# 007 — Phonological Quality Flagging & Confidence Corrections

**Date**: 2026-03-19

## Objective

Post-audit quality flagging to address three issues identified by a 4-agent adversarial certification audit:

1. **Phonological divergence**: ~31% of "certain" cognate pairs have surface forms so divergent (Score ≤ 0.2 or unscored) that they are indistinguishable from random word pairs, despite being etymologically correct cognates. Downstream consumers need a way to filter by phonological evidence strength.
2. **Robbeets cross-family contestation**: 27,059 pairs from the Transeurasian dataset cross language family boundaries (e.g., Turkic↔Japonic). The Transeurasian hypothesis is formally contested in published academic rebuttals. These were incorrectly labeled "certain."
3. **Sino-Tibetan doubt markers**: The original STEDT source data contains doubt markers (`!`, `?`, `doubtful`) in the NOTE column for 655 cognate sets, but the extraction script hardcoded all pairs as "certain."

## Scripts Used

| Script | Lines | Purpose |
|--------|------:|---------|
| `scripts/flag_phono_quality.py` | 185 | Stream-processes 23.5M rows: adds `Phono_Quality` column, downgrades Robbeets cross-family Confidence, fixes Sino-Tibetan doubt markers |

**Data integrity**: No data was added, removed, or fabricated. The script only adds a new column (`Phono_Quality`) and corrects two existing `Confidence` values based on source metadata. All changes are deterministic and reproducible.

## Data Sources

No new external data sources. All corrections derive from metadata already present in existing sources:

| Source | File Used | Purpose |
|--------|-----------|---------|
| Robbeets et al. 2021 | `sources_tier1/robbeetstriangulation/cldf/languages.csv` | Family column for cross-family detection |
| STEDT / Sagart et al. 2019 | `ancient-scripts-datasets/sources/sinotibetan/sinotibetan_dump.tsv` | NOTE column for doubt markers |

## Methodology

### Phono_Quality Classification

A new 15th column `Phono_Quality` is added to every row based on the existing SCA score:

| Value | Score Range | Meaning | Count | % |
|-------|-------------|---------|------:|--:|
| `strong` | Score ≥ 0.5 | Clear phonological similarity between surface forms | 6,551,211 | 27.92% |
| `moderate` | 0.2 ≤ Score < 0.5 | Detectable but weak surface similarity | 9,565,693 | 40.76% |
| `weak` | 0 < Score < 0.2 | Minimal similarity, possibly coincidental | 2,210,058 | 9.42% |
| `none` | Score = 0.0 | Zero surface similarity despite cognacy | 3,314,102 | 14.12% |
| `unscored` | Score = -1.0 | No SCA score computed (ACD pairs) | 1,825,701 | 7.78% |

**Rationale for thresholds**: The SCA (Sound Class Alphabet) distance metric from List (2012) returns a normalized similarity score in [0, 1]. The 0.5 threshold separates pairs where a human could plausibly identify shared phonological material from those where similarity is statistical only. The 0.2 threshold separates detectable patterns from near-noise. These thresholds are conservative — phonological similarity below 0.2 is rarely distinguishable from chance resemblance across unrelated languages.

**Why `none` ≠ "not cognate"**: A pair with Score=0.0 (e.g., Pohnpeian `ehd` and Atayal `isa`, both "one" from proto-Austronesian \*esa) can be a genuine cognate whose surface forms diverged beyond recognition over millennia. The `none` flag means "the phonological evidence is invisible at the surface level," not "the cognacy judgment is wrong."

### Robbeets Cross-Family Downgrade

The Robbeets Transeurasian dataset contains cognate sets that span 5 language families: Turkic, Mongolic, Tungusic, Koreanic, and Japonic. For each Robbeets pair:

1. Look up both Lang_A and Lang_B in the Robbeets `languages.csv` → get `Family` column
2. If `Family_A ≠ Family_B` → the pair is cross-family
3. Downgrade `Confidence` from `certain` to `contested`

**Academic justification**: The Transeurasian hypothesis (Robbeets et al. 2021, Nature) is contested by multiple published rebuttals. Georg (2023) and others argue that the cross-family cognate sets fail strict sound correspondence criteria. Within-family cognate sets (e.g., Turkic↔Turkic) are universally accepted and remain `certain`.

**Breakdown of cross-family pairs (27,059 total)**:
- Mongolic↔Turkic: 8,859
- Mongolic↔Tungusic: 6,863
- Tungusic↔Turkic: 5,624
- Japonic↔Turkic: 2,754
- Japonic↔Mongolic: 1,083
- Japonic↔Tungusic: 959
- Japonic↔Koreanic: 305
- Koreanic↔Tungusic: 262
- Koreanic↔Turkic: 243
- Koreanic↔Mongolic: 107

### Sino-Tibetan Doubt Marker Fix

The STEDT source data contains a NOTE column with doubt markers for 655 cognate sets (890 individual form rows). When any form in a cognate set has a doubt marker (`!`, `?`, `?!`, or `doubtful`), all pairs derived from that cognate set are downgraded from `certain` to `doubtful`.

**Source_Record_ID format**: `st_{COGID}` — the COGID maps directly to the STEDT etymological set. 2,906 pairs were fixed.

## Tests Performed

1. **Row count verification**: Output has exactly 23,466,765 rows (matches input)
2. **Column verification**: Header contains all 15 columns including new `Phono_Quality`
3. **Confidence distribution check**:
   - `certain`: 22,721,849 (was 22,751,814 — reduced by 27,059 + 2,906)
   - `doubtful`: 717,857 (was 714,951 — increased by 2,906)
   - `contested`: 27,059 (new category)
4. **Cross-tabulation**: Phono_Quality × Confidence verified for all 13 combinations
5. **Spot checks**: Verified Robbeets cross-family pairs (jpn↔kor) show `contested`, Sino-Tibetan doubt pairs show `doubtful`

## Output Summary

| File | Rows | Size | Change |
|------|-----:|-----:|--------|
| `cognate_pairs_inherited.tsv` | 23,466,765 | ~5.3 GB | +1 column (Phono_Quality), Confidence corrections |
| `cognate_pairs_inherited.parquet` | 23,466,765 | 31.3 MB | Rebuilt with new column |

### Schema Change

Column 15 added: `Phono_Quality` (string enum: `strong`, `moderate`, `weak`, `none`, `unscored`)

### Confidence Value Changes

| Change | Count | Reason |
|--------|------:|--------|
| `certain` → `contested` | 27,059 | Robbeets cross-family pairs |
| `certain` → `doubtful` | 2,906 | Sino-Tibetan doubt markers from STEDT |

## Limitations

1. **Phono_Quality thresholds are heuristic**: The 0.5 and 0.2 boundaries are reasonable but not calibrated against a held-out dataset. Different downstream tasks may want different cutoffs.
2. **ACD pairs remain `unscored`**: The ACD source provides no IPA transcriptions, so SCA scoring is impossible. These 1.8M pairs are likely genuine cognates (Blust's life work) but their phonological quality cannot be assessed.
3. **Score=0.0 does not mean "not cognate"**: Deep cognates with millennia of divergence can legitimately score 0.0. The `none` flag is informational, not a rejection.
4. **Robbeets within-family pairs remain `certain`**: Only the 27,059 cross-family pairs are downgraded. The 134,090 within-family pairs (Turkic↔Turkic, etc.) are universally accepted.

## Academic References

- List, J.-M. (2012). "SCA: Phonetic alignment based on sound classes." New Directions in Logic, Language, and Computation, Springer. (SCA distance metric)
- Robbeets, M. et al. (2021). "Triangulation supports agricultural spread of the Transeurasian languages." Nature 599, 616-621.
- Georg, S. (2023). "Review of Robbeets et al. 2021." (Formal rebuttal of cross-family cognate claims)
- Sagart, L. et al. (2019). "Dated language phylogenies shed light on the ancestry of Sino-Tibetan." PNAS 116(21):10317-10322.