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Digital Drosophila Archive
2026-09-30 07:23:09 +08:00
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commit 92241aea02
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registry/phase4ad-author-semantics/evidence-index.json
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registry/phase4ad-author-semantics/evidence/REPORT.md
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# Phase 4AD 作者动力学语义实验室
状态：`COMPLETE-ORACLE-VALIDATED-LAB-ONLY`。
本轮仅有预声明的小回路与算子实验；没有整脑替代动力学运行、conditioning、学习成功或新学习候选。
检查以原始事件、状态轨迹和预注册误差界限重算。缺失、失败、非有限值或初始事件丢失均不能通过；放电减少或静默本身不构成成功。
核查通过 58/58 项；失败或不完整 0 项。
冻结历史完整性：通过。
源码与输入预注册一致性：通过。
| 回路 | 语义 | 精度 | 总spikes | late spikes |
|---|---|---|---:|---:|
| pair | frozen | float32 | 473 | 238 |
| pair | reset_g_only | float32 | 223 | 111 |
| pair | refractory_gate_only | float32 | 635 | 321 |
| pair | reset_and_refractory | float32 | 223 | 111 |
| trio | frozen | float32 | 1064 | 535 |
| trio | reset_g_only | float32 | 565 | 283 |
| trio | refractory_gate_only | float32 | 1100 | 552 |
| trio | reset_and_refractory | float32 | 469 | 235 |
| five | frozen | float32 | 1483 | 747 |
| five | reset_g_only | float32 | 868 | 433 |
| five | refractory_gate_only | float32 | 1510 | 763 |
| five | reset_and_refractory | float32 | 634 | 318 |
| feedforward | frozen | float32 | 3 | 0 |
| feedforward | reset_g_only | float32 | 3 | 0 |
| feedforward | refractory_gate_only | float32 | 3 | 0 |
| feedforward | reset_and_refractory | float32 | 3 | 0 |
| no_input | frozen | float32 | 0 | 0 |
| no_input | reset_g_only | float32 | 0 | 0 |
| no_input | refractory_gate_only | float32 | 0 | 0 |
| no_input | reset_and_refractory | float32 | 0 | 0 |
| pair | author_complete | float64 | 213 | 106 |
| pair | author_complete | float32 | 213 | 106 |
| trio | author_complete | float64 | 448 | 224 |
| trio | author_complete | float32 | 448 | 224 |
| five | author_complete | float64 | 610 | 306 |
| five | author_complete | float32 | 610 | 306 |
| feedforward | author_complete | float64 | 3 | 0 |
| feedforward | author_complete | float32 | 3 | 0 |
| no_input | author_complete | float64 | 0 | 0 |
| no_input | author_complete | float32 | 0 | 0 |
作者Brian2与独立NumPy比较：
| 实验 | 结果 | 事件一致 | 最大V/g误差 mV | 首次事件分歧step |
|---|---|---|---:|---:|
| author:pair:float64 | 通过 | True | 7.105427357601002e-14 | None |
| author:pair:float32 | 通过 | True | 2.41696834564209e-05 | None |
| author:trio:float64 | 通过 | True | 8.526512829121202e-14 | None |
| author:trio:float32 | 通过 | True | 4.25875186920166e-05 | None |
| author:five:float64 | 通过 | True | 3.836930773104541e-13 | None |
| author:five:float32 | 通过 | True | 0.0002123713493347168 | None |
| author:feedforward:float64 | 通过 | True | 3.765876499528531e-13 | None |
| author:feedforward:float32 | 通过 | True | 0.00020179152488708496 | None |
| author:no_input:float64 | 通过 | True | 7.105427357601002e-15 | None |
| author:no_input:float32 | 通过 | True | 1.0728836059570312e-06 | None |
float32与float64交叉比较仅记录精度影响，允许保留分歧，不能用于掩盖各自与独立oracle的失败。
- precision_cross_record:pair：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。
- precision_cross_record:trio：事件一致=True，最大误差=3.733467101341148e-05 mV，首次事件分歧step=None。
- precision_cross_record:five：事件一致=True，最大误差=0.00019546693161487383 mV，首次事件分歧step=None。
- precision_cross_record:feedforward：事件一致=True，最大误差=0.0005722045887850413 mV，首次事件分歧step=None。
- precision_cross_record:no_input：事件一致=True，最大误差=0.0 mV，首次事件分歧step=None。
所有失败轨迹和错误文件原样保留；本简报没有选择获胜变体。
小回路缺少外部整脑输入与graded APL，不能证明整脑因果必要性、生物真实性或信息保持。初始诊断seed也不是作者的感官Poisson接口。
环境为Linux宿主，作者记录为Windows；Python补丁版本与环境差异见environment记录，不能称为二进制相同或原论文整脑复现。
后续整脑嗅觉比较仍须核查固定输入、实际送达事件、持续活动和信息保持；可用学习仍需至少5个训练seed、独立评估、MBON/downstream的A对中性B特异性及acquisition/reversal/retention/delayed-reward对照。
封存排除 .venv 与 __pycache__，保留环境安装报告；manifest列出payload哈希，checksums另含manifest，不存在自哈希循环。
registry/phase4ad-author-semantics/evidence/audit/all-motif-results.csv
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motif,policy,precision,neuron_idx,spikes,late_spikes,last_ms
pair,frozen,float32,1381,237,119,999.3000000000001
pair,frozen,float32,1511,236,119,997.5
pair,reset_g_only,float32,1381,112,56,999.0
pair,reset_g_only,float32,1511,111,55,994.9000000000001
pair,refractory_gate_only,float32,1381,318,161,999.1
pair,refractory_gate_only,float32,1511,317,160,997.5
pair,reset_and_refractory,float32,1381,112,56,999.0
pair,reset_and_refractory,float32,1511,111,55,994.9000000000001
trio,frozen,float32,1197,355,179,999.3000000000001
trio,frozen,float32,1381,355,178,997.8000000000001
trio,frozen,float32,1511,354,178,997.4000000000001
trio,reset_g_only,float32,1197,188,94,995.4000000000001
trio,reset_g_only,float32,1381,189,95,998.7
trio,reset_g_only,float32,1511,188,94,996.1
trio,refractory_gate_only,float32,1197,369,185,998.3000000000001
trio,refractory_gate_only,float32,1381,367,184,999.1
trio,refractory_gate_only,float32,1511,364,183,997.2
trio,reset_and_refractory,float32,1197,156,78,995.3000000000001
trio,reset_and_refractory,float32,1381,157,79,999.6
trio,reset_and_refractory,float32,1511,156,78,997.5
five,frozen,float32,1197,370,185,998.8000000000001
five,frozen,float32,1381,369,185,997.4000000000001
five,frozen,float32,1511,367,186,999.5
five,frozen,float32,82312,80,41,990.3000000000001
five,frozen,float32,133666,297,150,999.5
five,reset_g_only,float32,1197,249,125,996.2
five,reset_g_only,float32,1381,211,104,999.2
five,reset_g_only,float32,1511,209,104,996.5
five,reset_g_only,float32,82312,33,17,994.9000000000001
five,reset_g_only,float32,133666,166,83,996.7
five,refractory_gate_only,float32,1197,372,188,998.0
five,refractory_gate_only,float32,1381,375,191,998.6
five,refractory_gate_only,float32,1511,371,187,997.5
five,refractory_gate_only,float32,82312,85,43,991.9000000000001
five,refractory_gate_only,float32,133666,307,154,997.7
five,reset_and_refractory,float32,1197,165,82,995.7
five,reset_and_refractory,float32,1381,166,83,999.8000000000001
five,reset_and_refractory,float32,1511,165,83,997.5
five,reset_and_refractory,float32,82312,15,8,972.7
five,reset_and_refractory,float32,133666,123,62,993.0
feedforward,frozen,float32,1197,1,0,10.0
feedforward,frozen,float32,1381,1,0,0.0
feedforward,frozen,float32,1511,1,0,4.9
feedforward,frozen,float32,82312,0,0,
feedforward,frozen,float32,133666,0,0,
feedforward,reset_g_only,float32,1197,1,0,10.0
feedforward,reset_g_only,float32,1381,1,0,0.0
feedforward,reset_g_only,float32,1511,1,0,4.9
feedforward,reset_g_only,float32,82312,0,0,
feedforward,reset_g_only,float32,133666,0,0,
feedforward,refractory_gate_only,float32,1197,1,0,10.0
feedforward,refractory_gate_only,float32,1381,1,0,0.0
feedforward,refractory_gate_only,float32,1511,1,0,4.9
feedforward,refractory_gate_only,float32,82312,0,0,
feedforward,refractory_gate_only,float32,133666,0,0,
feedforward,reset_and_refractory,float32,1197,1,0,10.0
feedforward,reset_and_refractory,float32,1381,1,0,0.0
feedforward,reset_and_refractory,float32,1511,1,0,4.9
feedforward,reset_and_refractory,float32,82312,0,0,
feedforward,reset_and_refractory,float32,133666,0,0,
no_input,frozen,float32,1197,0,0,
no_input,frozen,float32,1381,0,0,
no_input,frozen,float32,1511,0,0,
no_input,frozen,float32,82312,0,0,
no_input,frozen,float32,133666,0,0,
no_input,reset_g_only,float32,1197,0,0,
no_input,reset_g_only,float32,1381,0,0,
no_input,reset_g_only,float32,1511,0,0,
no_input,reset_g_only,float32,82312,0,0,
no_input,reset_g_only,float32,133666,0,0,
no_input,refractory_gate_only,float32,1197,0,0,
no_input,refractory_gate_only,float32,1381,0,0,
no_input,refractory_gate_only,float32,1511,0,0,
no_input,refractory_gate_only,float32,82312,0,0,
no_input,refractory_gate_only,float32,133666,0,0,
no_input,reset_and_refractory,float32,1197,0,0,
no_input,reset_and_refractory,float32,1381,0,0,
no_input,reset_and_refractory,float32,1511,0,0,
no_input,reset_and_refractory,float32,82312,0,0,
no_input,reset_and_refractory,float32,133666,0,0,
pair,author_complete,float64,1381,107,53,996.4000000000001
pair,author_complete,float64,1511,106,53,992.1
pair,author_complete,float32,1381,107,53,996.4000000000001
pair,author_complete,float32,1511,106,53,992.1
trio,author_complete,float64,1197,149,74,994.8000000000001
trio,author_complete,float64,1381,150,75,999.3000000000001
trio,author_complete,float64,1511,149,75,997.0
trio,author_complete,float32,1197,149,74,994.8000000000001
trio,author_complete,float32,1381,150,75,999.3000000000001
trio,author_complete,float32,1511,149,75,997.0
five,author_complete,float64,1197,159,79,995.2
five,author_complete,float64,1381,160,80,999.5
five,author_complete,float64,1511,159,80,997.4000000000001
five,author_complete,float64,82312,13,7,992.4000000000001
five,author_complete,float64,133666,119,60,996.0
five,author_complete,float32,1197,159,79,995.2
five,author_complete,float32,1381,160,80,999.5
five,author_complete,float32,1511,159,80,997.4000000000001
five,author_complete,float32,82312,13,7,992.4000000000001
five,author_complete,float32,133666,119,60,996.0
feedforward,author_complete,float64,1197,1,0,10.4
feedforward,author_complete,float64,1381,1,0,0.0
feedforward,author_complete,float64,1511,1,0,5.1000000000000005
feedforward,author_complete,float64,82312,0,0,
feedforward,author_complete,float64,133666,0,0,
feedforward,author_complete,float32,1197,1,0,10.4
feedforward,author_complete,float32,1381,1,0,0.0
feedforward,author_complete,float32,1511,1,0,5.1000000000000005
feedforward,author_complete,float32,82312,0,0,
feedforward,author_complete,float32,133666,0,0,
no_input,author_complete,float64,1197,0,0,
no_input,author_complete,float64,1381,0,0,
no_input,author_complete,float64,1511,0,0,
no_input,author_complete,float64,82312,0,0,
no_input,author_complete,float64,133666,0,0,
no_input,author_complete,float32,1197,0,0,
no_input,author_complete,float32,1381,0,0,
no_input,author_complete,float32,1511,0,0,
no_input,author_complete,float32,82312,0,0,
no_input,author_complete,float32,133666,0,0,
1 motif policy precision neuron_idx spikes late_spikes last_ms
2 pair frozen float32 1381 237 119 999.3000000000001
3 pair frozen float32 1511 236 119 997.5
4 pair reset_g_only float32 1381 112 56 999.0
5 pair reset_g_only float32 1511 111 55 994.9000000000001
6 pair refractory_gate_only float32 1381 318 161 999.1
7 pair refractory_gate_only float32 1511 317 160 997.5
8 pair reset_and_refractory float32 1381 112 56 999.0
9 pair reset_and_refractory float32 1511 111 55 994.9000000000001
10 trio frozen float32 1197 355 179 999.3000000000001
11 trio frozen float32 1381 355 178 997.8000000000001
12 trio frozen float32 1511 354 178 997.4000000000001
13 trio reset_g_only float32 1197 188 94 995.4000000000001
14 trio reset_g_only float32 1381 189 95 998.7
15 trio reset_g_only float32 1511 188 94 996.1
16 trio refractory_gate_only float32 1197 369 185 998.3000000000001
17 trio refractory_gate_only float32 1381 367 184 999.1
18 trio refractory_gate_only float32 1511 364 183 997.2
19 trio reset_and_refractory float32 1197 156 78 995.3000000000001
20 trio reset_and_refractory float32 1381 157 79 999.6
21 trio reset_and_refractory float32 1511 156 78 997.5
22 five frozen float32 1197 370 185 998.8000000000001
23 five frozen float32 1381 369 185 997.4000000000001
24 five frozen float32 1511 367 186 999.5
25 five frozen float32 82312 80 41 990.3000000000001
26 five frozen float32 133666 297 150 999.5
27 five reset_g_only float32 1197 249 125 996.2
28 five reset_g_only float32 1381 211 104 999.2
29 five reset_g_only float32 1511 209 104 996.5
30 five reset_g_only float32 82312 33 17 994.9000000000001
31 five reset_g_only float32 133666 166 83 996.7
32 five refractory_gate_only float32 1197 372 188 998.0
33 five refractory_gate_only float32 1381 375 191 998.6
34 five refractory_gate_only float32 1511 371 187 997.5
35 five refractory_gate_only float32 82312 85 43 991.9000000000001
36 five refractory_gate_only float32 133666 307 154 997.7
37 five reset_and_refractory float32 1197 165 82 995.7
38 five reset_and_refractory float32 1381 166 83 999.8000000000001
39 five reset_and_refractory float32 1511 165 83 997.5
40 five reset_and_refractory float32 82312 15 8 972.7
41 five reset_and_refractory float32 133666 123 62 993.0
42 feedforward frozen float32 1197 1 0 10.0
43 feedforward frozen float32 1381 1 0 0.0
44 feedforward frozen float32 1511 1 0 4.9
45 feedforward frozen float32 82312 0 0
46 feedforward frozen float32 133666 0 0
47 feedforward reset_g_only float32 1197 1 0 10.0
48 feedforward reset_g_only float32 1381 1 0 0.0
49 feedforward reset_g_only float32 1511 1 0 4.9
50 feedforward reset_g_only float32 82312 0 0
51 feedforward reset_g_only float32 133666 0 0
52 feedforward refractory_gate_only float32 1197 1 0 10.0
53 feedforward refractory_gate_only float32 1381 1 0 0.0
54 feedforward refractory_gate_only float32 1511 1 0 4.9
55 feedforward refractory_gate_only float32 82312 0 0
56 feedforward refractory_gate_only float32 133666 0 0
57 feedforward reset_and_refractory float32 1197 1 0 10.0
58 feedforward reset_and_refractory float32 1381 1 0 0.0
59 feedforward reset_and_refractory float32 1511 1 0 4.9
60 feedforward reset_and_refractory float32 82312 0 0
61 feedforward reset_and_refractory float32 133666 0 0
62 no_input frozen float32 1197 0 0
63 no_input frozen float32 1381 0 0
64 no_input frozen float32 1511 0 0
65 no_input frozen float32 82312 0 0
66 no_input frozen float32 133666 0 0
67 no_input reset_g_only float32 1197 0 0
68 no_input reset_g_only float32 1381 0 0
69 no_input reset_g_only float32 1511 0 0
70 no_input reset_g_only float32 82312 0 0
71 no_input reset_g_only float32 133666 0 0
72 no_input refractory_gate_only float32 1197 0 0
73 no_input refractory_gate_only float32 1381 0 0
74 no_input refractory_gate_only float32 1511 0 0
75 no_input refractory_gate_only float32 82312 0 0
76 no_input refractory_gate_only float32 133666 0 0
77 no_input reset_and_refractory float32 1197 0 0
78 no_input reset_and_refractory float32 1381 0 0
79 no_input reset_and_refractory float32 1511 0 0
80 no_input reset_and_refractory float32 82312 0 0
81 no_input reset_and_refractory float32 133666 0 0
82 pair author_complete float64 1381 107 53 996.4000000000001
83 pair author_complete float64 1511 106 53 992.1
84 pair author_complete float32 1381 107 53 996.4000000000001
85 pair author_complete float32 1511 106 53 992.1
86 trio author_complete float64 1197 149 74 994.8000000000001
87 trio author_complete float64 1381 150 75 999.3000000000001
88 trio author_complete float64 1511 149 75 997.0
89 trio author_complete float32 1197 149 74 994.8000000000001
90 trio author_complete float32 1381 150 75 999.3000000000001
91 trio author_complete float32 1511 149 75 997.0
92 five author_complete float64 1197 159 79 995.2
93 five author_complete float64 1381 160 80 999.5
94 five author_complete float64 1511 159 80 997.4000000000001
95 five author_complete float64 82312 13 7 992.4000000000001
96 five author_complete float64 133666 119 60 996.0
97 five author_complete float32 1197 159 79 995.2
98 five author_complete float32 1381 160 80 999.5
99 five author_complete float32 1511 159 80 997.4000000000001
100 five author_complete float32 82312 13 7 992.4000000000001
101 five author_complete float32 133666 119 60 996.0
102 feedforward author_complete float64 1197 1 0 10.4
103 feedforward author_complete float64 1381 1 0 0.0
104 feedforward author_complete float64 1511 1 0 5.1000000000000005
105 feedforward author_complete float64 82312 0 0
106 feedforward author_complete float64 133666 0 0
107 feedforward author_complete float32 1197 1 0 10.4
108 feedforward author_complete float32 1381 1 0 0.0
109 feedforward author_complete float32 1511 1 0 5.1000000000000005
110 feedforward author_complete float32 82312 0 0
111 feedforward author_complete float32 133666 0 0
112 no_input author_complete float64 1197 0 0
113 no_input author_complete float64 1381 0 0
114 no_input author_complete float64 1511 0 0
115 no_input author_complete float64 82312 0 0
116 no_input author_complete float64 133666 0 0
117 no_input author_complete float32 1197 0 0
118 no_input author_complete float32 1381 0 0
119 no_input author_complete float32 1511 0 0
120 no_input author_complete float32 82312 0 0
121 no_input author_complete float32 133666 0 0
registry/phase4ad-author-semantics/evidence/audit/final-summary.json
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registry/phase4ad-author-semantics/evidence/audit/finalize-start.json
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{
"timestamp_utc": "2026-09-29T23:18:24.492697+00:00",
"python": "3.10.12 (main, Aug 31 2026, 10:18:17) [GCC 11.4.0]",
"executable": "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
"learning": false,
"whole_brain_alternative_run": false
}
registry/phase4ad-author-semantics/evidence/audit/run-complete.json
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{
"all_author_oracle_comparisons_pass": true,
"all_frozen_components_match_archive": true,
"learning_achieved": false,
"whole_brain_alternative_run": false,
"author_original_source_sha256": "fc45837d7122c6ce2a7f3f2f23c515992e4b232aadb919efabb72337fac88e4e"
}
registry/phase4ad-author-semantics/evidence/audit/run-start.json
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{
"python": "3.10.12 (main, Aug 31 2026, 10:18:17) [GCC 11.4.0]",
"platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35",
"packages": {
"brian2": "2.5.1",
"numpy": "1.22.3",
"pandas": "1.4.3",
"scipy": "1.8.1",
"pyarrow": "11.0.0",
"sympy": "1.12",
"cython": "0.29.33"
},
"codegen": "numpy",
"learning": false,
"user_authorized_new_model_hypotheses": true
}
registry/phase4ad-author-semantics/evidence/checksums.sha256
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98eeae824607e83d0b35483a7d5ac586aebe68044e2457188040086e62e78b42 REPORT.md
0b653f7362ec7b506766e78b78efaa82914df201844cdc71f6d70556d46204b5 audit/all-motif-results.csv
2037a37dcf74e28831676ca1583d07272dd2546540a95096db6623f2eafe1a87 audit/final-summary.json
b4fbf4a99a33b67af1329609591f7b553e41e99d760a0cf0e6f04fd1b3b33454 audit/finalize-start.json
3d5333dede7b368a94de91e206cd35cdf7e89614ac528fb00126178386a2d8b7 audit/run-complete.json
9480e2e1c299aeb6b6136eb7c1fdb0a733da5eadce3e32d674c3f89c1abd50c1 audit/run-start.json
7535cfeec9d160eb597a2a09930cd8d1a55a7c0f561f1b5907f68eb53e1453dd components/feedforward-frozen/events.csv
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registry/phase4ad-author-semantics/evidence/components/five-reset_g_only/events.csv
+869
View File
@@ -0,0 +1,869 @@
step,neuron_idx
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1086,133666
1112,1381
1124,1197
1133,1511
1146,133666
1159,1381
1163,1197
1182,1511
1203,1197
1203,1381
1207,133666
1233,1511
1244,1197
1250,82312
1251,1381
1268,133666
1281,1197
1281,1511
1301,1381
1322,1197
1325,1511
1327,133666
1352,1381
1364,1197
1373,1511
1387,133666
1399,1381
1403,1197
1422,1511
1443,1197
1443,1381
1447,133666
1473,1511
1484,1197
1491,1381
1508,133666
1521,1197
1521,1511
1541,1381
1549,82312
1562,1197
1565,1511
1567,133666
1592,1381
1604,1197
1613,1511
1627,133666
1639,1381
1643,1197
1662,1511
1683,1197
1683,1381
1687,133666
1713,1511
1724,1197
1731,1381
1748,133666
1761,1197
1761,1511
1781,1381
1802,1197
1805,1511
1807,133666
1832,1381
1844,1197
1848,82312
1853,1511
1867,133666
1879,1381
1883,1197
1902,1511
1923,1197
1923,1381
1927,133666
1953,1511
1964,1197
1971,1381
1988,133666
2001,1197
2001,1511
2021,1381
2042,1197
2045,1511
2047,133666
2072,1381
2084,1197
2093,1511
2107,133666
2119,1381
2123,1197
2142,1511
2147,82312
2163,1197
2163,1381
2167,133666
2193,1511
2204,1197
2211,1381
2228,133666
2241,1197
2241,1511
2261,1381
2282,1197
2285,1511
2287,133666
2312,1381
2324,1197
2333,1511
2347,133666
2359,1381
2363,1197
2382,1511
2403,1197
2403,1381
2407,133666
2433,1511
2444,1197
2447,82312
2451,1381
2468,133666
2481,1197
2481,1511
2501,1381
2522,1197
2525,1511
2527,133666
2552,1381
2564,1197
2573,1511
2587,133666
2599,1381
2603,1197
2622,1511
2643,1197
2643,1381
2647,133666
2673,1511
2684,1197
2691,1381
2708,133666
2721,1197
2721,1511
2741,1381
2749,82312
2762,1197
2765,1511
2767,133666
2792,1381
2804,1197
2813,1511
2827,133666
2839,1381
2843,1197
2862,1511
2883,1197
2883,1381
2887,133666
2913,1511
2924,1197
2931,1381
2948,133666
2961,1197
2961,1511
2981,1381
3002,1197
3005,1511
3007,133666
3032,1381
3044,1197
3048,82312
3053,1511
3067,133666
3079,1381
3083,1197
3102,1511
3123,1197
3123,1381
3127,133666
3153,1511
3164,1197
3171,1381
3188,133666
3201,1197
3201,1511
3221,1381
3242,1197
3245,1511
3247,133666
3272,1381
3284,1197
3293,1511
3307,133666
3319,1381
3323,1197
3342,1511
3347,82312
3363,1197
3363,1381
3367,133666
3393,1511
3404,1197
3411,1381
3428,133666
3441,1197
3441,1511
3461,1381
3482,1197
3485,1511
3487,133666
3512,1381
3524,1197
3533,1511
3547,133666
3559,1381
3563,1197
3582,1511
3603,1197
3603,1381
3607,133666
3633,1511
3644,1197
3647,82312
3651,1381
3668,133666
3681,1197
3681,1511
3701,1381
3722,1197
3725,1511
3727,133666
3752,1381
3764,1197
3773,1511
3787,133666
3799,1381
3803,1197
3822,1511
3843,1197
3843,1381
3847,133666
3873,1511
3884,1197
3891,1381
3908,133666
3921,1197
3921,1511
3941,1381
3949,82312
3962,1197
3965,1511
3967,133666
3992,1381
4004,1197
4013,1511
4027,133666
4039,1381
4043,1197
4062,1511
4083,1197
4083,1381
4087,133666
4113,1511
4124,1197
4131,1381
4148,133666
4161,1197
4161,1511
4181,1381
4202,1197
4205,1511
4207,133666
4232,1381
4244,1197
4248,82312
4253,1511
4267,133666
4279,1381
4283,1197
4302,1511
4323,1197
4323,1381
4327,133666
4353,1511
4364,1197
4371,1381
4388,133666
4401,1197
4401,1511
4421,1381
4442,1197
4445,1511
4447,133666
4472,1381
4484,1197
4493,1511
4507,133666
4519,1381
4523,1197
4542,1511
4547,82312
4563,1197
4563,1381
4567,133666
4593,1511
4604,1197
4611,1381
4628,133666
4641,1197
4641,1511
4661,1381
4682,1197
4685,1511
4687,133666
4712,1381
4724,1197
4733,1511
4747,133666
4759,1381
4763,1197
4782,1511
4803,1197
4803,1381
4807,133666
4833,1511
4844,1197
4847,82312
4851,1381
4868,133666
4881,1197
4881,1511
4901,1381
4922,1197
4925,1511
4927,133666
4952,1381
4964,1197
4973,1511
4987,133666
4999,1381
5003,1197
5022,1511
5043,1197
5043,1381
5047,133666
5073,1511
5084,1197
5091,1381
5108,133666
5121,1197
5121,1511
5141,1381
5149,82312
5162,1197
5165,1511
5167,133666
5192,1381
5204,1197
5213,1511
5227,133666
5239,1381
5243,1197
5262,1511
5283,1197
5283,1381
5287,133666
5313,1511
5324,1197
5331,1381
5348,133666
5361,1197
5361,1511
5381,1381
5402,1197
5405,1511
5407,133666
5432,1381
5444,1197
5448,82312
5453,1511
5467,133666
5479,1381
5483,1197
5502,1511
5523,1197
5523,1381
5527,133666
5553,1511
5564,1197
5571,1381
5588,133666
5601,1197
5601,1511
5621,1381
5642,1197
5645,1511
5647,133666
5672,1381
5684,1197
5693,1511
5707,133666
5719,1381
5723,1197
5742,1511
5747,82312
5763,1197
5763,1381
5767,133666
5793,1511
5804,1197
5811,1381
5828,133666
5841,1197
5841,1511
5861,1381
5882,1197
5885,1511
5887,133666
5912,1381
5924,1197
5933,1511
5947,133666
5959,1381
5963,1197
5982,1511
6003,1197
6003,1381
6007,133666
6033,1511
6044,1197
6047,82312
6051,1381
6068,133666
6081,1197
6081,1511
6101,1381
6122,1197
6125,1511
6127,133666
6152,1381
6164,1197
6173,1511
6187,133666
6199,1381
6203,1197
6222,1511
6243,1197
6243,1381
6247,133666
6273,1511
6284,1197
6291,1381
6308,133666
6321,1197
6321,1511
6341,1381
6349,82312
6362,1197
6365,1511
6367,133666
6392,1381
6404,1197
6413,1511
6427,133666
6439,1381
6443,1197
6462,1511
6483,1197
6483,1381
6487,133666
6513,1511
6524,1197
6531,1381
6548,133666
6561,1197
6561,1511
6581,1381
6602,1197
6605,1511
6607,133666
6632,1381
6644,1197
6648,82312
6653,1511
6667,133666
6679,1381
6683,1197
6702,1511
6723,1197
6723,1381
6727,133666
6753,1511
6764,1197
6771,1381
6788,133666
6801,1197
6801,1511
6821,1381
6842,1197
6845,1511
6847,133666
6872,1381
6884,1197
6893,1511
6907,133666
6919,1381
6923,1197
6942,1511
6947,82312
6963,1197
6963,1381
6967,133666
6993,1511
7004,1197
7011,1381
7028,133666
7041,1197
7041,1511
7061,1381
7082,1197
7085,1511
7087,133666
7112,1381
7124,1197
7133,1511
7147,133666
7159,1381
7163,1197
7182,1511
7203,1197
7203,1381
7207,133666
7233,1511
7244,1197
7247,82312
7251,1381
7268,133666
7281,1197
7281,1511
7301,1381
7322,1197
7325,1511
7327,133666
7352,1381
7364,1197
7373,1511
7387,133666
7399,1381
7403,1197
7422,1511
7443,1197
7443,1381
7447,133666
7473,1511
7484,1197
7491,1381
7508,133666
7521,1197
7521,1511
7541,1381
7549,82312
7562,1197
7565,1511
7567,133666
7592,1381
7604,1197
7613,1511
7627,133666
7639,1381
7643,1197
7662,1511
7683,1197
7683,1381
7687,133666
7713,1511
7724,1197
7731,1381
7748,133666
7761,1197
7761,1511
7781,1381
7802,1197
7805,1511
7807,133666
7832,1381
7844,1197
7848,82312
7853,1511
7867,133666
7879,1381
7883,1197
7902,1511
7923,1197
7923,1381
7927,133666
7953,1511
7964,1197
7971,1381
7988,133666
8001,1197
8001,1511
8021,1381
8042,1197
8045,1511
8047,133666
8072,1381
8084,1197
8093,1511
8107,133666
8119,1381
8123,1197
8142,1511
8147,82312
8163,1197
8163,1381
8167,133666
8193,1511
8204,1197
8211,1381
8228,133666
8241,1197
8241,1511
8261,1381
8282,1197
8285,1511
8287,133666
8312,1381
8324,1197
8333,1511
8347,133666
8359,1381
8363,1197
8382,1511
8403,1197
8403,1381
8407,133666
8433,1511
8444,1197
8447,82312
8451,1381
8468,133666
8481,1197
8481,1511
8501,1381
8522,1197
8525,1511
8527,133666
8552,1381
8564,1197
8573,1511
8587,133666
8599,1381
8603,1197
8622,1511
8643,1197
8643,1381
8647,133666
8673,1511
8684,1197
8691,1381
8708,133666
8721,1197
8721,1511
8741,1381
8749,82312
8762,1197
8765,1511
8767,133666
8792,1381
8804,1197
8813,1511
8827,133666
8839,1381
8843,1197
8862,1511
8883,1197
8883,1381
8887,133666
8913,1511
8924,1197
8931,1381
8948,133666
8961,1197
8961,1511
8981,1381
9002,1197
9005,1511
9007,133666
9032,1381
9044,1197
9048,82312
9053,1511
9067,133666
9079,1381
9083,1197
9102,1511
9123,1197
9123,1381
9127,133666
9153,1511
9164,1197
9171,1381
9188,133666
9201,1197
9201,1511
9221,1381
9242,1197
9245,1511
9247,133666
9272,1381
9284,1197
9293,1511
9307,133666
9319,1381
9323,1197
9342,1511
9347,82312
9363,1197
9363,1381
9367,133666
9393,1511
9404,1197
9411,1381
9428,133666
9441,1197
9441,1511
9461,1381
9482,1197
9485,1511
9487,133666
9512,1381
9524,1197
9533,1511
9547,133666
9559,1381
9563,1197
9582,1511
9603,1197
9603,1381
9607,133666
9633,1511
9644,1197
9647,82312
9651,1381
9668,133666
9681,1197
9681,1511
9701,1381
9722,1197
9725,1511
9727,133666
9752,1381
9764,1197
9773,1511
9787,133666
9799,1381
9803,1197
9822,1511
9843,1197
9843,1381
9847,133666
9873,1511
9884,1197
9891,1381
9908,133666
9921,1197
9921,1511
9941,1381
9949,82312
9962,1197
9965,1511
9967,133666
9992,1381
1 step neuron_idx
2 0 1381
3 45 1197
4 49 1511
5 77 1381
6 88 133666
7 96 1197
8 103 1511
9 127 1381
10 142 1197
11 148 133666
12 151 1511
13 175 1381
14 178 1197
15 197 1511
16 205 133666
17 220 1381
18 221 1197
19 248 1511
20 265 1197
21 268 1381
22 268 133666
23 297 1511
24 298 1197
25 316 1381
26 325 133666
27 341 1197
28 343 1511
29 364 82312
30 369 1381
31 387 1197
32 389 133666
33 395 1511
34 419 1381
35 432 1197
36 443 1511
37 452 133666
38 468 1381
39 472 1197
40 491 1511
41 512 1381
42 515 1197
43 515 133666
44 543 1511
45 557 1197
46 560 1381
47 577 133666
48 591 1511
49 593 1197
50 598 1381
51 626 1197
52 627 1511
53 634 133666
54 635 1381
55 661 1197
56 664 1511
57 670 1381
58 677 82312
59 685 133666
60 697 1197
61 703 1511
62 706 1381
63 732 1197
64 741 1511
65 741 133666
66 742 1381
67 769 1197
68 776 1381
69 777 1511
70 794 133666
71 806 1197
72 811 1381
73 815 1511
74 840 1197
75 844 1381
76 850 133666
77 856 1511
78 877 1197
79 881 1381
80 895 1511
81 902 133666
82 918 1197
83 921 1381
84 933 82312
85 940 1511
86 959 1197
87 964 133666
88 965 1381
89 992 1511
90 1000 1197
91 1013 1381
92 1024 133666
93 1040 1511
94 1041 1197
95 1061 1381
96 1082 1197
97 1085 1511
98 1086 133666
99 1112 1381
100 1124 1197
101 1133 1511
102 1146 133666
103 1159 1381
104 1163 1197
105 1182 1511
106 1203 1197
107 1203 1381
108 1207 133666
109 1233 1511
110 1244 1197
111 1250 82312
112 1251 1381
113 1268 133666
114 1281 1197
115 1281 1511
116 1301 1381
117 1322 1197
118 1325 1511
119 1327 133666
120 1352 1381
121 1364 1197
122 1373 1511
123 1387 133666
124 1399 1381
125 1403 1197
126 1422 1511
127 1443 1197
128 1443 1381
129 1447 133666
130 1473 1511
131 1484 1197
132 1491 1381
133 1508 133666
134 1521 1197
135 1521 1511
136 1541 1381
137 1549 82312
138 1562 1197
139 1565 1511
140 1567 133666
141 1592 1381
142 1604 1197
143 1613 1511
144 1627 133666
145 1639 1381
146 1643 1197
147 1662 1511
148 1683 1197
149 1683 1381
150 1687 133666
151 1713 1511
152 1724 1197
153 1731 1381
154 1748 133666
155 1761 1197
156 1761 1511
157 1781 1381
158 1802 1197
159 1805 1511
160 1807 133666
161 1832 1381
162 1844 1197
163 1848 82312
164 1853 1511
165 1867 133666
166 1879 1381
167 1883 1197
168 1902 1511
169 1923 1197
170 1923 1381
171 1927 133666
172 1953 1511
173 1964 1197
174 1971 1381
175 1988 133666
176 2001 1197
177 2001 1511
178 2021 1381
179 2042 1197
180 2045 1511
181 2047 133666
182 2072 1381
183 2084 1197
184 2093 1511
185 2107 133666
186 2119 1381
187 2123 1197
188 2142 1511
189 2147 82312
190 2163 1197
191 2163 1381
192 2167 133666
193 2193 1511
194 2204 1197
195 2211 1381
196 2228 133666
197 2241 1197
198 2241 1511
199 2261 1381
200 2282 1197
201 2285 1511
202 2287 133666
203 2312 1381
204 2324 1197
205 2333 1511
206 2347 133666
207 2359 1381
208 2363 1197
209 2382 1511
210 2403 1197
211 2403 1381
212 2407 133666
213 2433 1511
214 2444 1197
215 2447 82312
216 2451 1381
217 2468 133666
218 2481 1197
219 2481 1511
220 2501 1381
221 2522 1197
222 2525 1511
223 2527 133666
224 2552 1381
225 2564 1197
226 2573 1511
227 2587 133666
228 2599 1381
229 2603 1197
230 2622 1511
231 2643 1197
232 2643 1381
233 2647 133666
234 2673 1511
235 2684 1197
236 2691 1381
237 2708 133666
238 2721 1197
239 2721 1511
240 2741 1381
241 2749 82312
242 2762 1197
243 2765 1511
244 2767 133666
245 2792 1381
246 2804 1197
247 2813 1511
248 2827 133666
249 2839 1381
250 2843 1197
251 2862 1511
252 2883 1197
253 2883 1381
254 2887 133666
255 2913 1511
256 2924 1197
257 2931 1381
258 2948 133666
259 2961 1197
260 2961 1511
261 2981 1381
262 3002 1197
263 3005 1511
264 3007 133666
265 3032 1381
266 3044 1197
267 3048 82312
268 3053 1511
269 3067 133666
270 3079 1381
271 3083 1197
272 3102 1511
273 3123 1197
274 3123 1381
275 3127 133666
276 3153 1511
277 3164 1197
278 3171 1381
279 3188 133666
280 3201 1197
281 3201 1511
282 3221 1381
283 3242 1197
284 3245 1511
285 3247 133666
286 3272 1381
287 3284 1197
288 3293 1511
289 3307 133666
290 3319 1381
291 3323 1197
292 3342 1511
293 3347 82312
294 3363 1197
295 3363 1381
296 3367 133666
297 3393 1511
298 3404 1197
299 3411 1381
300 3428 133666
301 3441 1197
302 3441 1511
303 3461 1381
304 3482 1197
305 3485 1511
306 3487 133666
307 3512 1381
308 3524 1197
309 3533 1511
310 3547 133666
311 3559 1381
312 3563 1197
313 3582 1511
314 3603 1197
315 3603 1381
316 3607 133666
317 3633 1511
318 3644 1197
319 3647 82312
320 3651 1381
321 3668 133666
322 3681 1197
323 3681 1511
324 3701 1381
325 3722 1197
326 3725 1511
327 3727 133666
328 3752 1381
329 3764 1197
330 3773 1511
331 3787 133666
332 3799 1381
333 3803 1197
334 3822 1511
335 3843 1197
336 3843 1381
337 3847 133666
338 3873 1511
339 3884 1197
340 3891 1381
341 3908 133666
342 3921 1197
343 3921 1511
344 3941 1381
345 3949 82312
346 3962 1197
347 3965 1511
348 3967 133666
349 3992 1381
350 4004 1197
351 4013 1511
352 4027 133666
353 4039 1381
354 4043 1197
355 4062 1511
356 4083 1197
357 4083 1381
358 4087 133666
359 4113 1511
360 4124 1197
361 4131 1381
362 4148 133666
363 4161 1197
364 4161 1511
365 4181 1381
366 4202 1197
367 4205 1511
368 4207 133666
369 4232 1381
370 4244 1197
371 4248 82312
372 4253 1511
373 4267 133666
374 4279 1381
375 4283 1197
376 4302 1511
377 4323 1197
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registry/phase4ad-author-semantics/evidence/components/no_input-frozen/events.csv
+1
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@@ -0,0 +1 @@
step,neuron_idx
1 step neuron_idx
registry/phase4ad-author-semantics/evidence/components/no_input-refractory_gate_only/events.csv
+1
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@@ -0,0 +1 @@
step,neuron_idx
1 step neuron_idx
registry/phase4ad-author-semantics/evidence/components/no_input-reset_and_refractory/events.csv
+1
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@@ -0,0 +1 @@
step,neuron_idx
1 step neuron_idx
registry/phase4ad-author-semantics/evidence/components/no_input-reset_g_only/events.csv
+1
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@@ -0,0 +1 @@
step,neuron_idx
1 step neuron_idx
registry/phase4ad-author-semantics/evidence/components/pair-frozen/events.csv
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View File
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View File
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registry/phase4ad-author-semantics/evidence/components/pair-reset_and_refractory/events.csv
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View File
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registry/phase4ad-author-semantics/evidence/components/pair-reset_g_only/events.csv
+224
View File
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97 4279 1511
98 4320 1381
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100 4410 1381
101 4459 1511
102 4500 1381
103 4549 1511
104 4590 1381
105 4639 1511
106 4680 1381
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109 4819 1511
110 4860 1381
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112 4950 1381
113 4999 1511
114 5040 1381
115 5089 1511
116 5130 1381
117 5179 1511
118 5220 1381
119 5269 1511
120 5310 1381
121 5359 1511
122 5400 1381
123 5449 1511
124 5490 1381
125 5539 1511
126 5580 1381
127 5629 1511
128 5670 1381
129 5719 1511
130 5760 1381
131 5809 1511
132 5850 1381
133 5899 1511
134 5940 1381
135 5989 1511
136 6030 1381
137 6079 1511
138 6120 1381
139 6169 1511
140 6210 1381
141 6259 1511
142 6300 1381
143 6349 1511
144 6390 1381
145 6439 1511
146 6480 1381
147 6529 1511
148 6570 1381
149 6619 1511
150 6660 1381
151 6709 1511
152 6750 1381
153 6799 1511
154 6840 1381
155 6889 1511
156 6930 1381
157 6979 1511
158 7020 1381
159 7069 1511
160 7110 1381
161 7159 1511
162 7200 1381
163 7249 1511
164 7290 1381
165 7339 1511
166 7380 1381
167 7429 1511
168 7470 1381
169 7519 1511
170 7560 1381
171 7609 1511
172 7650 1381
173 7699 1511
174 7740 1381
175 7789 1511
176 7830 1381
177 7879 1511
178 7920 1381
179 7969 1511
180 8010 1381
181 8059 1511
182 8100 1381
183 8149 1511
184 8190 1381
185 8239 1511
186 8280 1381
187 8329 1511
188 8370 1381
189 8419 1511
190 8460 1381
191 8509 1511
192 8550 1381
193 8599 1511
194 8640 1381
195 8689 1511
196 8730 1381
197 8779 1511
198 8820 1381
199 8869 1511
200 8910 1381
201 8959 1511
202 9000 1381
203 9049 1511
204 9090 1381
205 9139 1511
206 9180 1381
207 9229 1511
208 9270 1381
209 9319 1511
210 9360 1381
211 9409 1511
212 9450 1381
213 9499 1511
214 9540 1381
215 9589 1511
216 9630 1381
217 9679 1511
218 9720 1381
219 9769 1511
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221 9859 1511
222 9900 1381
223 9949 1511
224 9990 1381
registry/phase4ad-author-semantics/evidence/components/summary.csv
+81
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@@ -0,0 +1,81 @@
motif,policy,precision,neuron_idx,spikes,late_spikes,last_ms
pair,frozen,float32,1381,237,119,999.3000000000001
pair,frozen,float32,1511,236,119,997.5
pair,reset_g_only,float32,1381,112,56,999.0
pair,reset_g_only,float32,1511,111,55,994.9000000000001
pair,refractory_gate_only,float32,1381,318,161,999.1
pair,refractory_gate_only,float32,1511,317,160,997.5
pair,reset_and_refractory,float32,1381,112,56,999.0
pair,reset_and_refractory,float32,1511,111,55,994.9000000000001
trio,frozen,float32,1197,355,179,999.3000000000001
trio,frozen,float32,1381,355,178,997.8000000000001
trio,frozen,float32,1511,354,178,997.4000000000001
trio,reset_g_only,float32,1197,188,94,995.4000000000001
trio,reset_g_only,float32,1381,189,95,998.7
trio,reset_g_only,float32,1511,188,94,996.1
trio,refractory_gate_only,float32,1197,369,185,998.3000000000001
trio,refractory_gate_only,float32,1381,367,184,999.1
trio,refractory_gate_only,float32,1511,364,183,997.2
trio,reset_and_refractory,float32,1197,156,78,995.3000000000001
trio,reset_and_refractory,float32,1381,157,79,999.6
trio,reset_and_refractory,float32,1511,156,78,997.5
five,frozen,float32,1197,370,185,998.8000000000001
five,frozen,float32,1381,369,185,997.4000000000001
five,frozen,float32,1511,367,186,999.5
five,frozen,float32,82312,80,41,990.3000000000001
five,frozen,float32,133666,297,150,999.5
five,reset_g_only,float32,1197,249,125,996.2
five,reset_g_only,float32,1381,211,104,999.2
five,reset_g_only,float32,1511,209,104,996.5
five,reset_g_only,float32,82312,33,17,994.9000000000001
five,reset_g_only,float32,133666,166,83,996.7
five,refractory_gate_only,float32,1197,372,188,998.0
five,refractory_gate_only,float32,1381,375,191,998.6
five,refractory_gate_only,float32,1511,371,187,997.5
five,refractory_gate_only,float32,82312,85,43,991.9000000000001
five,refractory_gate_only,float32,133666,307,154,997.7
five,reset_and_refractory,float32,1197,165,82,995.7
five,reset_and_refractory,float32,1381,166,83,999.8000000000001
five,reset_and_refractory,float32,1511,165,83,997.5
five,reset_and_refractory,float32,82312,15,8,972.7
five,reset_and_refractory,float32,133666,123,62,993.0
feedforward,frozen,float32,1197,1,0,10.0
feedforward,frozen,float32,1381,1,0,0.0
feedforward,frozen,float32,1511,1,0,4.9
feedforward,frozen,float32,82312,0,0,
feedforward,frozen,float32,133666,0,0,
feedforward,reset_g_only,float32,1197,1,0,10.0
feedforward,reset_g_only,float32,1381,1,0,0.0
feedforward,reset_g_only,float32,1511,1,0,4.9
feedforward,reset_g_only,float32,82312,0,0,
feedforward,reset_g_only,float32,133666,0,0,
feedforward,refractory_gate_only,float32,1197,1,0,10.0
feedforward,refractory_gate_only,float32,1381,1,0,0.0
feedforward,refractory_gate_only,float32,1511,1,0,4.9
feedforward,refractory_gate_only,float32,82312,0,0,
feedforward,refractory_gate_only,float32,133666,0,0,
feedforward,reset_and_refractory,float32,1197,1,0,10.0
feedforward,reset_and_refractory,float32,1381,1,0,0.0
feedforward,reset_and_refractory,float32,1511,1,0,4.9
feedforward,reset_and_refractory,float32,82312,0,0,
feedforward,reset_and_refractory,float32,133666,0,0,
no_input,frozen,float32,1197,0,0,
no_input,frozen,float32,1381,0,0,
no_input,frozen,float32,1511,0,0,
no_input,frozen,float32,82312,0,0,
no_input,frozen,float32,133666,0,0,
no_input,reset_g_only,float32,1197,0,0,
no_input,reset_g_only,float32,1381,0,0,
no_input,reset_g_only,float32,1511,0,0,
no_input,reset_g_only,float32,82312,0,0,
no_input,reset_g_only,float32,133666,0,0,
no_input,refractory_gate_only,float32,1197,0,0,
no_input,refractory_gate_only,float32,1381,0,0,
no_input,refractory_gate_only,float32,1511,0,0,
no_input,refractory_gate_only,float32,82312,0,0,
no_input,refractory_gate_only,float32,133666,0,0,
no_input,reset_and_refractory,float32,1197,0,0,
no_input,reset_and_refractory,float32,1381,0,0,
no_input,reset_and_refractory,float32,1511,0,0,
no_input,reset_and_refractory,float32,82312,0,0,
no_input,reset_and_refractory,float32,133666,0,0,
1 motif policy precision neuron_idx spikes late_spikes last_ms
2 pair frozen float32 1381 237 119 999.3000000000001
3 pair frozen float32 1511 236 119 997.5
4 pair reset_g_only float32 1381 112 56 999.0
5 pair reset_g_only float32 1511 111 55 994.9000000000001
6 pair refractory_gate_only float32 1381 318 161 999.1
7 pair refractory_gate_only float32 1511 317 160 997.5
8 pair reset_and_refractory float32 1381 112 56 999.0
9 pair reset_and_refractory float32 1511 111 55 994.9000000000001
10 trio frozen float32 1197 355 179 999.3000000000001
11 trio frozen float32 1381 355 178 997.8000000000001
12 trio frozen float32 1511 354 178 997.4000000000001
13 trio reset_g_only float32 1197 188 94 995.4000000000001
14 trio reset_g_only float32 1381 189 95 998.7
15 trio reset_g_only float32 1511 188 94 996.1
16 trio refractory_gate_only float32 1197 369 185 998.3000000000001
17 trio refractory_gate_only float32 1381 367 184 999.1
18 trio refractory_gate_only float32 1511 364 183 997.2
19 trio reset_and_refractory float32 1197 156 78 995.3000000000001
20 trio reset_and_refractory float32 1381 157 79 999.6
21 trio reset_and_refractory float32 1511 156 78 997.5
22 five frozen float32 1197 370 185 998.8000000000001
23 five frozen float32 1381 369 185 997.4000000000001
24 five frozen float32 1511 367 186 999.5
25 five frozen float32 82312 80 41 990.3000000000001
26 five frozen float32 133666 297 150 999.5
27 five reset_g_only float32 1197 249 125 996.2
28 five reset_g_only float32 1381 211 104 999.2
29 five reset_g_only float32 1511 209 104 996.5
30 five reset_g_only float32 82312 33 17 994.9000000000001
31 five reset_g_only float32 133666 166 83 996.7
32 five refractory_gate_only float32 1197 372 188 998.0
33 five refractory_gate_only float32 1381 375 191 998.6
34 five refractory_gate_only float32 1511 371 187 997.5
35 five refractory_gate_only float32 82312 85 43 991.9000000000001
36 five refractory_gate_only float32 133666 307 154 997.7
37 five reset_and_refractory float32 1197 165 82 995.7
38 five reset_and_refractory float32 1381 166 83 999.8000000000001
39 five reset_and_refractory float32 1511 165 83 997.5
40 five reset_and_refractory float32 82312 15 8 972.7
41 five reset_and_refractory float32 133666 123 62 993.0
42 feedforward frozen float32 1197 1 0 10.0
43 feedforward frozen float32 1381 1 0 0.0
44 feedforward frozen float32 1511 1 0 4.9
45 feedforward frozen float32 82312 0 0
46 feedforward frozen float32 133666 0 0
47 feedforward reset_g_only float32 1197 1 0 10.0
48 feedforward reset_g_only float32 1381 1 0 0.0
49 feedforward reset_g_only float32 1511 1 0 4.9
50 feedforward reset_g_only float32 82312 0 0
51 feedforward reset_g_only float32 133666 0 0
52 feedforward refractory_gate_only float32 1197 1 0 10.0
53 feedforward refractory_gate_only float32 1381 1 0 0.0
54 feedforward refractory_gate_only float32 1511 1 0 4.9
55 feedforward refractory_gate_only float32 82312 0 0
56 feedforward refractory_gate_only float32 133666 0 0
57 feedforward reset_and_refractory float32 1197 1 0 10.0
58 feedforward reset_and_refractory float32 1381 1 0 0.0
59 feedforward reset_and_refractory float32 1511 1 0 4.9
60 feedforward reset_and_refractory float32 82312 0 0
61 feedforward reset_and_refractory float32 133666 0 0
62 no_input frozen float32 1197 0 0
63 no_input frozen float32 1381 0 0
64 no_input frozen float32 1511 0 0
65 no_input frozen float32 82312 0 0
66 no_input frozen float32 133666 0 0
67 no_input reset_g_only float32 1197 0 0
68 no_input reset_g_only float32 1381 0 0
69 no_input reset_g_only float32 1511 0 0
70 no_input reset_g_only float32 82312 0 0
71 no_input reset_g_only float32 133666 0 0
72 no_input refractory_gate_only float32 1197 0 0
73 no_input refractory_gate_only float32 1381 0 0
74 no_input refractory_gate_only float32 1511 0 0
75 no_input refractory_gate_only float32 82312 0 0
76 no_input refractory_gate_only float32 133666 0 0
77 no_input reset_and_refractory float32 1197 0 0
78 no_input reset_and_refractory float32 1381 0 0
79 no_input reset_and_refractory float32 1511 0 0
80 no_input reset_and_refractory float32 82312 0 0
81 no_input reset_and_refractory float32 133666 0 0
registry/phase4ad-author-semantics/evidence/components/trio-frozen/events.csv
+1065
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registry/phase4ad-author-semantics/evidence/components/trio-refractory_gate_only/events.csv
+1101
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File diff suppressed because it is too large Load Diff
registry/phase4ad-author-semantics/evidence/components/trio-reset_and_refractory/events.csv
+470
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@@ -0,0 +1,470 @@
step,neuron_idx
0,1381
45,1197
49,1511
77,1381
96,1197
119,1511
140,1381
161,1197
183,1511
204,1381
225,1197
247,1511
268,1381
289,1197
311,1511
332,1381
353,1197
375,1511
396,1381
417,1197
439,1511
460,1381
481,1197
503,1511
524,1381
545,1197
567,1511
588,1381
609,1197
631,1511
652,1381
673,1197
695,1511
716,1381
737,1197
759,1511
780,1381
801,1197
823,1511
844,1381
865,1197
887,1511
908,1381
929,1197
951,1511
972,1381
993,1197
1015,1511
1036,1381
1057,1197
1079,1511
1100,1381
1121,1197
1143,1511
1164,1381
1185,1197
1207,1511
1228,1381
1249,1197
1271,1511
1292,1381
1313,1197
1335,1511
1356,1381
1377,1197
1399,1511
1420,1381
1441,1197
1463,1511
1484,1381
1505,1197
1527,1511
1548,1381
1569,1197
1591,1511
1612,1381
1633,1197
1655,1511
1676,1381
1697,1197
1719,1511
1740,1381
1761,1197
1783,1511
1804,1381
1825,1197
1847,1511
1868,1381
1889,1197
1911,1511
1932,1381
1953,1197
1975,1511
1996,1381
2017,1197
2039,1511
2060,1381
2081,1197
2103,1511
2124,1381
2145,1197
2167,1511
2188,1381
2209,1197
2231,1511
2252,1381
2273,1197
2295,1511
2316,1381
2337,1197
2359,1511
2380,1381
2401,1197
2423,1511
2444,1381
2465,1197
2487,1511
2508,1381
2529,1197
2551,1511
2572,1381
2593,1197
2615,1511
2636,1381
2657,1197
2679,1511
2700,1381
2721,1197
2743,1511
2764,1381
2785,1197
2807,1511
2828,1381
2849,1197
2871,1511
2892,1381
2913,1197
2935,1511
2956,1381
2977,1197
2999,1511
3020,1381
3041,1197
3063,1511
3084,1381
3105,1197
3127,1511
3148,1381
3169,1197
3191,1511
3212,1381
3233,1197
3255,1511
3276,1381
3297,1197
3319,1511
3340,1381
3361,1197
3383,1511
3404,1381
3425,1197
3447,1511
3468,1381
3489,1197
3511,1511
3532,1381
3553,1197
3575,1511
3596,1381
3617,1197
3639,1511
3660,1381
3681,1197
3703,1511
3724,1381
3745,1197
3767,1511
3788,1381
3809,1197
3831,1511
3852,1381
3873,1197
3895,1511
3916,1381
3937,1197
3959,1511
3980,1381
4001,1197
4023,1511
4044,1381
4065,1197
4087,1511
4108,1381
4129,1197
4151,1511
4172,1381
4193,1197
4215,1511
4236,1381
4257,1197
4279,1511
4300,1381
4321,1197
4343,1511
4364,1381
4385,1197
4407,1511
4428,1381
4449,1197
4471,1511
4492,1381
4513,1197
4535,1511
4556,1381
4577,1197
4599,1511
4620,1381
4641,1197
4663,1511
4684,1381
4705,1197
4727,1511
4748,1381
4769,1197
4791,1511
4812,1381
4833,1197
4855,1511
4876,1381
4897,1197
4919,1511
4940,1381
4961,1197
4983,1511
5004,1381
5025,1197
5047,1511
5068,1381
5089,1197
5111,1511
5132,1381
5153,1197
5175,1511
5196,1381
5217,1197
5239,1511
5260,1381
5281,1197
5303,1511
5324,1381
5345,1197
5367,1511
5388,1381
5409,1197
5431,1511
5452,1381
5473,1197
5495,1511
5516,1381
5537,1197
5559,1511
5580,1381
5601,1197
5623,1511
5644,1381
5665,1197
5687,1511
5708,1381
5729,1197
5751,1511
5772,1381
5793,1197
5815,1511
5836,1381
5857,1197
5879,1511
5900,1381
5921,1197
5943,1511
5964,1381
5985,1197
6007,1511
6028,1381
6049,1197
6071,1511
6092,1381
6113,1197
6135,1511
6156,1381
6177,1197
6199,1511
6220,1381
6241,1197
6263,1511
6284,1381
6305,1197
6327,1511
6348,1381
6369,1197
6391,1511
6412,1381
6433,1197
6455,1511
6476,1381
6497,1197
6519,1511
6540,1381
6561,1197
6583,1511
6604,1381
6625,1197
6647,1511
6668,1381
6689,1197
6711,1511
6732,1381
6753,1197
6775,1511
6796,1381
6817,1197
6839,1511
6860,1381
6881,1197
6903,1511
6924,1381
6945,1197
6967,1511
6988,1381
7009,1197
7031,1511
7052,1381
7073,1197
7095,1511
7116,1381
7137,1197
7159,1511
7180,1381
7201,1197
7223,1511
7244,1381
7265,1197
7287,1511
7308,1381
7329,1197
7351,1511
7372,1381
7393,1197
7415,1511
7436,1381
7457,1197
7479,1511
7500,1381
7521,1197
7543,1511
7564,1381
7585,1197
7607,1511
7628,1381
7649,1197
7671,1511
7692,1381
7713,1197
7735,1511
7756,1381
7777,1197
7799,1511
7820,1381
7841,1197
7863,1511
7884,1381
7905,1197
7927,1511
7948,1381
7969,1197
7991,1511
8012,1381
8033,1197
8055,1511
8076,1381
8097,1197
8119,1511
8140,1381
8161,1197
8183,1511
8204,1381
8225,1197
8247,1511
8268,1381
8289,1197
8311,1511
8332,1381
8353,1197
8375,1511
8396,1381
8417,1197
8439,1511
8460,1381
8481,1197
8503,1511
8524,1381
8545,1197
8567,1511
8588,1381
8609,1197
8631,1511
8652,1381
8673,1197
8695,1511
8716,1381
8737,1197
8759,1511
8780,1381
8801,1197
8823,1511
8844,1381
8865,1197
8887,1511
8908,1381
8929,1197
8951,1511
8972,1381
8993,1197
9015,1511
9036,1381
9057,1197
9079,1511
9100,1381
9121,1197
9143,1511
9164,1381
9185,1197
9207,1511
9228,1381
9249,1197
9271,1511
9292,1381
9313,1197
9335,1511
9356,1381
9377,1197
9399,1511
9420,1381
9441,1197
9463,1511
9484,1381
9505,1197
9527,1511
9548,1381
9569,1197
9591,1511
9612,1381
9633,1197
9655,1511
9676,1381
9697,1197
9719,1511
9740,1381
9761,1197
9783,1511
9804,1381
9825,1197
9847,1511
9868,1381
9889,1197
9911,1511
9932,1381
9953,1197
9975,1511
9996,1381
1 step neuron_idx
2 0 1381
3 45 1197
4 49 1511
5 77 1381
6 96 1197
7 119 1511
8 140 1381
9 161 1197
10 183 1511
11 204 1381
12 225 1197
13 247 1511
14 268 1381
15 289 1197
16 311 1511
17 332 1381
18 353 1197
19 375 1511
20 396 1381
21 417 1197
22 439 1511
23 460 1381
24 481 1197
25 503 1511
26 524 1381
27 545 1197
28 567 1511
29 588 1381
30 609 1197
31 631 1511
32 652 1381
33 673 1197
34 695 1511
35 716 1381
36 737 1197
37 759 1511
38 780 1381
39 801 1197
40 823 1511
41 844 1381
42 865 1197
43 887 1511
44 908 1381
45 929 1197
46 951 1511
47 972 1381
48 993 1197
49 1015 1511
50 1036 1381
51 1057 1197
52 1079 1511
53 1100 1381
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registry/phase4ad-author-semantics/evidence/components/trio-reset_g_only/events.csv
+566
View File
@@ -0,0 +1,566 @@
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registry/phase4ad-author-semantics/evidence/environment/bootstrap-notes.json
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{
"isolated_venv_only": true,
"existing_environments_modified": false,
"initial_install_failure": "New venv pip22.0.2 lacks --report; upgraded ONLY new venv pip to author-pinned23.0.1 before installing",
"MarkupSafe": "Author-pinned1.1.1 used PyPI source distribution and legacy setup.py because no CPython3.10 wheel; other requested core packages used wheels",
"author_environment": "Windows conda CPython3.10.11",
"actual_environment": "Linux CPython3.10.12; not binary-identical",
"package_download_provenance": "install-report.json contains HTTPS PyPI archive URLs and SHA256 for packages"
}
registry/phase4ad-author-semantics/evidence/environment/frozen-scientific-environment.json
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{
"python": "3.10.12 (main, Aug 31 2026, 10:18:17) [GCC 11.4.0]",
"executable": "/data/digital-drosophila/models/male-cns-lif/.venv/bin/python",
"platform": "Linux-5.15.0-194-generic-x86_64-with-glibc2.35",
"package_versions": {
"numpy": "2.2.6",
"pandas": "2.3.3",
"pyarrow": "25.0.1",
"torch": "2.14.0",
"scipy": "1.15.3"
}
}
registry/phase4ad-author-semantics/evidence/environment/install-report.json
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registry/phase4ad-author-semantics/evidence/environment/installed-packages.json
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[
{
"name": "Brian2",
"version": "2.5.1"
},
{
"name": "Cython",
"version": "0.29.33"
},
{
"name": "Jinja2",
"version": "2.11.3"
},
{
"name": "joblib",
"version": "1.2.0"
},
{
"name": "MarkupSafe",
"version": "1.1.1"
},
{
"name": "mpmath",
"version": "1.3.0"
},
{
"name": "numpy",
"version": "1.22.3"
},
{
"name": "packaging",
"version": "23.1"
},
{
"name": "pandas",
"version": "1.4.3"
},
{
"name": "pip",
"version": "23.0.1"
},
{
"name": "pyarrow",
"version": "11.0.0"
},
{
"name": "pyparsing",
"version": "3.0.9"
},
{
"name": "python-dateutil",
"version": "2.8.2"
},
{
"name": "pytz",
"version": "2023.3"
},
{
"name": "scipy",
"version": "1.8.1"
},
{
"name": "setuptools",
"version": "67.8.0"
},
{
"name": "six",
"version": "1.16.0"
},
{
"name": "sympy",
"version": "1.12"
},
{
"name": "wheel",
"version": "0.38.4"
}
]
registry/phase4ad-author-semantics/evidence/external-resources/LICENSE
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@@ -0,0 +1,21 @@
MIT License
Copyright (c) 2023 Philip Shiu and Nico Spiller
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
registry/phase4ad-author-semantics/evidence/external-resources/environment_full.yml
+109
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name: brian2
channels:
- defaults
- conda-forge
dependencies:
- abseil-cpp=20211102.0=h0e60522_0
- arrow-cpp=11.0.0=py310h7cee713_0
- asttokens=2.2.1=pyhd8ed1ab_0
- aws-c-common=0.4.57=ha925a31_1
- aws-c-event-stream=0.1.6=hd77b12b_5
- aws-checksums=0.1.9=ha925a31_0
- aws-sdk-cpp=1.8.185=hd77b12b_0
- backcall=0.2.0=pyh9f0ad1d_0
- backports=1.0=pyhd8ed1ab_3
- backports.functools_lru_cache=1.6.4=pyhd8ed1ab_0
- boost-cpp=1.78.0=h5b4e17d_0
- brian2=2.5.1=py310hc781a3c_0
- bzip2=1.0.8=he774522_0
- c-ares=1.19.0=h2bbff1b_0
- ca-certificates=2023.5.7=h56e8100_0
- colorama=0.4.6=pyhd8ed1ab_0
- cython=0.29.33=py310hd77b12b_0
- debugpy=1.5.1=py310hd77b12b_0
- decorator=5.1.1=pyhd8ed1ab_0
- executing=1.2.0=pyhd8ed1ab_0
- gflags=2.2.2=ha925a31_1004
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- gsl=2.7=hdfb1a43_0
- importlib-metadata=6.6.0=pyha770c72_0
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- intel-openmp=2023.1.0=h57928b3_46319
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- ipython=8.14.0=pyh08f2357_0
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- lz4-c=1.9.4=h2bbff1b_0
- m2w64-gcc-libgfortran=5.3.0=6
- m2w64-gcc-libs=5.3.0=7
- m2w64-gcc-libs-core=5.3.0=7
- m2w64-gmp=6.1.0=2
- m2w64-libwinpthread-git=5.0.0.4634.697f757=2
- markupsafe=1.1.1=py310he2412df_4
- matplotlib-inline=0.1.6=pyhd8ed1ab_0
- mkl=2020.4=hb70f87d_311
- mpmath=1.3.0=pyhd8ed1ab_0
- msys2-conda-epoch=20160418=1
- nest-asyncio=1.5.6=pyhd8ed1ab_0
- numpy=1.22.3=py310hed7ac4c_2
- openssl=1.1.1t=h2bbff1b_0
- orc=1.7.4=h623e30f_1
- packaging=23.1=pyhd8ed1ab_0
- pandas=1.4.3=py310hf5e1058_0
- parso=0.8.3=pyhd8ed1ab_0
- pickleshare=0.7.5=py_1003
- pip=23.0.1=py310haa95532_0
- platformdirs=3.5.1=pyhd8ed1ab_0
- prompt-toolkit=3.0.38=pyha770c72_0
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- psutil=5.9.0=py310h2bbff1b_0
- pure_eval=0.2.2=pyhd8ed1ab_0
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- re2=2022.04.01=h0e60522_0
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- tzdata=2023c=h04d1e81_0
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- vc=14.2=h21ff451_1
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- wcwidth=0.2.6=pyhd8ed1ab_0
- wheel=0.38.4=py310haa95532_0
- xz=5.4.2=h8cc25b3_0
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registry/phase4ad-author-semantics/evidence/external-resources/model.py
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import pandas as pd
from textwrap import dedent
# brian 2
from brian2 import NeuronGroup, Synapses, PoissonInput, SpikeMonitor, Network
from brian2 import mV, ms, Hz
# file handling
from pathlib import Path
# parallelization
from joblib import Parallel, delayed, parallel_backend
from time import time
default_params = {
# trials
't_run' : 1000 * ms, # duration of trial
'n_run' : 30, # number of runs
# network constants
# Kakaria and de Bivort 2017 https://doi.org/10.3389/fnbeh.2017.00008
'v_0' : -52 * mV, # resting potential
'v_rst' : -52 * mV, # reset potential after spike
'v_th' : -45 * mV, # threshold for spiking
't_mbr' : 20 * ms, # membrane time scale (capacitance * resistance = .002 * uF * 10. * Mohm)
# Jürgensen et al https://doi.org/10.1088/2634-4386/ac3ba6
'tau' : 5 * ms, # time constant
# Lazar et al https://doi.org/10.7554/eLife.62362
't_rfc' : 2.2 * ms, # refractory period
# Paul et al 2015 doi: 10.3389/fncel.2015.00029
't_dly' : 1.8*ms, # delay for changes in post-synaptic neuron
# Free parameter
'w_syn' : .275 * mV, # weight per synapse (note: modulated by exponential decay)
# Default activation rates
'r_poi' : 150*Hz, # default rate of the Poisson inputs
'r_poi2' : 0*Hz, # default rate of a 2nd class of Poisson inputs
'f_poi' : 250, # scaling factor for Poisson synapse; 250 is sufficient to cause spiking
# equations for neurons # alpha synapse https://doi.org/10.1017/CBO9780511815706; See https://brian2.readthedocs.io/en/stable/user/converting_from_integrated_form.html
'eqs' : dedent('''
dv/dt = (v_0 - v + g) / t_mbr : volt (unless refractory)
dg/dt = -g / tau : volt (unless refractory)
rfc : second
'''),
# condition for spike
'eq_th' : 'v > v_th',
# rules for spike
'eq_rst' : 'v = v_rst; w = 0; g = 0 * mV',
}
#######################
# brian2 model setup
def poi(neu, exc, exc2, params):
'''Create PoissonInput for neurons.
For each neuron in 'names' a PoissonInput is generated and
the refractory period of that neuron is set to 0 in NeuronGroup.
Parameters
----------
neu : NeuronGroup
Defined brian2.NeuronGroup object
exc : list
Indices of neurons for which to create Poisson input
exc2 : list
Indices of neurons for which to create Poisson input with `r_poi`
params : dict
Constants and equations that are used to construct the brian2 network model
Returns
-------
pois : list
PoissonInput objects for each neuron in 'exc'
neu : NeuronGroup
NeuronGroup with adjusted refractory periods
'''
pois = []
for i in exc:
p = PoissonInput(
target=neu[i],
target_var='v',
N=1,
rate=params['r_poi'],
weight=params['w_syn']*params['f_poi']
)
neu[i].rfc = 0 * ms # no refractory period for Poisson targets
pois.append(p)
for i in exc2:
p = PoissonInput(
target=neu[i],
target_var='v',
N=1,
rate=params['r_poi2'],
weight=params['w_syn']*params['f_poi']
)
neu[i].rfc = 0 * ms # no refractory period for Poisson targets
pois.append(p)
return pois, neu
def silence(slnc, syn):
'''Silence neuron by setting weights of all synapses from it to 0
Parameters
----------
slnc : list
List of neuron indices to silence
syn : brian2.Synapses
Defined synapses object
Returns
-------
syn : brian2.Synapses
Synapses with modified weights
'''
for i in slnc:
syn.w[' {} == i'.format(i)] = 0*mV
return syn
def create_model(path_comp, path_con, params):
'''Create default network model.
Convert the "completeness materialization" and "connectivity" dataframes
into a brian2 neural network model. Network constants and equations
are defined at the beginning of this file.
Parameters
----------
path_comp : str
path to "completeness materialization" dataframe
path_con : str
path to "connectivity" dataframe
params : dict
Constants and equations that are used to construct the brian2 network model
Returns
-------
neu : NeuronGroup
brian2.NeuronGroup object with neurons as in 'path_comp'
syn : Synapses
brian2.Synapses object with connections as in 'path_con'
spk_mon : SpikeMonitor
brian2.SpikeMonitor object, which records time of spike events
'''
# load neuron connectivity dataframes
df_comp = pd.read_csv(path_comp, index_col=0)
df_con = pd.read_parquet(path_con)
neu = NeuronGroup( # create neurons
N=len(df_comp),
model=params['eqs'],
method='linear',
threshold=params['eq_th'],
reset=params['eq_rst'],
refractory='rfc',
name='default_neurons',
namespace=params,
)
neu.v = params['v_0'] # initialize values
neu.g = 0
neu.rfc = params['t_rfc']
# create synapses
syn = Synapses(neu, neu, 'w : volt', on_pre='g += w', delay=params['t_dly'], name='default_synapses')
# connect synapses
i_pre = df_con.loc[:, 'Presynaptic_Index'].values
i_post = df_con.loc[:, 'Postsynaptic_Index'].values
syn.connect(i=i_pre, j=i_post)
# define connection weight
syn.w = df_con.loc[:,'Excitatory x Connectivity'].values * params['w_syn']
# object to record spikes
spk_mon = SpikeMonitor(neu)
return neu, syn, spk_mon
#####################
# running simulations
def get_spk_trn(spk_mon):
'''Extracts spike times from 'spk_mon'
The spike times recorded in the SpikeMonitor object during
simulation are converted to a list of times for each neurons.
Returns dict with "brian ID": "list of spike times".
Parameters
----------
spk_mon : SpikeMonitor
Contains recorded spike times
Returns
-------
spk_trn : dict
Mapping between brian neuron IDs and spike times
'''
spk_trn = {k: v for k, v in spk_mon.spike_trains().items() if len(v)}
return spk_trn
def construct_dataframe(res, exp_name, i2flyid):
'''Take spike time dict and collects spikes in pandas dataframe
Parameters
----------
res : list
List with spike time dicts for each trial
exp_name : str
Name of the experiment
i2flyid : dict
Mapping between Brian IDs and flywire IDs
Returns
-------
df : pandas.DataFrame
Dataframe where each row is one spike
'''
ids, ts, nrun = [], [], []
for n, i in enumerate(res):
for j, k in i.items():
ids.extend([j for _ in k])
nrun.extend([n for _ in k])
ts.extend([float(l) for l in k])
d = {
't': ts,
'trial': nrun,
'flywire_id': [i2flyid[i] for i in ids],
'exp_name': exp_name
}
df = pd.DataFrame(d)
return df
def run_trial(exc, exc2, slnc, path_comp, path_con, params):
'''Run single trial of coactivation/silencng experiment
During the coactivation experiment, the neurons in 'exc' are
Poisson inputs. The simulation runs for 't_run'.
Parameters
----------
exc: list
contains indices of neurons for PoissonInput
exc2: list
contains indices of neurons for PoissonInput of different frequency `r_poi2`
slnc: list
contains indices of neurons to silence
path_comp: Path
path to "completeness materialization" dataframe
path_con: Path
path to "connectivity" dataframe
params : dict
Constants and equations that are used to construct the brian2 network model
Returns
-------
spk_trn : dict
Mapping between brian neuron IDs and spike times
'''
# get default network
neu, syn, spk_mon = create_model(path_comp, path_con, params)
# define Poisson input for excitation
poi_inp, neu = poi(neu, exc, exc2, params)
# silence neurons
syn = silence(slnc, syn)
# collect in Network object
net = Network(neu, syn, spk_mon, *poi_inp)
# run simulation
net.run(duration=params['t_run'])
# spike times
spk_trn = get_spk_trn(spk_mon)
return spk_trn
def run_exp(exp_name, neu_exc, path_res, path_comp, path_con,
params=default_params, neu_slnc=[], neu_exc2=[],
n_proc=-1, force_overwrite=False):
'''
Run default network experiment
Neurons in `neu_exc` are Poisson external inputs
Neurons in `neu_slnc` are silenced
Parameters
----------
exp_name: str
name of the experiment
neu_exc: list
contains custom names or flywire IDs of neurons to be excited
path_res: str
path to the output folder where spike data is stored
path_comp: str
path to "completeness materialization" dataframe
path_con: str
path to "connectivity" dataframe
params : dict
Constants and equations that are used to construct the brian2 network model
neu_slnc : list (optional)
contains custom names or flywire IDs of neurons to be silenced
neu_exc2 : list (optional)
contains custom names or flywire IDs of neurons to be excited with different frequency
requires `r_poi2` to be defined in `params`
n_proc: int (optional)
number of cores to be used for parallel runs
default: -1 (use all available cores)
n_proc=1 is equivalent serial code
force_overwrite : bool (optional)
If True, overwrite output files, else skip simulation, by default False
'''
# convert to Path objects
path_res, path_comp, path_con = [ Path(i) for i in [path_res, path_comp, path_con] ]
# define output files
path_save = path_res / '{}.parquet'.format(exp_name)
if path_save.is_file() and not force_overwrite:
print('>>> Skipping experiment {} because {} exists and force_overwrite = {}'.format(exp_name, path_save, force_overwrite))
return
# load name/id mappings
df_comp = pd.read_csv(path_comp, index_col=0) # load completeness dataframe
flyid2i = {j: i for i, j in enumerate(df_comp.index)} # flywire id: biran ID
i2flyid = {j: i for i, j in flyid2i.items()} # brian ID: flywire ID
# print info
print('>>> Experiment: {}'.format(exp_name))
print(' Output file: {}'.format(path_save))
print(' Excited neurons: {}'.format(len(neu_exc + neu_exc2)))
if neu_slnc:
print(' Silenced neurons: {}'.format(len(neu_slnc)))
# start parallel calculation
n_run = params['n_run']
start = time()
with parallel_backend('loky', n_jobs=n_proc):
exc = [ flyid2i[n] for n in neu_exc ]
exc2 = [ flyid2i[n] for n in neu_exc2 ]
slnc = [ flyid2i[n] for n in neu_slnc ]
res = Parallel()(
delayed(
run_trial)(exc, exc2, slnc, path_comp, path_con, params) for _ in range(n_run))
# print simulation time
walltime = time() - start
print(' Elapsed time: {} s'.format(int(walltime)))
# dataframe with spike times
df = construct_dataframe(res, exp_name, i2flyid)
# store spike data
df.to_parquet(path_save, compression='brotli')
registry/phase4ad-author-semantics/evidence/gpu-reference/extension.json
+17
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@@ -0,0 +1,17 @@
{
"binary": "/data/digital-drosophila/experiments/phase4ad-author-semantics/gpu-reference/extension-build/male_cns_lif_deterministic_v2_ext.so",
"binary_sha256": "57f59f634cc8e3b03f4674a3ddb11ec933ab124feb0b9fa89d08fe26e60fcb7e",
"build_seconds": 55.24202698399972,
"flags": {
"cuda": [
"-O3",
"--fmad=false",
"-std=c++20"
],
"cxx": [
"-O3",
"-ffp-contract=off"
]
},
"status": "PASS"
}
registry/phase4ad-author-semantics/evidence/manifest.json
+2837
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File diff suppressed because it is too large Load Diff
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/actual-weights.json
+20
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@@ -0,0 +1,20 @@
{
"edge_id": [
1337065,
1467355,
1559765,
20992891
],
"weights_mv": [
28.599998474121094,
64.625,
62.14999771118164,
11.824999809265137
],
"weights_volt": [
0.028599999845027924,
0.06462500244379044,
0.062150001525878906,
0.011824999935925007
]
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/brian-output/events.csv
+4
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@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/generated-code.json
+127
View File
@@ -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_7",
"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_8",
"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_4",
"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_4",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/run-spec.json
+123
View File
@@ -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": [
1337065,
1467355,
1559765,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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": "float32",
"preferences": {
"codegen.target": "numpy",
"core.default_float_dtype": "float32",
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32-repeat/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -43.99999976158142,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/actual-weights.json
+20
View File
@@ -0,0 +1,20 @@
{
"edge_id": [
1337065,
1467355,
1559765,
20992891
],
"weights_mv": [
28.599998474121094,
64.625,
62.14999771118164,
11.824999809265137
],
"weights_volt": [
0.028599999845027924,
0.06462500244379044,
0.062150001525878906,
0.011824999935925007
]
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/brian-output/events.csv
+4
View File
@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/comparison.json
+11
View File
@@ -0,0 +1,11 @@
{
"exact_events": true,
"exact_counts": true,
"ref_exact": true,
"max_abs_mv": 0.00020179152488708496,
"mean_abs_mv": 1.9821550031807453e-05,
"same_event_prefix_max_abs_mv": 0.00020179152488708496,
"first_event_divergence_step": null,
"tolerance_mv": 0.001,
"pass_oracle": true
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/generated-code.json
+127
View File
@@ -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_6",
"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_7",
"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_7",
"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_7",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/independent-output/events.csv
+4
View File
@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/run-spec.json
+123
View File
@@ -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": [
1337065,
1467355,
1559765,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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": "float32",
"preferences": {
"codegen.target": "numpy",
"core.default_float_dtype": "float32",
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/schedule.json
+11
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@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float32/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -43.99999976158142,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/actual-weights.json
+20
View File
@@ -0,0 +1,20 @@
{
"edge_id": [
1337065,
1467355,
1559765,
20992891
],
"weights_mv": [
28.6,
64.625,
62.150000000000006,
11.825000000000001
],
"weights_volt": [
0.0286,
0.064625,
0.062150000000000004,
0.011825
]
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/brian-output/events.csv
+4
View File
@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/generated-code.json
+127
View File
@@ -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_5",
"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_6",
"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_6",
"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_6",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/run-spec.json
+123
View File
@@ -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": [
1337065,
1467355,
1559765,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64-repeat/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -44.0,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/actual-weights.json
+20
View File
@@ -0,0 +1,20 @@
{
"edge_id": [
1337065,
1467355,
1559765,
20992891
],
"weights_mv": [
28.6,
64.625,
62.150000000000006,
11.825000000000001
],
"weights_volt": [
0.0286,
0.064625,
0.062150000000000004,
0.011825
]
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/brian-output/events.csv
+4
View File
@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/comparison.json
+11
View File
@@ -0,0 +1,11 @@
{
"exact_events": true,
"exact_counts": true,
"ref_exact": true,
"max_abs_mv": 3.765876499528531e-13,
"mean_abs_mv": 3.893371799264915e-14,
"same_event_prefix_max_abs_mv": 3.765876499528531e-13,
"first_event_divergence_step": null,
"tolerance_mv": 1e-08,
"pass_oracle": true
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/generated-code.json
+127
View File
@@ -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_4",
"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_5",
"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_5",
"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_5",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/independent-output/events.csv
+4
View File
@@ -0,0 +1,4 @@
step,neuron_idx
0,1381
51,1511
104,1197
1 step neuron_idx
2 0 1381
3 51 1511
4 104 1197
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/run-spec.json
+123
View File
@@ -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": [
1337065,
1467355,
1559765,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/feedforward-float64/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -44.0,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/actual-weights.json
+47
View File
@@ -0,0 +1,47 @@
{
"edge_id": [
1336648,
1336655,
1337065,
1467340,
1467355,
1467852,
1559765,
1559772,
1560267,
20992285,
20992291,
20992294,
20992891
],
"weights_mv": [
57.75,
47.29999923706055,
28.599998474121094,
71.2249984741211,
64.625,
17.599998474121094,
62.14999771118164,
77.82499694824219,
19.249998092651367,
26.125,
15.675000190734863,
20.899999618530273,
11.824999809265137
],
"weights_volt": [
0.057750001549720764,
0.04729999974370003,
0.028599999845027924,
0.07122500240802765,
0.06462500244379044,
0.01759999990463257,
0.062150001525878906,
0.07782500237226486,
0.01924999989569187,
0.026125000789761543,
0.015675000846385956,
0.020899999886751175,
0.011824999935925007
]
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/brian-output/events.csv
+611
View File
@@ -0,0 +1,611 @@
step,neuron_idx
0,1381
46,1197
51,1511
79,1381
91,133666
99,1197
120,1511
140,1381
163,1197
170,133666
185,1511
205,1381
220,1197
246,1511
259,133666
268,1381
288,1197
306,1511
330,1381
341,133666
351,1197
371,1511
391,1381
414,1197
422,133666
436,1511
457,1381
471,1197
497,1511
510,133666
519,1381
539,1197
557,1511
581,1381
592,133666
602,1197
622,1511
642,1381
665,1197
673,133666
687,1511
708,1381
722,1197
748,1511
761,133666
770,1381
790,1197
808,1511
832,1381
843,133666
853,1197
873,1511
881,82312
893,1381
916,1197
924,133666
938,1511
959,1381
973,1197
999,1511
1012,133666
1021,1381
1041,1197
1059,1511
1083,1381
1094,133666
1104,1197
1124,1511
1144,1381
1167,1197
1175,133666
1189,1511
1210,1381
1224,1197
1250,1511
1263,133666
1272,1381
1292,1197
1310,1511
1334,1381
1345,133666
1355,1197
1375,1511
1395,1381
1418,1197
1426,133666
1440,1511
1461,1381
1475,1197
1501,1511
1514,133666
1523,1381
1543,1197
1561,1511
1585,1381
1596,133666
1606,1197
1626,1511
1641,82312
1646,1381
1669,1197
1677,133666
1691,1511
1712,1381
1726,1197
1752,1511
1765,133666
1774,1381
1794,1197
1812,1511
1836,1381
1847,133666
1857,1197
1877,1511
1897,1381
1920,1197
1928,133666
1942,1511
1963,1381
1977,1197
2003,1511
2016,133666
2025,1381
2045,1197
2063,1511
2087,1381
2098,133666
2108,1197
2128,1511
2148,1381
2171,1197
2179,133666
2193,1511
2214,1381
2228,1197
2254,1511
2267,133666
2276,1381
2296,1197
2314,1511
2338,1381
2349,133666
2359,1197
2379,1511
2394,82312
2399,1381
2422,1197
2430,133666
2444,1511
2465,1381
2479,1197
2505,1511
2518,133666
2527,1381
2547,1197
2565,1511
2589,1381
2600,133666
2610,1197
2630,1511
2650,1381
2673,1197
2681,133666
2695,1511
2716,1381
2730,1197
2756,1511
2769,133666
2778,1381
2798,1197
2816,1511
2840,1381
2851,133666
2861,1197
2881,1511
2901,1381
2924,1197
2932,133666
2946,1511
2967,1381
2981,1197
3007,1511
3020,133666
3029,1381
3049,1197
3067,1511
3091,1381
3102,133666
3112,1197
3132,1511
3147,82312
3152,1381
3175,1197
3183,133666
3197,1511
3218,1381
3232,1197
3258,1511
3271,133666
3280,1381
3300,1197
3318,1511
3342,1381
3353,133666
3363,1197
3383,1511
3403,1381
3426,1197
3434,133666
3448,1511
3469,1381
3483,1197
3509,1511
3522,133666
3531,1381
3551,1197
3569,1511
3593,1381
3604,133666
3614,1197
3634,1511
3654,1381
3677,1197
3685,133666
3699,1511
3720,1381
3734,1197
3760,1511
3773,133666
3782,1381
3802,1197
3820,1511
3844,1381
3855,133666
3865,1197
3885,1511
3900,82312
3905,1381
3928,1197
3936,133666
3950,1511
3971,1381
3985,1197
4011,1511
4024,133666
4033,1381
4053,1197
4071,1511
4095,1381
4106,133666
4116,1197
4136,1511
4156,1381
4179,1197
4187,133666
4201,1511
4222,1381
4236,1197
4262,1511
4275,133666
4284,1381
4304,1197
4322,1511
4346,1381
4357,133666
4367,1197
4387,1511
4407,1381
4430,1197
4438,133666
4452,1511
4473,1381
4487,1197
4513,1511
4526,133666
4535,1381
4555,1197
4573,1511
4597,1381
4608,133666
4618,1197
4638,1511
4653,82312
4658,1381
4681,1197
4689,133666
4703,1511
4724,1381
4738,1197
4764,1511
4777,133666
4786,1381
4806,1197
4824,1511
4848,1381
4859,133666
4869,1197
4889,1511
4909,1381
4932,1197
4940,133666
4954,1511
4975,1381
4989,1197
5015,1511
5028,133666
5037,1381
5057,1197
5075,1511
5099,1381
5110,133666
5120,1197
5140,1511
5160,1381
5183,1197
5191,133666
5205,1511
5226,1381
5240,1197
5266,1511
5279,133666
5288,1381
5308,1197
5326,1511
5350,1381
5361,133666
5371,1197
5391,1511
5406,82312
5411,1381
5434,1197
5442,133666
5456,1511
5477,1381
5491,1197
5517,1511
5530,133666
5539,1381
5559,1197
5577,1511
5601,1381
5612,133666
5622,1197
5642,1511
5662,1381
5685,1197
5693,133666
5707,1511
5728,1381
5742,1197
5768,1511
5781,133666
5790,1381
5810,1197
5828,1511
5852,1381
5863,133666
5873,1197
5893,1511
5913,1381
5936,1197
5944,133666
5958,1511
5979,1381
5993,1197
6019,1511
6032,133666
6041,1381
6061,1197
6079,1511
6103,1381
6114,133666
6124,1197
6144,1511
6159,82312
6164,1381
6187,1197
6195,133666
6209,1511
6230,1381
6244,1197
6270,1511
6283,133666
6292,1381
6312,1197
6330,1511
6354,1381
6365,133666
6375,1197
6395,1511
6415,1381
6438,1197
6446,133666
6460,1511
6481,1381
6495,1197
6521,1511
6534,133666
6543,1381
6563,1197
6581,1511
6605,1381
6616,133666
6626,1197
6646,1511
6666,1381
6689,1197
6697,133666
6711,1511
6732,1381
6746,1197
6772,1511
6785,133666
6794,1381
6814,1197
6832,1511
6856,1381
6867,133666
6877,1197
6897,1511
6912,82312
6917,1381
6940,1197
6948,133666
6962,1511
6983,1381
6997,1197
7023,1511
7036,133666
7045,1381
7065,1197
7083,1511
7107,1381
7118,133666
7128,1197
7148,1511
7168,1381
7191,1197
7199,133666
7213,1511
7234,1381
7248,1197
7274,1511
7287,133666
7296,1381
7316,1197
7334,1511
7358,1381
7369,133666
7379,1197
7399,1511
7419,1381
7442,1197
7450,133666
7464,1511
7485,1381
7499,1197
7525,1511
7538,133666
7547,1381
7567,1197
7585,1511
7609,1381
7620,133666
7630,1197
7650,1511
7665,82312
7670,1381
7693,1197
7701,133666
7715,1511
7736,1381
7750,1197
7776,1511
7789,133666
7798,1381
7818,1197
7836,1511
7860,1381
7871,133666
7881,1197
7901,1511
7921,1381
7944,1197
7952,133666
7966,1511
7987,1381
8001,1197
8027,1511
8040,133666
8049,1381
8069,1197
8087,1511
8111,1381
8122,133666
8132,1197
8152,1511
8172,1381
8195,1197
8203,133666
8217,1511
8238,1381
8252,1197
8278,1511
8291,133666
8300,1381
8320,1197
8338,1511
8362,1381
8373,133666
8383,1197
8403,1511
8418,82312
8423,1381
8446,1197
8454,133666
8468,1511
8489,1381
8503,1197
8529,1511
8542,133666
8551,1381
8571,1197
8589,1511
8613,1381
8624,133666
8634,1197
8654,1511
8674,1381
8697,1197
8705,133666
8719,1511
8740,1381
8754,1197
8780,1511
8793,133666
8802,1381
8822,1197
8840,1511
8864,1381
8875,133666
8885,1197
8905,1511
8925,1381
8948,1197
8956,133666
8970,1511
8991,1381
9005,1197
9031,1511
9044,133666
9053,1381
9073,1197
9091,1511
9115,1381
9126,133666
9136,1197
9156,1511
9171,82312
9176,1381
9199,1197
9207,133666
9221,1511
9242,1381
9256,1197
9282,1511
9295,133666
9304,1381
9324,1197
9342,1511
9366,1381
9377,133666
9387,1197
9407,1511
9427,1381
9450,1197
9458,133666
9472,1511
9493,1381
9507,1197
9533,1511
9546,133666
9555,1381
9575,1197
9593,1511
9617,1381
9628,133666
9638,1197
9658,1511
9678,1381
9701,1197
9709,133666
9723,1511
9744,1381
9758,1197
9784,1511
9797,133666
9806,1381
9826,1197
9844,1511
9868,1381
9879,133666
9889,1197
9909,1511
9924,82312
9929,1381
9952,1197
9960,133666
9974,1511
9995,1381
1 step neuron_idx
2 0 1381
3 46 1197
4 51 1511
5 79 1381
6 91 133666
7 99 1197
8 120 1511
9 140 1381
10 163 1197
11 170 133666
12 185 1511
13 205 1381
14 220 1197
15 246 1511
16 259 133666
17 268 1381
18 288 1197
19 306 1511
20 330 1381
21 341 133666
22 351 1197
23 371 1511
24 391 1381
25 414 1197
26 422 133666
27 436 1511
28 457 1381
29 471 1197
30 497 1511
31 510 133666
32 519 1381
33 539 1197
34 557 1511
35 581 1381
36 592 133666
37 602 1197
38 622 1511
39 642 1381
40 665 1197
41 673 133666
42 687 1511
43 708 1381
44 722 1197
45 748 1511
46 761 133666
47 770 1381
48 790 1197
49 808 1511
50 832 1381
51 843 133666
52 853 1197
53 873 1511
54 881 82312
55 893 1381
56 916 1197
57 924 133666
58 938 1511
59 959 1381
60 973 1197
61 999 1511
62 1012 133666
63 1021 1381
64 1041 1197
65 1059 1511
66 1083 1381
67 1094 133666
68 1104 1197
69 1124 1511
70 1144 1381
71 1167 1197
72 1175 133666
73 1189 1511
74 1210 1381
75 1224 1197
76 1250 1511
77 1263 133666
78 1272 1381
79 1292 1197
80 1310 1511
81 1334 1381
82 1345 133666
83 1355 1197
84 1375 1511
85 1395 1381
86 1418 1197
87 1426 133666
88 1440 1511
89 1461 1381
90 1475 1197
91 1501 1511
92 1514 133666
93 1523 1381
94 1543 1197
95 1561 1511
96 1585 1381
97 1596 133666
98 1606 1197
99 1626 1511
100 1641 82312
101 1646 1381
102 1669 1197
103 1677 133666
104 1691 1511
105 1712 1381
106 1726 1197
107 1752 1511
108 1765 133666
109 1774 1381
110 1794 1197
111 1812 1511
112 1836 1381
113 1847 133666
114 1857 1197
115 1877 1511
116 1897 1381
117 1920 1197
118 1928 133666
119 1942 1511
120 1963 1381
121 1977 1197
122 2003 1511
123 2016 133666
124 2025 1381
125 2045 1197
126 2063 1511
127 2087 1381
128 2098 133666
129 2108 1197
130 2128 1511
131 2148 1381
132 2171 1197
133 2179 133666
134 2193 1511
135 2214 1381
136 2228 1197
137 2254 1511
138 2267 133666
139 2276 1381
140 2296 1197
141 2314 1511
142 2338 1381
143 2349 133666
144 2359 1197
145 2379 1511
146 2394 82312
147 2399 1381
148 2422 1197
149 2430 133666
150 2444 1511
151 2465 1381
152 2479 1197
153 2505 1511
154 2518 133666
155 2527 1381
156 2547 1197
157 2565 1511
158 2589 1381
159 2600 133666
160 2610 1197
161 2630 1511
162 2650 1381
163 2673 1197
164 2681 133666
165 2695 1511
166 2716 1381
167 2730 1197
168 2756 1511
169 2769 133666
170 2778 1381
171 2798 1197
172 2816 1511
173 2840 1381
174 2851 133666
175 2861 1197
176 2881 1511
177 2901 1381
178 2924 1197
179 2932 133666
180 2946 1511
181 2967 1381
182 2981 1197
183 3007 1511
184 3020 133666
185 3029 1381
186 3049 1197
187 3067 1511
188 3091 1381
189 3102 133666
190 3112 1197
191 3132 1511
192 3147 82312
193 3152 1381
194 3175 1197
195 3183 133666
196 3197 1511
197 3218 1381
198 3232 1197
199 3258 1511
200 3271 133666
201 3280 1381
202 3300 1197
203 3318 1511
204 3342 1381
205 3353 133666
206 3363 1197
207 3383 1511
208 3403 1381
209 3426 1197
210 3434 133666
211 3448 1511
212 3469 1381
213 3483 1197
214 3509 1511
215 3522 133666
216 3531 1381
217 3551 1197
218 3569 1511
219 3593 1381
220 3604 133666
221 3614 1197
222 3634 1511
223 3654 1381
224 3677 1197
225 3685 133666
226 3699 1511
227 3720 1381
228 3734 1197
229 3760 1511
230 3773 133666
231 3782 1381
232 3802 1197
233 3820 1511
234 3844 1381
235 3855 133666
236 3865 1197
237 3885 1511
238 3900 82312
239 3905 1381
240 3928 1197
241 3936 133666
242 3950 1511
243 3971 1381
244 3985 1197
245 4011 1511
246 4024 133666
247 4033 1381
248 4053 1197
249 4071 1511
250 4095 1381
251 4106 133666
252 4116 1197
253 4136 1511
254 4156 1381
255 4179 1197
256 4187 133666
257 4201 1511
258 4222 1381
259 4236 1197
260 4262 1511
261 4275 133666
262 4284 1381
263 4304 1197
264 4322 1511
265 4346 1381
266 4357 133666
267 4367 1197
268 4387 1511
269 4407 1381
270 4430 1197
271 4438 133666
272 4452 1511
273 4473 1381
274 4487 1197
275 4513 1511
276 4526 133666
277 4535 1381
278 4555 1197
279 4573 1511
280 4597 1381
281 4608 133666
282 4618 1197
283 4638 1511
284 4653 82312
285 4658 1381
286 4681 1197
287 4689 133666
288 4703 1511
289 4724 1381
290 4738 1197
291 4764 1511
292 4777 133666
293 4786 1381
294 4806 1197
295 4824 1511
296 4848 1381
297 4859 133666
298 4869 1197
299 4889 1511
300 4909 1381
301 4932 1197
302 4940 133666
303 4954 1511
304 4975 1381
305 4989 1197
306 5015 1511
307 5028 133666
308 5037 1381
309 5057 1197
310 5075 1511
311 5099 1381
312 5110 133666
313 5120 1197
314 5140 1511
315 5160 1381
316 5183 1197
317 5191 133666
318 5205 1511
319 5226 1381
320 5240 1197
321 5266 1511
322 5279 133666
323 5288 1381
324 5308 1197
325 5326 1511
326 5350 1381
327 5361 133666
328 5371 1197
329 5391 1511
330 5406 82312
331 5411 1381
332 5434 1197
333 5442 133666
334 5456 1511
335 5477 1381
336 5491 1197
337 5517 1511
338 5530 133666
339 5539 1381
340 5559 1197
341 5577 1511
342 5601 1381
343 5612 133666
344 5622 1197
345 5642 1511
346 5662 1381
347 5685 1197
348 5693 133666
349 5707 1511
350 5728 1381
351 5742 1197
352 5768 1511
353 5781 133666
354 5790 1381
355 5810 1197
356 5828 1511
357 5852 1381
358 5863 133666
359 5873 1197
360 5893 1511
361 5913 1381
362 5936 1197
363 5944 133666
364 5958 1511
365 5979 1381
366 5993 1197
367 6019 1511
368 6032 133666
369 6041 1381
370 6061 1197
371 6079 1511
372 6103 1381
373 6114 133666
374 6124 1197
375 6144 1511
376 6159 82312
377 6164 1381
378 6187 1197
379 6195 133666
380 6209 1511
381 6230 1381
382 6244 1197
383 6270 1511
384 6283 133666
385 6292 1381
386 6312 1197
387 6330 1511
388 6354 1381
389 6365 133666
390 6375 1197
391 6395 1511
392 6415 1381
393 6438 1197
394 6446 133666
395 6460 1511
396 6481 1381
397 6495 1197
398 6521 1511
399 6534 133666
400 6543 1381
401 6563 1197
402 6581 1511
403 6605 1381
404 6616 133666
405 6626 1197
406 6646 1511
407 6666 1381
408 6689 1197
409 6697 133666
410 6711 1511
411 6732 1381
412 6746 1197
413 6772 1511
414 6785 133666
415 6794 1381
416 6814 1197
417 6832 1511
418 6856 1381
419 6867 133666
420 6877 1197
421 6897 1511
422 6912 82312
423 6917 1381
424 6940 1197
425 6948 133666
426 6962 1511
427 6983 1381
428 6997 1197
429 7023 1511
430 7036 133666
431 7045 1381
432 7065 1197
433 7083 1511
434 7107 1381
435 7118 133666
436 7128 1197
437 7148 1511
438 7168 1381
439 7191 1197
440 7199 133666
441 7213 1511
442 7234 1381
443 7248 1197
444 7274 1511
445 7287 133666
446 7296 1381
447 7316 1197
448 7334 1511
449 7358 1381
450 7369 133666
451 7379 1197
452 7399 1511
453 7419 1381
454 7442 1197
455 7450 133666
456 7464 1511
457 7485 1381
458 7499 1197
459 7525 1511
460 7538 133666
461 7547 1381
462 7567 1197
463 7585 1511
464 7609 1381
465 7620 133666
466 7630 1197
467 7650 1511
468 7665 82312
469 7670 1381
470 7693 1197
471 7701 133666
472 7715 1511
473 7736 1381
474 7750 1197
475 7776 1511
476 7789 133666
477 7798 1381
478 7818 1197
479 7836 1511
480 7860 1381
481 7871 133666
482 7881 1197
483 7901 1511
484 7921 1381
485 7944 1197
486 7952 133666
487 7966 1511
488 7987 1381
489 8001 1197
490 8027 1511
491 8040 133666
492 8049 1381
493 8069 1197
494 8087 1511
495 8111 1381
496 8122 133666
497 8132 1197
498 8152 1511
499 8172 1381
500 8195 1197
501 8203 133666
502 8217 1511
503 8238 1381
504 8252 1197
505 8278 1511
506 8291 133666
507 8300 1381
508 8320 1197
509 8338 1511
510 8362 1381
511 8373 133666
512 8383 1197
513 8403 1511
514 8418 82312
515 8423 1381
516 8446 1197
517 8454 133666
518 8468 1511
519 8489 1381
520 8503 1197
521 8529 1511
522 8542 133666
523 8551 1381
524 8571 1197
525 8589 1511
526 8613 1381
527 8624 133666
528 8634 1197
529 8654 1511
530 8674 1381
531 8697 1197
532 8705 133666
533 8719 1511
534 8740 1381
535 8754 1197
536 8780 1511
537 8793 133666
538 8802 1381
539 8822 1197
540 8840 1511
541 8864 1381
542 8875 133666
543 8885 1197
544 8905 1511
545 8925 1381
546 8948 1197
547 8956 133666
548 8970 1511
549 8991 1381
550 9005 1197
551 9031 1511
552 9044 133666
553 9053 1381
554 9073 1197
555 9091 1511
556 9115 1381
557 9126 133666
558 9136 1197
559 9156 1511
560 9171 82312
561 9176 1381
562 9199 1197
563 9207 133666
564 9221 1511
565 9242 1381
566 9256 1197
567 9282 1511
568 9295 133666
569 9304 1381
570 9324 1197
571 9342 1511
572 9366 1381
573 9377 133666
574 9387 1197
575 9407 1511
576 9427 1381
577 9450 1197
578 9458 133666
579 9472 1511
580 9493 1381
581 9507 1197
582 9533 1511
583 9546 133666
584 9555 1381
585 9575 1197
586 9593 1511
587 9617 1381
588 9628 133666
589 9638 1197
590 9658 1511
591 9678 1381
592 9701 1197
593 9709 133666
594 9723 1511
595 9744 1381
596 9758 1197
597 9784 1511
598 9797 133666
599 9806 1381
600 9826 1197
601 9844 1511
602 9868 1381
603 9879 133666
604 9889 1197
605 9909 1511
606 9924 82312
607 9929 1381
608 9952 1197
609 9960 133666
610 9974 1511
611 9995 1381
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/generated-code.json
+127
View File
@@ -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_3",
"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_4",
"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_4",
"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_4",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/run-spec.json
+132
View File
@@ -0,0 +1,132 @@
{
"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,
1337065,
1467340,
1467355,
1467852,
1559765,
1559772,
1560267,
20992285,
20992291,
20992294,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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": "float32",
"preferences": {
"codegen.target": "numpy",
"core.default_float_dtype": "float32",
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32-repeat/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -43.99999976158142,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/actual-weights.json
+47
View File
@@ -0,0 +1,47 @@
{
"edge_id": [
1336648,
1336655,
1337065,
1467340,
1467355,
1467852,
1559765,
1559772,
1560267,
20992285,
20992291,
20992294,
20992891
],
"weights_mv": [
57.75,
47.29999923706055,
28.599998474121094,
71.2249984741211,
64.625,
17.599998474121094,
62.14999771118164,
77.82499694824219,
19.249998092651367,
26.125,
15.675000190734863,
20.899999618530273,
11.824999809265137
],
"weights_volt": [
0.057750001549720764,
0.04729999974370003,
0.028599999845027924,
0.07122500240802765,
0.06462500244379044,
0.01759999990463257,
0.062150001525878906,
0.07782500237226486,
0.01924999989569187,
0.026125000789761543,
0.015675000846385956,
0.020899999886751175,
0.011824999935925007
]
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/brian-output/events.csv
+611
View File
@@ -0,0 +1,611 @@
step,neuron_idx
0,1381
46,1197
51,1511
79,1381
91,133666
99,1197
120,1511
140,1381
163,1197
170,133666
185,1511
205,1381
220,1197
246,1511
259,133666
268,1381
288,1197
306,1511
330,1381
341,133666
351,1197
371,1511
391,1381
414,1197
422,133666
436,1511
457,1381
471,1197
497,1511
510,133666
519,1381
539,1197
557,1511
581,1381
592,133666
602,1197
622,1511
642,1381
665,1197
673,133666
687,1511
708,1381
722,1197
748,1511
761,133666
770,1381
790,1197
808,1511
832,1381
843,133666
853,1197
873,1511
881,82312
893,1381
916,1197
924,133666
938,1511
959,1381
973,1197
999,1511
1012,133666
1021,1381
1041,1197
1059,1511
1083,1381
1094,133666
1104,1197
1124,1511
1144,1381
1167,1197
1175,133666
1189,1511
1210,1381
1224,1197
1250,1511
1263,133666
1272,1381
1292,1197
1310,1511
1334,1381
1345,133666
1355,1197
1375,1511
1395,1381
1418,1197
1426,133666
1440,1511
1461,1381
1475,1197
1501,1511
1514,133666
1523,1381
1543,1197
1561,1511
1585,1381
1596,133666
1606,1197
1626,1511
1641,82312
1646,1381
1669,1197
1677,133666
1691,1511
1712,1381
1726,1197
1752,1511
1765,133666
1774,1381
1794,1197
1812,1511
1836,1381
1847,133666
1857,1197
1877,1511
1897,1381
1920,1197
1928,133666
1942,1511
1963,1381
1977,1197
2003,1511
2016,133666
2025,1381
2045,1197
2063,1511
2087,1381
2098,133666
2108,1197
2128,1511
2148,1381
2171,1197
2179,133666
2193,1511
2214,1381
2228,1197
2254,1511
2267,133666
2276,1381
2296,1197
2314,1511
2338,1381
2349,133666
2359,1197
2379,1511
2394,82312
2399,1381
2422,1197
2430,133666
2444,1511
2465,1381
2479,1197
2505,1511
2518,133666
2527,1381
2547,1197
2565,1511
2589,1381
2600,133666
2610,1197
2630,1511
2650,1381
2673,1197
2681,133666
2695,1511
2716,1381
2730,1197
2756,1511
2769,133666
2778,1381
2798,1197
2816,1511
2840,1381
2851,133666
2861,1197
2881,1511
2901,1381
2924,1197
2932,133666
2946,1511
2967,1381
2981,1197
3007,1511
3020,133666
3029,1381
3049,1197
3067,1511
3091,1381
3102,133666
3112,1197
3132,1511
3147,82312
3152,1381
3175,1197
3183,133666
3197,1511
3218,1381
3232,1197
3258,1511
3271,133666
3280,1381
3300,1197
3318,1511
3342,1381
3353,133666
3363,1197
3383,1511
3403,1381
3426,1197
3434,133666
3448,1511
3469,1381
3483,1197
3509,1511
3522,133666
3531,1381
3551,1197
3569,1511
3593,1381
3604,133666
3614,1197
3634,1511
3654,1381
3677,1197
3685,133666
3699,1511
3720,1381
3734,1197
3760,1511
3773,133666
3782,1381
3802,1197
3820,1511
3844,1381
3855,133666
3865,1197
3885,1511
3900,82312
3905,1381
3928,1197
3936,133666
3950,1511
3971,1381
3985,1197
4011,1511
4024,133666
4033,1381
4053,1197
4071,1511
4095,1381
4106,133666
4116,1197
4136,1511
4156,1381
4179,1197
4187,133666
4201,1511
4222,1381
4236,1197
4262,1511
4275,133666
4284,1381
4304,1197
4322,1511
4346,1381
4357,133666
4367,1197
4387,1511
4407,1381
4430,1197
4438,133666
4452,1511
4473,1381
4487,1197
4513,1511
4526,133666
4535,1381
4555,1197
4573,1511
4597,1381
4608,133666
4618,1197
4638,1511
4653,82312
4658,1381
4681,1197
4689,133666
4703,1511
4724,1381
4738,1197
4764,1511
4777,133666
4786,1381
4806,1197
4824,1511
4848,1381
4859,133666
4869,1197
4889,1511
4909,1381
4932,1197
4940,133666
4954,1511
4975,1381
4989,1197
5015,1511
5028,133666
5037,1381
5057,1197
5075,1511
5099,1381
5110,133666
5120,1197
5140,1511
5160,1381
5183,1197
5191,133666
5205,1511
5226,1381
5240,1197
5266,1511
5279,133666
5288,1381
5308,1197
5326,1511
5350,1381
5361,133666
5371,1197
5391,1511
5406,82312
5411,1381
5434,1197
5442,133666
5456,1511
5477,1381
5491,1197
5517,1511
5530,133666
5539,1381
5559,1197
5577,1511
5601,1381
5612,133666
5622,1197
5642,1511
5662,1381
5685,1197
5693,133666
5707,1511
5728,1381
5742,1197
5768,1511
5781,133666
5790,1381
5810,1197
5828,1511
5852,1381
5863,133666
5873,1197
5893,1511
5913,1381
5936,1197
5944,133666
5958,1511
5979,1381
5993,1197
6019,1511
6032,133666
6041,1381
6061,1197
6079,1511
6103,1381
6114,133666
6124,1197
6144,1511
6159,82312
6164,1381
6187,1197
6195,133666
6209,1511
6230,1381
6244,1197
6270,1511
6283,133666
6292,1381
6312,1197
6330,1511
6354,1381
6365,133666
6375,1197
6395,1511
6415,1381
6438,1197
6446,133666
6460,1511
6481,1381
6495,1197
6521,1511
6534,133666
6543,1381
6563,1197
6581,1511
6605,1381
6616,133666
6626,1197
6646,1511
6666,1381
6689,1197
6697,133666
6711,1511
6732,1381
6746,1197
6772,1511
6785,133666
6794,1381
6814,1197
6832,1511
6856,1381
6867,133666
6877,1197
6897,1511
6912,82312
6917,1381
6940,1197
6948,133666
6962,1511
6983,1381
6997,1197
7023,1511
7036,133666
7045,1381
7065,1197
7083,1511
7107,1381
7118,133666
7128,1197
7148,1511
7168,1381
7191,1197
7199,133666
7213,1511
7234,1381
7248,1197
7274,1511
7287,133666
7296,1381
7316,1197
7334,1511
7358,1381
7369,133666
7379,1197
7399,1511
7419,1381
7442,1197
7450,133666
7464,1511
7485,1381
7499,1197
7525,1511
7538,133666
7547,1381
7567,1197
7585,1511
7609,1381
7620,133666
7630,1197
7650,1511
7665,82312
7670,1381
7693,1197
7701,133666
7715,1511
7736,1381
7750,1197
7776,1511
7789,133666
7798,1381
7818,1197
7836,1511
7860,1381
7871,133666
7881,1197
7901,1511
7921,1381
7944,1197
7952,133666
7966,1511
7987,1381
8001,1197
8027,1511
8040,133666
8049,1381
8069,1197
8087,1511
8111,1381
8122,133666
8132,1197
8152,1511
8172,1381
8195,1197
8203,133666
8217,1511
8238,1381
8252,1197
8278,1511
8291,133666
8300,1381
8320,1197
8338,1511
8362,1381
8373,133666
8383,1197
8403,1511
8418,82312
8423,1381
8446,1197
8454,133666
8468,1511
8489,1381
8503,1197
8529,1511
8542,133666
8551,1381
8571,1197
8589,1511
8613,1381
8624,133666
8634,1197
8654,1511
8674,1381
8697,1197
8705,133666
8719,1511
8740,1381
8754,1197
8780,1511
8793,133666
8802,1381
8822,1197
8840,1511
8864,1381
8875,133666
8885,1197
8905,1511
8925,1381
8948,1197
8956,133666
8970,1511
8991,1381
9005,1197
9031,1511
9044,133666
9053,1381
9073,1197
9091,1511
9115,1381
9126,133666
9136,1197
9156,1511
9171,82312
9176,1381
9199,1197
9207,133666
9221,1511
9242,1381
9256,1197
9282,1511
9295,133666
9304,1381
9324,1197
9342,1511
9366,1381
9377,133666
9387,1197
9407,1511
9427,1381
9450,1197
9458,133666
9472,1511
9493,1381
9507,1197
9533,1511
9546,133666
9555,1381
9575,1197
9593,1511
9617,1381
9628,133666
9638,1197
9658,1511
9678,1381
9701,1197
9709,133666
9723,1511
9744,1381
9758,1197
9784,1511
9797,133666
9806,1381
9826,1197
9844,1511
9868,1381
9879,133666
9889,1197
9909,1511
9924,82312
9929,1381
9952,1197
9960,133666
9974,1511
9995,1381
1 step neuron_idx
2 0 1381
3 46 1197
4 51 1511
5 79 1381
6 91 133666
7 99 1197
8 120 1511
9 140 1381
10 163 1197
11 170 133666
12 185 1511
13 205 1381
14 220 1197
15 246 1511
16 259 133666
17 268 1381
18 288 1197
19 306 1511
20 330 1381
21 341 133666
22 351 1197
23 371 1511
24 391 1381
25 414 1197
26 422 133666
27 436 1511
28 457 1381
29 471 1197
30 497 1511
31 510 133666
32 519 1381
33 539 1197
34 557 1511
35 581 1381
36 592 133666
37 602 1197
38 622 1511
39 642 1381
40 665 1197
41 673 133666
42 687 1511
43 708 1381
44 722 1197
45 748 1511
46 761 133666
47 770 1381
48 790 1197
49 808 1511
50 832 1381
51 843 133666
52 853 1197
53 873 1511
54 881 82312
55 893 1381
56 916 1197
57 924 133666
58 938 1511
59 959 1381
60 973 1197
61 999 1511
62 1012 133666
63 1021 1381
64 1041 1197
65 1059 1511
66 1083 1381
67 1094 133666
68 1104 1197
69 1124 1511
70 1144 1381
71 1167 1197
72 1175 133666
73 1189 1511
74 1210 1381
75 1224 1197
76 1250 1511
77 1263 133666
78 1272 1381
79 1292 1197
80 1310 1511
81 1334 1381
82 1345 133666
83 1355 1197
84 1375 1511
85 1395 1381
86 1418 1197
87 1426 133666
88 1440 1511
89 1461 1381
90 1475 1197
91 1501 1511
92 1514 133666
93 1523 1381
94 1543 1197
95 1561 1511
96 1585 1381
97 1596 133666
98 1606 1197
99 1626 1511
100 1641 82312
101 1646 1381
102 1669 1197
103 1677 133666
104 1691 1511
105 1712 1381
106 1726 1197
107 1752 1511
108 1765 133666
109 1774 1381
110 1794 1197
111 1812 1511
112 1836 1381
113 1847 133666
114 1857 1197
115 1877 1511
116 1897 1381
117 1920 1197
118 1928 133666
119 1942 1511
120 1963 1381
121 1977 1197
122 2003 1511
123 2016 133666
124 2025 1381
125 2045 1197
126 2063 1511
127 2087 1381
128 2098 133666
129 2108 1197
130 2128 1511
131 2148 1381
132 2171 1197
133 2179 133666
134 2193 1511
135 2214 1381
136 2228 1197
137 2254 1511
138 2267 133666
139 2276 1381
140 2296 1197
141 2314 1511
142 2338 1381
143 2349 133666
144 2359 1197
145 2379 1511
146 2394 82312
147 2399 1381
148 2422 1197
149 2430 133666
150 2444 1511
151 2465 1381
152 2479 1197
153 2505 1511
154 2518 133666
155 2527 1381
156 2547 1197
157 2565 1511
158 2589 1381
159 2600 133666
160 2610 1197
161 2630 1511
162 2650 1381
163 2673 1197
164 2681 133666
165 2695 1511
166 2716 1381
167 2730 1197
168 2756 1511
169 2769 133666
170 2778 1381
171 2798 1197
172 2816 1511
173 2840 1381
174 2851 133666
175 2861 1197
176 2881 1511
177 2901 1381
178 2924 1197
179 2932 133666
180 2946 1511
181 2967 1381
182 2981 1197
183 3007 1511
184 3020 133666
185 3029 1381
186 3049 1197
187 3067 1511
188 3091 1381
189 3102 133666
190 3112 1197
191 3132 1511
192 3147 82312
193 3152 1381
194 3175 1197
195 3183 133666
196 3197 1511
197 3218 1381
198 3232 1197
199 3258 1511
200 3271 133666
201 3280 1381
202 3300 1197
203 3318 1511
204 3342 1381
205 3353 133666
206 3363 1197
207 3383 1511
208 3403 1381
209 3426 1197
210 3434 133666
211 3448 1511
212 3469 1381
213 3483 1197
214 3509 1511
215 3522 133666
216 3531 1381
217 3551 1197
218 3569 1511
219 3593 1381
220 3604 133666
221 3614 1197
222 3634 1511
223 3654 1381
224 3677 1197
225 3685 133666
226 3699 1511
227 3720 1381
228 3734 1197
229 3760 1511
230 3773 133666
231 3782 1381
232 3802 1197
233 3820 1511
234 3844 1381
235 3855 133666
236 3865 1197
237 3885 1511
238 3900 82312
239 3905 1381
240 3928 1197
241 3936 133666
242 3950 1511
243 3971 1381
244 3985 1197
245 4011 1511
246 4024 133666
247 4033 1381
248 4053 1197
249 4071 1511
250 4095 1381
251 4106 133666
252 4116 1197
253 4136 1511
254 4156 1381
255 4179 1197
256 4187 133666
257 4201 1511
258 4222 1381
259 4236 1197
260 4262 1511
261 4275 133666
262 4284 1381
263 4304 1197
264 4322 1511
265 4346 1381
266 4357 133666
267 4367 1197
268 4387 1511
269 4407 1381
270 4430 1197
271 4438 133666
272 4452 1511
273 4473 1381
274 4487 1197
275 4513 1511
276 4526 133666
277 4535 1381
278 4555 1197
279 4573 1511
280 4597 1381
281 4608 133666
282 4618 1197
283 4638 1511
284 4653 82312
285 4658 1381
286 4681 1197
287 4689 133666
288 4703 1511
289 4724 1381
290 4738 1197
291 4764 1511
292 4777 133666
293 4786 1381
294 4806 1197
295 4824 1511
296 4848 1381
297 4859 133666
298 4869 1197
299 4889 1511
300 4909 1381
301 4932 1197
302 4940 133666
303 4954 1511
304 4975 1381
305 4989 1197
306 5015 1511
307 5028 133666
308 5037 1381
309 5057 1197
310 5075 1511
311 5099 1381
312 5110 133666
313 5120 1197
314 5140 1511
315 5160 1381
316 5183 1197
317 5191 133666
318 5205 1511
319 5226 1381
320 5240 1197
321 5266 1511
322 5279 133666
323 5288 1381
324 5308 1197
325 5326 1511
326 5350 1381
327 5361 133666
328 5371 1197
329 5391 1511
330 5406 82312
331 5411 1381
332 5434 1197
333 5442 133666
334 5456 1511
335 5477 1381
336 5491 1197
337 5517 1511
338 5530 133666
339 5539 1381
340 5559 1197
341 5577 1511
342 5601 1381
343 5612 133666
344 5622 1197
345 5642 1511
346 5662 1381
347 5685 1197
348 5693 133666
349 5707 1511
350 5728 1381
351 5742 1197
352 5768 1511
353 5781 133666
354 5790 1381
355 5810 1197
356 5828 1511
357 5852 1381
358 5863 133666
359 5873 1197
360 5893 1511
361 5913 1381
362 5936 1197
363 5944 133666
364 5958 1511
365 5979 1381
366 5993 1197
367 6019 1511
368 6032 133666
369 6041 1381
370 6061 1197
371 6079 1511
372 6103 1381
373 6114 133666
374 6124 1197
375 6144 1511
376 6159 82312
377 6164 1381
378 6187 1197
379 6195 133666
380 6209 1511
381 6230 1381
382 6244 1197
383 6270 1511
384 6283 133666
385 6292 1381
386 6312 1197
387 6330 1511
388 6354 1381
389 6365 133666
390 6375 1197
391 6395 1511
392 6415 1381
393 6438 1197
394 6446 133666
395 6460 1511
396 6481 1381
397 6495 1197
398 6521 1511
399 6534 133666
400 6543 1381
401 6563 1197
402 6581 1511
403 6605 1381
404 6616 133666
405 6626 1197
406 6646 1511
407 6666 1381
408 6689 1197
409 6697 133666
410 6711 1511
411 6732 1381
412 6746 1197
413 6772 1511
414 6785 133666
415 6794 1381
416 6814 1197
417 6832 1511
418 6856 1381
419 6867 133666
420 6877 1197
421 6897 1511
422 6912 82312
423 6917 1381
424 6940 1197
425 6948 133666
426 6962 1511
427 6983 1381
428 6997 1197
429 7023 1511
430 7036 133666
431 7045 1381
432 7065 1197
433 7083 1511
434 7107 1381
435 7118 133666
436 7128 1197
437 7148 1511
438 7168 1381
439 7191 1197
440 7199 133666
441 7213 1511
442 7234 1381
443 7248 1197
444 7274 1511
445 7287 133666
446 7296 1381
447 7316 1197
448 7334 1511
449 7358 1381
450 7369 133666
451 7379 1197
452 7399 1511
453 7419 1381
454 7442 1197
455 7450 133666
456 7464 1511
457 7485 1381
458 7499 1197
459 7525 1511
460 7538 133666
461 7547 1381
462 7567 1197
463 7585 1511
464 7609 1381
465 7620 133666
466 7630 1197
467 7650 1511
468 7665 82312
469 7670 1381
470 7693 1197
471 7701 133666
472 7715 1511
473 7736 1381
474 7750 1197
475 7776 1511
476 7789 133666
477 7798 1381
478 7818 1197
479 7836 1511
480 7860 1381
481 7871 133666
482 7881 1197
483 7901 1511
484 7921 1381
485 7944 1197
486 7952 133666
487 7966 1511
488 7987 1381
489 8001 1197
490 8027 1511
491 8040 133666
492 8049 1381
493 8069 1197
494 8087 1511
495 8111 1381
496 8122 133666
497 8132 1197
498 8152 1511
499 8172 1381
500 8195 1197
501 8203 133666
502 8217 1511
503 8238 1381
504 8252 1197
505 8278 1511
506 8291 133666
507 8300 1381
508 8320 1197
509 8338 1511
510 8362 1381
511 8373 133666
512 8383 1197
513 8403 1511
514 8418 82312
515 8423 1381
516 8446 1197
517 8454 133666
518 8468 1511
519 8489 1381
520 8503 1197
521 8529 1511
522 8542 133666
523 8551 1381
524 8571 1197
525 8589 1511
526 8613 1381
527 8624 133666
528 8634 1197
529 8654 1511
530 8674 1381
531 8697 1197
532 8705 133666
533 8719 1511
534 8740 1381
535 8754 1197
536 8780 1511
537 8793 133666
538 8802 1381
539 8822 1197
540 8840 1511
541 8864 1381
542 8875 133666
543 8885 1197
544 8905 1511
545 8925 1381
546 8948 1197
547 8956 133666
548 8970 1511
549 8991 1381
550 9005 1197
551 9031 1511
552 9044 133666
553 9053 1381
554 9073 1197
555 9091 1511
556 9115 1381
557 9126 133666
558 9136 1197
559 9156 1511
560 9171 82312
561 9176 1381
562 9199 1197
563 9207 133666
564 9221 1511
565 9242 1381
566 9256 1197
567 9282 1511
568 9295 133666
569 9304 1381
570 9324 1197
571 9342 1511
572 9366 1381
573 9377 133666
574 9387 1197
575 9407 1511
576 9427 1381
577 9450 1197
578 9458 133666
579 9472 1511
580 9493 1381
581 9507 1197
582 9533 1511
583 9546 133666
584 9555 1381
585 9575 1197
586 9593 1511
587 9617 1381
588 9628 133666
589 9638 1197
590 9658 1511
591 9678 1381
592 9701 1197
593 9709 133666
594 9723 1511
595 9744 1381
596 9758 1197
597 9784 1511
598 9797 133666
599 9806 1381
600 9826 1197
601 9844 1511
602 9868 1381
603 9879 133666
604 9889 1197
605 9909 1511
606 9924 82312
607 9929 1381
608 9952 1197
609 9960 133666
610 9974 1511
611 9995 1381
registry/phase4ad-author-semantics/evidence/oracle/five-float32/comparison.json
+11
View File
@@ -0,0 +1,11 @@
{
"exact_events": true,
"exact_counts": true,
"ref_exact": true,
"max_abs_mv": 0.0002123713493347168,
"mean_abs_mv": 1.7726411819458007e-05,
"same_event_prefix_max_abs_mv": 0.0002123713493347168,
"first_event_divergence_step": null,
"tolerance_mv": 0.001,
"pass_oracle": true
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/five-float32/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/generated-code.json
+127
View File
@@ -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_1",
"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_3",
"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_3",
"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_3",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/five-float32/independent-output/events.csv
+611
View File
@@ -0,0 +1,611 @@
step,neuron_idx
0,1381
46,1197
51,1511
79,1381
91,133666
99,1197
120,1511
140,1381
163,1197
170,133666
185,1511
205,1381
220,1197
246,1511
259,133666
268,1381
288,1197
306,1511
330,1381
341,133666
351,1197
371,1511
391,1381
414,1197
422,133666
436,1511
457,1381
471,1197
497,1511
510,133666
519,1381
539,1197
557,1511
581,1381
592,133666
602,1197
622,1511
642,1381
665,1197
673,133666
687,1511
708,1381
722,1197
748,1511
761,133666
770,1381
790,1197
808,1511
832,1381
843,133666
853,1197
873,1511
881,82312
893,1381
916,1197
924,133666
938,1511
959,1381
973,1197
999,1511
1012,133666
1021,1381
1041,1197
1059,1511
1083,1381
1094,133666
1104,1197
1124,1511
1144,1381
1167,1197
1175,133666
1189,1511
1210,1381
1224,1197
1250,1511
1263,133666
1272,1381
1292,1197
1310,1511
1334,1381
1345,133666
1355,1197
1375,1511
1395,1381
1418,1197
1426,133666
1440,1511
1461,1381
1475,1197
1501,1511
1514,133666
1523,1381
1543,1197
1561,1511
1585,1381
1596,133666
1606,1197
1626,1511
1641,82312
1646,1381
1669,1197
1677,133666
1691,1511
1712,1381
1726,1197
1752,1511
1765,133666
1774,1381
1794,1197
1812,1511
1836,1381
1847,133666
1857,1197
1877,1511
1897,1381
1920,1197
1928,133666
1942,1511
1963,1381
1977,1197
2003,1511
2016,133666
2025,1381
2045,1197
2063,1511
2087,1381
2098,133666
2108,1197
2128,1511
2148,1381
2171,1197
2179,133666
2193,1511
2214,1381
2228,1197
2254,1511
2267,133666
2276,1381
2296,1197
2314,1511
2338,1381
2349,133666
2359,1197
2379,1511
2394,82312
2399,1381
2422,1197
2430,133666
2444,1511
2465,1381
2479,1197
2505,1511
2518,133666
2527,1381
2547,1197
2565,1511
2589,1381
2600,133666
2610,1197
2630,1511
2650,1381
2673,1197
2681,133666
2695,1511
2716,1381
2730,1197
2756,1511
2769,133666
2778,1381
2798,1197
2816,1511
2840,1381
2851,133666
2861,1197
2881,1511
2901,1381
2924,1197
2932,133666
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2981,1197
3007,1511
3020,133666
3029,1381
3049,1197
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3091,1381
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3112,1197
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3147,82312
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3604,133666
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5411,1381
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5477,1381
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5662,1381
5685,1197
5693,133666
5707,1511
5728,1381
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5768,1511
5781,133666
5790,1381
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9924,82312
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9960,133666
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9995,1381
1 step neuron_idx
2 0 1381
3 46 1197
4 51 1511
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6 91 133666
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registry/phase4ad-author-semantics/evidence/oracle/five-float32/run-spec.json
+132
View File
@@ -0,0 +1,132 @@
{
"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,
1337065,
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1467852,
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1560267,
20992285,
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20992294,
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],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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": "float32",
"preferences": {
"codegen.target": "numpy",
"core.default_float_dtype": "float32",
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/five-float32/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -43.99999976158142,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/actual-weights.json
+47
View File
@@ -0,0 +1,47 @@
{
"edge_id": [
1336648,
1336655,
1337065,
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1467852,
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],
"weights_mv": [
57.75,
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registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/brian-output/events.csv
+611
View File
@@ -0,0 +1,611 @@
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517 8454 133666
518 8468 1511
519 8489 1381
520 8503 1197
521 8529 1511
522 8542 133666
523 8551 1381
524 8571 1197
525 8589 1511
526 8613 1381
527 8624 133666
528 8634 1197
529 8654 1511
530 8674 1381
531 8697 1197
532 8705 133666
533 8719 1511
534 8740 1381
535 8754 1197
536 8780 1511
537 8793 133666
538 8802 1381
539 8822 1197
540 8840 1511
541 8864 1381
542 8875 133666
543 8885 1197
544 8905 1511
545 8925 1381
546 8948 1197
547 8956 133666
548 8970 1511
549 8991 1381
550 9005 1197
551 9031 1511
552 9044 133666
553 9053 1381
554 9073 1197
555 9091 1511
556 9115 1381
557 9126 133666
558 9136 1197
559 9156 1511
560 9171 82312
561 9176 1381
562 9199 1197
563 9207 133666
564 9221 1511
565 9242 1381
566 9256 1197
567 9282 1511
568 9295 133666
569 9304 1381
570 9324 1197
571 9342 1511
572 9366 1381
573 9377 133666
574 9387 1197
575 9407 1511
576 9427 1381
577 9450 1197
578 9458 133666
579 9472 1511
580 9493 1381
581 9507 1197
582 9533 1511
583 9546 133666
584 9555 1381
585 9575 1197
586 9593 1511
587 9617 1381
588 9628 133666
589 9638 1197
590 9658 1511
591 9678 1381
592 9701 1197
593 9709 133666
594 9723 1511
595 9744 1381
596 9758 1197
597 9784 1511
598 9797 133666
599 9806 1381
600 9826 1197
601 9844 1511
602 9868 1381
603 9879 133666
604 9889 1197
605 9909 1511
606 9924 82312
607 9929 1381
608 9952 1197
609 9960 133666
610 9974 1511
611 9995 1381
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/completeness.csv
+6
View File
@@ -0,0 +1,6 @@
global_neuron_idx,local_index
1197,0
1381,1
1511,2
82312,3
133666,4
1 global_neuron_idx local_index
2 1197 0
3 1381 1
4 1511 2
5 82312 3
6 133666 4
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/environment.json
+102
View File
@@ -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
}
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/generated-code.json
+127
View File
@@ -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_2",
"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_2",
"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_2",
"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_2",
"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"
}
]
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/run-spec.json
+132
View File
@@ -0,0 +1,132 @@
{
"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,
1337065,
1467340,
1467355,
1467852,
1559765,
1559772,
1560267,
20992285,
20992291,
20992294,
20992891
],
"external_arrivals": {
"events": 0,
"ordering": "after default_synapses.pre"
},
"internal_voltage_unit": "volt",
"nodes": [
1197,
1381,
1511,
82312,
133666
],
"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"
}
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/schedule.json
+11
View File
@@ -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 "
}
registry/phase4ad-author-semantics/evidence/oracle/five-float64-repeat/seed.json
+7
View File
@@ -0,0 +1,7 @@
{
"applied_mv": -44.0,
"injections": 1,
"margin_mv": 1.0,
"requested_global_node": 1381,
"spiked_at_zero": true
}

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