Diagnostic-Reasoning-Q3X1

A QLoRA fine-tune of Qwen3-8B for medical question answering, released as the evaluated artifact for a study of training-corpus overlap in medical language model benchmarks.

Read this first. An earlier version of this card reported an average of 76.4% across seven medical benchmarks and a +24.2-point gain over the parent checkpoint. Those figures are superseded. They were produced by log-likelihood scoring on benchmarks subsequently found to overlap the fine-tuning corpus by up to 100%. Under overlap-audited evaluation the measured gain over the parent checkpoint is +5.2 percentage points on a held-out benchmark subset. The numbers below are the corrected ones, and the accompanying paper is largely about why the earlier figures were misleading.

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What this model is for

This checkpoint is released so that the results of the accompanying paper can be independently reproduced. It is a research artifact. It has not been clinically validated and must not be used for clinical decision-making.

The paper's contribution is methodological: for a model whose fine-tuning corpus is assembled in part from public medical QA datasets, standard benchmark evaluation cannot distinguish reasoning from exposure to test items, and this is measurable against the training corpus itself.

Headline results

All figures from a single fixed evaluation harness: generative chain-of-thought, greedy decoding (temperature 0), identical prompt template and answer-extraction rule across every model and benchmark.

MedXpertQA (Text) — the primary benchmark, not among the named training sources

	Parent checkpoint (Qwen3-8B)	This model	Gain
Full set (n = 2,450)	17.5% [16.1–19.1]	24.5% [22.8–26.2]	+7.0
Exact-stem-unflagged (n = 1,838)	15.6% [14.0–17.3]	20.8% [19.0–22.8]	+5.2

Unflagged comparison: paired McNemar test, 235 items gained against 139 lost, χ² = 24.13 (continuity-corrected), exact two-sided P = 7.9 × 10⁻⁷. Intervals are binomial 95% Wilson.

Excluding exact-stem-flagged items reduced the estimated gain from 7.0 to 5.2 percentage points — a reduction of 1.8 points, approximately 26% of the full-set estimate.

Benchmark overlap against this model's training corpus

Measured with a three-layer pipeline (13-gram overlap, verbatim exact-stem match, longest-common-subsequence ratio ≥ 0.80) against the 97,041-item fine-tuning corpus.

Benchmark	Exact-stem (primary)	13-gram (upper bound)
PubMedQA	100%	100%
MedQA (USMLE)	73.4%	99.9%
MMLU Professional Medicine	70.6%	95.6%
MMLU Anatomy	48.9%	48.9%
MMLU Clinical Knowledge	33.3%	33.3%
MMLU Medical Genetics	29.0%	29.0%
MedXpertQA	25.0%	50.0%
MedMCQA (validation split)	0.02%	0.24%

Overlap tracks the training-corpus composition, not benchmark difficulty. MedQA and PubMedQA items are present in the corpus at their evaluation-set sizes. MedMCQA is near-unflagged because training material was drawn from its train split while evaluation uses the held-out validation split — which also demonstrates that the detector is specific rather than flagging items indiscriminately.

MedXpertQA was not among the named training sources, yet 612 of its 2,450 items met the exact-stem criterion. The source pathway for these matches could not be resolved from the available corpus metadata; they were excluded from the primary subset without assigning a specific origin.

On several overlapping benchmarks the unmodified parent checkpoint equals or outperforms this fine-tune — significantly so on MedQA (75.5% versus 68.7% on the unflagged subset, P = 7.6 × 10⁻³). This pattern is consistent with benchmark-item exposure contributing to measured performance, though it does not establish the mechanism of any individual response; catastrophic forgetting, altered answer formatting and calibration shifts may also contribute. Scores on PubMedQA, MedQA and MMLU Professional Medicine should not be cited as evidence of this model's capability.

Bundled ablation

A third arm was trained on the identical corpus with the reasoning traces removed and curriculum weighting replaced by uniform sampling. On the exact-stem-unflagged subset:

Arm	Configuration	Accuracy [95% CI]	Contrast	P
A0	Unmodified parent checkpoint	15.6% [14.0–17.3]	—	—
A1	Plain SFT, traces and weighting removed	19.3% [17.5–21.1]	+3.6 vs A0	1.3 × 10⁻³
A4	Full recipe (this model)	20.8% [19.0–22.8]	+1.6 vs A1	0.175

A1 retained approximately 70% of the observed A0-to-A4 improvement. This is a descriptive decomposition of the observed accuracies, not an estimate that 70% of the causal effect is uniquely attributable to medical-QA exposure.

This is a bundled ablation, not a component-isolating experiment. A1 and A4 differ jointly in five respects — reasoning-trace content, training-token exposure (A1 uses ≈21% of A4's tokens), curriculum weighting, cognitive-forcing structure and output-format supervision — and one training seed was used per arm. The comparison estimates a combined incremental contrast and does not identify the independent causal contribution of any single component.

Training

Parent checkpoint	Qwen/Qwen3-8B (instruction-tuned, not Qwen3-8B-Base)
Method	QLoRA, r = 128, α = 256
Target modules	q_proj, k_proj, v_proj, o_proj, gate_proj, up_proj, down_proj
Trainable parameters	349,175,808 (4.09%)
Learning rate	2×10⁻⁴, cosine-with-restarts, warmup ratio 0.05
Effective batch	32 (per-device 2 × grad-accum 16)
Epochs	3 main + 1 answer-format stabilisation
Max sequence length	6,144
Precision	bf16 compute, 4-bit base
Corpus	97,041 examples

Training used a structured eight-component clinical reasoning template — seven reasoning stages plus a post-reasoning answer stage — with likelihood ratios cited inline, and a quality-tier-weighted curriculum. The complete template schema, a worked example and the curriculum weighting scheme are in the paper's supplementary material.

Evaluation protocol

Reproducing the reported numbers requires this exact configuration:

scoring        generative chain-of-thought
decoding       greedy, temperature 0.0, top_p 1.0
max_new_tokens 10240
max_model_len  12000
dtype          bfloat16
extraction     options-count-aware, six-stage staged fallback

The six extraction stages are: (1) explicit answer marker; (2) terminal standalone option letter; (3) bracketed option; (4) concluding-sentence cue; (5) leading option letter in the post-reasoning answer block; (6) explicit "option X" reference. Stages 5 and 6 were added after a differential extraction failure was identified — the original four-stage rule failed on 7.1% of the plain fine-tune's responses against 0.04% of this model's, because the two answer in different registers. The corrected rule is applied identically to all arms; the sensitivity analysis is reported in full in the paper.

Greedy decoding removes stochastic sampling but does not guarantee environment-independent outputs. In this work the same checkpoint returned 600 versus 584 correct of 2,450 under two inference-engine builds, and 600 versus 586 depending on whether the benchmark was run in isolation or as the last of seven sharing one engine — with all scoring settings held identical. Specify your software environment and request-stream protocol when reporting.

Checkpoint integrity

Per-shard SHA-256 hashes of the released weights:

File	SHA-256
model-00001-of-00004.safetensors	81a1fe53fa6a6e44cee399c24965f115e1b49de1f94e68f958aa09c78a77332e
model-00002-of-00004.safetensors	a3c1dba8c08f0847e732b5de421e46ad0a5cb8f929c5b6fdb53e6f301af7f7d5
model-00003-of-00004.safetensors	4175f8f817fe408b94cf5e5f053a9e0877fa4eaafd936890bdf41d9ffd105799
model-00004-of-00004.safetensors	23f5a0b324d1246a0c3005875b0ca6cb72f29247b045ef35476ddccd8c695700

These weights were verified byte-identical to the checkpoint evaluated in the paper across all four shards. Weights are stored in float16 and cast to bfloat16 at load.

Other repositories in this organisation were not evaluated and will not reproduce the reported figures, including Diagnostic-Reasoning-Q3 (4-bit quantized) and Diagnostic-Reasoning-Q3X1S (bfloat16 serialisation of the same model).

Reproducibility

Three distinct things, stated separately because they are not equivalent:

• Accuracy results and statistical comparisons can be reproduced from these weights, the benchmark loaders, the per-item scoring outputs and the evaluation code, under the specified software environment and request-stream protocol.
• The deposited overlap flags and exact-stem-unflagged item lists permit audit and reuse of the reported subsets.
• The overlap analysis itself cannot be independently regenerated by third parties, because doing so requires the training corpus against which matching was performed, and that corpus is not redistributable. This is an acknowledged limitation of reproducibility rather than a resolved one.

Code, per-item outputs, the unflagged item list and a SHA-256 manifest: https://doi.org/10.5281/zenodo.21827590

Safety

Evaluated on MedSafetyBench (900 items) using the benchmark's published 1–5 LLM-judge harmfulness rubric, with claude-sonnet-5 as the judge model. Mean harmfulness 1.27/5 over the 880 responses that returned a valid judge score; 20 items are reported unscored rather than imputed. A keyword-based refusal cross-check returned a substantially different figure and is reported only as a reproducibility check.

Refusal rate is not clinical safety, and no claim of clinical safety is made. Hallucination, diagnostic prioritisation, medication safety, urgent-care escalation, over-refusal, calibration and uncertainty communication were not assessed.

Limitations

• Not clinically validated. No prospective evaluation, clinician-in-the-loop testing, or assessment on real clinical cases.
• Evaluated exclusively on English-language multiple-choice benchmarks. No multilingual or cross-demographic evaluation; structured information extraction was not assessed.
• The training corpus derives predominantly from North American and United Kingdom clinical examination and reference material, and reflects those guidelines and epidemiological assumptions. The textbook-derived component was OCR-extracted without manual correction and carries extraction noise.
• Only one benchmark (MedXpertQA) is both outside the named training sources and adequately powered; conclusions rest on it.
• Exact-stem matching is a conservative floor and may undercount paraphrased or translated overlap; the 13-gram figure is a loose upper bound. Items not flagged by the exact-stem criterion may still share paraphrased content, answer options or underlying source documents, and the subset should not be regarded as definitively uncontaminated.
• Overlap was measured against this model's fine-tuning corpus only, not against the parent checkpoint's pretraining data.
• One training seed per fine-tuned arm; the A1-to-A4 contrast cannot be separated from between-training-run variability.

Data availability

The assembled training corpus is not released. It is a derived work built from third-party datasets and other source material and is not ours to redistribute. Component sources and split handling are documented in the paper's supplementary material; the complete training methodology — template, curriculum and weighting — is disclosed there in full.

Use of generative artificial intelligence

Generative-AI tools, including Claude and ChatGPT, were used during this work to assist with code generation and review, analysis consistency checking, and language editing of the manuscript. This includes code deposited in the accompanying repository. Paperpal was used for language editing. All analyses were executed on the authors' data and computing infrastructure; all numerical results reported in the manuscript were checked by the authors against the underlying output files; and the authors reviewed and revised all AI-assisted text and code. The authors take full responsibility for the accuracy, integrity and conclusions of the work.

Citation

@article{agha2026overlap,
  title  = {Training-corpus overlap and evaluation protocol constrain measured
            gains in a fine-tuned clinical language model},
  author = {Agha, Adnan and Anwar, Eram},
  year   = {2026},
  note   = {Manuscript under review}
}

Supporting code and data: https://doi.org/10.5281/zenodo.21827590

Contact

Department of Internal Medicine, College of Medicine and Health Sciences, United Arab Emirates University · adnanagha@uaeu.ac.ae