Publish corrected P0 fixture baselines and historical metric invalidation

HISTORICAL_METRICS_INVALIDATED.md

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+Historical physics_teacher evaluation metrics are INVALIDATED by P0: voltage/conductance mixing, broadcast trajectory errors, and mismatched gradient/search objectives. Do not use old model rankings. Old teacher traces are retained, but all corrected metrics are under p0_corrected_20261030/fixture_v2. This remains FIXTURE_TEST_ONLY, not biological calibration.

README.md

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+# NeuronMimic reusable data (2026-10-30)
+
+This dataset contains compact, source-bound tables and a deterministic passive
+cable fixture for reproducing the NeuronMimic baselines. It deliberately does
+not contain restricted raw MaleCNS/FlyWire connectome downloads or any claim of
+biological validation.
+
+The current structure/dynamics requirement matrix is maintained in the parent
+BioFly project at `artifacts/wu_20261030_science_gate/WU_REQUIREMENTS_STATUS_20261030.md`.
+
+
+## Contents
+
+- `physics_teacher/`: deterministic 12-compartment Teacher stimulus panel,
+  train/held-out arrays, model comparison, finite-difference gradient check,
+  and Teacher-rechecked active-search results. Every file is
+  `FIXTURE_TEST_ONLY`.
+- `malecns/`: normalized MaleCNS v1.0 directed aggregate edges and annotations,
+  with source hashes. These are `VERIFIED_REAL_DATA` structural tables, while
+  contact-to-branch mapping is explicitly blocked.
+- `flywire_kc_atlas/`: compact all-5,177-cell structural profiles and the
+  source-bound 20-unit entry registry. This is single-connectome structural
+  evidence, not independent biological replication.
+- `provenance/`: protocol and source manifests.
+
+## Links
+
+- Code: https://github.com/ydchen0806/neuronmimic
+- Parent analysis repository: https://github.com/ydchen0806/bio_fly_cyber_lateralization
+- Dataset: https://huggingface.co/datasets/cyd0806/neuronmimic-data
+
+The GitHub repository documents the code and the exact analysis boundaries;
+this dataset provides the compact inputs and receipts. Raw data remain at their
+original public repositories and are not mirrored here.
+
+## Status and limits
+
+`FIXTURE_TEST_ONLY` is synthetic/passive-cable testing. `VERIFIED_REAL_DATA`
+means the local source table was hashed and schema-checked. `BLOCKED_MISSING_DATA`
+means the data required for a real multi-compartment biological calibration are
+not present, especially contact coordinates, branch IDs, conductance values,
+and held-out physiological recordings.
+
+
+## Corrected P0 release
+
+Use `p0_corrected_20261030/fixture_v2/` for reproducible Teacher data, four model baselines, and corrected results. Historical metric files are invalidated; see `HISTORICAL_METRICS_INVALIDATED.md`. All cable experiments are FIXTURE_TEST_ONLY. Code and scientific metric tests: https://github.com/ydchen0806/neuronmimic . Known-equation PhysicsOnly is more accurate than the trained Students; no biological or speed-accuracy advantage is established.

SHA256SUMS.json

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+CM019,non_KC,parent_residual,1235,435,435,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM019,opposite_parent,non_KC,36460,16549,16549,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM019,opposite_parent,opposite_parent,5487,4284,4284,0,17292.0,0.2477446217904233,DEFINED_FOR_KC_SETS
+CM019,opposite_parent,other_KC,1392,1177,1177,0,646404.0,0.0018208426928051189,DEFINED_FOR_KC_SETS
+CM019,other_KC,opposite_parent,1361,1163,1163,0,646404.0,0.0017991844109875557,DEFINED_FOR_KC_SETS
+CM019,other_KC,parent_hit,756,680,680,0,646404.0,0.0010519736882816319,DEFINED_FOR_KC_SETS
+CM019,other_KC,parent_residual,638,451,451,0,78352.0,0.005756075148049826,DEFINED_FOR_KC_SETS
+CM019,parent_hit,non_KC,36560,17061,17061,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM019,parent_hit,other_KC,712,639,639,0,646404.0,0.0009885458629587689,DEFINED_FOR_KC_SETS
+CM019,parent_hit,parent_hit,6976,5324,5324,0,17292.0,0.30788804071246817,DEFINED_FOR_KC_SETS
+CM019,parent_hit,parent_residual,302,250,250,0,2112.0,0.11837121212121213,DEFINED_FOR_KC_SETS
+CM019,parent_residual,non_KC,3582,1713,1713,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM019,parent_residual,other_KC,541,393,393,0,78352.0,0.005015826015928119,DEFINED_FOR_KC_SETS
+CM019,parent_residual,parent_hit,272,215,215,0,2112.0,0.10179924242424243,DEFINED_FOR_KC_SETS
+CM019,parent_residual,parent_residual,191,112,112,0,240.0,0.4666666666666667,DEFINED_FOR_KC_SETS
+CM020,mixed_member,mixed_member,22,17,17,0,56.0,0.30357142857142855,DEFINED_FOR_KC_SETS
+CM020,mixed_member,non_KC,1953,892,892,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,mixed_member,other_KC,75,65,65,0,39112.0,0.0016618940478625485,DEFINED_FOR_KC_SETS
+CM020,mixed_member,parent_hit,242,198,198,0,968.0,0.20454545454545456,DEFINED_FOR_KC_SETS
+CM020,mixed_member,parent_residual,21,19,19,0,88.0,0.2159090909090909,DEFINED_FOR_KC_SETS
+CM020,non_KC,mixed_member,558,189,189,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,non_KC,opposite_parent,12640,4330,4330,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,non_KC,parent_hit,9233,3222,3222,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,non_KC,parent_residual,762,290,290,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,opposite_parent,non_KC,40142,18774,18774,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,opposite_parent,opposite_parent,7741,5901,5901,0,21756.0,0.27123552123552125,DEFINED_FOR_KC_SETS
+CM020,opposite_parent,other_KC,1253,1032,1032,0,723572.0,0.0014262575113464866,DEFINED_FOR_KC_SETS
+CM020,other_KC,mixed_member,101,84,84,0,39112.0,0.0021476784618531396,DEFINED_FOR_KC_SETS
+CM020,other_KC,opposite_parent,1394,1131,1131,0,723572.0,0.0015630787260977484,DEFINED_FOR_KC_SETS
+CM020,other_KC,parent_hit,722,657,657,0,591569.0,0.0011106058633904075,DEFINED_FOR_KC_SETS
+CM020,other_KC,parent_residual,376,289,289,0,53779.0,0.005373844809312185,DEFINED_FOR_KC_SETS
+CM020,parent_hit,mixed_member,276,216,216,0,968.0,0.2231404958677686,DEFINED_FOR_KC_SETS
+CM020,parent_hit,non_KC,34056,15408,15408,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,parent_hit,other_KC,772,693,693,0,591569.0,0.0011714609791926216,DEFINED_FOR_KC_SETS
+CM020,parent_hit,parent_hit,5104,3971,3971,0,14520.0,0.2734848484848485,DEFINED_FOR_KC_SETS
+CM020,parent_hit,parent_residual,195,163,163,0,1331.0,0.12246431254695718,DEFINED_FOR_KC_SETS
+CM020,parent_residual,mixed_member,16,12,12,0,88.0,0.13636363636363635,DEFINED_FOR_KC_SETS
+CM020,parent_residual,non_KC,2404,1141,1141,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM020,parent_residual,other_KC,328,256,256,0,53779.0,0.004760222391639859,DEFINED_FOR_KC_SETS
+CM020,parent_residual,parent_hit,126,106,106,0,1331.0,0.07963936889556725,DEFINED_FOR_KC_SETS
+CM020,parent_residual,parent_residual,62,44,44,0,110.0,0.4,DEFINED_FOR_KC_SETS
+CM022,non_KC,opposite_parent,91034,19667,19667,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,non_KC,parent_hit,12529,3129,3129,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,non_KC,parent_residual,91247,18536,18536,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,opposite_parent,non_KC,136526,64558,64558,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,opposite_parent,opposite_parent,73519,54432,54432,0,637602.0,0.0853698702325275,DEFINED_FOR_KC_SETS
+CM022,opposite_parent,other_KC,2356,2060,2060,0,2823666.0,0.0007295480414468284,DEFINED_FOR_KC_SETS
+CM022,other_KC,opposite_parent,1236,1097,1097,0,2823666.0,0.0003885020395471702,DEFINED_FOR_KC_SETS
+CM022,other_KC,parent_hit,805,684,684,0,402876.0,0.001697792869269949,DEFINED_FOR_KC_SETS
+CM022,other_KC,parent_residual,853,792,792,0,2579820.0,0.00030699816266251134,DEFINED_FOR_KC_SETS
+CM022,parent_hit,non_KC,21925,9796,9796,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,parent_hit,other_KC,1214,1031,1031,0,402876.0,0.002559100070493154,DEFINED_FOR_KC_SETS
+CM022,parent_hit,parent_hit,7916,4759,4759,0,12882.0,0.36943021269989135,DEFINED_FOR_KC_SETS
+CM022,parent_hit,parent_residual,3441,2838,2838,0,83220.0,0.034102379235760635,DEFINED_FOR_KC_SETS
+CM022,parent_residual,non_KC,117818,53368,53368,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM022,parent_residual,other_KC,1540,1466,1466,0,2579820.0,0.0005682567000798505,DEFINED_FOR_KC_SETS
+CM022,parent_residual,parent_hit,3127,2536,2536,0,83220.0,0.030473443883681808,DEFINED_FOR_KC_SETS
+CM022,parent_residual,parent_residual,63972,47766,47766,0,532170.0,0.08975703252719995,DEFINED_FOR_KC_SETS
+CM031,non_KC,opposite_parent,7389,2552,2552,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM031,non_KC,parent_hit,8058,2695,2695,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM031,opposite_parent,non_KC,14248,7304,7304,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM031,opposite_parent,opposite_parent,6476,2813,2813,0,3660.0,0.7685792349726775,DEFINED_FOR_KC_SETS
+CM031,opposite_parent,other_KC,832,699,699,0,307989.0,0.002269561575251064,DEFINED_FOR_KC_SETS
+CM031,other_KC,opposite_parent,1261,994,994,0,307989.0,0.0032273879911295534,DEFINED_FOR_KC_SETS
+CM031,other_KC,parent_hit,1197,1011,1011,0,338283.0,0.0029886219526254645,DEFINED_FOR_KC_SETS
+CM031,parent_hit,non_KC,16304,7336,7336,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM031,parent_hit,other_KC,807,683,683,0,338283.0,0.0020190195782820893,DEFINED_FOR_KC_SETS
+CM031,parent_hit,parent_hit,7822,3455,3455,0,4422.0,0.7813206693803709,DEFINED_FOR_KC_SETS
+CM033,non_KC,opposite_parent,8058,2695,2695,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM033,non_KC,parent_hit,7389,2552,2552,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM033,opposite_parent,non_KC,16304,7336,7336,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM033,opposite_parent,opposite_parent,7822,3455,3455,0,4422.0,0.7813206693803709,DEFINED_FOR_KC_SETS
+CM033,opposite_parent,other_KC,807,683,683,0,338283.0,0.0020190195782820893,DEFINED_FOR_KC_SETS
+CM033,other_KC,opposite_parent,1197,1011,1011,0,338283.0,0.0029886219526254645,DEFINED_FOR_KC_SETS
+CM033,other_KC,parent_hit,1261,994,994,0,307989.0,0.0032273879911295534,DEFINED_FOR_KC_SETS
+CM033,parent_hit,non_KC,14248,7304,7304,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+CM033,parent_hit,other_KC,832,699,699,0,307989.0,0.002269561575251064,DEFINED_FOR_KC_SETS
+CM033,parent_hit,parent_hit,6476,2813,2813,0,3660.0,0.7685792349726775,DEFINED_FOR_KC_SETS
+J25_K30_C014,mixed_member,non_KC,813,369,369,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,mixed_member,other_KC,59,46,46,0,14508.0,0.0031706644609870416,DEFINED_FOR_KC_SETS
+J25_K30_C014,mixed_member,parent_hit,159,116,116,0,477.0,0.2431865828092243,DEFINED_FOR_KC_SETS
+J25_K30_C014,mixed_member,parent_residual,22,18,18,0,45.0,0.4,DEFINED_FOR_KC_SETS
+J25_K30_C014,non_KC,mixed_member,262,99,99,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,non_KC,opposite_parent,16526,5694,5694,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,non_KC,parent_hit,13229,5208,5208,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,non_KC,parent_residual,1228,481,481,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,opposite_parent,non_KC,42003,18283,18283,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,opposite_parent,opposite_parent,12855,8849,8849,0,26732.0,0.33102648511147686,DEFINED_FOR_KC_SETS
+J25_K30_C014,opposite_parent,other_KC,1823,1531,1531,0,793104.0,0.0019303899614678528,DEFINED_FOR_KC_SETS
+J25_K30_C014,opposite_parent,parent_hit,8,8,8,0,26076.0,0.00030679552078539653,DEFINED_FOR_KC_SETS
+J25_K30_C014,other_KC,mixed_member,63,52,52,0,14508.0,0.0035842293906810036,DEFINED_FOR_KC_SETS
+J25_K30_C014,other_KC,opposite_parent,2307,1854,1854,0,793104.0,0.002337650547721358,DEFINED_FOR_KC_SETS
+J25_K30_C014,other_KC,parent_hit,1534,1355,1355,0,768924.0,0.0017622027664632655,DEFINED_FOR_KC_SETS
+J25_K30_C014,other_KC,parent_residual,510,383,383,0,72540.0,0.005279845602426248,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_hit,mixed_member,157,124,124,0,477.0,0.259958071278826,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_hit,non_KC,37999,18240,18240,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,parent_hit,opposite_parent,11,9,9,0,26076.0,0.0003451449608835711,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_hit,other_KC,1366,1194,1194,0,768924.0,0.001552819264322612,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_hit,parent_hit,9655,7180,7180,0,25122.0,0.2858052702810286,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_hit,parent_residual,552,444,444,0,2385.0,0.1861635220125786,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_residual,mixed_member,16,11,11,0,45.0,0.24444444444444444,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_residual,non_KC,3827,1838,1838,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C014,parent_residual,other_KC,436,339,339,0,72540.0,0.00467328370554177,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_residual,parent_hit,559,416,416,0,2385.0,0.17442348008385744,DEFINED_FOR_KC_SETS
+J25_K30_C014,parent_residual,parent_residual,104,72,72,0,210.0,0.34285714285714286,DEFINED_FOR_KC_SETS
+J25_K30_C015,non_KC,opposite_parent,14457,5689,5689,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,non_KC,parent_hit,15363,5265,5265,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,non_KC,parent_residual,1163,429,429,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,opposite_parent,non_KC,41826,20078,20078,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,opposite_parent,opposite_parent,10870,8112,8112,0,30102.0,0.26948375523221046,DEFINED_FOR_KC_SETS
+J25_K30_C015,opposite_parent,other_KC,1975,1668,1668,0,841986.0,0.001981030563453549,DEFINED_FOR_KC_SETS
+J25_K30_C015,opposite_parent,parent_hit,11,9,9,0,26448.0,0.00034029038112522685,DEFINED_FOR_KC_SETS
+J25_K30_C015,other_KC,opposite_parent,2225,1872,1872,0,841986.0,0.0022233148769694507,DEFINED_FOR_KC_SETS
+J25_K30_C015,other_KC,parent_hit,1756,1500,1500,0,735528.0,0.0020393513231311386,DEFINED_FOR_KC_SETS
+J25_K30_C015,other_KC,parent_residual,551,354,354,0,58068.0,0.00609630088861335,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_hit,non_KC,38907,16929,16929,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,parent_hit,opposite_parent,8,8,8,0,26448.0,0.00030248033877797946,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_hit,other_KC,1481,1277,1277,0,735528.0,0.0017361677597589758,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_hit,parent_hit,11405,7863,7863,0,22952.0,0.34258452422446845,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_hit,parent_residual,711,486,486,0,1824.0,0.26644736842105265,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_residual,non_KC,3096,1354,1354,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C015,parent_residual,other_KC,342,254,254,0,58068.0,0.004374181993524833,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_residual,parent_hit,607,434,434,0,1824.0,0.23793859649122806,DEFINED_FOR_KC_SETS
+J25_K30_C015,parent_residual,parent_residual,132,66,66,0,132.0,0.5,DEFINED_FOR_KC_SETS
+J25_K30_C016,mixed_member,mixed_member,124,28,28,0,42.0,0.6666666666666666,DEFINED_FOR_KC_SETS
+J25_K30_C016,mixed_member,non_KC,3249,1853,1853,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,mixed_member,other_KC,480,413,413,0,34125.0,0.012102564102564103,DEFINED_FOR_KC_SETS
+J25_K30_C016,mixed_member,parent_hit,334,224,224,0,910.0,0.24615384615384617,DEFINED_FOR_KC_SETS
+J25_K30_C016,mixed_member,parent_residual,31,21,21,0,119.0,0.17647058823529413,DEFINED_FOR_KC_SETS
+J25_K30_C016,non_KC,mixed_member,1541,471,471,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,non_KC,opposite_parent,12260,3394,3394,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,non_KC,parent_hit,12893,3780,3780,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,non_KC,parent_residual,2172,469,469,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,opposite_parent,non_KC,18297,11678,11678,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,opposite_parent,opposite_parent,3981,3131,3131,0,21756.0,0.14391432248575106,DEFINED_FOR_KC_SETS
+J25_K30_C016,opposite_parent,other_KC,1817,1615,1615,0,721500.0,0.0022383922383922383,DEFINED_FOR_KC_SETS
+J25_K30_C016,other_KC,mixed_member,339,309,309,0,34125.0,0.009054945054945055,DEFINED_FOR_KC_SETS
+J25_K30_C016,other_KC,opposite_parent,1621,1454,1454,0,721500.0,0.0020152460152460154,DEFINED_FOR_KC_SETS
+J25_K30_C016,other_KC,parent_hit,1406,1290,1290,0,633750.0,0.0020355029585798815,DEFINED_FOR_KC_SETS
+J25_K30_C016,other_KC,parent_residual,627,529,529,0,82875.0,0.0063831070889894415,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_hit,mixed_member,338,238,238,0,910.0,0.26153846153846155,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_hit,non_KC,21400,12711,12711,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,parent_hit,other_KC,1912,1719,1719,0,633750.0,0.0027124260355029586,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_hit,parent_hit,5206,3866,3866,0,16770.0,0.23053070960047703,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_hit,parent_residual,300,248,248,0,2210.0,0.11221719457013575,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_residual,mixed_member,25,20,20,0,119.0,0.16806722689075632,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_residual,non_KC,2767,1534,1534,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C016,parent_residual,other_KC,673,567,567,0,82875.0,0.006841628959276018,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_residual,parent_hit,278,229,229,0,2210.0,0.10361990950226245,DEFINED_FOR_KC_SETS
+J25_K30_C016,parent_residual,parent_residual,61,42,42,0,272.0,0.15441176470588236,DEFINED_FOR_KC_SETS
+J25_K30_C017,non_KC,opposite_parent,9995,3512,3512,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,non_KC,parent_hit,11405,3895,3895,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,non_KC,parent_residual,1235,435,435,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,opposite_parent,non_KC,36460,16549,16549,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,opposite_parent,opposite_parent,5487,4284,4284,0,17292.0,0.2477446217904233,DEFINED_FOR_KC_SETS
+J25_K30_C017,opposite_parent,other_KC,1392,1177,1177,0,646404.0,0.0018208426928051189,DEFINED_FOR_KC_SETS
+J25_K30_C017,other_KC,opposite_parent,1361,1163,1163,0,646404.0,0.0017991844109875557,DEFINED_FOR_KC_SETS
+J25_K30_C017,other_KC,parent_hit,756,680,680,0,646404.0,0.0010519736882816319,DEFINED_FOR_KC_SETS
+J25_K30_C017,other_KC,parent_residual,638,451,451,0,78352.0,0.005756075148049826,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_hit,non_KC,36560,17061,17061,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,parent_hit,other_KC,712,639,639,0,646404.0,0.0009885458629587689,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_hit,parent_hit,6976,5324,5324,0,17292.0,0.30788804071246817,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_hit,parent_residual,302,250,250,0,2112.0,0.11837121212121213,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_residual,non_KC,3582,1713,1713,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C017,parent_residual,other_KC,541,393,393,0,78352.0,0.005015826015928119,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_residual,parent_hit,272,215,215,0,2112.0,0.10179924242424243,DEFINED_FOR_KC_SETS
+J25_K30_C017,parent_residual,parent_residual,191,112,112,0,240.0,0.4666666666666667,DEFINED_FOR_KC_SETS
+J25_K30_C018,mixed_member,mixed_member,22,17,17,0,56.0,0.30357142857142855,DEFINED_FOR_KC_SETS
+J25_K30_C018,mixed_member,non_KC,1953,892,892,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,mixed_member,other_KC,75,65,65,0,39112.0,0.0016618940478625485,DEFINED_FOR_KC_SETS
+J25_K30_C018,mixed_member,parent_hit,242,198,198,0,968.0,0.20454545454545456,DEFINED_FOR_KC_SETS
+J25_K30_C018,mixed_member,parent_residual,21,19,19,0,88.0,0.2159090909090909,DEFINED_FOR_KC_SETS
+J25_K30_C018,non_KC,mixed_member,558,189,189,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,non_KC,opposite_parent,12640,4330,4330,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,non_KC,parent_hit,9233,3222,3222,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,non_KC,parent_residual,762,290,290,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,opposite_parent,non_KC,40142,18774,18774,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,opposite_parent,opposite_parent,7741,5901,5901,0,21756.0,0.27123552123552125,DEFINED_FOR_KC_SETS
+J25_K30_C018,opposite_parent,other_KC,1253,1032,1032,0,723572.0,0.0014262575113464866,DEFINED_FOR_KC_SETS
+J25_K30_C018,other_KC,mixed_member,101,84,84,0,39112.0,0.0021476784618531396,DEFINED_FOR_KC_SETS
+J25_K30_C018,other_KC,opposite_parent,1394,1131,1131,0,723572.0,0.0015630787260977484,DEFINED_FOR_KC_SETS
+J25_K30_C018,other_KC,parent_hit,722,657,657,0,591569.0,0.0011106058633904075,DEFINED_FOR_KC_SETS
+J25_K30_C018,other_KC,parent_residual,376,289,289,0,53779.0,0.005373844809312185,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_hit,mixed_member,276,216,216,0,968.0,0.2231404958677686,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_hit,non_KC,34056,15408,15408,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,parent_hit,other_KC,772,693,693,0,591569.0,0.0011714609791926216,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_hit,parent_hit,5104,3971,3971,0,14520.0,0.2734848484848485,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_hit,parent_residual,195,163,163,0,1331.0,0.12246431254695718,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_residual,mixed_member,16,12,12,0,88.0,0.13636363636363635,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_residual,non_KC,2404,1141,1141,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C018,parent_residual,other_KC,328,256,256,0,53779.0,0.004760222391639859,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_residual,parent_hit,126,106,106,0,1331.0,0.07963936889556725,DEFINED_FOR_KC_SETS
+J25_K30_C018,parent_residual,parent_residual,62,44,44,0,110.0,0.4,DEFINED_FOR_KC_SETS
+J25_K30_C023,mixed_member,mixed_member,87,64,64,0,182.0,0.3516483516483517,DEFINED_FOR_KC_SETS
+J25_K30_C023,mixed_member,non_KC,3585,1716,1716,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,mixed_member,opposite_parent,2,2,2,0,1932.0,0.0010351966873706005,DEFINED_FOR_KC_SETS
+J25_K30_C023,mixed_member,other_KC,554,411,411,0,68110.0,0.0060343561885185725,DEFINED_FOR_KC_SETS
+J25_K30_C023,mixed_member,parent_hit,355,268,268,0,1106.0,0.2423146473779385,DEFINED_FOR_KC_SETS
+J25_K30_C023,mixed_member,parent_residual,62,50,50,0,1134.0,0.04409171075837742,DEFINED_FOR_KC_SETS
+J25_K30_C023,non_KC,mixed_member,1155,455,455,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,non_KC,opposite_parent,11562,4162,4162,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,non_KC,parent_hit,5649,2352,2352,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,non_KC,parent_residual,5830,2107,2107,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,opposite_parent,non_KC,34254,15788,15788,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,opposite_parent,opposite_parent,7825,5360,5360,0,18906.0,0.2835078810959484,DEFINED_FOR_KC_SETS
+J25_K30_C023,opposite_parent,other_KC,2882,2229,2229,0,671370.0,0.0033200768577684434,DEFINED_FOR_KC_SETS
+J25_K30_C023,opposite_parent,parent_hit,12,11,11,0,10902.0,0.001008989176297927,DEFINED_FOR_KC_SETS
+J25_K30_C023,opposite_parent,parent_residual,3,3,3,0,11178.0,0.00026838432635534085,DEFINED_FOR_KC_SETS
+J25_K30_C023,other_KC,mixed_member,554,446,446,0,68110.0,0.006548230803112612,DEFINED_FOR_KC_SETS
+J25_K30_C023,other_KC,opposite_parent,2714,2227,2227,0,671370.0,0.0033170978744954346,DEFINED_FOR_KC_SETS
+J25_K30_C023,other_KC,parent_hit,1317,1146,1146,0,384335.0,0.0029817737130368037,DEFINED_FOR_KC_SETS
+J25_K30_C023,other_KC,parent_residual,1313,1090,1090,0,394065.0,0.0027660411353456916,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_hit,mixed_member,397,290,290,0,1106.0,0.26220614828209765,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_hit,non_KC,19591,9396,9396,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,parent_hit,opposite_parent,25,21,21,0,10902.0,0.001926252063841497,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_hit,other_KC,1272,1090,1090,0,384335.0,0.0028360674932025446,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_hit,parent_hit,2642,1953,1953,0,6162.0,0.3169425511197663,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_hit,parent_residual,1005,831,831,0,6399.0,0.12986404125644632,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_residual,mixed_member,83,67,67,0,1134.0,0.059082892416225746,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_residual,non_KC,19097,9162,9162,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C023,parent_residual,opposite_parent,4,4,4,0,11178.0,0.0003578457684737878,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_residual,other_KC,1215,1005,1005,0,394065.0,0.002550340679837083,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_residual,parent_hit,982,804,804,0,6399.0,0.1256446319737459,DEFINED_FOR_KC_SETS
+J25_K30_C023,parent_residual,parent_residual,2410,1773,1773,0,6480.0,0.27361111111111114,DEFINED_FOR_KC_SETS
+J25_K30_C024,mixed_member,mixed_member,62,44,44,0,110.0,0.4,DEFINED_FOR_KC_SETS
+J25_K30_C024,mixed_member,non_KC,2404,1141,1141,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,mixed_member,other_KC,149,128,128,0,53548.0,0.002390378725629342,DEFINED_FOR_KC_SETS
+J25_K30_C024,mixed_member,parent_hit,273,206,206,0,781.0,0.26376440460947503,DEFINED_FOR_KC_SETS
+J25_K30_C024,mixed_member,parent_residual,48,40,40,0,979.0,0.04085801838610827,DEFINED_FOR_KC_SETS
+J25_K30_C024,non_KC,mixed_member,762,290,290,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,non_KC,opposite_parent,11562,4162,4162,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,non_KC,parent_hit,5072,1844,1844,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,non_KC,parent_residual,6407,2615,2615,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,opposite_parent,non_KC,34254,15788,15788,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,opposite_parent,opposite_parent,7825,5360,5360,0,18906.0,0.2835078810959484,DEFINED_FOR_KC_SETS
+J25_K30_C024,opposite_parent,other_KC,2882,2229,2229,0,671784.0,0.0033180307956128755,DEFINED_FOR_KC_SETS
+J25_K30_C024,opposite_parent,parent_hit,3,3,3,0,9798.0,0.0003061849357011635,DEFINED_FOR_KC_SETS
+J25_K30_C024,opposite_parent,parent_residual,12,11,11,0,12282.0,0.0008956196059273734,DEFINED_FOR_KC_SETS
+J25_K30_C024,other_KC,mixed_member,218,186,186,0,53548.0,0.0034735190856801375,DEFINED_FOR_KC_SETS
+J25_K30_C024,other_KC,opposite_parent,2716,2229,2229,0,671784.0,0.0033180307956128755,DEFINED_FOR_KC_SETS
+J25_K30_C024,other_KC,parent_hit,654,577,577,0,345628.0,0.0016694249308505098,DEFINED_FOR_KC_SETS
+J25_K30_C024,other_KC,parent_residual,2072,1731,1731,0,433252.0,0.003995365283945602,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_hit,mixed_member,296,220,220,0,781.0,0.28169014084507044,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_hit,non_KC,16569,8012,8012,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,parent_hit,opposite_parent,4,4,4,0,9798.0,0.0004082465809348847,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_hit,other_KC,580,517,517,0,345628.0,0.0014958278843149283,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_hit,parent_hit,2252,1644,1644,0,4970.0,0.33078470824949696,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_hit,parent_residual,1004,824,824,0,6319.0,0.13040037980693148,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_residual,mixed_member,78,65,65,0,979.0,0.06639427987742594,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_residual,non_KC,22119,10546,10546,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C024,parent_residual,opposite_parent,25,21,21,0,12282.0,0.001709819247679531,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_residual,other_KC,2013,1650,1650,0,433252.0,0.003808407116412619,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_residual,parent_hit,1007,835,835,0,6319.0,0.13214116157619876,DEFINED_FOR_KC_SETS
+J25_K30_C024,parent_residual,parent_residual,2776,2058,2058,0,7832.0,0.26276813074565886,DEFINED_FOR_KC_SETS
+J25_K30_C027,non_KC,opposite_parent,7389,2552,2552,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C027,non_KC,parent_hit,8058,2695,2695,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C027,opposite_parent,non_KC,14248,7304,7304,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C027,opposite_parent,opposite_parent,6476,2813,2813,0,3660.0,0.7685792349726775,DEFINED_FOR_KC_SETS
+J25_K30_C027,opposite_parent,other_KC,832,699,699,0,307989.0,0.002269561575251064,DEFINED_FOR_KC_SETS
+J25_K30_C027,other_KC,opposite_parent,1261,994,994,0,307989.0,0.0032273879911295534,DEFINED_FOR_KC_SETS
+J25_K30_C027,other_KC,parent_hit,1197,1011,1011,0,338283.0,0.0029886219526254645,DEFINED_FOR_KC_SETS
+J25_K30_C027,parent_hit,non_KC,16304,7336,7336,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C027,parent_hit,other_KC,807,683,683,0,338283.0,0.0020190195782820893,DEFINED_FOR_KC_SETS
+J25_K30_C027,parent_hit,parent_hit,7822,3455,3455,0,4422.0,0.7813206693803709,DEFINED_FOR_KC_SETS
+J25_K30_C029,non_KC,opposite_parent,8058,2695,2695,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C029,non_KC,parent_hit,7389,2552,2552,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C029,opposite_parent,non_KC,16304,7336,7336,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C029,opposite_parent,opposite_parent,7822,3455,3455,0,4422.0,0.7813206693803709,DEFINED_FOR_KC_SETS
+J25_K30_C029,opposite_parent,other_KC,807,683,683,0,338283.0,0.0020190195782820893,DEFINED_FOR_KC_SETS
+J25_K30_C029,other_KC,opposite_parent,1197,1011,1011,0,338283.0,0.0029886219526254645,DEFINED_FOR_KC_SETS
+J25_K30_C029,other_KC,parent_hit,1261,994,994,0,307989.0,0.0032273879911295534,DEFINED_FOR_KC_SETS
+J25_K30_C029,parent_hit,non_KC,14248,7304,7304,0,,,NON_KC_POPULATION_DENOMINATOR_UNSPECIFIED
+J25_K30_C029,parent_hit,other_KC,832,699,699,0,307989.0,0.002269561575251064,DEFINED_FOR_KC_SETS
+J25_K30_C029,parent_hit,parent_hit,6476,2813,2813,0,3660.0,0.7685792349726775,DEFINED_FOR_KC_SETS

flywire_kc_atlas/entries.csv

@@ -0,0 +1,18 @@
+entry_id,entry_kind,evidence_status,parent_type,side,member_n,parent_hit_n,parent_n,residual_n,mixed_n,opposite_parent_n,parent_coverage,purity,mapped_type,mapped_parent_n,mapped_residual_n,mapped_parent_coverage,secondary_parent_status
+CM012,FROZEN_STABLE8,stable_main,KCapbp-m,right,163,160,174,14,3,164,0.9195402298850575,0.9815950920245399,KCa'b'-m,174,14,0.9195402298850575,DEFINED_WITHIN_COARSE_PARENT
+CM014,FROZEN_STABLE8,stable_main,KCapbp-m,left,152,152,164,12,0,174,0.926829268292683,1.0,KCa'b'-m,164,12,0.926829268292683,DEFINED_WITHIN_COARSE_PARENT
+CM016,FROZEN_STABLE8,stable_main,KCab,right,147,147,799,652,0,844,0.18397997496871088,1.0,KCab-s,310,163,0.47419354838709676,DEFINED_WITHIN_COARSE_PARENT
+CM019,FROZEN_STABLE8,stable_main,KCapbp-ap1,left,132,132,148,16,0,132,0.8918918918918919,1.0,KCa'b'-ap1,148,16,0.8918918918918919,DEFINED_WITHIN_COARSE_PARENT
+CM020,FROZEN_STABLE8,stable_main,KCapbp-ap1,right,129,121,132,11,8,148,0.9166666666666666,0.937984496124031,KCa'b'-ap1,132,11,0.9166666666666666,DEFINED_WITHIN_COARSE_PARENT
+CM022,FROZEN_STABLE8,stable_main,KCab,left,114,114,844,730,0,799,0.13507109004739337,1.0,KCab-s,311,197,0.3665594855305466,DEFINED_WITHIN_COARSE_PARENT
+CM031,FROZEN_STABLE8,stable_main,KCab-p,left,67,67,67,0,0,61,1.0,1.0,KCab-p,67,0,1.0,DEFINED_WITHIN_COARSE_PARENT
+CM033,FROZEN_STABLE8,stable_main,KCab-p,right,61,61,61,0,0,67,1.0,1.0,KCab-p,61,0,1.0,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C014,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-m,right,162,159,174,15,3,164,0.9137931034482759,0.9814814814814815,KCa'b'-m,174,15,0.9137931034482759,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C015,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-m,left,152,152,164,12,0,174,0.926829268292683,1.0,KCa'b'-m,164,12,0.926829268292683,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C016,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCg-d,left,137,130,147,17,7,148,0.8843537414965986,0.948905109489051,KCg-d,147,17,0.8843537414965986,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C017,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-ap1,left,132,132,148,16,0,132,0.8918918918918919,1.0,KCa'b'-ap1,148,16,0.8918918918918919,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C018,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-ap1,right,129,121,132,11,8,148,0.9166666666666666,0.937984496124031,KCa'b'-ap1,132,11,0.9166666666666666,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C023,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-ap2,right,93,79,160,81,14,138,0.49375,0.8494623655913979,KCa'b'-ap2,160,81,0.49375,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C024,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCapbp-ap2,right,82,71,160,89,11,138,0.44375,0.8658536585365854,KCa'b'-ap2,160,89,0.44375,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C027,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCab-p,left,67,67,67,0,0,61,1.0,1.0,KCab-p,67,0,1.0,DEFINED_WITHIN_COARSE_PARENT
+J25_K30_C029,CROSS_METHOD_CONSENSUS,DESCRIPTIVE_ONLY,KCab-p,right,61,61,61,0,0,67,1.0,1.0,KCab-p,61,0,1.0,DEFINED_WITHIN_COARSE_PARENT

flywire_kc_atlas/parent_layer_diagnostics.csv

@@ -0,0 +1,35 @@
+entry_id,parent_layer,candidate_n,parent_n,residual_n,candidate_internal_synapses,residual_internal_synapses,candidate_to_residual_synapses,residual_to_candidate_synapses,candidate_internal_directed_pairs,residual_internal_directed_pairs,candidate_to_residual_directed_pairs,residual_to_candidate_directed_pairs,candidate_density,residual_density,candidate_to_residual_density,residual_to_candidate_density,weighted_cut,weighted_volume_candidate,weighted_volume_residual,conductance,excluded_autapse_synapses,candidate_soma_pair_distance_q25_um,candidate_soma_pair_distance_median_um,candidate_soma_pair_distance_q75_um,residual_soma_pair_distance_q25_um,residual_soma_pair_distance_median_um,residual_soma_pair_distance_q75_um
+CM012,coarse,160,174,14,9724,87,522,537,7238,64,415,395,0.2845125786163522,0.3516483516483517,0.18526785714285715,0.17633928571428573,1059,20507,1233,0.8588807785888077,0,25.965245770395317,62.50927710051509,78.7500288222149,33.64325953309441,62.75455017765643,79.78581002050171
+CM012,mapped_within_coarse,160,174,14,9724,87,522,537,7238,64,415,395,0.2845125786163522,0.3516483516483517,0.18526785714285715,0.17633928571428573,1059,20507,1233,0.8588807785888077,0,25.965245770395317,62.50927710051509,78.7500288222149,33.64325953309441,62.75455017765643,79.78581002050171
+CM014,coarse,152,164,12,11405,132,711,607,7863,66,486,434,0.34258452422446845,0.5,0.26644736842105265,0.23793859649122806,1318,24128,1582,0.8331226295828066,0,35.79651366628612,62.29455257078234,84.48490667810292,41.316898603531854,68.65130568313381,91.20217329036598
+CM014,mapped_within_coarse,152,164,12,11405,132,711,607,7863,66,486,434,0.34258452422446845,0.5,0.26644736842105265,0.23793859649122806,1318,24128,1582,0.8331226295828066,0,35.79651366628612,62.29455257078234,84.48490667810292,41.316898603531854,68.65130568313381,91.20217329036598
+CM016,coarse,147,799,652,10979,55783,3513,3244,7051,41873,2847,2661,0.32853415338738234,0.09865190881418864,0.029704519844747715,0.027763866282709403,6757,28715,118323,0.2353125544140693,0,27.552511605586982,61.01157293497683,81.264215531309,24.39167858101754,49.674524658017646,65.42735241430836
+CM016,mapped_within_coarse,147,310,163,10979,8570,2852,2669,7051,6116,2241,2141,0.32853415338738234,0.2316140271150496,0.09352698134468511,0.08935353282417262,5521,27479,22661,0.24363443802127002,0,27.552511605586982,61.01157293497683,81.264215531309,26.67289556235575,54.890151830724626,69.78109934660134
+CM019,coarse,132,148,16,6976,191,302,272,5324,112,250,215,0.30788804071246817,0.4666666666666667,0.11837121212121213,0.10179924242424243,574,14526,956,0.600418410041841,0,35.467834310531835,59.292676916362666,78.5988546116335,17.926698105479876,37.59889568571826,54.27743181168289
+CM019,mapped_within_coarse,132,148,16,6976,191,302,272,5324,112,250,215,0.30788804071246817,0.4666666666666667,0.11837121212121213,0.10179924242424243,574,14526,956,0.600418410041841,0,35.467834310531835,59.292676916362666,78.5988546116335,17.926698105479876,37.59889568571826,54.27743181168289
+CM020,coarse,121,132,11,5104,62,195,126,3971,44,163,106,0.2734848484848485,0.4,0.12246431254695718,0.07963936889556725,321,10529,445,0.7213483146067415,0,27.63727177524414,67.90336331968734,85.45287442365837,17.14468650040851,31.018529945824294,67.2901811027736
+CM020,mapped_within_coarse,121,132,11,5104,62,195,126,3971,44,163,106,0.2734848484848485,0.4,0.12246431254695718,0.07963936889556725,321,10529,445,0.7213483146067415,0,27.63727177524414,67.90336331968734,85.45287442365837,17.14468650040851,31.018529945824294,67.2901811027736
+CM022,coarse,114,844,730,7916,63972,3441,3127,4759,47766,2838,2536,0.36943021269989135,0.08975703252719995,0.034102379235760635,0.030473443883681808,6568,22400,134512,0.2932142857142857,0,29.824948482771948,49.44986891792535,69.33552324746672,27.19376987473417,49.82494796786047,64.22417189812572
+CM022,mapped_within_coarse,114,311,197,7916,12490,3117,2820,4759,8561,2527,2247,0.36943021269989135,0.22171863669325598,0.11252115059221658,0.10005343307507347,5937,21769,30917,0.2727272727272727,0,29.824948482771948,49.44986891792535,69.33552324746672,28.697655615633103,47.974185648050735,64.97293269871497
+CM031,coarse,67,67,0,7822,0,0,0,3455,0,0,0,0.7813206693803709,,,,0,15644,0,,0,32.83829333982888,53.078926289064995,69.12647420459386,,,
+CM031,mapped_within_coarse,67,67,0,7822,0,0,0,3455,0,0,0,0.7813206693803709,,,,0,15644,0,,0,32.83829333982888,53.078926289064995,69.12647420459386,,,
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+CM033,mapped_within_coarse,61,61,0,6476,0,0,0,2813,0,0,0,0.7685792349726775,,,,0,12952,0,,0,22.044165172312226,65.29057072115248,81.7621190028158,,,
+J25_K30_C014,coarse,159,174,15,9655,104,552,559,7180,72,444,416,0.2858052702810286,0.34285714285714286,0.1861635220125786,0.17442348008385744,1111,20421,1319,0.8423047763457164,0,25.928627576483926,62.300685710512035,78.60902838732963,34.80881175794427,65.40828620289632,82.5609240258368
+J25_K30_C014,mapped_within_coarse,159,174,15,9655,104,552,559,7180,72,444,416,0.2858052702810286,0.34285714285714286,0.1861635220125786,0.17442348008385744,1111,20421,1319,0.8423047763457164,0,25.928627576483926,62.300685710512035,78.60902838732963,34.80881175794427,65.40828620289632,82.5609240258368
+J25_K30_C015,coarse,152,164,12,11405,132,711,607,7863,66,486,434,0.34258452422446845,0.5,0.26644736842105265,0.23793859649122806,1318,24128,1582,0.8331226295828066,0,35.79651366628612,62.29455257078234,84.48490667810292,41.316898603531854,68.65130568313381,91.20217329036598
+J25_K30_C015,mapped_within_coarse,152,164,12,11405,132,711,607,7863,66,486,434,0.34258452422446845,0.5,0.26644736842105265,0.23793859649122806,1318,24128,1582,0.8331226295828066,0,35.79651366628612,62.29455257078234,84.48490667810292,41.316898603531854,68.65130568313381,91.20217329036598
+J25_K30_C016,coarse,130,147,17,5206,61,300,278,3866,42,248,229,0.23053070960047703,0.15441176470588236,0.11221719457013575,0.10361990950226245,578,10990,700,0.8257142857142857,0,24.540682957081696,43.73531442667357,58.14930575681882,14.88468627673539,61.18808771730254,82.79039831430633
+J25_K30_C016,mapped_within_coarse,130,147,17,5206,61,300,278,3866,42,248,229,0.23053070960047703,0.15441176470588236,0.11221719457013575,0.10361990950226245,578,10990,700,0.8257142857142857,0,24.540682957081696,43.73531442667357,58.14930575681882,14.88468627673539,61.18808771730254,82.79039831430633
+J25_K30_C017,coarse,132,148,16,6976,191,302,272,5324,112,250,215,0.30788804071246817,0.4666666666666667,0.11837121212121213,0.10179924242424243,574,14526,956,0.600418410041841,0,35.467834310531835,59.292676916362666,78.5988546116335,17.926698105479876,37.59889568571826,54.27743181168289
+J25_K30_C017,mapped_within_coarse,132,148,16,6976,191,302,272,5324,112,250,215,0.30788804071246817,0.4666666666666667,0.11837121212121213,0.10179924242424243,574,14526,956,0.600418410041841,0,35.467834310531835,59.292676916362666,78.5988546116335,17.926698105479876,37.59889568571826,54.27743181168289
+J25_K30_C018,coarse,121,132,11,5104,62,195,126,3971,44,163,106,0.2734848484848485,0.4,0.12246431254695718,0.07963936889556725,321,10529,445,0.7213483146067415,0,27.63727177524414,67.90336331968734,85.45287442365837,17.14468650040851,31.018529945824294,67.2901811027736
+J25_K30_C018,mapped_within_coarse,121,132,11,5104,62,195,126,3971,44,163,106,0.2734848484848485,0.4,0.12246431254695718,0.07963936889556725,321,10529,445,0.7213483146067415,0,27.63727177524414,67.90336331968734,85.45287442365837,17.14468650040851,31.018529945824294,67.2901811027736
+J25_K30_C023,coarse,79,160,81,2642,2410,1005,982,1953,1773,831,804,0.3169425511197663,0.27361111111111114,0.12986404125644632,0.1256446319737459,1987,7271,6807,0.291905391508741,0,30.002693212443425,63.46278531549023,82.36858711911964,26.76472551579164,51.05259236203085,76.23106665065366
+J25_K30_C023,mapped_within_coarse,79,160,81,2642,2410,1005,982,1953,1773,831,804,0.3169425511197663,0.27361111111111114,0.12986404125644632,0.1256446319737459,1987,7271,6807,0.291905391508741,0,30.002693212443425,63.46278531549023,82.36858711911964,26.76472551579164,51.05259236203085,76.23106665065366
+J25_K30_C024,coarse,71,160,89,2252,2776,1004,1007,1644,2058,824,835,0.33078470824949696,0.26276813074565886,0.13040037980693148,0.13214116157619876,2011,6515,7563,0.308672294704528,0,27.218332057640826,57.31011498854279,76.05388405597702,28.61215028500346,60.93846696846869,82.04342167367811
+J25_K30_C024,mapped_within_coarse,71,160,89,2252,2776,1004,1007,1644,2058,824,835,0.33078470824949696,0.26276813074565886,0.13040037980693148,0.13214116157619876,2011,6515,7563,0.308672294704528,0,27.218332057640826,57.31011498854279,76.05388405597702,28.61215028500346,60.93846696846869,82.04342167367811
+J25_K30_C027,coarse,67,67,0,7822,0,0,0,3455,0,0,0,0.7813206693803709,,,,0,15644,0,,0,32.83829333982888,53.078926289064995,69.12647420459386,,,
+J25_K30_C027,mapped_within_coarse,67,67,0,7822,0,0,0,3455,0,0,0,0.7813206693803709,,,,0,15644,0,,0,32.83829333982888,53.078926289064995,69.12647420459386,,,
+J25_K30_C029,coarse,61,61,0,6476,0,0,0,2813,0,0,0,0.7685792349726775,,,,0,12952,0,,0,22.044165172312226,65.29057072115248,81.7621190028158,,,
+J25_K30_C029,mapped_within_coarse,61,61,0,6476,0,0,0,2813,0,0,0,0.7685792349726775,,,,0,12952,0,,0,22.044165172312226,65.29057072115248,81.7621190028158,,,

flywire_kc_atlas/representative_routes.csv

@@ -0,0 +1,18 @@
+entry_id,root_id,status,family,upstream_id,upstream_type,downstream_id,downstream_type,input_synapse_pairs,output_synapse_pairs,endpoint_combinations,median_cable_um,example_path_cable_um
+CM012,720575940625163139,AVAILABLE,ALPN,720575940638624189,DM2_lPN,720575940624694503,MBON03,9,28,252,253.58352083232364,209.162816443399
+CM014,720575940614326439,AVAILABLE,ALPN,720575940611079236,VA2_adPN,720575940624590316,MBON03,17,22,374,264.30189665924775,219.47289727178057
+CM016,720575940626044924,AVAILABLE,ALPN,720575940630547909,VA1d_adPN,720575940622997453,MBON18,26,11,286,290.17585104974853,276.88719990763053
+CM019,720575940622998920,AVAILABLE,ALPN,720575940639680957,VA7m_lPN,720575940628734376,MBON04,12,9,108,245.65854419578682,232.8267044242613
+CM020,720575940659577217,AVAILABLE,ALPN,720575940608293129,VP2_adPN,720575940624694503,MBON03,23,19,437,308.4800259873854,278.58960498468167
+CM022,720575940620420129,AVAILABLE,ALPN,720575940618308825,DP1m_adPN,720575940632535756,MBON14,19,12,228,304.03815649486955,271.9476207894422
+CM031,720575940610872418,AVAILABLE,VISUAL_PROJECTION,720575940631298860,aMe26,720575940638028607,MBON06,5,23,115,320.3802145801373,286.1568770019814
+CM033,720575940634514533,AVAILABLE,VISUAL_PROJECTION,720575940612495331,aMe26,720575940628783363,MBON07,7,14,98,259.79929270204525,236.34040696972747
+J25_K30_C014,720575940645236078,AVAILABLE,ALPN,720575940619071005,DM1_lPN,720575940624694503,MBON03,10,14,140,282.95310134187235,233.90600711563596
+J25_K30_C015,720575940614326439,AVAILABLE,ALPN,720575940611079236,VA2_adPN,720575940624590316,MBON03,17,22,374,264.30189665924775,219.47289727178057
+J25_K30_C016,720575940626316974,AVAILABLE,VISUAL_PROJECTION,720575940637511525,MTe26,720575940629856515,MBON09,21,9,189,242.46797451263598,223.96880278792585
+J25_K30_C017,720575940622998920,AVAILABLE,ALPN,720575940639680957,VA7m_lPN,720575940628734376,MBON04,12,9,108,245.65854419578682,232.8267044242613
+J25_K30_C018,720575940659577217,AVAILABLE,ALPN,720575940608293129,VP2_adPN,720575940624694503,MBON03,23,19,437,308.4800259873854,278.58960498468167
+J25_K30_C023,720575940628404188,AVAILABLE,ALPN,720575940617642832,VM4_lvPN,720575940624694503,MBON03,7,22,154,291.2795238293219,264.4714009954714
+J25_K30_C024,720575940626225173,AVAILABLE,ALPN,720575940625493400,DM6_adPN,720575940626315010,MBON13,4,12,48,215.68660249359172,206.8842550457445
+J25_K30_C027,720575940610872418,AVAILABLE,VISUAL_PROJECTION,720575940631298860,aMe26,720575940638028607,MBON06,5,23,115,320.3802145801373,286.1568770019814
+J25_K30_C029,720575940634514533,AVAILABLE,VISUAL_PROJECTION,720575940612495331,aMe26,720575940628783363,MBON07,7,14,98,259.79929270204525,236.34040696972747

flywire_kc_atlas/representatives.csv

@@ -0,0 +1,18 @@
+entry_id,root_id,rule
+CM012,720575940625163139,Nearest median parent-hit cable length; lexical root tie
+CM014,720575940614326439,Nearest median parent-hit cable length; lexical root tie
+CM016,720575940626044924,Nearest median parent-hit cable length; lexical root tie
+CM019,720575940622998920,Nearest median parent-hit cable length; lexical root tie
+CM020,720575940659577217,Nearest median parent-hit cable length; lexical root tie
+CM022,720575940620420129,Nearest median parent-hit cable length; lexical root tie
+CM031,720575940610872418,Nearest median parent-hit cable length; lexical root tie
+CM033,720575940634514533,Nearest median parent-hit cable length; lexical root tie
+J25_K30_C014,720575940645236078,Preserved existing median-cable representative
+J25_K30_C015,720575940614326439,Preserved existing median-cable representative
+J25_K30_C016,720575940626316974,Preserved existing median-cable representative
+J25_K30_C017,720575940622998920,Preserved existing median-cable representative
+J25_K30_C018,720575940659577217,Preserved existing median-cable representative
+J25_K30_C023,720575940628404188,Preserved existing median-cable representative
+J25_K30_C024,720575940626225173,Preserved existing median-cable representative
+J25_K30_C027,720575940610872418,Preserved existing median-cable representative
+J25_K30_C029,720575940634514533,Preserved existing median-cable representative

malecns/malecns_annotations_normalized.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:bebab58e743bb78b7711c76287305534205092d000c1ebc6fdb0cf5cbb351e49
+size 1579892

malecns/malecns_directed_edges_normalized.parquet

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:6375b28355c4f1ccd7c9b486ee5b93e5fb5bc43e8f5337cad5be7aa04569684d
+size 2142834

malecns/malecns_provenance.json

@@ -0,0 +1,20 @@
+{
+  "adapter": "bio_fly.male_cns_adapter",
+  "adapter_version": "0.1.0",
+  "config": {
+    "annotations": "audit/meeting_revision_20261027/reproduced_structure/MaleCNS_v1_0_source_annotations.parquet",
+    "dataset_version": "MaleCNS_v1.0",
+    "edges": "audit/meeting_revision_20261027/reproduced_structure/MaleCNS_v1_0_annotated_input_edges.parquet",
+    "source_release": "male-cns-v1.0-minconf-0.5",
+    "swc_dir": "data/raw/male_cns_v0_9/kc_swc"
+  },
+  "output_hashes": {
+    "annotations": "bebab58e743bb78b7711c76287305534205092d000c1ebc6fdb0cf5cbb351e49",
+    "edges": "6375b28355c4f1ccd7c9b486ee5b93e5fb5bc43e8f5337cad5be7aa04569684d"
+  },
+  "source_hashes": {
+    "annotations": "65d0959068ac9987d105e24831ba073bffbfad07350f0cfcfc400c53d827e9f3",
+    "edges": "b4832e8d5056f231068242f2075c5e1795409c16e4fd62789e1bcc360b75a865"
+  },
+  "status": "VERIFIED_REAL_DATA_WITH_MORPHOLOGY_GAP"
+}

malecns/malecns_source_audit.json

@@ -0,0 +1,173 @@
+{
+  "annotation_schema": [
+    "KC_family",
+    "assignedOlHex1",
+    "assignedOlHex2",
+    "birthtime",
+    "body",
+    "body_id",
+    "cell_type",
+    "celltype_predicted_nt",
+    "celltype_predicted_nt_confidence",
+    "celltype_total_nt_predictions",
+    "class",
+    "coarse_class",
+    "confidence",
+    "consensus_nt",
+    "dimorphism",
+    "entryNerve",
+    "exitNerve",
+    "flywireType",
+    "fruDsx",
+    "ground_truth",
+    "group",
+    "id",
+    "instance",
+    "itoleeHl",
+    "mancBodyid",
+    "mancGroup",
+    "mancSerial",
+    "mancType",
+    "matched_hemibrain_type",
+    "matchingNotes",
+    "mcnsSerial",
+    "nt_table_cell_type",
+    "receptorType",
+    "rootSide",
+    "serialMotif",
+    "side",
+    "somaLocation",
+    "somaNeuromere",
+    "somaSide",
+    "status",
+    "statusLabel",
+    "subclass",
+    "superclass",
+    "supertype",
+    "synonyms",
+    "top_nt",
+    "tosomaLocation",
+    "total_nt_predictions",
+    "trumanHl",
+    "type_mapping_ambiguous",
+    "vfbId"
+  ],
+  "claims": {
+    "branch_level_cable_mapping": "BLOCKED_MISSING_DATA",
+    "contact_level_synapse_placement": "BLOCKED_MISSING_DATA",
+    "cross_connectome_unit_reuse": "NOT_TESTED",
+    "directed_aggregate_structure": "VERIFIED_REAL_DATA",
+    "synaptic_polarity_or_conductance": "NOT_IDENTIFIABLE_FROM_INPUT"
+  },
+  "counts": {
+    "aggregate_synapse_count": 2610758,
+    "annotation_null_body_ids": 24561,
+    "annotation_rows": 211577,
+    "edge_rows": 944638,
+    "kc_annotation_rows": 4064,
+    "kc_unique_body_ids": 4064,
+    "positive_edge_rows": 944638,
+    "post_ids_in_annotation": 4072,
+    "pre_ids_in_annotation": 9748,
+    "swc_ids_matching_annotation": 886,
+    "swc_ids_matching_edge": 886,
+    "unique_annotated_body_ids": 187016,
+    "unique_edge_body_ids": 41105
+  },
+  "dataset_version": "MaleCNS_v1.0",
+  "edge_schema": [
+    "direction",
+    "post",
+    "post_id",
+    "pre",
+    "pre_id",
+    "source_class",
+    "source_confidence",
+    "source_side",
+    "source_top_nt",
+    "synapses",
+    "target_class",
+    "target_family",
+    "target_side"
+  ],
+  "inputs": {
+    "annotations": {
+      "path": "audit/meeting_revision_20261027/reproduced_structure/MaleCNS_v1_0_source_annotations.parquet",
+      "rows": 211577,
+      "sha256": "65d0959068ac9987d105e24831ba073bffbfad07350f0cfcfc400c53d827e9f3"
+    },
+    "edges": {
+      "path": "audit/meeting_revision_20261027/reproduced_structure/MaleCNS_v1_0_annotated_input_edges.parquet",
+      "rows": 944638,
+      "sha256": "b4832e8d5056f231068242f2075c5e1795409c16e4fd62789e1bcc360b75a865"
+    }
+  },
+  "labels": {
+    "coarse_class": {
+      "ALPN": 686,
+      "APL": 2,
+      "DPM": 2,
+      "KC": 4064,
+      "MBON": 97,
+      "PAM": 316,
+      "PPL1": 16,
+      "other": 206394
+    },
+    "kc_family": {
+      "alpha_beta": 1810,
+      "alpha_prime_beta_prime": 695,
+      "gamma": 1557,
+      "unresolved": 207515
+    },
+    "side": {
+      "left": 75215,
+      "midline": 392,
+      "right": 75119,
+      "unknown": 60851
+    }
+  },
+  "morphology": {
+    "body_ids_are_filename_stems": true,
+    "complete_files": 886,
+    "contact_to_branch_mapping": "BLOCKED_MISSING_DATA",
+    "coordinate_units": "UNKNOWN_SOURCE_UNITS",
+    "node_count_max": 3844,
+    "node_count_median": 1020.5,
+    "node_count_min": 760,
+    "partial_file_names": [
+      ".49545.swc.part",
+      ".51391.swc.part",
+      ".51583.swc.part",
+      ".52594.swc.part",
+      ".52972.swc.part",
+      ".53178.swc.part",
+      ".53271.swc.part",
+      ".53688.swc.part",
+      ".56274.swc.part",
+      ".57152.swc.part",
+      ".57977.swc.part",
+      ".60349.swc.part",
+      ".60729.swc.part",
+      ".60768.swc.part",
+      ".60787.swc.part",
+      ".61555.swc.part",
+      ".62641.swc.part",
+      ".62643.swc.part",
+      ".64310.swc.part",
+      ".67774.swc.part",
+      ".68265.swc.part",
+      ".68287.swc.part",
+      ".68339.swc.part",
+      ".68428.swc.part",
+      ".68487.swc.part",
+      ".68495.swc.part",
+      ".68531.swc.part",
+      ".68635.swc.part"
+    ],
+    "partial_files": 28,
+    "path": "data/raw/male_cns_v0_9/kc_swc",
+    "status": "PARTIAL_REAL_DATA"
+  },
+  "source_release": "male-cns-v1.0-minconf-0.5",
+  "status": "VERIFIED_REAL_DATA_WITH_MORPHOLOGY_GAP"
+}

p0_corrected_20261030/P0_REPORT.md

@@ -0,0 +1,59 @@
+# P0：指标修正与结构证据审计
+
+2026-10-30。按用户提供的P0文字执行；本机未找到`/root/codex_kc_nature.sh`，未假装运行该脚本。复用现有模型和Teacher，修正评估及搜索契约；未重写模拟器、未改变候选、未下载数据、未自动推送。所有动力学新数值均为FIXTURE_TEST_ONLY。
+
+## 已完成
+
+- 旧源码保存到`before/`，历史结果原位保留；`invalidated_results.csv`逐文件列出失效指标、原因及哈希。
+- 电压/电导分开；逐时刻对齐；一步预测用所有留出Teacher状态；无响应保留NA并计入FP/FN；非有限预测使评估失败，不静默忽略；负电导比例单独记录。
+- 梯度比较同一事件、幅度、时刻和读出；有限差分用两档epsilon，并测试未来输入的因果零梯度。
+- 搜索统一为25ms末端房室电压到目标的平方误差；刺激16ms、K=2、每点幅度1。松弛幅度在[0,1]且和为K，最终精确Top-K；三方法各25次Teacher候选评估，梯度每个起点40步。每个候选均由Teacher重评；几何启发式仅依树距离，不能把它写成旧版Teacher单点启发式的同一实验。
+- 保留原6训练/3留出刺激、seed20261030、120epochs、Adam0.002；新增不学习的PhysicsOnly，记录训练与推理时间、模型权重和完整源码哈希。
+- 23项回归测试通过。两个独立进程复放，非计时模型指标、梯度和搜索输出一致，产物哈希校验通过。
+
+## 修正后的模型结果
+
+|模型|全部留出状态的一步电压RMSE|对齐多步电压RMSE|有效时延比较/测试刺激|
+|---|---:|---:|---:|
+|MLP|0.068539|5.823275|0/3|
+|Graph|0.213696|33.859930|0/3|
+|PhysicsResidual|0.000164|0.014663|3/3|
+|PhysicsOnly|0.00000244|0.00000815|3/3|
+
+电压单位mV。MLP/Graph均漏检3个参考graded-response，不能以NA时延说明表现良好。Graph负电导比例为1，MLP约0.417；数值有限不等于物理状态合法。PhysicsResidual与PhysicsOnly均未出现负电导。
+
+原PhysicsResidual多步4.58数值受错误广播和通道混算影响，旧梯度cosine约0.044的干预变量也不一致，均不再引用为模型失败证据。修正后该单例梯度相对L2误差约0.00706；但只有一个非零方向及一个未来事件控制，cosine=1并不证明普遍梯度准确。
+
+在相同25次Teacher候选评估下，最佳目标电压误差：几何2.313808、随机0.134327、梯度Top-K0.128074mV。梯度仅略优于随机的最佳值，不作优越性声明；重复提案均计费，唯一提案数分别25/19/14。每次完整基准生成9条Teacher轨迹、36次梯度参考求解、1次搜索目标求解和75次候选求解，共121次Teacher调用；复放不增加独立科学样本数。
+
+**解释：当前已知方程的小电缆上，不学习的物理参考最好。PhysicsResidual比纯数据Student准确，但没有证明比物理求解器更有必要、更快或更可泛化。** Teacher与PhysicsOnly采用同一分辨率与方程，该比较首先是正确性对照。不得把它写成真实KC或高分辨率代理成功。
+
+## 结构与数据审计
+
+173项检查通过，包括52候选冻结得分、coverage、成员保留率复算、stable8/965不变、20单元2125唯一成员、源哈希和ID往返。
+
+- 训练KC图234,964有向对，测试58,798对，直接重叠0；二者相加等于原293,762对。
+- 仅从训练图重建spectral32，与存档最大差1.57e-11。
+- 15,119条测试边的反向边在训练图中。它不是同方向边直接泄漏，但不是无向pair隔离或独立细胞检验；新协议需处理这类依赖。
+- 旧ap2协议明确说明结果已被查看，当前不能将该测试集重称为盲测。
+- 20单元仍为图发现，胞体/形态不在本协议发现输入；尺度条件稳定不等于旧clean61跨尺度稳定。
+- 已生成CM/SU成员交叉表。CM019与SU019分别132/104成员，不能混名；CM016与SU021为147/98，CM022与SU027为114/84。
+- MaleCNS本地输入边表944,638有向聚合对、2,610,758突触；不是全CNS总量。41,105端点body ID中31,355未出现在当前有效注释ID集合。保留unknown，不能归零或硬映射类型。
+- FlyWire和MaleCNS字符串ID经Parquet及实际Node.js JSON往返一致。
+
+## P1门槛
+
+允许继续做回顾性方案设计、完整parent特征清单与跨脑QC；暂不生成“独立确认了离散/混合组织”的新结论。必须先明确新评价集的历史使用情况、完整发现/拟合/筛选隔离，并修复跨脑注释覆盖。BANC已出现在本地既有分析，不应说本轮首次引入；其版本、原始数据和论文出处仍须分别核验。
+
+用户给出的2025/2026文献描述尚未完成本轮书目核对，标UNVERIFIED，不用于证明创新性或设计依赖。GitHub已发布版本仍有旧指标；本轮按要求不自动推送，后续发布必须带失效说明及新结果版本。
+
+## 复现
+
+```bash
+cd /unify/ydchen/unidit/bio_fly
+PYTHONPATH=simulation/src pytest -q simulation/tests/test_physics_guided_scientific_metrics.py simulation/tests/test_physics_guided_protocol.py simulation/tests/test_physics_guided_students.py simulation/tests/test_physics_guided_teacher.py simulation/tests/test_neuronmimic.py simulation/tests/test_male_cns_adapter.py simulation/tests/test_stable8_dynamic_cohesion.py
+PYTHONPATH=simulation/src python simulation/scripts/audit_nature_kc_p0.py
+PYTHONPATH=simulation/src python simulation/scripts/run_physics_guided_baseline.py --output-dir artifacts/nature_kc_20261030/p0_audit/fixture_v2_reproduction_new
+```
+
+基准拒绝覆盖已完成输出；复放须指定新目录。状态入口`P0_STATUS.json`；图件`figures/p0_corrected_baseline.pdf`；新结果`fixture_v2/results/`；完整输入哈希`source_manifest.json`和`fixture_v2/run_manifest.json`。

p0_corrected_20261030/P0_STATUS.json

@@ -0,0 +1,27 @@
+{
+  "stage": "P0",
+  "status": "DONE_WITH_BLOCKERS",
+  "protocol_version": "nature_kc_p0_metrics_v2",
+  "metrics_repair": "PASS",
+  "scientific_regression_tests": 23,
+  "structural_checks_passed": 173,
+  "seed_replay": "PASS",
+  "historical_invalidated_results": "invalidated_results.csv",
+  "historical_results_preserved": true,
+  "new_stable_units": 0,
+  "biological_validation": "NOT_PERFORMED",
+  "external_push": "NOT_PERFORMED",
+  "P1_gate": {
+    "retrospective_design_and_data_QC": "READY",
+    "confirmatory_structural_claims": "BLOCKED",
+    "reasons": [
+      "old held-out edges already used during development",
+      "cross-connectome endpoint annotation gaps",
+      "unverified user-supplied literature claims"
+    ]
+  },
+  "release_note": "Existing GitHub release still contains old metric implementation; fix local, no automatic push requested.",
+  "source_script": "simulation/scripts/finalize_nature_kc_p0.py",
+  "source_script_sha256": "eb0387c841316442f4ed24cefc41db735c5c2795d0bf301181f7af4981c0e709",
+  "code_commit": "f15ab12e1988000f71ec5e0ab138ab116f150e7d"
+}

p0_corrected_20261030/fixture_v2/config_snapshot.yaml

@@ -0,0 +1,28 @@
+status: FIXTURE_TEST_ONLY
+seed: 20261030
+teacher:
+  n_compartments: 12
+  dt_ms: 0.05
+  duration_ms: 80.0
+  tau_mem_ms: 12.0
+  tau_syn_ms: 4.0
+  leak_conductance: 1.0
+  axial_conductance: 0.35
+  capacitance: 1.0
+  resting_voltage: -65.0
+  synapse_reversal: 0.0
+  synapse_increment: 0.8
+  spike_threshold: -45.0
+students:
+  train_stimuli: 6
+  heldout_stimuli: 3
+  epochs: 120
+  optimizer: Adam
+  learning_rate: 0.002
+  rollout_readout_compartment: 11
+  latency_threshold_mv: -64.5
+active_search:
+  k: 2
+  target_readout_compartment: 11
+  target_time_ms: 25.0
+  methods: [random, structural_single_site, gradient_relaxation_topk]

p0_corrected_20261030/fixture_v2/models/Graph.pt

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p0_corrected_20261030/fixture_v2/models/MLP.pt

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p0_corrected_20261030/fixture_v2/models/PhysicsOnly.pt

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p0_corrected_20261030/fixture_v2/models/PhysicsResidual.pt

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p0_corrected_20261030/fixture_v2/results/gradient_check.csv

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p0_corrected_20261030/fixture_v2/results/student_comparison.csv

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p0_corrected_20261030/fixture_v2/run_manifest.json

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+{
+  "status": "FIXTURE_TEST_ONLY",
+  "protocol_version": "nature_kc_p0_metrics_v2",
+  "dataset_version": "synthetic_chain12_fixture_v1",
+  "seed": 20261030,
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+  "source_hashes": {
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+    "search_proposals": 0
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+    "epochs",
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+    "train_loss_final",
+    "parameter_count",
+    "gpu_peak_memory_mb",
+    "teacher_training_trajectories_shared",
+    "device",
+    "one_step_voltage_rmse",
+    "multi_step_voltage_rmse",
+    "one_step_conductance_rmse",
+    "multi_step_conductance_rmse",
+    "latency_error_ms",
+    "latency_valid_pairs",
+    "n_test_stimuli",
+    "teacher_response_count",
+    "student_response_count",
+    "response_tp",
+    "response_fp",
+    "response_fn",
+    "response_tn",
+    "graded_response_error",
+    "negative_conductance_fraction",
+    "finite_fraction",
+    "metric_version",
+    "voltage_sample_count",
+    "status"
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+  "stable_metric_sha256": "d6ee192e77ebfd593b7845643b2dfe811db060ec28413f5c1e4abeacb8e48f91",
+  "limitations": [
+    "one morphology and seed",
+    "mixed-state legacy training loss retained; evaluation channels separated",
+    "same-resolution exact-physics reference; no coarse-grid speedup or biology claim"
+  ],
+  "outputs": {
+    "config_snapshot.yaml": "7dca856d63db82fd72aa981d736f6a562edb32abf05cdcf35f0a2b454fe7d013",
+    "models/Graph.pt": "080db8bdfbc631a653f82e223a3ff790dda6387fc690b8807764cfd4803ec72b",
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+    "models/MLP.pt": "2f85508fd03d392e71971f3a29cbcaaca7ec427b58f232c23fe8e1a86218cadd",
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physics_teacher/teacher_protocol.json

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provenance/protocol.json

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+  "parents": "Primary parent=same-side frozen official type. Secondary within-parent matched hemibrain_type from pinned upstream annotation, only when all primary-hit members share one nonempty label; otherwise composition only. Keep full coarse residual and same-mapped-type residual separately. Audit alreadyobserved CM016147/310rightKCab-s andCM022114/311leftKCab-s alongside original147/799,114/844coarseKCab.",
+  "background": "Existing118102 registered whole-brain somata; exact same v783source annotation coordinates checked using[.004,.004,.04]um transforms. All5177 KC agree. Never present soma point cloud as brain surface or missing somata as absent neurons.",
+  "geometry": "Retain exact original branch IDs/segment fractions. Check source binaryhash, vertexrounding, edgeidentity, treeconnectivity, rawbranchlength and projectedendpointerror for everycell. Displayoriginalcontact coordinates, record mappingqualitycontinuously and prior<=2umflag; no newqualitycutoff.",
+  "features": "Per-cell and perbranch input/output counts, occupiedbranches, pathfromsoma-nearest quantiles, mappingerrors, originalmorphology, knowninputclasses/partnercounts. Perentry fullrole directional synapsecount/uniqueedge matrices and exact KCpossiblepair denominator excludingautapses. NonKC or outside-query denominators remainNA. No physiologicalprobability.",
+  "partial_parent_diagnostics": "CM016/CM022: candidate versus coarse residual and samehemibrain-type residual; pairwise soma distances; within-parent directed edgecounts,density; conductance after symmetrizing directedweighted graph, removeautapses. cut=sumAtoB+sumBtoA;volA=2internalA+cut;phi=cut/min(volA,volB). Report against coarse and mappedparents separately, no newnull/pvalues or boundarythresholds.",
+  "representatives": "For9prior entries preserve existing median-cable representative and selectedbranch. For8stable entries nearest median parent-hit cable length,ties lexicalroot; branch max min(in,out),then total,then branchID. Route family priority ALPN,then exactvisual_projection,thenAPL among availableinputs onthatfixedcell and exactMBONoutput; withinfamily selectmax min(legcounts),then total,then lexicalIDs. Selection uses no distances.",
+  "metricsinterpretation": "Known anatomical subtypes may explain apparent coarse-type subdivision; source hemibrain_type is a mapped annotation in this same FlyWire brain, not new independentconnectome replication. Residualdifferences are descriptive. Stable8/965 unchanged; newstable0.",
+  "validation": "Member/statushashes,allrawdirection/coordinates/branchlineage,all5177rawgeometry+lengthreplay,fullsynapse-endpointconservation,entryrole partition+edgecountconservation,known-type denominators,graphcut fixture,root/branch/route query,portablepayload hashreplay.",
+  "seed": 2026103005,
+  "randomness": "No stochastic scientific analysis; deterministiclexicaldisplay and checks.",
+  "evidence_tier": "DESCRIPTIVE_ONLY_EM_ANATOMY",
+  "model_version": "NONE_NO_NEURAL_SIMULATION"
+}

provenance/provenance_manifest.json

@@ -0,0 +1,60 @@
+{
+  "protocol_version": "kc_all5177_structural_atlas_v1_20261030",
+  "dataset_version": "FlyWire v783",
+  "connectome_snapshot": "frozen all-KC incident synapses and original geometry",
+  "annotation_snapshot": "f02717b7624e502f4c72443e986976feff2b563e",
+  "run_id": "all5177_structural_atlas_20261030",
+  "seed": 2026103005,
+  "model_version": "NONE_GEOMETRY_ONLY",
+  "code_commit": "b080cbfe2b2a88620238fda216045083e1d33a9f",
+  "sources": [
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/nature_methods_connectome/fine_structure_mechanism/runs/20261018_wu1018_frozen5177_review_v11/results_v9/all5177_evidence_atlas.parquet",
+      "sha256": "6ed285fbb921c593905572eb50e121b7c82db807fc4f7f29509f1b799e0350bf"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261019/registry/stable8_members.parquet",
+      "sha256": "01f7ab2dd5e8527f303cead2f8c89e8f92990b06020598ef5390dcd07c2af2eb"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/external/flywire_annotations_upstream/supplemental_files/Supplemental_file1_neuron_annotations.tsv",
+      "sha256": "533db093e12d8de350fd20875a967f8f74acace633ff22118eefff550d5dcbc1"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261026_spatial_units/registry/whole_brain_somata.parquet",
+      "sha256": "2228b34b23a5d1cd337b613cd90abbeaf5d3aff1d0854e2a1871c39a926299a6"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261029_structure_entries/registry/all5177_cells.parquet",
+      "sha256": "f663dce46e2a7464f54639a69d80bcface5003e09d612f24799e89931d231315"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261029_structure_entries/registry/entry_cells.parquet",
+      "sha256": "0aa5b633b2054de4505ce1754100cefd5d4aad7a00b458de76ac068fc036772e"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261029_structure_entries/registry/entries.csv",
+      "sha256": "cc4198e40b68c978b5a6cfee4138eaec313970de1dde117471ca6aa3a4378e95"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/nature_methods_connectome/fine_structure_mechanism/runs/20260929_flywire_atlas_completion_v2/results/all_KC_incident_synapses.parquet",
+      "sha256": "7e5b53b4113eabec97d33339492330139af97d06b72c9929f692ce19954b6342"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/nature_methods_connectome/fine_structure_mechanism/runs/20260929_flywire_atlas_completion_v2/results/synapse_branch_mapping.parquet",
+      "sha256": "190dade53484269c0e5cd51933a3d13e040119b09377d33495d3b2a458ef3a22"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/nature_methods_connectome/fine_structure_mechanism/runs/20260929_flywire_atlas_completion_v2/results/topological_branches.parquet",
+      "sha256": "a8d500742d98ed09c5c23b15d7226c5f68bb1c10072b482c41ad95298f74bd4b"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/artifacts/wu_20261030_all5177_structural_atlas/audit/protocol.json",
+      "sha256": "92987403780a425f2a586b34173fb66dbb8fd3645592bc1d32d7044a277af451"
+    },
+    {
+      "path": "/unify/ydchen/unidit/bio_fly/simulation/scripts/build_all5177_structural_atlas.py",
+      "sha256": "e9473c048dcd01ca7eced51e698c2297ed48fca14b4a7a1f12446317ec741715"
+    }
+  ]
+}