Add recurrence controls, numerical decomposition and updated vector article

.gitattributes

@@ -114,3 +114,13 @@ wu_20261107_contact_asynchrony/figures/ExtendedData7.pdf filter=lfs diff=lfs mer
 wu_20261107_contact_asynchrony/figures/Figure1.pdf filter=lfs diff=lfs merge=lfs -text
 wu_20261107_contact_asynchrony/manuscript.pdf filter=lfs diff=lfs merge=lfs -text
 wu_20261107_contact_asynchrony/source_data/meshes/BRAIN.glb filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/assets/registered_brain.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/briefing.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/briefing.pptx filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/figures/ExtendedData11.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/figures/ExtendedData5.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/figures/ExtendedData6.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/figures/ExtendedData7.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/figures/Figure1.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/manuscript.pdf filter=lfs diff=lfs merge=lfs -text
+wu_20261107_recurrence_timing/source_data/meshes/BRAIN.glb filter=lfs diff=lfs merge=lfs -text

wu_20261107_recurrence_timing/METHODS_RESULTS_zh.md

@@ -0,0 +1,56 @@
+# 当前方法与结论：循环传递与接点时间协调
+
+本轮完成11次新计算：8个循环关闭条件，以及L输入的记录采样、时间步长、空间网格3个独立控制。对9个历史配对条件重新读取原始轨迹；合计核验640个细胞—条件读数，其中352个来自本轮计算。每个输入、静默行、潜伏期和原始波形均保留。
+
+## 方法
+
+沿用吴老师要求的真实树结构、突触三维落点、输入/输出方向与伙伴身份。结构底座保留5,177个KC；原始61细胞的32/15/14不改写，14细胞的精细功能问题继续保留。仿真使用原32个KC和2个真实被动MBON14，含1,926个KC循环接点、144个KC→MBON接点。按原三家族资格，10细胞接受平衡边界驱动，22细胞仍完整在线。
+
+外部参考电导固定E=1nS，每活跃接点18个事件。把共享同步/接点独立时序分别与R=0/1nS交叉，四种输入A、V、L、ABC均完整覆盖；独立时序严格复用前版首个冻结种子。R=0保留连接登记，但逐接点积分电导和电荷必须为零。源阈值事件、零权重到达记录与操作性起始部位波形分开审计。
+
+波形以峰值≥0mV、前2ms最大上升速率≥10mV/ms、最小峰间隔2ms识别，统计窗100≤t<1000ms；胞体均电位窗100≤t<1100ms。响应时间同时相对最早全局输入和本细胞最早局部输入保存；静默细胞保留零计数和空潜伏期。计数、覆盖、连续电位、首响应分别比较。
+
+## 本轮机制结果
+
+下表每项为“总波形数 / 响应细胞数”，覆盖原32细胞。
+
+|时间组织|循环R|A|V|L|ABC|
+|---|---:|---:|---:|---:|---:|
+|共享同步|0nS|18 / 1细胞|0 / 0细胞|0 / 0细胞|18 / 1细胞|
+|共享同步|1nS|559 / 32细胞|0 / 0细胞|0 / 0细胞|559 / 32细胞|
+|接点独立，种子09|0nS|5 / 1细胞|2 / 1细胞|2 / 1细胞|1 / 1细胞|
+|接点独立，种子09|1nS|252 / 32细胞|158 / 32细胞|188 / 32细胞|281 / 32细胞|
+
+
+完整逐细胞因果干预差见`recurrence_factorial.csv`。R=0的循环积分电导/电荷全部为零；不存在把零权重到达事件当作有效循环传递的情况。结果把直接驱动与循环募集分开，结论对应这里的模型参数、输入预算与时序。按响应重新划分生物学亚型不属于本轮估计。
+
+## L输入数值分解
+
+同一接点事件、相同电导与原32细胞，对记录采样、时间和空间独立控制。
+
+|配置|KC/MBON最大段长µm|dt ms|采样ms|波形数|响应细胞|
+|---|---:|---:|---:|---:|---:|
+|原始|0.25/0.5|0.0025|0.025|188|32|
+|仅提高采样|0.25/0.5|0.0025|0.0125|188|32|
+|仅细化时间|0.25/0.5|0.00125|0.0125|192|32|
+|仅细化空间|0.125/0.25|0.0025|0.0125|158|32|
+|时间/空间联合|0.125/0.25|0.00125|0.0125|125|32|
+
+
+`numerical_decomposition.csv`保留所有细胞的计数变化、首响应变化与胞体轨迹RMS。响应覆盖与累积计数分别呈现；细化差异直接写入结果，不用总数相近替代轨迹检验。前版首种子四输入联合细化仍保留：A/V/L/ABC=250/160/125/281，混合减逐细胞最强单输入的求和为+28。
+
+## 保留的证据链与文献
+
+三组接点独立时序在R=1nS均使V/L覆盖原32细胞；混合计数差分别+29、+25、−2。共享时序的抖动比较与接点独立时序区分；连续剖面95.4852%的第一共同模态只对应原共享同步面板。公开KC生理按7个Fly-ID留出：固定WT9与经验训练波形均值的平均误差分别35.216与32.723mV；按作者QC保留4个时为15.820与14.192mV。所有24个QC判定均能重建。
+
+新增核验2026年蜜蜂嗅觉—视觉MBON复合响应文献，DOI10.3389/fphys.2026.1898182。取得带CC BY许可的全文，作为跨物种讨论背景。该文只提供向作者索取数据的声明，全文未列出公开数据编号或代码仓库；本轮没有据此声称原始数据复分析。逐项证据见`new_literature_evidence.csv`，此前真实脑/蘑菇体矢量来源与组件许可继续保留。
+
+## 文章、图版与汇报
+
+[29页英文稿](exports/manuscript.pdf)、[文章源文件](manuscript/article.md)、[LaTeX](manuscript/main.tex)、[Overleaf包](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261107_recurrence_timing/overleaf_submission.zip)；六张复合主图25子图、十四张扩展图；[12页PPTX](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261107_recurrence_timing/briefing.pptx)、[矢量汇报PDF](exports/吴老师汇报_循环与时间协调机制_20261107.pdf)。主图2改为循环关闭配对，扩展图13为独立数值分解，原主图2的非零增益比较保留为扩展图14。真实脑区矢量与真实骨架继续用作主图解剖锚点。
+
+## 执行与复现记录
+
+方案在计算前冻结。首5个条件保存完13个原始科学文件后，因状态序列化中的执行字段重复而退出1；独立重提取全部波形、核对数组与电荷后才补全状态和事件登记，原13文件的字节保持不变。修复说明、冻结哈希、原退出记录和恢复审计一并保留。缺失的原计时不补造；恢复状态用空计时。余下条件使用只过滤重复执行字段的修复入口，数值参数与模型均不变。
+
+代码沿用已授权GitHub分支；数据以`wu_20261107_recurrence_timing`新前缀增量发布，历史版本完整保留。确切提交、对象核验和历史保留数以`metadata/publication_receipt.json`为准。

wu_20261107_recurrence_timing/README.md

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+# Recurrent transmission and contact-level timing in a synapse-resolved mushroom body
+
+This successor completes **11 new numerical runs**: an eight-condition zero-recurrence timing/input panel and three independent L numerical controls. Nine original matched runs are re-audited, yielding 640 cell-condition readouts, including 352 new ones. The original32/15/14, real cable trees, contact identities, boundary event budgets and physiological parameters are preserved.
+
+- [29-page article](exports/manuscript.pdf), [manuscript source](manuscript/article.md), [LaTeX](manuscript/main.tex), [independently compiled Overleaf package](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261107_recurrence_timing/overleaf_submission.zip).
+- [12-slide Chinese PPTX](https://huggingface.co/datasets/cyd0806/neuronmimic-data/resolve/main/wu_20261107_recurrence_timing/briefing.pptx), [vector briefing PDF](exports/吴老师汇报_循环与时间协调机制_20261107.pdf), [methods and findings in Chinese](当前方法与结论.md).
+- [Six composite vector main figures](figures/), [real brain/MB artwork](assets/registered_brain.svg), [canonical data](source_data/), [scientific audits](validation/), [publication identities](metadata/publication_receipt.json).
+
+## Results
+
+Each entry below gives operational waveform counts and responding cells out of32. E=1nS and each active boundary contact retains18 events. R0 preserves connection objects but carries exactly zero integrated recurrent conductance and charge.
+
+|时间组织|循环R|A|V|L|ABC|
+|---|---:|---:|---:|---:|---:|
+|共享同步|0nS|18 / 1细胞|0 / 0细胞|0 / 0细胞|18 / 1细胞|
+|共享同步|1nS|559 / 32细胞|0 / 0细胞|0 / 0细胞|559 / 32细胞|
+|接点独立，种子09|0nS|5 / 1细胞|2 / 1细胞|2 / 1细胞|1 / 1细胞|
+|接点独立，种子09|1nS|252 / 32细胞|158 / 32细胞|188 / 32细胞|281 / 32细胞|
+
+
+Figure2 now presents the matched schedule-by-recurrence intervention. Extended Data13 separates acquisition sampling, time-step and cable controls; Extended Data14 preserves the former nonzero conductance comparison. All six main figures/25 panels and fourteen Extended Data figures accompany the manuscript. The three-seed contact-timing results, source-attributed brain projections, structural nulls and public Fly-ID physiology remain explicit layers of the same evidence chain.
+
+## Reproduce
+
+See [REPRODUCIBILITY.md](REPRODUCIBILITY.md) for exact dependency revisions, raw-data restoration and the execution-only repair. No additional full second simulation repeat is claimed. Saved-data extraction and isolated compact figure reconstruction were executed.
+
+```bash
+python projects/wu_20261107_recurrence_timing/code/analyze_mechanism.py
+python projects/wu_20261107_recurrence_timing/code/build_figures.py
+python projects/wu_20261107_recurrence_timing/code/build_paper.py
+python projects/wu_20261107_recurrence_timing/code/build_slides.py
+python projects/wu_20261107_recurrence_timing/code/verify_release.py
+```
+
+The11 complete new raw runs are directly available under HF `main/` and `fine/`. The compact `paper_and_vectors.tar.gz` archive includes editable figures, canonical sources, all manuscript files, source attribution and code. Restore the9 matched legacy runs at their original paths to re-extract the full20-condition audit. Their immutable predecessors and file-level hashes are in `metadata/dependencies.json` and `metadata/mechanism_raw_manifest.json`.
+
+The primary protocol and original runner remain frozen. `execution_repair.json` documents a final-status serialization failure after the first5 complete raw payloads; their13 scientific files were audited and left byte-identical. The production rerun entry is `run_mechanism_repaired.py`. Original exit1 records and missing per-run timings are preserved explicitly; no timer is invented. The recovery utility is one-time provenance, not a normal rerun step.
+
+## Publication and sources
+
+GitHub: `ydchen0806/bio_fly_cyber_lateralization`, branch `research/wu-structure-function-20261104`. HF: `cyd0806/neuronmimic-data`, additive prefix `wu_20261107_recurrence_timing`. Historical prefixes are preserved. Source meshes retain their component-specific CC BY-NC4.0 notes and credits. The inspected honeybee MBON article (DOI10.3389/fphys.2026.1898182) is comparative context with CC BY full-text attribution, not a new raw-data validation; its data statement offers author-mediated access and states no public code repository. No journal artwork is copied.

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wu_20261107_recurrence_timing/fine/async_R1_L_sample_control/MBON_response.csv

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wu_20261107_recurrence_timing/fine/async_R1_L_sample_control/MBON_traces.npz

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wu_20261107_recurrence_timing/fine/async_R1_L_sample_control/STATUS.json

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+{
+  "status": "COMPUTED_AUTONOMOUS_COMBINATION",
+  "condition": "async_R1_L_sample_control",
+  "panel": "balanced",
+  "mask": 4,
+  "weight_uS": 0.001,
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+  "stage": "fine",
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+  "gate": {},
+  "elapsed_s": 330.77532180026174,
+  "scope": "Online excitatory KC subnetwork with partial passive MBON output; synthetic inputs and unvalidated parameter/release transfers. No biological validation."
+}