Binesh Sadanandan PhD Dissertation Companion
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Thrust 1 · Chapter 3

Measurement

How often do equivalent questions change model answers?

PSF-Med evaluates six medical vision-language models on 92,856 audited paraphrase pairs built from 26,850 chest X-ray questions spanning three countries. Pairwise flip rates on the binary yes/no subset range from 6.4% to 54.7% (an 8.5x spread), and scale does not buy consistency. Two model-dataset cells with degenerate yes-bias (>98% positive on originals) are set aside rather than counted as consistency.

How I ran it

Generate roughly 92,000 candidate paraphrases, adjudicate 122,778 pairs for semantic equivalence with an LLM judge validated against clinician review (50.3% retained), then measure answer flips at both pairwise and query-level denominators.

Datasets
MIMIC-CXR, PadChest, VinDr-CXR
Models
MedGemma-27B, MedGemma-1.5-4B, MedGemma-4B, CheXone, LLaVA-Rad, RadFM
Thesis tables
Table 3.3 (tab:t1_flip_rates), Table 3.4 (tab:t1_denominators)
Papers
PSF-Med

The limitation that matters most

The paraphrases are generated by a language model and filtered by an automated judge, not collected from clinicians, so the flip rates measure sensitivity to plausible rewrites rather than to the way clinicians actually phrase questions.

Confirmed Paraphrase sensitivity is common in medical vision-language models: pairwise flip rates on the binary yes/no subset span 6.4% to 54.7% across six models and three chest X-ray datasets, an 8.5x spread.

Supported Scale does not buy paraphrase consistency: MedGemma-27B is the most consistent model on MIMIC (6.4%) but not on PadChest or VinDr, and no stable consistency ordering by parameter count exists across datasets.

Primary results

6.4% to 54.7%

pairwise

Paraphrase flip rates span 6.4% to 54.7% across six medical VLMs

Rephrasing a clinical yes/no question in a way that preserves its meaning changes the answer on anywhere from 1 in 16 to more than half of paraphrase pairs, depending on which model and which patient population you test. Paraphrase sensitivity is not a quirk of one weak model: every model tested flips, and the spread between the best and worst model-dataset cell is 8.5-fold.

Multiple models · Multiple datasets · A range over 18 model-dataset cells, so it has no single denominator. Per-dataset binary-subset denominators are MIMIC-CXR 1,539 questions / 5,076 pairs, PadChest 8,445 / 36,244, and VinDr-CXR 2,807 / 8,612, each evaluated on every model. The endpoints are MedGemma-27B on MIMIC (6.4%) and RadFM on VinDr (54.7%).

Source, denominator, and limits
How far this goesTwo of the 18 cells are set aside as degenerate yes-bias and excluded from this range: LLaVA-Rad on PadChest (99.6% positive predictions on originals) and MedGemma-1.5-4B on VinDr (100%). Both post a near-zero flip rate (0.8%) that reflects a single-class prior rather than paraphrase stability, so a model that answers 'yes' to everything would look maximally consistent here. The range also confounds model and population: it spans three different countries' patient distributions, so a cell's position reflects both the model and where the data came from.
Metric
pairwise paraphrase flip rate (range across six models x three datasets)
Denominator
pairwise (per question-paraphrase pair)
Sample
A range over 18 model-dataset cells, so it has no single denominator. Per-dataset binary-subset denominators are MIMIC-CXR 1,539 questions / 5,076 pairs, PadChest 8,445 / 36,244, and VinDr-CXR 2,807 / 8,612, each evaluated on every model. The endpoints are MedGemma-27B on MIMIC (6.4%) and RadFM on VinDr (54.7%).
Model
Multiple models
Dataset
Multiple datasets
Split
eval
Comparison
An 8.5x spread between the most consistent cell (MedGemma-27B on MIMIC) and the least consistent (RadFM on VinDr).
Uncertainty
not reported for this value
Thesis
Chapter 3, Table 3.3
Source artifact
results/uai/revision/psf_binary_recompute_v2.json
Last verified
2026-07-15

8.3%

pairwise

MedGemma-4B flips on 8.3% of MIMIC-CXR paraphrase pairs

On in-distribution US chest X-ray questions, the mechanistic subject model gives a different yes/no answer to about 1 in 12 clinically equivalent rephrasings.

MedGemma-4B · MIMIC-CXR · n = 5,076

Source, denominator, and limits
How far this goesThe MIMIC binary subset is not a pure presence set: it mixes 956 presence questions, 177 view-identification questions and 406 abnormality questions, so the rate averages over question types that may not be equally fragile. This is the pairwise denominator (flipped paraphrases over paraphrase pairs); the query-level rate on the same questions is more than double at 18.1%, and the two must never be interchanged. Do not compare this figure to the 42.1% MedGemma-4B flip rate on the 107-pair diagnostic set of Chapter 4, which is a different, deliberately hard population.
Metric
pairwise paraphrase flip rate
Denominator
pairwise (per question-paraphrase pair)
Sample
n = 5,076
Model
MedGemma-4B
Dataset
MIMIC-CXR
Split
eval
Comparison
13.4% for the same model on PadChest and 15.3% on VinDr-CXR; 18.1% query-level on this same MIMIC set.
Uncertainty
not reported for this value
Thesis
Chapter 3, Table 3.3
Source artifact
results/uai/revision/psf_binary_recompute_v2.json
Last verified
2026-07-15

92,856

pairwise

PSF-Med evaluates 92,856 question-paraphrase pairs

The benchmark that every headline flip rate is computed on contains 92,856 (question, paraphrase) pairs across three continents: 8,938 from MIMIC-CXR, 59,573 from PadChest v2 and 24,345 from VinDr-CXR, averaging 3.5 paraphrases per question.

Not model-specific · Multiple datasets · n = 92,856

Source, denominator, and limits
How far this goes92,856 is NOT the same thing as the roughly 92,000 candidate paraphrases generated at construction time; the two numbers are close by coincidence and describe different pipeline stages. The construction stage produced about 92,000 candidates (mean 4.7 per question) before filtering; 92,856 is the post-audit evaluation set (mean 3.5 per question). It is also not a subset of the 61,761 audit-retained core, because the audited PadChest v1 pairs were superseded by a separately filtered PadChest v2 set. Sources that report 'about 92,000 pairs' as the evaluation size are blurring two stages.
Metric
post-audit evaluation pairs in the PSF-Med benchmark
Denominator
pairwise (per question-paraphrase pair)
Sample
n = 92,856
Model
Not model-specific
Dataset
Multiple datasets
Split
eval
Comparison
Distinct from the roughly 92,000 construction-stage candidate paraphrases and from the 122,778 pairs sent through the rubric audit.
Uncertainty
not reported for this value
Thesis
Chapter 3, Table 3.1
Source artifact
dissertation/tables/thrust1/table_dataset_stats.tex
Last verified
2026-07-15

50.3%

pairwise

The equivalence audit rejects nearly half of generated paraphrases

A rubric-based GPT-5-mini audit of 122,778 candidate pairs kept only 50.3% (61,761) as clinically equivalent, rejected 48.7% (59,788) as adversarial or meaning-changing, and flagged 1.0% (1,229) as uncertain. Roughly half of what an LLM generates as a 'paraphrase' of a clinical question does not preserve the question.

Not model-specific · Multiple datasets · n = 122,778

Source, denominator, and limits
How far this goesThe 92,856-pair evaluation set is NOT a subset of the 61,761-pair retained core: the audit's retained PadChest v1 pairs were superseded by a regenerated, separately judge-filtered PadChest v2 set (59,573 pairs), which combined with audit-retained MIMIC (8,938) and VinDr (24,345) gives the 92,856 evaluated pairs. So the 50.3% describes the audit population, not the shipped benchmark. These tallies supersede an earlier snapshot of the same audit (60,712 retained / 60,766 rejected / 1,300 uncertain) taken while the VinDr run was still completing. Retention is a judge verdict, not a clinician verdict; the clinician sample agrees with this judge only 72.3% of the time.
Metric
share of audited paraphrase pairs retained as core-equivalent
Denominator
pairwise (per question-paraphrase pair)
Sample
n = 122,778
Model
Not model-specific
Dataset
Multiple datasets
Split
eval
Comparison
Retention varies sharply by dataset: 72.9% MIMIC, 35.7% PadChest, 78.6% VinDr.
Uncertainty
not reported for this value
Thesis
Chapter 3, Chapter 3, Rubric-Based Equivalence Audit
Source artifact
scripts/analysis/recompute_audit_retention.py
Last verified
2026-07-15

72.3%

pairwise

The automated judge agrees with clinicians on only 72.3% of pairs

Three reviewers (a radiologist, a clinician, and a device-research reviewer) adjudicated a 1,200-pair sample and agreed with each other almost perfectly (98.5% raw, kappa 0.97 on the 400 triple-reviewed pairs), but the GPT-5-mini equivalence judge matched their consensus on just 72.3% of pairs (kappa 0.52). The judge and the clinicians agree on easy cases and diverge exactly on the adversarial and uncertain ones the sample was designed to over-represent.

Not model-specific · Multiple datasets · n = 1,200 · Cohen's kappa 0.52 (moderate); consensus labels 689 equivalent / 409 not equivalent / 102 uncertain

Source, denominator, and limits
How far this goesThis validates the judge, NOT the benchmark's flip rates. The 1,200-pair sample was drawn before the PadChest v2 regeneration, so only 95 of 174 MIMIC pairs, 45 of 658 PadChest pairs and 0 of 43 VinDr pairs are in the evaluated benchmark at all. It therefore cannot be used to restate any flip rate; on the 95 overlapping MIMIC pairs, restricting to clinician-confirmed equivalents moves per-model flip rates by only -2.5 to +1.1 percentage points, within sampling noise. An earlier '0.9 pp sensitivity' claim from this sample was unreproducible and has been removed. The sample also deliberately over-samples adversarial and uncertain pairs, so 72.3% is a lower bound on agreement over a natural pair mix, not an unbiased estimate.
Metric
raw agreement between clinician consensus and the GPT-5-mini equivalence judge
Denominator
pairwise (per question-paraphrase pair)
Sample
n = 1,200
Model
Not model-specific
Dataset
Multiple datasets
Split
eval
Comparison
Inter-reviewer agreement on the same task is 98.5% raw (394/400, Cohen's kappa 0.97); judge-vs-judge cross-family agreement is 91.6-94.4%.
Uncertainty
Cohen's kappa 0.52 (moderate); consensus labels 689 equivalent / 409 not equivalent / 102 uncertain
Thesis
Chapter 3, Chapter 3, Clinician Adjudication
Source artifact
results/clinician_review/run_v2/kappa_report.json
Last verified
2026-07-15

Charts from this thrust

Open any of these in the evidence explorer to filter by model, dataset, or metric.

Pairwise paraphrase flip rate by model and dataset

Six base vision-language models on the equivalence-filtered PSF-Med binary yes/no subset: MIMIC-CXR 1,539 questions / 5,076 pairs, PadChest 8,445 / 36,244, VinDr-CXR 2,807 / 8,612.

Every model changes its yes/no answer on a meaningful share of clinically equivalent rephrasings, and the spread across models is 8.5-fold (6.4% for MedGemma-27B on MIMIC-CXR to 54.7% for RadFM on VinDr-CXR). No model is stable on all three populations, and rank order changes with the dataset.

Query-level flip rate: at least one paraphrase flips

Same PSF-Med binary subset as the pairwise chart, re-scored per question (MIMIC-CXR n=1,539, PadChest n=8,445, VinDr-CXR n=2,807 questions). MedGemma-27B on PadChest is absent from the recompute file and is not plotted.

Counting a question as unstable if any of its roughly 3.3 paraphrases flips roughly doubles every rate: MedGemma-4B moves from 8.3% pairwise to 18.1% on MIMIC-CXR and from 13.4% to 32.2% on PadChest. Per-question exposure is what a clinician meets, and it is far higher than the pairwise number.

Accuracy against pairwise flip rate

17 model-dataset cells (six base models x three datasets; MedGemma-27B / PadChest absent) on the PSF-Med binary subset, 5,076 / 36,244 / 8,612 pairs.

Consistency and correctness do not travel together. The most consistent cells include the degenerate ones, and on VinDr-CXR (all-positive) a model that always answers yes scores 100% accuracy at a 0.8% flip rate. Reading either axis alone ranks models wrongly.

How many generated paraphrases survive the equivalence audit

All 122,778 candidate pairs adjudicated by the rubric audit: MIMIC-CXR 12,259, PadChest 79,378, VinDr-CXR 31,141. Overall 61,761 retained (50.3%), 59,788 rejected (48.7%), 1,229 uncertain (1.0%).

Roughly half of everything an LLM generates as a 'paraphrase' of a clinical question is not clinically equivalent, and the rate depends strongly on the source: PadChest keeps only 35.7% against 78.6% for VinDr-CXR. Without this audit a benchmark would be scoring models on questions that genuinely changed meaning.

Which kinds of rephrasing break the model

Mean pairwise flip rate over the six base models on the PSF-Med binary yes/no subset, by transformation type. Per-cell n is binary-subset pairs per model (11 to 14,662). PadChest has no negation cell.

No transformation type is safe: even plain lexical substitution flips 11-17% of pairs. Negation-pattern rephrasings are the worst where a usable pool survives the audit (34.7% on VinDr-CXR), roughly triple the lexical rate on the same dataset.

Clinicians agree with each other; the automated judge is the weak link

1,200-pair stratified adjudication sample, three reviewers, 400 pairs triple-reviewed. Reviewer-versus-reviewer agreement on the 400; clinician-consensus-versus-GPT-5-mini agreement on all 1,200 and on the 400.

Clinicians agree with each other almost perfectly (98.5% raw, kappa 0.97, 394 of 400) but agree with the automated equivalence judge only 72.3% of the time (kappa 0.52), rising to 78.2% on the best-supported subset. The judge and the clinicians agree on easy cases and diverge on the adversarial and uncertain ones the sample over-represents.

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