docs: refresh README and session handoff for current state
- README: add deep-comparison, post-hoc audit, and defense-preparation phases;
correct the not-computed list (exploratory post-hoc tests now exist, with
explicit small-n limits); add kisikisithesis/ and POSTHOC_STATISTICAL_AUDIT.md
to the structure, artifact index, key documents, and reproduction commands.
- SESSION_HANDOFF.md: reflect HEAD 34bab45 and the post-16 sessions, document
the prototype-snapshot tracking rule, refresh the next-session prompt.
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@@ -3,12 +3,17 @@
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This is the canonical continuation point for the next agent session. It is written to be
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readable without prior chat history, terminal scrollback, or git history.
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Last updated: 2026-10-02 (Session 16). Session 16 type: **handoff refresh** — no training, no
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experiments, no source/model/aggregation change, no proposal content change.
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Last updated: 2026-10-17 (Session 18). Session 18 type: **repository hygiene and documentation
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refresh** — no training, no experiments, no source/model/aggregation change, no proposal content
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change. It committed the previously untracked post-hoc statistical audit and defense-preparation
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work, codified the prototype-snapshot tracking rule in `.gitignore`, refreshed this handoff and
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`README.md`, declared `matplotlib` in `pyproject.toml`, and applied three behavior-preserving code
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nits (docstring fix, device-safe embedding extraction, empty-table guard).
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> **Current state in one line.** The 108-run experimental grid is complete and synthesized; the
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> thesis proposal Markdown has been finalized and committed. Remaining work is academic writing
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> and, later, formatting into the university template — not new experiments.
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> thesis proposal Markdown has been finalized and committed; the post-hoc statistical audit and
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> robustness/defense-preparation aids are committed. Remaining work is academic writing and, later,
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> formatting into the university template — not new experiments.
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---
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@@ -80,6 +85,15 @@ It is **frozen** unless academic/supervisor feedback requires revision. It is wr
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- `docs/research/FINAL_EXPERIMENTAL_SYNTHESIS.md` — authoritative six-condition synthesis
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(RQ1/RQ2/RQ3 answers, threats to validity, contribution, unsupported claims, gap assessment).
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- `docs/research/ORIGINAL_VS_PROPOSED_DEEP_COMPARISON.md` — paired original-vs-proposed deep
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comparison (`artifacts/analysis/deepcmp__*.csv`).
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- `docs/research/POSTHOC_STATISTICAL_AUDIT.md` — exploratory paired statistical audit of the
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completed grid (`scripts/posthoc_statistical_audit.py`, `artifacts/analysis/posthoc__*.csv`);
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explicit small-n limits (minimum attainable sign-flip p = 0.25 with three seeds); no
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significance claims.
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- `kisikisithesis/ROBUSTNESS_AUDIT_DAN_PERSIAPAN_PENGUJI.md` — robustness audit and examiner
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Q&A preparation; `kisikisithesis/robustness_checks.py` runs deterministic read-only checks
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over the actual implementation and persisted snapshots (prints only, writes nothing).
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- `docs/research/CROSS_DATASET_BETA_ANALYSIS.md` — cross-dataset comparison.
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- `docs/research/XIIOTID_CROSS_ALPHA_ANALYSIS.md` — X-IIoTID cross-alpha analysis.
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- `docs/research/5GNIDD_CROSS_ALPHA_ANALYSIS.md` — 5G-NIDD cross-alpha analysis.
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@@ -143,7 +157,10 @@ These constraints must be respected in every future text (proposal, chapters, sl
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3. **Later, draft thesis chapters** (starting with Chapter 4) from the final synthesis documents and
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`artifacts/analysis/final__*` + `artifacts/figures/final/`, obeying `CLAIMS_REGISTER.md` and
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`CHAPTER4_RESULTS_OUTLINE.md`.
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4. **No more experiments** unless required by new academic feedback.
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4. **For defense preparation**, use `kisikisithesis/ROBUSTNESS_AUDIT_DAN_PERSIAPAN_PENGUJI.md`
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(robustness audit, examiner Q&A, oral cheat sheet) and
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`docs/research/POSTHOC_STATISTICAL_AUDIT.md`; keep the exploratory-test caveats explicit.
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5. **No more experiments** unless required by new academic feedback.
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---
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@@ -174,11 +191,20 @@ These constraints must be respected in every future text (proposal, chapters, sl
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## 12. Git state
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- Branch `main`, `HEAD = e27c5a83abcb84ab31c667b4d39d580012fa6f26`, in sync with `origin/main`.
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- Session 15 commit: `docs: finalize thesis proposal markdown` (four proposal files).
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- No tracked working-tree changes expected between sessions; only pre-existing untracked
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`artifacts/analysis/*prototype_snapshot.json` files (94) remain untracked and must not be staged
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accidentally.
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- Branch `main`, `HEAD = 34bab45` (`docs: improve readability of PROTEAN comparison figures`);
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sessions after 16 added the deep paired comparison, the redesigned final figures, and the
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experiments documentation before this branch.
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- Session 18 work lives on branch **`chore/posthoc-audit-and-docs-refresh`** (not yet merged or
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pushed):
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- `111adb2` `research: add post-hoc statistical audit and defense preparation aids`
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(posthoc script + doc + 6 CSVs, `kisikisithesis/`, 4 remaining beta0-snapshot effect/weight
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CSVs, `.gitignore` snapshot rule)
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- documentation refresh (README, this handoff, `pyproject.toml`, three code nits) — commits
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after `111adb2` on the same branch.
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- Prototype-snapshot tracking rule (now explicit in `.gitignore`): the **18 beta0-round-0
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snapshots and their effect/weight CSVs are tracked**; the remaining ~76 non-beta0 snapshot
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JSONs (~28 MB, inputs to already-committed displacement tables) stay **untracked** — cited by
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path in the audit documents, like `results/`. Do not stage them.
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- `results/` is git-ignored. Do not commit raw datasets, large artifacts, or `results/`.
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## 13. Integrity / important commands
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@@ -196,12 +222,18 @@ git diff --stat
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.venv/bin/python scripts/analyze_partition_heterogeneity.py --dataset 5gnidd --alphas 0.25 0.5 0.75
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.venv/bin/python scripts/analyze_cross_alpha.py --dataset 5gnidd --alphas 0.25 0.5 0.75
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.venv/bin/python scripts/verify_beta0_equivalence.py --dataset 5gnidd --alpha 0.25 --seeds 0 1 2
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# Post-hoc statistical audit (read-only; writes only posthoc__*.csv)
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.venv/bin/python scripts/posthoc_statistical_audit.py
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# Deterministic robustness checks (prints only, writes nothing)
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.venv/bin/python kisikisithesis/robustness_checks.py
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```
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## 14. Recommended next-session prompt
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```
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You are continuing the perdalam-protean research repository (Session 17).
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You are continuing the perdalam-protean research repository (Session 19).
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FIRST, read completely:
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1. docs/handoff/SESSION_HANDOFF.md
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@@ -218,11 +250,18 @@ Critical rules:
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- Beta selection uses validation only; PRIMARY is pooled across clients and seeds.
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- The 108-run 2-dataset x 3-alpha x 3-seed grid is COMPLETE. Do NOT run new training.
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- The proposal Markdown is finalized and frozen unless academic feedback requires revision.
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- Non-beta0 prototype snapshots stay untracked (see .gitignore); do not stage them.
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Context: Session 15 finalized and committed the proposal Markdown
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(docs/proposal/THESIS_PROPOSAL_DRAFT.md) at HEAD e27c5a8. Session 16 refreshed this handoff.
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"Optimasi" in the title means empirical beta selection among predefined candidates, not a global
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optimum. All six conditions are synthesized; no material scientific gap remains (classification A).
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Context: Session 18 (branch chore/posthoc-audit-and-docs-refresh) committed the previously
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untracked post-hoc statistical audit (scripts/posthoc_statistical_audit.py,
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docs/research/POSTHOC_STATISTICAL_AUDIT.md, artifacts/analysis/posthoc__*.csv) and the
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defense-preparation aids (kisikisithesis/), refreshed the handoff/README, and added matplotlib
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to pyproject.toml. Sessions after 16 added the deep paired comparison
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(docs/research/ORIGINAL_VS_PROPOSED_DEEP_COMPARISON.md, deepcmp__*.csv) and the redesigned
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final figures. "Optimasi" in the title means empirical beta selection among predefined
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candidates, not a global optimum. All six conditions are synthesized; no material scientific
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gap remains (classification A). The post-hoc tests are EXPLORATORY ONLY (n=3 seeds; minimum
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attainable sign-flip p = 0.25); never present them as significance.
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Task: perform the requested writing/formatting or review work using the final synthesis documents
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and artifacts/analysis/final__*. Obey CLAIMS_REGISTER.md wording, keep all limitations explicit,
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