Comparison of techniques for fine-tuning open-weight models for entity extraction from radiology reports

arXiv:2609.40236v1 Announce Type: new Abstract: Converting free-text radiology reports into structured labels supports cohort building, quality assurance, and monitoring of clinical imaging models, but the strongest label extractors are hosted proprietary models whose use raises privacy, cost, and reproducibility concerns. We asked whether a fine-tuned open-weight model (Gemma-3-12B) can match GPT-4o at multi-label intracranial hemorrhage (ICH) acuity extraction from non-contrast head-CT reports, and which ingredients matter. Using a 2x2 design, we crossed two adaptation strategies (a discriminative classification head, CH; generative instruction fine-tuning, IFT) with two training-data sources (distillation of real GPT-4o-labeled reports; synthetic reports generated by GPT-4o from real exemplars), across five training sizes, benchmarked on 100 expert-adjudicated reports against GPT-4o and the un-tuned open-weight base. The distilled instruction-tuned model (DIFT) matched GPT-4o (macro-F1 0.845 vs 0.850; p = 1.000) and exceeded the base model by 0.178. The decisive factor was the training-data source, not the fine-tuning method: both synthetic-data models failed to exceed the un-tuned open-weight base at any training size and underperformed the distilled models across all acuity classes. Fine-tuning and inference fit within the memory envelope of a single 24 GB consumer GPU. For narrow, high-value clinical label-extraction tasks, distilling real reports, rather than generating synthetic ones, is what closes the gap to a hosted model, enabling a private, low-cost, version-stable on-premises alternative.

Authors:Aawez Mansuri, Kush Mehta, Mohammadreza Chavoshi, Jahanzaib Malik, Theodorus Dapamede, Frank Li, Rohan Isaac, Beatrice Brown-Mulry, Chiratidzo Rudado Sanyika, YoungSeok Jeon, Judy W. Gichoya, Ali Emami, Hari Trivedi

Abstract:Converting free-text radiology reports into structured labels supports cohort building, quality assurance, and monitoring of clinical imaging models, but the strongest label extractors are hosted proprietary models whose use raises privacy, cost, and reproducibility concerns. We asked whether a fine-tuned open-weight model (Gemma-3-12B) can match GPT-4o at multi-label intracranial hemorrhage (ICH) acuity extraction from non-contrast head-CT reports, and which ingredients matter. Using a 2x2 design, we crossed two adaptation strategies (a discriminative classification head, CH; generative instruction fine-tuning, IFT) with two training-data sources (distillation of real GPT-4o-labeled reports; synthetic reports generated by GPT-4o from real exemplars), across five training sizes, benchmarked on 100 expert-adjudicated reports against GPT-4o and the un-tuned open-weight base. The distilled instruction-tuned model (DIFT) matched GPT-4o (macro-F1 0.845 vs 0.850; p = 1.000) and exceeded the base model by 0.178. The decisive factor was the training-data source, not the fine-tuning method: both synthetic-data models failed to exceed the un-tuned open-weight base at any training size and underperformed the distilled models across all acuity classes. Fine-tuning and inference fit within the memory envelope of a single 24 GB consumer GPU. For narrow, high-value clinical label-extraction tasks, distilling real reports, rather than generating synthetic ones, is what closes the gap to a hosted model, enabling a private, low-cost, version-stable on-premises alternative.

Computation and Language (cs.CL); Machine Learning (cs.LG)

arXiv:2609.40236 [cs.CL]

(or arXiv:2609.40236v1 [cs.CL] for this version)

https://doi.org/10.48550/arXiv.2609.40236 arXiv-issued DOI via DataCite (pending registration)

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Comparison of techniques for fine-tuning open-weight models for entity extraction from radiology reports

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