Add prospective three-seed active timing-assignment refinement, raw pairs and revised article

.gitattributes

@@ -145,3 +145,21 @@ wu_20261108_centroid_controls/figures/Figure1.pdf filter=lfs diff=lfs merge=lfs
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wu_20261108_active_refinement/METHODS_RESULTS_zh.md

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+# 当前方法与结论：活跃接点时序交换与联合细化
+
+本轮完成12次新模拟：三个原始时序种子×V/L两类输入×原始/交换两时序臂。重新读取12组精确主网格对照，共24次运行、768个KC细胞—条件读数，其中384个新增。新增接受波形1,884个，全部3,896个；所有12个新进程退出码为0。94个输入与模拟依赖在计算前冻结；方案代码在任何新输出完成前推送到GitHub，辅助采样分析也在首个输出前冻结。
+
+## 按吴老师要求保留的模型
+
+延续5,177KC结构底座、61细胞的原32/15/14划分和14细胞尚未解决的问题。代表网络包含原32KC和2个真实被动MBON14，保留真实树、1,926个KC循环接点、144个KC→MBON接点的物理位置、方向与伙伴身份。输入明确分ALPN、directVPN和operationalLVIN；本轮检验V/L，不新增A/ABC混合结论。10个原资格细胞接受平衡外部输入，22个仍连接于网络，所有细胞均保留。
+
+每活跃接点18事件、原float32权重、E=R=1nS及原检测判据保持不变。完整时序列在同细胞、同家族的等权接点间交换，每个细胞/家族的事件时间与权重集合完全一致。树和突触本身不移动，接点收到的输入时序改变。
+
+## 本轮直接回答的问题
+
+上一版主网格的154/192项配对细胞计数改变，尚未说明活跃时序交换效应的数值稳定性。本轮将原始和交换两臂都做联合细化：KC/MBON最大段长0.25/0.5→0.125/0.25µm；dt0.0025→0.00125ms；起始部位采样0.025→0.0125ms。胞体采样维持0.2ms。两套网格都读取全部32细胞的计数、响应状态、首峰、胞体电位，并保留完整原始轨迹。
+
+|输入|种子|主网格原始→交换|细网格原始→交换|配对效应主→细|细网格计数变化|细网格响应覆盖|
+|---|---|---|---|---|---|---|
+|V|20261109|158→157|160→157|-1→-3|1/32|32→32/32|
+|V|20261110|127→158|157→158|+31→+1|2/32|32→32/32|
+|V|20261111|187→128|156→158|-59→+2|4/32|32→32/32|
+|L|20261109|188→158|125→190|-30→+65|32/32|32→32/32|
+|L|20261110|188→216|93→186|+28→+93|32/32|31→32/32|
+|L|20261111|159→188|157→187|+29→+30|31/32|32→32/32|
+
+细网格共有6/6组总计数效应非零，102/192项细胞计数及1/192项响应状态改变。主/细网格总计数效应4/6组保持相同非零方向，2/6组反转。逐细胞在两网格均非零的95项中，62项保持方向、33项反转。
+
+对同一细网格轨迹降采样到0.025ms再用相同判据检测，0/384项原生细网格计数改变。这一辅助检查分离记录采样的影响，不计为新增模拟。主/细网格差异仍同时涉及积分与空间离散，两网格检验不能确定一般性的收敛阶或外推极限。
+
+结论应分别读取：固定逐细胞输入包络下是否存在时序分配敏感性、效应方向是否保持，以及响应覆盖是否保持。完整配对结果明确了哪些预测可复现、哪些量依赖数值设置；没有从单个有利种子推断特定树突机制。
+
+## 线程配置重放
+
+另完成6次主网格原始输入重放，把历史16线程统一为5线程；这一对照在首个新细网格输出前指定。全部6组KC/MBON电位、时刻与源事件数组逐值完全相同：True；计数变化0/192。额外192个技术读数单列。合计18次新模拟、12次历史参考、960个读数，其中576个新增；没有增加生物重复。
+
+## 论文与图版
+
+[28页论文](manuscript.pdf)、[正文](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/manuscript/article.md)、[LaTeX](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/manuscript/main.tex)、[Overleaf包](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261108_active_refinement/overleaf_submission.zip)、[21页PPT](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261108_active_refinement/briefing.pptx)、[汇报PDF](briefing.pdf)、[吴老师要求逐项对照](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/%E5%90%B4%E8%80%81%E5%B8%88%E8%A6%81%E6%B1%82%E9%80%90%E9%A1%B9%E5%AF%B9%E7%85%A7.md)。六张复合主图25子图、10张扩展数据图与13张补充图；新主图4并列平均到达/分散对照、两个网格上的六组配对效应、全部192个逐细胞效应。原主图4保留为补充图13；扩展图9展示响应覆盖/首峰/采样检查，扩展图10展示全部计数、连续电位和预设直接/间接细胞完整轨迹。
+
+主图、新增扩展图9—10及补充图13及汇报PDF均为矢量；历史扩展图2/4的5个热图/色条栅格对象保留并记录。真实脑/蘑菇体表面继续保留FlyWire/Amy Sterling署名及CC BY-NC4.0条款。公开生理、12篇核验文献和上一版校验过的13表实验源工作簿保留各自证据范围，未重新拟合。本轮新增动物0，尚未投稿。
+
+[独立补充信息PDF](supplementary_information.pdf)共14页；[含补充材料的完整阅读版](manuscript_with_supplement.pdf)共42页。主稿和补充信息均从Overleaf解压包独立编译核验。
+
+## 发布与后续
+
+代码使用授权GitHub分支，HF采用新前缀`wu_20261108_active_refinement`，历史对象保留。精确版本及完整核验见metadata/publication_receipt.json与metadata/final_verification.json。后续优先用独立膜参数约束和受体特异性数据检验可辨识预测；需要更精确效应时，再以独立冻结方案分解时间步长与空间网格、并检验抑制性反馈。

wu_20261108_active_refinement/README.md

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+# Active timing assignment under prospective joint numerical refinement
+
+Twelve new active runs cross all three original timing realizations, V/L and original/reassigned trains. Twelve exact main-grid references are reaudited. The result contains 768 KC readouts (384 new), 48 MBON readouts and 1,884 new accepted waveform events. Every original 32 KC and both real passive MBON14 cells remain, with real trees, physical synapse positions, directed partners and unchanged input budgets.
+
+- [28-page article](manuscript.pdf), [manuscript](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/manuscript/article.md), [LaTeX](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/manuscript/main.tex), [independently compiled Overleaf ZIP](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261108_active_refinement/overleaf_submission.zip).
+- [21-slide editable briefing](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261108_active_refinement/briefing.pptx), [vector PDF](briefing.pdf), [Chinese methods/results](METHODS_RESULTS_zh.md), [meeting requirement traceability](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/%E5%90%B4%E8%80%81%E5%B8%88%E8%A6%81%E6%B1%82%E9%80%90%E9%A1%B9%E5%AF%B9%E7%85%A7.md).
+- [Protocol](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/protocol.json), [all source tables](source_data/), [raw-data audit](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/validation/active_audit.json), [reproduction](https://github.com/ydchen0806/bio_fly_cyber_lateralization/blob/128d00f0061905da1e42e5030f8b3fd6e832f5ad/projects/wu_20261108_active_refinement/REPRODUCIBILITY.md), [publication identities](publication_status.json).
+
+## Paired results
+
+|输入|种子|主网格原始→交换|细网格原始→交换|配对效应主→细|细网格计数变化|细网格响应覆盖|
+|---|---|---|---|---|---|---|
+|V|20261109|158→157|160→157|-1→-3|1/32|32→32/32|
+|V|20261110|127→158|157→158|+31→+1|2/32|32→32/32|
+|V|20261111|187→128|156→158|-59→+2|4/32|32→32/32|
+|L|20261109|188→158|125→190|-30→+65|32/32|32→32/32|
+|L|20261110|188→216|93→186|+28→+93|32/32|31→32/32|
+|L|20261111|159→188|157→187|+29→+30|31/32|32→32/32|
+
+Fine-grid population count effects are nonzero in 6/6 pairs. Between grids, 4/6 population effects retain and 2/6 reverse their nonzero sign. All 192 cellwise paired effects, zeros, coverage and missing onsets remain. Fine-grid count effects change 102/192 cell counts and 1/192 response states. Evaluating saved fine trajectories at the main acquisition interval changes 0/384 native counts.
+
+The 94-file simulation freeze precedes execution. Protocol code was pushed before any of the12new completed outputs; the analysis plan and code were frozen before the first output. Six workers use five Arbor threads each. Two grids establish a numerical sensitivity comparison, not asymptotic convergence. Timing realizations and cells are descriptive within-model units. Public physiology, the twelve verified references and historical controls retain their original evidence roles. No additional animals, fitting, permutation selection or journal submission.
+
+Six main vector composites contain 25 panels. Ten Extended Data figures and thirteen supplementary figures carry the complete controls in separately compiled documents. Main figures and briefing PDF contain no displayed raster images; historical Extended Data 2/4 retain five inventoried heatmap/colorbar raster objects. Real anatomical surface assets retain FlyWire/Amy Sterling attribution and CC BY-NC 4.0 terms. Third-party experimental data retain source-specific licenses.
+
+GitHub `ydchen0806/bio_fly_cyber_lateralization`, branch `research/wu-structure-function-20261104`; HF dataset `cyd0806/neuronmimic-data`, additive prefix `wu_20261108_active_refinement`. All historical releases remain.
+
+[Supplementary information](supplementary_information.pdf): 14 pages; [combined reader PDF](manuscript_with_supplement.pdf): 42 pages. [Publication figure names](figures/journal/) map to original source artwork through metadata/journal_figure_layout.json.
+
+Six additional main-grid original-input replays test 16-versus-5-thread runtime layout. All 6 voltage/time/source-event array sets match exactly: True; changed counts: 0/192. These technical controls bring the new-run count to 18, new KC readouts to 576 and current raw comparisons to 30 runs/960 readouts. Primary active results remain 12 new fine runs/384 new readouts.

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+{
+  "dataset": "cyd0806/neuronmimic-data",
+  "predecessor_prefix": "wu_20261108_centroid_controls",
+  "predecessor_payload": "fa2cf67a5a5f1b5422a39e88deffde0bac3ec950",
+  "base_engine_prefix": "wu_20261104_combination_network",
+  "source_data": "12new joint-fine runs and12exact main references; inherited evidence preserved",
+  "new_simulations": 22,
+  "new_animals": 0,
+  "base_dataset_revision": "6f24982d0375d957c7c3906e81a2c2678c5c4667",
+  "base_dataset_prefix": "wu_20261104_structure_function",
+  "base_restore": "Restore all 12 base archives with original workspace-relative paths; original .mod and compiled catalogues are in base archives",
+  "legacy_synchronous_prefix": "wu_20261104_combination_network",
+  "legacy_synchronous_restore": "Four balanced_w0.001_m{1,2,4,7} main runs; restore at original workspace paths from the archived base release.",
+  "matched_legacy_runs": 18,
+  "contact_timing_prefix": "wu_20261107_contact_asynchrony",
+  "contact_timing_payload": "236b3f0d6e3abf10318fe43f0ba863b3eff27cc1",
+  "current_freeze": "metadata/active_refinement_freeze.json",
+  "current_raw_manifest": "metadata/active_raw_manifest.json",
+  "refinement_scope": "All3original seeds,V/L,original/reassigned active pairs",
+  "recurrence_prefix": "wu_20261107_recurrence_timing",
+  "recurrence_payload": "6b8f7246b276485d79dba779372ea96ce52a0732"
+}

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