docs: reconcile arXiv benchmark figures after post-fix review

README.md

@@ -380,18 +380,18 @@ LongMemEval (Wu et al., ICLR 2025): 500 human-curated questions embedded in ~40
 | | Cortex | What it means |
 |---|---|---|
 | Recall@10 | **98.2%** | The right memory shows up in the top 10 for nearly every question |
-| MRR | **0.915** | The correct *memory* is usually ranked first or second — retrieval rank only, no LLM reader |
+| MRR | **0.9167** | The correct *memory* is usually ranked first or second — retrieval rank only, no LLM reader |
 
-<sub>n=500, E1 v3 verification campaign — per-row JSONs with code SHAs in `benchmarks/results/ablation/longmemeval-s_v3/`. Re-verified on a clean DB 2026-06-10.</sub>
+<sub>n=500, clean-DB run `benchmarks/results/repro/20260714-v4.14.1-pretag/longmemeval-s.json`, code SHA `28145f0b7a113fc06e22568de6feea7f8444eaf5`, dirty=false.</sub>
 
 | Category | MRR | R@10 |
 |---|---|---|
 | Single-session (assistant) | 1.000 | 100.0% |
-| Multi-session reasoning | 0.962 | 100.0% |
-| Knowledge updates | 0.925 | 100.0% |
-| Temporal reasoning | 0.926 | 98.5% |
-| Single-session (user) | 0.814 | 94.3% |
-| Single-session (preference) | 0.668 | 93.3% |
+| Multi-session reasoning | 0.964 | 100.0% |
+| Knowledge updates | 0.932 | 100.0% |
+| Temporal reasoning | 0.917 | 97.7% |
+| Single-session (user) | 0.841 | 95.7% |
+| Single-session (preference) | 0.685 | 90.0% |
 
 Knowledge updates score near-perfect because the retrieval stack's recency signal and update-intent routing push the newest version of a fact above older ones.
 
@@ -401,10 +401,10 @@ LoCoMo (Maharana et al., ACL 2024): 1,986 questions across 10 conversations —
 
 | | Cortex | What it means |
 |---|---|---|
-| Recall@10 | **91.5%** | Right memory in top 10 over 9 times out of 10 |
-| MRR | **0.805** | The correct *memory* is typically ranked first — retrieval rank only, no LLM reader |
+| Recall@10 | **94.35%** | Right memory in top 10 over 9 times out of 10 |
+| MRR | **0.8279** | The correct *memory* is typically ranked first — retrieval rank only, no LLM reader |
 
-<sub>n=1986, BASELINE_NO_CONSOLIDATION, post-plasticity-fix — `docs/benchmarks/e1-v3-locomo-results-post-fix.md`.</sub>
+<sub>n=1986, BASELINE_NO_CONSOLIDATION, post-plasticity-fix run at code SHA `2f45bcb39dbe15fa0ef857cc8c8c3783175d05db` — `docs/benchmarks/e1-v3-locomo-results-post-fix.md`.</sub>
 
 | Category | MRR | R@10 |
 |---|---|---|

benchmarks/README.md

@@ -84,7 +84,9 @@ session(s) appear in the top 10.
 
 - The comparable published baseline is the best retrieval configuration
   in the LongMemEval paper itself (Wu et al., ICLR 2025): **Recall@10
-  78.4%**. Cortex: **98.4%** (n=500).
+  78.4%**. Cortex: **98.2%**, MRR **0.9167** (n=500; clean-DB run
+  `results/repro/20260714-v4.14.1-pretag/longmemeval-s.json`, code SHA
+  `28145f0b7a113fc06e22568de6feea7f8444eaf5`, dirty=false).
 - This is **not** the end-to-end QA accuracy that LLM-answering
   leaderboards report (an LLM answers from the retrieved context and a
   judge scores the answer). Retrieval recall and QA accuracy are

docs/arxiv-context-assembly/main.tex

@@ -356,8 +356,10 @@ \subsection{Reciprocal Rank Fusion and Hybrid Search}
 Client-side, FlashRank (ONNX cross-encoder) reranks the top-$3k$
 candidates to produce the final ranking.
 
-This pipeline is strong at moderate scale: 98.4\% R@10 on
-LongMemEval, 94.2\% R@10 on LoCoMo (E1 v3, May 2026).  The five-signal fusion
+This pipeline is strong at moderate scale: 98.2\% R@10 on
+LongMemEval (clean run, July 2026; code SHA \texttt{28145f0}) and
+94.35\% R@10 on LoCoMo (E1 v3 post-fix run, May 2026; code SHA
+\texttt{2f45bcb}).  The five-signal fusion
 mitigates any single signal's weakness (\eg, vector similarity
 misses lexical matches that trigram catches; FTS misses paraphrases
 that vectors catch).  But at BEAM-10M scale, all five signals suffer
@@ -1291,8 +1293,11 @@ \subsection{Baselines}
 \paragraph{WRRF baseline.}
 Cortex's production pipeline without the assembler: 5-signal
 server-side fusion + FlashRank client-side reranking.  This is a
-strong baseline: 98.4\% R@10 on LongMemEval, 94.2\% R@10 on LoCoMo
-(E1 v3, May 2026), and 0.591 MRR on BEAM-100K.
+strong baseline: 98.2\% R@10 on LongMemEval (clean run, July 2026;
+code SHA \texttt{28145f0}), 94.35\% R@10 on LoCoMo (E1 v3 post-fix
+run, May 2026; code SHA \texttt{2f45bcb}), and 0.591 MRR on
+BEAM-100K (five-conversation protocol, $n{=}100$; code SHA
+\texttt{a071d89}).
 
 \paragraph{LIGHT} \citep{Tavakoli2026}.
 The strongest published system on BEAM, achieving 0.266 overall on

docs/benchmarks/arxiv-figure-audit-2026-08-02.md

@@ -0,0 +1,35 @@
+# arXiv benchmark-figure audit — 2026-08-02
+
+This audit records the pre-submission check requested in issue #347. It covers the benchmark figures in `docs/arxiv-thermodynamic/main.tex`, `docs/arxiv-context-assembly/main.tex`, and their Markdown source documents.
+
+## Authoritative run records
+
+| Benchmark | Current figure | Run record | Code / protocol |
+|---|---:|---|---|
+| LongMemEval-S, current headline | MRR 0.9167, R@10 0.982, n=500 | `benchmarks/results/repro/20260714-v4.14.1-pretag/longmemeval-s.json` | code SHA `28145f0b7a113fc06e22568de6feea7f8444eaf5`, dirty=false, 2026-07-14 |
+| LongMemEval-S, E1 v3 ablation snapshot | MRR 0.9124, R@10 0.984, n=500 | `docs/benchmarks/e1-v3-results.md`; `benchmarks/results/ablation/longmemeval-s_v3/` | code SHA `0e858e8db0f8a5dae0879fa0134113d101be19f8`, dirty=false, 2026-05-03; historical protocol-specific decomposition, not the current headline |
+| LoCoMo | MRR 0.8279, R@10 0.9435, n=1986 | `docs/benchmarks/e1-v3-locomo-results-post-fix.md` | code SHA `2f45bcb39dbe15fa0ef857cc8c8c3783175d05db`, dirty=false, descendant of `5f737fe` |
+| BEAM-100K, flat WRRF | retrieval-proxy MRR 0.591, R@10 0.790, n=100 | `benchmarks/results/a3_beam_100k_post_refactor.md` and `benchmarks/beam/variance/baseline_limit5.txt` | code SHA `a071d89`, five-conversation A/B protocol; result committed by `544abe7` |
+| BEAM-100K, assembler | MRR 0.602, n=100 | `benchmarks/beam/variance/assembler_limit5.txt` | same five-conversation A/B protocol |
+| BEAM-10M, flat / oracle / temporal | MRR 0.353 / 0.429 / 0.471, n=196 | `benchmarks/beam/variance/baseline_10m_fixed.txt`, `assembler_10m_stagefixed.txt`, `assembler_10m_temporal.txt` | original paired protocol |
+| BEAM-10M reproduction, oracle / temporal | MRR 0.496 / 0.523, n=196 | `benchmarks/results/beam10m_paired/RESULTS.md` | later paired code revision; compare within this pair only |
+| BEAM-500K / 1M crossover | flat 0.500 / 0.466; assembler 0.570 / 0.535 | `benchmarks/results/beam_crossover/RESULTS.md` | clean DB, 35 conversations per split |
+
+## Findings and resolution
+
+- **LongMemEval:** Opus 5's review found that the first audit had incorrectly promoted the May E1 v3 ablation baseline (MRR 0.9124, R@10 98.4%) to the current headline while `README.md` carried 98.2%. The current headline is now the latest committed clean run with an explicit clean flag: MRR 0.9167, R@10 98.2%, n=500, code SHA `28145f0`. The E1 v3 values remain only inside their named historical ablation snapshot and its per-row analysis.
+- **LoCoMo:** the thermodynamic paper's headline, benchmark table, 14-row ablation table, contributor narrative, cadence appendix, and both context-assembly citations still used the pre-fix 0.8278 / 0.942 run. They now use the post-fix 0.8279 / 0.9435 run and its per-row deltas. Pre-fix values remain only in explicitly labelled historical comparisons.
+- **Historical 0.794 / 0.926 comparator:** this pair is the April 2026 clean-DB Cortex result (n=1982) first published in commit `b4057a`. Its original per-query artefact is not committed. All active citations now label it as a superseded historical comparator rather than attributing it to the current `CLAUDE.md`.
+- **BEAM:** the arXiv LaTeX headline already had the correct 0.591 retrieval-proxy MRR from the named five-conversation / 100-question protocol at code SHA `a071d89`. The standalone Popper appendix's stale 0.543 was replaced, and the thermodynamic Markdown source now matches the LaTeX paper by removing the invalid comparison against BEAM's incommensurable end-to-end 0.329 score. The later 395-question full split remains a separate protocol.
+- **Publication surfaces:** the thermodynamic and context-assembly LaTeX sources, their Markdown sources, the Popper/Shannon/Erdős appendices, the README benchmark table, and the arXiv endorsement drafts now use the current LongMemEval and LoCoMo headlines. Historical values are retained only with a named run or an explicit historical label.
+- **Noise-floor language:** the post-fix LoCoMo consolidation-only values are all within the stated ±0.002 MRR floor. HOMEOSTATIC_PLASTICITY and SCHEMA_ENGINE end at +0.0017; the papers now describe these as positive-direction observations within noise, not causal contributions outside noise.
+
+## Submission gate
+
+The source-level figure audit passes when:
+
+1. the stale-number grep contains no unlabeled LoCoMo headline (`0.805`, `91.5%`, `94.2%`) or current LongMemEval headline (`97.8%`, `98.4%`), and every retained occurrence is explicitly historical, belongs to a named protocol, or represents a different metric;
+2. the two LaTeX sources compile without undefined references or citations;
+3. `git diff --check` passes.
+
+**Result: PASS after Opus 5 follow-up on 2026-08-02.** The stale-number grep has no unlabeled current LoCoMo or LongMemEval headline; both PDFs were rebuilt with `pdflatex`/`bibtex` and the final passes contain no undefined references or citations; the 14-row LoCoMo values were checked across the post-fix writeup, Markdown paper, and LaTeX source; `scripts/check_doc_claims.py` and `git diff --check` pass.

docs/benchmarks/e1-v3-locomo-results-post-fix.md

@@ -3,7 +3,7 @@
 ## Headline
 
 - **Cortex BASELINE_NO_CONSOLIDATION (longitudinal-read-path anchor): MRR = 0.8279, R@10 = 0.9435** on LoCoMo (n = 1986).
-- vs. CLAUDE.md established LoCoMo baseline (MRR = 0.794, R@10 = 0.926): **+4.3% MRR, +1.7% R@10** — within rounding identical to the pre-fix sweep, as expected (the longitudinal-read-path rows ran with consolidation off in both sweeps and the plasticity bug cannot exercise there).
+- vs. the historical April 2026 clean-DB Cortex comparator (MRR = 0.794, R@10 = 0.926; n=1982; provenance below): **+4.3% MRR, +1.75 percentage points R@10** — directionally identical to the pre-fix sweep, as expected (the longitudinal-read-path rows ran with consolidation off in both sweeps and the plasticity bug cannot exercise there).
 - **BASELINE_WITH_CONSOLIDATION (consolidation-cadence anchor): MRR = 0.8265, R@10 = 0.941.** ΔvsNO = +0.0014, **identical to the pre-fix value**, within the per-row noise floor. The cadence fix (commit `6c51bce`) re-validated at full n = 1986 a second time on post-`5f737fe` bytes.
 - The 14-row two-baseline ablation **re-confirms** the architectural-mismatch resolution from the pre-fix writeup (`docs/benchmarks/e1-v3-locomo-results.md`): RECONSOLIDATION ΔMRR = +0.0091, ADAPTIVE_DECAY ΔMRR = -0.0163. The longitudinal-read-path group is unchanged; the consolidation-only group has small sign flips on three rows (HOMEOSTATIC_PLASTICITY, SCHEMA_ENGINE, SYNAPTIC_PLASTICITY) — see "Pre-vs-post-fix comparison" below.
 
@@ -43,13 +43,13 @@ Positive Δ ⇒ mechanism contributes positively (ablating it hurts). Negative 
 | BASELINE_WITH_CONSOLIDATION | 0.8265        | 0.9410         |     0   |     0   | self   | Reference (consolidation-cadence anchor); ΔvsNO = +0.0014, within noise — cadence fix `6c51bce` re-validated |
 | CASCADE                     | 0.8268        | 0.9425         | -0.0002 | -0.0015 | WITH   | Within noise floor |
 | INTERFERENCE                | 0.8271        | 0.9410         | -0.0005 |  0.0000 | WITH   | Within noise floor |
-| HOMEOSTATIC_PLASTICITY      | 0.8248        | 0.9390         | +0.0017 | +0.0020 | WITH   | **Sign flipped** vs pre-fix (-0.0025 → +0.0017); positive contribution unmasked once plasticity ran cleanly |
+| HOMEOSTATIC_PLASTICITY      | 0.8248        | 0.9390         | +0.0017 | +0.0020 | WITH   | **Sign flipped** vs pre-fix (-0.0025 → +0.0017); positive direction, within the MRR noise floor |
 | SYNAPTIC_PLASTICITY         | 0.8269        | 0.9405         | -0.0003 | +0.0005 | WITH   | Null contribution (clean: ablation explicitly disables plasticity) |
 | MICROGLIAL_PRUNING          | 0.8269        | 0.9420         | -0.0004 | -0.0010 | WITH   | Within noise floor (sign flipped from +0.0011 but |Δ| at noise floor) |
 | TWO_STAGE_MODEL             | 0.8267        | 0.9395         | -0.0002 | +0.0015 | WITH   | Within noise floor |
 | EMOTIONAL_DECAY             | 0.8263        | 0.9415         | +0.0002 | -0.0005 | WITH   | Within noise floor |
 | TRIPARTITE_SYNAPSE          | 0.8266        | 0.9415         | -0.0001 | -0.0005 | WITH   | Within noise floor |
-| SCHEMA_ENGINE               | 0.8249        | 0.9395         | +0.0017 | +0.0015 | WITH   | **Sign flipped** vs pre-fix (-0.0004 → +0.0017); positive contribution unmasked |
+| SCHEMA_ENGINE               | 0.8249        | 0.9395         | +0.0017 | +0.0015 | WITH   | **Sign flipped** vs pre-fix (-0.0004 → +0.0017); positive direction, within the MRR noise floor |
 
 (Exact 6-decimal values at `benchmarks/results/ablation/locomo_v3_post_plasticity_fix/<MECH>.json::overall_mrr` and `manifest.rows`.)
 
@@ -66,15 +66,15 @@ The plasticity result-shape contract bug (commit `5f737fe`) silently dropped pla
 | BASELINE_WITH_CONSOLIDATION | 0 (anchor)   | 0 (anchor)    | —        | ΔvsNO = +0.0014 in both runs — cadence fix re-confirmed |
 | CASCADE                     | -0.0008      | -0.0002       | +0.0006  | Within noise; closer to zero |
 | INTERFERENCE                | +0.0004      | -0.0005       | -0.0009  | Within noise; sign flipped at noise floor |
-| **HOMEOSTATIC_PLASTICITY**  | **-0.0025**  | **+0.0017**   | **+0.0042** | **Sign flipped** — plasticity-bug-muted negative reading was an artefact; with clean plasticity, this row contributes positively |
+| **HOMEOSTATIC_PLASTICITY**  | **-0.0025**  | **+0.0017**   | **+0.0042** | **Sign flipped** — the between-run movement exceeds the floor, but the post-fix delta remains within the ±0.002 MRR floor |
 | SYNAPTIC_PLASTICITY         |  0.0000      | -0.0003       | -0.0003  | Within noise; explicitly clean ablation |
 | MICROGLIAL_PRUNING          | +0.0011      | -0.0004       | -0.0015  | Within noise; sign flipped at noise floor |
 | TWO_STAGE_MODEL             | -0.0012      | -0.0002       | +0.0010  | Within noise; closer to zero |
 | EMOTIONAL_DECAY             | +0.0015      | +0.0002       | -0.0013  | Within noise; closer to zero |
 | TRIPARTITE_SYNAPSE          | -0.0004      | -0.0001       | +0.0003  | Within noise; near-identical |
-| **SCHEMA_ENGINE**           | **-0.0004**  | **+0.0017**   | **+0.0021** | **Sign flipped** — small but consistent-direction unmasking, mirrors HOMEOSTATIC_PLASTICITY |
+| **SCHEMA_ENGINE**           | **-0.0004**  | **+0.0017**   | **+0.0021** | **Sign flipped** — positive direction after the fix, still within the post-fix MRR noise floor |
 
-**Reading.** Three sign-flips (HOMEOSTATIC_PLASTICITY, SCHEMA_ENGINE, SYNAPTIC_PLASTICITY) of which two (HOMEOSTATIC_PLASTICITY at +0.0042, SCHEMA_ENGINE at +0.0021) move out of noise and toward positive contribution. The longitudinal-read-path group (RECONSOLIDATION, CO_ACTIVATION, ADAPTIVE_DECAY) is essentially identical between runs because those rows ran with consolidation off and the plasticity bug had no opportunity to exercise — exactly as documented in the pre-fix limitations note. The cadence-fix anchor agreement (ΔvsNO = +0.0014) is identical to 4 decimals in both runs.
+**Reading.** Three rows change sign (HOMEOSTATIC_PLASTICITY, SCHEMA_ENGINE, SYNAPTIC_PLASTICITY). HOMEOSTATIC_PLASTICITY and SCHEMA_ENGINE move by +0.0042 and +0.0021 between runs, ending at positive-direction ΔMRR = +0.0017; because |+0.0017| < 0.002, both post-fix row effects remain inside the stated MRR noise floor. The longitudinal-read-path group (RECONSOLIDATION, CO_ACTIVATION, ADAPTIVE_DECAY) is essentially identical between runs because those rows ran with consolidation off and the plasticity bug had no opportunity to exercise. The cadence-fix anchor agreement (ΔvsNO = +0.0014) is identical to 4 decimals in both runs.
 
 ## Architectural-mismatch hypothesis: re-confirmed on clean bytes
 
@@ -96,11 +96,11 @@ The architectural-mismatch hypothesis (longitudinal mechanisms are foreclosed on
 
 **Consolidation-only (anchor: BASELINE_WITH_CONSOLIDATION)**
 
-1. **HOMEOSTATIC_PLASTICITY: ΔMRR = +0.0017** (largest absolute; sign-flipped from pre-fix; positive contribution unmasked).
+1. **HOMEOSTATIC_PLASTICITY: ΔMRR = +0.0017** (largest absolute; sign-flipped from pre-fix; positive direction within noise).
 2. **SCHEMA_ENGINE: ΔMRR = +0.0017** (tied largest absolute; sign-flipped from pre-fix).
 3. **INTERFERENCE: ΔMRR = -0.0005** (within noise floor; reported for completeness).
 
-The consolidation-only group's deltas all sit at or just outside the per-row noise floor (≈ ±0.002 MRR at n = 1986 single-seed). The two newly-unmasked positive contributions (HOMEOSTATIC_PLASTICITY, SCHEMA_ENGINE) sit at the boundary of noise and effect; they are reportable as positive-direction contributions but no single consolidation-time mechanism dominates at LoCoMo's scale, the same calibrated-stack property documented for LME-S and the pre-fix LoCoMo run.
+The consolidation-only group's deltas all sit inside the per-row noise floor (≈ ±0.002 MRR at n = 1986 single-seed). HOMEOSTATIC_PLASTICITY and SCHEMA_ENGINE are positive-direction observations, not causal contributions at this precision; no single consolidation-time mechanism dominates at LoCoMo's scale.
 
 ## Limitations and honest framing
 
@@ -124,6 +124,10 @@ The consolidation-only group's deltas all sit at or just outside the per-row noi
 - **Summary CSV:** `summary.csv` (14 rows, anchor assignments, per-row delta_mrr_vs_anchor / delta_r10_vs_anchor).
 - **Total artefacts:** 14 row JSONs + 1 manifest + 1 summary = 16.
 
+## Historical comparator provenance
+
+The MRR = 0.794 / R@10 = 0.926 pair is **not the current baseline** and is no longer sourced from `CLAUDE.md`. It is the historical clean-database, per-conversation-isolated LoCoMo result (n=1982) first published in commit [`b4057a`](https://github.com/cdeust/Cortex/commit/b4057a532da9c0eecd63ba72ad4174f5e54dab1c). The original per-query run artefact was not committed, so the pair is retained only as a transparent historical comparator; the post-fix run above is authoritative for current Cortex figures.
+
 ## Sources
 
 - LoCoMo (Maharana et al., ACL 2024) — benchmark.

docs/benchmarks/e1-v3-locomo-results.md

@@ -1,9 +1,12 @@
 # E1 v3 — LoCoMo Ablation Results (n=1986, 14 rows)
 
+> [!WARNING]
+> **Superseded for current figures.** This sweep ran on code SHA `ef178da7418a05bcf7aeb3e66f5b3179fdad2c4d`, before the plasticity result-shape fix `5f737fe`. Use the [post-fix re-run](e1-v3-locomo-results-post-fix.md) (code SHA `2f45bcb39dbe15fa0ef857cc8c8c3783175d05db`) for every current LoCoMo value and per-mechanism delta. This document is retained as historical pre-fix evidence only.
+
 ## Headline
 
 - **Cortex BASELINE_NO_CONSOLIDATION (longitudinal-read-path anchor): MRR = 0.8278, R@10 = 0.942** on LoCoMo (n = 1986).
-- vs. CLAUDE.md established LoCoMo baseline (MRR = 0.794, R@10 = 0.926): **+4.3% MRR, +1.6% R@10**.
+- vs. the historical April 2026 clean-DB Cortex comparator (MRR = 0.794, R@10 = 0.926; n=1982; provenance and limitations in the [post-fix re-run](e1-v3-locomo-results-post-fix.md#historical-comparator-provenance)): **+4.3% MRR, +1.6% R@10**.
 - **BASELINE_WITH_CONSOLIDATION (consolidation-cadence anchor): MRR = 0.8264, R@10 = 0.940.** ΔvsNO = +0.0014, within the per-row noise floor. This is the **n=1986 validation that the cadence fix (commit `6c51bce`) holds**: pre-fix smoke had MRR_with_cons collapse to 0.222 because of a wall-clock vs event-time confusion; the post-fix anchor sits indistinguishable from NO_CONSOLIDATION at full scale.
 - The 14-row two-baseline ablation **empirically resolves the architectural-mismatch hypothesis from the LME-S §6.3 writeup**: longitudinal mechanisms (RECONSOLIDATION, CO_ACTIVATION, ADAPTIVE_DECAY) that were at the noise floor on isolated-haystack LME-S **do show measurable effect on the longitudinal benchmark whose mechanism-of-action they target**.