docs/changelog/007_phono_quality_flagging.md

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.