# Genome cross-compare — 2026-04-15 01:41

Generated by `scripts/cross_compare_genomes.py`. Compares
`genome.db` (current working state) against reproducible
bench-target genomes built earlier tonight.

## TL;DR

**Three genomes:** working (`genome.db`, 19.4k genes, 222k links),
tight helix-only (`genome_bench_helix.db`, 687 genes, 0 links),
wide organic (`genome_bench_organic.db`, 8.9k genes, 0 links).

**Five canonical queries:** the fresh genomes **beat** the working
genome for every query about recent code shipped in this session.

| query | working top-1 | fresh top-1 | takeaway |
|---|---|---|---|
| "session delivery working-set register" | generic old session code | `test_legibility.py` Sprint 1 test | working doesn't know about my new files yet |
| "legibility per-gene header fired tiers" | unrelated code (`row += 2`) | `legibility.py::_confidence_symbol` | working returns NOISE for shipped features |
| "context manager pipeline step assemble" | token-budget doc | same | tie (stable docs) |
| "cwola bucket accumulation" | collab findings doc | collab findings doc | tie |
| "harmonic links retrieval tier scoring" | scoring-logic code | scoring-logic code | tie |

**Three findings that matter:**

1. **harmonic_links are NOT ingested — they accumulate from use.**
   Both fresh genomes have 0 links despite 687 / 8,872 genes.
   Working genome's 222k links came from running benches + queries
   through the pipeline, which writes to the graph via seeded-edges +
   Hebbian co-activation. Fresh genome ≠ clean genome indefinitely —
   it just resets the counter.

2. **Working genome is 13.4k genes heavier than organic** (19,401 vs
   8,872, only 27% Jaccard overlap). The 13.4k extra aren't bench-
   fixture ingest — they're memory auto-sync + conversation
   replications + prior-session artifacts accumulated over time.
   `ingest_all.py` was never the sole source.

3. **Working genome is missing recent files.** Queries about
   `legibility`, `session_delivery`, `expand` surface RELEVANT code
   in fresh but IRRELEVANT hits in working — because I shipped those
   files after the last re-ingest. The live server is retrieval-
   blind to its own most recent source code.

**Latency diff** (retrieval-only, no splice):

| genome | avg ms |
|---|---|
| `genome.db` | 308 |
| `genome_bench_organic.db` | 133 (57% faster) |
| `genome_bench_helix.db` | 27 (91% faster) |

**Recommended morning action:** the right path isn't "replace working
with fresh." It's **add a `genome.read_only` config knob** so benches
can mount a fresh genome that retrieval reads but does NOT write back
to. Then point the PWPC bench (and any A/B) at `genome_bench_organic.db`
in read-only mode. Working genome keeps evolving organically, bench
target stays stable forever. ~30 LOC, low risk.

Secondary: trigger a re-ingest of `F:\Projects\helix-context\` into
the working genome before next session — your live server is blind
to Sprint 1/2/3 source right now.

---


## Bulk stats

| metric | genome.db | genome_bench_helix.db | genome_bench_organic.db |
|---|---|---|---|
| size on disk (MB) | 864.5 | 23.2 | 314.6 |
| genes | 19,401 | 687 | 8,872 |
| open | 13,741 | 664 | 7,931 |
| euchromatin | 1,917 | 16 | 182 |
| heterochromatin | 3,743 | 7 | 759 |
| harmonic_links | 222,157 | 0 | 0 |
| cwola_log rows | 2,346 | 0 | 0 |
| session_delivery rows | 0 | 0 | 0 |
| chars raw (M) | 107.8 | 2.3 | 31.8 |
| chars compressed (M) | 49.4 | 0.8 | 13.6 |
| compression ratio | 2.2x | 2.8x | 2.3x |
| links / gene | 11.45 | 0.00 | 0.00 |

## Gene-ID overlap

Cells are |A ∩ B| / |A ∪ B| (Jaccard).

| | genome.db | genome_bench_helix.db | genome_bench_organic.db |
|---|---|---|---|
| genome.db | 100.00% | 1.61% | 27.22% |
| genome_bench_helix.db | 1.61% | 100.00% | 7.73% |
| genome_bench_organic.db | 27.22% | 7.73% | 100.00% |

## Top-10 outbound hubs per genome

### `genome.db`

| gene_id (12) | out-deg | avg w | summary |
|---|---|---|---|
| `51a50f0a4f2a` | 275 | 0.332 | User requested Education value; context insufficient; assist |
| `4df4b7525b8a` | 244 | 0.256 | ["tags.camera.left"]  },
"roll_camera_right"     :{"cat":"ca |
| `7de5acba850c` | 222 | 0.368 | What We Did
- **Made CosmicTasha demo-ready** for a raw inve |
| `d5b27088d1ca` | 218 | 0.303 | User queried lock port value in Education context; informati |
| `a4bf438478f3` | 216 | 0.294 | Unknown probe configuration in Steam's common directory |
| `63d17aad9a6a` | 198 | 0.438 | Summary (no commits)

**CosmicTasha Demo-Ready:**
- Created  |
| `b74704f55937` | 190 | 0.369 | \| Filler content, removed per-query \|
\| **Promoter** \| D |
| `c7b6651af954` | 190 | 0.323 | \| Token \| Value \| Usage \|
\|-------\|-------\|-------\|
 |
| `f03cb70e44c0` | 185 | 0.334 | Education module supports configurable models for complex pr |
| `d5880be4d824` | 181 | 0.321 | User queried for 'log dir' value in Education context; infor |

### `genome_bench_helix.db`

(no harmonic_links)

### `genome_bench_organic.db`

(no harmonic_links)

## Canonical queries — same prompt, different genomes

Direct Python API calls (no HTTP), retrieval only — no
ribosome splice. Shows what each genome *surfaces* for the
same question.

### `session delivery working-set register`

| genome | ms | top results (gene_id · score · summary) |
|---|---|---|
| genome.db | 334.6 | `fdf53e215042` · 22.871 · ""
    session_data = get_session_from_r<br>`1b5d38c78100` · 21.5 · \| `active` \|
\| ≤ `2 * ttl_s` \| `idle` \|
<br>`db281e257f1c` · 19.139 · \|------\|--------\|---------\|
\| `fleet/mig |
| genome_bench_helix.db | 26.0 | `6515aa0f7a0c` · 22.0 · Bracketed like the Sprint 1 header
    a<br>`631b3b3710f8` · 13.0 · Exposing the FastAPI server beyond `loca<br>`1a129641974e` · 11.0 · ")
print(window.expressed_context)
print |
| genome_bench_organic.db | 128.2 | `6515aa0f7a0c` · 22.0 · Bracketed like the Sprint 1 header
    a<br>`24b371d9a12a` · 14.0 · ""
    return CliRunner()


@pytest.fixt<br>`fdf53e215042` · 13.177 · ""
    session_data = get_session_from_r |

### `harmonic links retrieval tier scoring`

| genome | ms | top results (gene_id · score · summary) |
|---|---|---|
| genome.db | 267.8 | `9f05749f6a82` · 21.154 · Calculates evidence support scores by ca<br>`1902b60a776c` · 21.1 · Defines comprehensive configuration sett<br>`ccbb3b129c0b` · 16.707 · The `run_tier` function orchestrates dim |
| genome_bench_helix.db | 25.5 | `368585a7330f` · 17.0 · Source authority bonus applies per-sourc<br>`c32a8c18e453` · 17.0 · 2=HETEROCHROMATIN)
        row = conn.ex<br>`c42e1440be8d` · 11.5 · def __getitem__(self, idx):
        row  |
| genome_bench_organic.db | 127.0 | `368585a7330f` · 17.0 · Source authority bonus applies per-sourc<br>`f24288e577cb` · 13.0 · """Tests for tier definitions and schedu<br>`8ab431a0546c` · 12.5 · Lock()

        # Event storage
         |

### `cwola bucket accumulation`

| genome | ms | top results (gene_id · score · summary) |
|---|---|---|
| genome.db | 240.4 | `1edf254050a7` · 20.24 · 10
          AND chromatin < 2
        "<br>`ecc4f3fdeb55` · 17.954 · Four regimes still valid but antiresonan<br>`c6807e65183f` · 15.827 · Collection of utility methods for displa |
| genome_bench_helix.db | 24.5 | `6a5a0ed4ba1f` · 19.781 · **

- 791 rows accumulated over 2.8 hour<br>`806c8d16c55e` · 18.781 · Since sweep_buckets can't detect re-quer<br>`f74c078a28be` · 17.281 · """Tests for CWoLa label logger (STATIST |
| genome_bench_organic.db | 116.8 | `6a5a0ed4ba1f` · 19.319 · **

- 791 rows accumulated over 2.8 hour<br>`806c8d16c55e` · 18.319 · Since sweep_buckets can't detect re-quer<br>`f74c078a28be` · 16.819 · """Tests for CWoLa label logger (STATIST |

### `context manager pipeline step assemble`

| genome | ms | top results (gene_id · score · summary) |
|---|---|---|
| genome.db | 440.5 | `81f3a53c3657` · 22.409 · tokens \| No (background) \|

**Token budg<br>`8b27b8286267` · 21.936 · - Builds a mask vector assigning 1 to to<br>`39b694447f36` · 21.249 · """

import json
import pytest

from hel |
| genome_bench_helix.db | 33.6 | `81f3a53c3657` · 19.0 · tokens \| No (background) \|

**Token budg<br>`7daaafef23c4` · 17.5 · \| Category \| Tokens \| Rate \| Cost \|
\|---<br>`05ff1371a8ab` · 16.667 · --------
#
# "full"      ~750 tokens — f |
| genome_bench_organic.db | 168.7 | `81f3a53c3657` · 19.0 · tokens \| No (background) \|

**Token budg<br>`1e38c1a6dcba` · 17.5 · If still 0 → `PromoterMismatch` (logged,<br>`7daaafef23c4` · 17.5 · \| Category \| Tokens \| Rate \| Cost \|
\|--- |

### `legibility per-gene header fired tiers`

| genome | ms | top results (gene_id · score · summary) |
|---|---|---|
| genome.db | 258.2 | `4ed7e6e02c81` · 13.5 · = row
        row += 2

        # Fixed <br>`6065adffbf0e` · 13.5 · Args:
        report_data: Dict from eng<br>`71855e27dc5d` · 13.5 · Args:
        report_data: Dict from eng |
| genome_bench_helix.db | 27.9 | `f488e726ef4b` · 13.5 · """
    if z_score >= 1.0:
        retur<br>`f5bc584063ef` · 13.5 · Integration: confirm header is a single <br>`5855625e17d9` · 8.5 · == 0.0


def test_z_normalize_negative() |
| genome_bench_organic.db | 123.5 | `f488e726ef4b` · 13.5 · """
    if z_score >= 1.0:
        retur<br>`f5bc584063ef` · 13.5 · Integration: confirm header is a single <br>`db003c441a70` · 12.5 · border_color = _hex_to_color(styles_dict |

