Cited by 30Artificial Intelligence in Healthcare and EducationMachine Learning in HealthcareAI in cancer detection

Large language model trained on clinical oncology data predicts cancer progression

Open access
Zhu, Menglei, Lin, Hui, Jiang, Jue, Jinia, Abbas J., Jee, Justin, Pichotta, Karl, Waters, Michele, Rose, Doori +11 more·2025·npj Digital Medicine

Abstract

Subspecialty knowledge barriers have limited the adoption of large language models (LLMs) in oncology. We introduce Woollie, an open-source, oncology-specific LLM trained on real-world data from Memorial Sloan Kettering Cancer Center (MSK) across lung, breast, prostate, pancreatic, and colorectal cancers, with external validation using University of California, San Francisco (UCSF) data. Woollie surpasses ChatGPT in medical benchmarks and excels in eight non-medical benchmarks. Analyzing 39,319 radiology impression notes from 4002 patients, it achieved an overall area under the receiver operating characteristic curve (AUROC) of 0.97 for cancer progression prediction on MSK data, including a notable 0.98 AUROC for pancreatic cancer. On UCSF data, it achieved an overall AUROC of 0.88, excelling in lung cancer detection with an AUROC of 0.95. As the first oncology specific LLM validated across institutions, Woollie demonstrates high accuracy and consistency across cancer types, underscoring its potential to enhance cancer progression analysis.

AI snapshot

Written from the paper’s full text.

TL;DR

Woollie, an open-source oncology-specific LLM built on Llama and trained on MSK clinical oncology data, predicts cancer progression from radiology impressions with high accuracy and validates externally at UCSF. It outperforms ChatGPT on medical benchmarks and demonstrates cross-institutional generalization across multiple cancer types.

Key findings

  • On MSK data, Woollie MSK 33B achieved an overall AUROC of 0.97 for cancer progression prediction, versus 0.87 for Llama 33B; Woollie MSK 7B achieved 0.94 versus 0.50 for Llama 7B. Pancreatic cancer detection reached AUROC 0.98 and accuracy 0.92.
  • On external UCSF validation, Woollie MSK 7B and 33B achieved AUROCs of 0.89 and 0.88, with accuracies of 0.80 and 0.78; lung cancer progression detection reached AUROC 0.95 and accuracy 0.88.
  • On medical benchmarks, Woollie 65B achieved accuracies of 0.81 on PubMedQA, 0.50 on MedMCQA, and 0.52 on USMLE, exceeding Llama 65B scores of 0.70, 0.37, and 0.42; PubMedQA performance matched GPT-4’s 0.804 and surpassed ChatGPT 3.5-turbo’s 0.7165.
  • Stacked alignment mitigated catastrophic forgetting: Woollie 33B achieved 0.43 on MMLU versus 0.40 for Woollie All 33B, and 0.79 on PubMedQA versus 0.70 for Woollie All 33B.

Methods

  • Trained fourteen Woollie models from Llama 1 at 7B, 13B, 33B, and 65B parameters using stacked alignment: non-medical datasets (Alpaca, Chain of Thought, InstructionWild, OASST1 subset), medical datasets (PubMedQA, MedQuAD, MedMCQA, USMLE), then oncology fine-tuning on MSK radiology impressions.
  • Main MSK dataset: 38,719 radiology impressions from 3402 patients across breast, colorectal, lung, pancreatic, and prostate cancers, with radiologist labels simplified to binary “Progressing” vs “Not Progressing”; split 80% training, 10% validation, 10% testing. External validation used 600 UCSF radiology impressions from 600 patients with lung, breast, and prostate cancers.
  • Evaluated with accuracy, AUROC, precision, recall, F1, and MCC; used zero-shot prompting, logits converted to probabilities for ROC/AUROC, and applied topic modeling with UMAP/HDBSCAN plus LIME for explainability.

Limitations

  • Stated: small sample sizes in certain age and race subgroups limit the ability to fully exclude performance variation; no significant performance differences were observed across age, birth sex, or race (p-values > 0.1), but underrepresentation may affect robustness. Performance differed significantly by cancer type (all p-values < 0.01).
  • Stated: reliance solely on free-text radiology impressions may introduce biases tied to institutional reporting styles; the impact of hedging language such as “possibility,” “cannot exclude,” or “likely” was not systematically studied. Future work should consider multimodal imaging.
  • Evident from the text: the abstract reports 39,319 radiology impression notes from 4002 patients, while the main text and methods report 38,719 notes from 3402/3401 patients; external validation is limited to one institution (UCSF) and excludes colorectal and pancreatic cancers; hallucination in generative use cases beyond those examined remains a stated area for further research.

Model-written summary. Check it against the paper before relying on it.

Integrity signals

Registry

Crossref · 10.1038/s41746-025-01780-2

Cites

36 of 36 references verified0 citation errors · 0 not checkable

Statistics

Nothing to recompute.

Claims the paper makes

0 of 14 cited sources checked · 0 supported · 0 flagged

  • Findingown data

    Woollie achieved an overall AUROC of 0.97 for cancer progression prediction on MSK data.

    “Analyzing 39,319 radiology impression notes from 4002 patients, it achieved an overall area under the receiver operating characteristic curve (AUROC) of 0.97 for cancer progression prediction on MSK data”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Findingnone given

    Woollie surpasses ChatGPT in medical benchmarks.

    “Woollie surpasses ChatGPT in medical benchmarks and excels in eight non-medical benchmarks.”
    Quote in the paperNot a substantial claim
  • Findingown data

    Woollie models exhibited superior capabilities in logic, conversation, and reasoning tasks compared to Llama models.

    “When compared to Llama models, Woollie models exhibited superior capabilities in logic, conversation, and reasoning tasks.”
    Quote in the paperNot a substantial claim
  • Findingown data

    Woollie achieved an AUROC of 0.98 for pancreatic cancer progression prediction on MSK data.

    “including a notable 0.98 AUROC for pancreatic cancer.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Findingown data

    Woollie achieved an AUROC of 0.95 for lung cancer detection on UCSF data.

    “excelling in lung cancer detection with an AUROC of 0.95.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Classified as probably not a substantial claim. 38
  • May combine two claims. 48
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingnone given

    Woollie excels in eight non-medical benchmarks.

    “Woollie surpasses ChatGPT in medical benchmarks and excels in eight non-medical benchmarks.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingnone given

    Woollie is an open-source, oncology-specific LLM trained on real-world data from Memorial Sloan Kettering Cancer Center (MSK) across lung, breast, prostate, pancreatic, and colorectal cancers, with external validation using University of California, San Francisco (UCSF) data.

    “We introduce Woollie, an open-source, oncology-specific LLM trained on real-world data from Memorial Sloan Kettering Cancer Center (MSK) across lung, breast, prostate, pancreatic, and colorectal cancers, with external validation using University of California, San Francisco (UCSF) data.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    For COQA, Woollie 65B achieved accuracy 0.78 versus Llama 65B 0.74, and F1 0.82 versus 0.77.

    “For the COQA benchmark, the Woollie 65B model achieved an accuracy of 0.78 compared to 0.74 for the Llama 65B model, and an F1 score of 0.82 versus 0.77.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Stylistic differences between MSK and UCSF reports exist.

    “Although we illustrate stylistic differences between MSK and UCSF reports (Supplementary Note 6), future work should consider incorporating imaging data into a multimodal LLM framework to mitigate such limitations and enhance model robustness.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    When evaluated within oncology, the Guanaco 65B model's performance did not measure up to Woollie MSK 7B, and it fell short compared to Woollie 33B without finetuning on the MSK dataset.

    “When we evaluated its performance within our specific field of oncology, despite its substantial 65 billion parameters—a figure nine times greater than that of a 7 billion parameter model—its performance did not measure up to our Woollie MSK 7B model. It even fell short compared to the Woollie 33B model without finetuning on the MSK dataset (Supplementary Fig. 6).”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [36] Dettmers, T., Pagnoni, A., Holtzman, A. & Zettlemoyer, L. Qlora: Efficient finetuning of quantized LLMs. In Advances in neural information processing Systems 36 (NIPS, 2024).

      Not checked in the free run.

  • May combine two claims.

    Findingown data

    The cross-institution validation of the Woollie model, validated on UCSF data, demonstrates that the smaller 7B model performs comparably and even slightly outperforms its larger 33B counterparts.

    “The cross-institution validation of the Woollie model, validated on UCSF data, demonstrates that the smaller 7B model performs comparably and even slightly outperforms its larger 33B counterparts.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingreasoning

    The model's generalizability is validated, with performance metrics of AUROC illustrating the model's capability to classify tumor progression accurately.

    “The model’s generalizability is validated, with performance metrics of AUROC illustrating the model’s capability to classify tumor progression accurately.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Woollie MSK 7B and 33B achieved AUROCs of 0.89 and 0.88, with accuracies of 0.80 and 0.78, respectively, in detecting cancer progression on the UCSF dataset.

    “The Woollie MSK 7B and 33B models were tested on this dataset and achieved AUROCs of 0.89 and 0.88, with accuracies of 0.80 and 0.78, respectively, in detecting cancer progression”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Classified as probably not a substantial claim. May combine two claims.

    Findingown data

    Woollie highlights terms like "FDG" and "Increase" in notes labeled as "Progressing," while also recognizing the influence of words such as "small" and "mild" in notes classified as "Not Progressing."

    “Woollie highlights terms like “FDG” and “Increase” in notes labeled as “Progressing,” while also recognizing the influence of words such as “small” and “mild” in notes classified as “Not Progressing.””
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Woollie MSK 33B improved over baseline Woollie on PubMedQA from 0.80 to 0.83, MedMCQA from 0.45 to 0.48, and USMLE from 0.49 to 0.53.

    “Compared to the baseline Woollie models, the accuracy of Woollie MSK 33B increased from 0.80 to 0.83 in PubMedQA, from 0.45 to 0.48 in MedMCQA, and from 0.49 to 0.53 in USMLE.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.

    Findingreasoning

    Woollie adeptly summarizes the salient themes within medical radiology reports, pinpointing intricate details of disease progression and the exact locations of metastatic spread amidst a wealth of medical data.

    “Woollie adeptly summarizes the salient themes within medical radiology reports, pinpointing intricate details of disease progression and the exact locations of metastatic spread amidst a wealth of medical data.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Woollie MSK 7B improved over baseline Woollie on PubMedQA from 0.72 to 0.79, MedMCQA from 0.32 to 0.35, and USMLE from 0.33 to 0.38.

    “A similar trend was observed in the smaller Woollie MSK 7B model, where accuracy improved from 0.72 to 0.79 in PubMedQA, from 0.32 to 0.35 in MedMCQA, and from 0.33 to 0.38 in USMLE”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Woollie MSK 33B achieved AUROC 0.97, compared to Llama 33B AUROC 0.87.

    “Similarly, Woollie MSK 33B surpassed the baseline Llama 33B model with an AUROC of 0.97, compared to 0.87”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • May combine two claims.

    Findingown data

    Although the 33B model's AUROC was slightly lower than the 7B's, its precision in detecting cancer progression was higher at 0.95 compared to 0.78.

    “A precision comparison across models, including the baseline Llama (Fig. 5e), using both MSK and UCSF datasets revealed that although the 33B model’s AUROC was slightly lower than the 7B’s, its precision in detecting cancer progression was higher at 0.95 compared to 0.78”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • May combine two claims.

    Findingown data

    Woollie MSK 7B outperformed all competing 65B models (Llama, Woollie Foundation, Woollie Medicine, Woollie) in binary classification of cancer progression, achieving overall accuracy 0.86 across all disease sites in the rad_imp test.

    “When evaluating cancer progression as a binary classification within the test dataset, Woollie MSK 7B outperformed all competing 65B models (Llama, Woolie Foundation, Woollie Medicine, Woollie), achieving an overall accuracy of 0.86 across all disease sites in the “rad_imp” test.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Classified as probably not a substantial claim. May combine two claims.

    Findingown data

    Woollie distilled the primary themes of each report, exhibiting not just the presence or absence of disease progression but further detailing the sites of disease progression.

    “Woollie distilled the primary themes of each report (Fig. 6a–f), exhibiting not just the presence or absence of disease progression but further detailing the sites of disease progression.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Woollie 65B performance on PubMedQA matched GPT-4's accuracy of 0.804 and significantly surpassed ChatGPT (3.5-turbo)'s accuracy of 0.7165.

    “Notably, the Woollie 65B model’s performance on PubMedQA matched GPT-4’s accuracy of 0.804 and significantly surpassed ChatGPT (3.5-turbo)’s accuracy of 0.7165”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Woollie 65B achieved accuracies of 0.81 on PubMedQA, 0.50 on MedMCQA, and 0.52 on USMLE, exceeding Llama 65B scores of 0.70, 0.37, and 0.42.

    “Specifically, the Woollie 65B model marked substantial improvements, achieving accuracies of 0.81 on PubMedQA, 0.50 on MedMCQA, and 0.52 on USMLE—exceeding the Llama 65B model’s scores of 0.70, 0.37, and 0.42, respectively”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Llama performance generally improved with size, except on PubMedQA where accuracy was 0.71 for 7B, 0.67 for 13B, 0.66 for 33B, and 0.70 for 65B.

    “Llama showed that performance generally improved with size, except on the PubMedQA tests, where the accuracy was 0.71 for 7B, 0.67 for 13B, 0.66 for 33B, and 0.70 for 65B”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S2 (checkable).

    Findingreasoning

    By preserving general domain competencies of reasoning, conversation, and information extraction while enhancing medical domain proficiency, the aligned models demonstrated a strong foundation for further specialization.

    “By preserving general domain competencies of reasoning, conversation, and information extraction while enhancing medical domain proficiency, the aligned models demonstrated a strong foundation for further specialization.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    On PubMedQA, Woollie 33B achieved accuracy 0.7980, while 65B reached 0.8092.

    “For instance, on the PubMedQA benchmark, the Woollie 33B model achieved an accuracy of 0.7980, while the 65B model reached 0.8092.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    As more medical datasets were integrated, non-medical performance slightly declined while medical domain proficiency increased.

    “As more medical datasets were integrated into the alignment process, a distinct trend appeared: non-medical performance slightly declined while medical domain proficiency increased.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Woollie All outperformed baseline Llama models but had significant performance gaps compared to Woollie models aligned with the stacked alignment strategy.

    “While Woollie All outperformed the baseline Llama models, significant performance gaps were evident when compared to Woollie models aligned with the stacked alignment strategy.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Woollie MSK 7B achieved AUROC 0.94 across all disease sites, outperforming base Llama 7B AUROC 0.50.

    “Comparing the Woollie MSK models to the Llama models, Woollie MSK 7B achieved an impressive AUROC of 0.94 across all disease sites, significantly outperforming the base Llama 7B model’s AUROC of 0.50.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • May combine two claims.

    Findingown data

    Larger models generally yield better performance in binary classification, but Woollie 65B accuracy slightly lagged behind 33B, with 0.77 versus 0.79.

    “The binary classification results indicated that larger models generally yield better performance; however, interestingly, the Woollie 65B model’s accuracy slightly lagged behind the 33B model, with accuracy of 0.77 versus 0.79 for the 33B model.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    On PubMedQA, Woollie 33B achieved accuracy 0.79 versus Woollie All 33B 0.70.

    “Similarly, on PubMedQA, Woollie 33B achieved an accuracy of 0.79, significantly outperforming Woollie All 33B at 0.70.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    Model performance differed significantly by cancer type (Supplementary Table 5b), with all associated p-values below 0.01.

    “In contrast, model performance differed significantly by cancer type (Supplementary Table 5b), with all associated p-values below 0.01.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Findingown data

    The 7B model is more economically viable for clinical applications due to its lower memory footprint, reduced energy consumption, and less demanding CPU and GPU requirements.

    “When comparing the resource usage of deploying 33B models versus smaller 7B models, we found that the 7B model is more economically viable for clinical applications due to its lower memory footprint, reduced energy consumption, and less demanding CPU and GPU requirements.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Findingown data

    The proportion of Not Progressing labels is roughly equal to that of Progressing labels, except in lung cancer cases, which show a slight skew toward Not Progressing.

    “The proportion of “Not Progressing” labels is roughly equal to that of “Progressing” labels, except in lung cancer cases, which show a slight skew toward “Not Progressing””
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingreasoning

    Performance improvement was observed from 0-shot to 1-shot learning, but further increases in the number of shots showed minimal improvement or, in some cases, a decline in performance.

    “While we observed a performance improvement from 0-shot to 1-shot learning, further increases in the number of shots showed minimal improvement or, in some cases, a decline in performance.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Findingown data

    Examination of fourteen distinct Woollie models revealed a slight decrease in general performance following domain-specific training that was not otherwise substantial while demonstrating marked improvement in domain-specific knowledge.

    “Our examination of fourteen distinct Woollie models revealed a slight decrease in general performance following domain-specific training that was not otherwise substantial while demonstrating marked improvement in domain-specific knowledge.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S4 (based). May combine two claims.

    Findingnone given

    Training tailored to one proprietary dataset improved performance in the oncology domain and enhanced performance across other general medical domains and oncology institutions.

    “Training tailored to one proprietary dataset improved performance in the oncology domain and enhanced performance across other general medical domains and oncology institutions.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Findingown data

    Out of 38,719 impression notes, 2467 contained physician names, which were masked as [[PERSON]].

    “Out of 38,719 impression notes, 2467 contained physician names, which we masked as [[PERSON]].”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S4 (based).

    Interpretationreasoning

    High scores on standard medical benchmarks do not necessarily equate to increased effectiveness when using real-world data in healthcare, especially in oncology.

    “However, achieving high scores on these benchmarks does not necessarily equate to increased effectiveness when using RWD in healthcare practices, especially in the oncology sector.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Premisecitation

    Specialized medical models frequently lack in-depth expertise in oncology and have not been validated across multiple institutions.

    “Like their general domain counterparts, these specialized medical models frequently lack in-depth expertise in oncology and have not been validated across multiple institutions.”
    Quote in the paperSubstantial claim0 of 3 sources checked
    • cites [13] Bolton, E. et al. Biomedlm: A 2.7 b parameter language model trained on biomedical text. Preprint at https://arxiv.org/abs/2403.18421 (2024).

      Not checked in the free run.

    • cites [14] Luo, R. et al. BioGPT: generative pre-trained transformer for biomedical text generation and mining. Brief. Bioinformatics 23, https://doi.org/10.1093/bib/bbac409 (2022). source

      Not checked in the free run.

    • cites [15] Yang, X. et al. A large language model for electronic health records. npj Digital Med. 5, 194. https://doi.org/10.1038/s41746-022-00742-2 (2022). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductnone given

    Configuring inference settings with temperature 0.01 and top_p 1.0 effectively minimizes randomness, ensuring deterministic model behavior.

    “When utilizing Woollie as a classifier, we configured the inference settings with a temperature of 0.01 and top_p of 1.0. This setup effectively minimizes randomness, ensuring deterministic model behavior.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationnone given

    Reliance solely on free-text radiology impressions may introduce biases tied to institutional reporting styles.

    “Additionally, reliance solely on free-text radiology impressions may introduce biases tied to institutional reporting styles.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

    Interpretationreasoning

    Woollie's proficiency indicates potential for comprehending the intent behind medical imaging and for mapping out and succinctly encapsulating the complex pathways of disease evolution across diverse organ systems.

    “This proficiency indicates Woollie’s potential not just for comprehending the intent behind medical imaging but also for mapping out and succinctly encapsulating the complex pathways of disease evolution across diverse organ systems (Fig. 6).”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationown data

    The LLM can serve as a foundational model that can adapt to various tasks, particularly in medical contexts.

    “This underscores the LLM’s role as a foundational model that can adapt to various tasks, particularly in medical contexts.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    Woollie's efficacy in general medical contexts is underscored and the stacked alignment strategy is validated.

    “These results underscore Woollie’s efficacy in general medical contexts and validate the effectiveness of our stacked alignment strategy”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Premisecitation

    Our approach, using a single model, contrasts with similar studies on metastatic disease that employ multiple models.

    “Our approach, using a single model, contrasts with similar studies on metastatic disease that employ multiple models35, offering potential for new insights into disease progression pathways that have not been thoroughly explored yet.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [35] Do, R. K. G. et al. Patterns of metastatic disease in patients with cancer derived from natural language processing of structured CT radiology reports over a 10-year period. Radiology 301, 115–122(2021). source

      Not checked in the free run.

  • May combine two claims.

    Interpretationown data

    Despite the marginal decrease in non-medical domain performance, the aligned models' capabilities remained robust and competitive.

    “Despite the marginal decrease in non-medical domain performance among the aligned models, their capabilities remained robust and competitive.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    Using LLMs in oncology for purposes like tracking cancer progression and analyzing reports proves viable and advantageous.

    “Considering the cost implications, using LLMs in oncology for purposes like tracking cancer progression and analyzing reports proves viable and advantageous.”
    Quote in the paperSubstantial claim
  • May combine two claims.

    Interpretationown data

    Woollie models demonstrated effective knowledge transfer, affirming their utility in diverse oncological settings across institutions.

    “Although there was a slight drop in performance compared to the MSK data, the Woollie models demonstrated effective knowledge transfer, affirming their utility in diverse oncological settings across institutions.”
    Quote in the paperSubstantial claim
    • Rests on an assumption: Radiology impression notes contain sufficient information to determine cancer progression.
    • Rests on an assumption: The radiologist-assigned progression labels are a valid reference standard for cancer progression.
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing).

    Interpretationreasoning

    These variations likely reflect differences in reporting style and diagnostic emphasis across anatomical sites, which influence the content and structure of radiology impressions.

    “These variations likely reflect differences in reporting style and diagnostic emphasis across anatomical sites, which influence the content and structure of radiology impressions.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationown data

    Models with a more extensive parameter base before alignment yielded better outcomes, with performance scaling almost linearly between 7B and 33B.

    “This trend affirmed that models with a more extensive parameter base before alignment yielded better outcomes, with the performance scaling almost linearly with sizes between 7B and 33B.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    Aligning and fine-tuning LLMs within oncology without losing prior knowledge can be achieved by selecting high-quality datasets and employing a stacked alignment methodology.

    “This can be achieved by selecting high-quality datasets and employing a stacked alignment methodology.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.

    Interpretationreasoning

    Woollie's capabilities extend beyond mere data interpretation to an in-depth understanding of cancer biology, positioning it well beyond conventional topic modeling methods.

    “Woollie’s capabilities extend beyond mere data interpretation to an in-depth understanding of cancer biology, positioning it well beyond conventional topic modeling methods.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    The 7B model's smaller parameters make it an attractive option for widespread clinical use, capable of running on a single GPU for inference, eliminating the need for specialized centralized computing resources.

    “The 7B model’s smaller parameters makes it an attractive option for widespread clinical use, capable of running on a single GPU for inference, thus eliminating the need for specialized centralized computing resources.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: Performance on retrospective radiology impression datasets is indicative of potential clinical utility as real-time assistants for oncologists.
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    The discrepancy suggests a common trade-off in larger models like the 33B, which typically exhibit low bias but high variance, making them adept at fitting training data closely.

    “This discrepancy suggests a common trade-off in larger models like the 33B, which typically exhibit low bias but high variance, making them adept at fitting training data closely.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationreasoning

    Underrepresentation in specific subgroups may impact model robustness.

    “While radiology impression narratives appear largely independent of these demographic factors, underrepresentation in specific subgroups may impact model robustness.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: The datasets from MSK and UCSF differ in the sociodemographic composition of their patient populations.
  • Probably not a substantial claim: may not pass S2 (checkable).

    Interpretationreasoning

    Choosing a baseline model with adequate parameters is crucial for successful alignment and fine-tuning, as the knowledge acquired during pre-training plays a significant role in performance on downstream tasks.

    “Additionally, choosing a baseline model with adequate parameters is crucial for successful alignment and fine-tuning, as the knowledge acquired during pre-training plays a significant role in performance on downstream tasks.”
    Quote in the paperNot a substantial claim
  • May combine two claims.

    Interpretationreasoning

    The approach fortified the model's foundation and optimized it for oncology-specific applications, demonstrating improved performance upon further fine-tuning with oncology datasets.

    “Our approach fortified the model’s foundation and optimized it for oncology-specific applications, demonstrating improved performance upon further fine-tuning with oncology datasets.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Interpretationreasoning

    Predictions are based solely on the knowledge acquired during the model's alignment and fine-tuning processes.

    “Predictions are based solely on the knowledge acquired during the model’s alignment and fine-tuning processes.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Interpretationreasoning

    Combining insights from LLM-based topic modeling and LIME explanations highlights the knowledge acquired by the Woollie models and bolsters confidence in their explainability for clinical use.

    “Combining insights from LLM-based topic modeling and LIME explanations highlights the knowledge acquired by the Woollie models and bolsters confidence in their explainability for clinical use.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductnone given

    All MSK patients included in this study were part of IRB-approved research protocols, and the study received independent approval from UCSF; patients provided written, informed consent and were enrolled in a continuous, non-random fashion.

    “All MSK patients included in this study were part of institutional review board (IRB)-approved research protocols (MSK IRB Protocols 12–245). Additionally, the study received independent approval from the UCSF (UCSF IRB Protocols 20–32527). Patients provided written, informed consent and were enrolled in a continuous, non-random fashion.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Interpretationnone given

    This approach helps gauge the extent of cancer biology knowledge the model has assimilated during its fine-tuning phase.

    “This approach helps us gauge the extent of cancer biology knowledge the model has assimilated during its fine-tuning phase.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductreasoning

    AUROC was selected as a primary performance metric due to its robustness and widespread use in evaluating a model's ability to distinguish between classes across various decision thresholds.

    “AUROC was selected as a primary performance metric due to its robustness and widespread use in evaluating a model’s ability to distinguish between classes across various decision thresholds.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Study design and conductcitation

    The Language Model Evaluation Harness framework is a standard tool used across the open-source LLM community for evaluating model effectiveness.

    “To test their performance, we employed the Language Model Evaluation Harness framework50, a standard tool used across the open-source LLM community for evaluating model effectiveness.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [50] Gao, L. et al. A framework for few-shot language model evaluation (Zenodo, 2021).

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Study design and conductown data

    During evaluations and testing, setting the model's generation temperature to 0.01 and top_p to 1.0 minimized randomness and ensured deterministic behavior; repeated tasks showed no randomness, with performance metrics remaining constant across runs.

    “During evaluations and testing, we set the model’s generation temperature to 0.01 and top_p to 1.0 to minimize randomness and ensure deterministic behavior, as the model is being used as a classifier. Additionally, we repeated the same tasks multiple times and observed no randomness, with the performance metrics remaining constants across runs.”
    Quote in the paperNot a substantial claim
  • Probably not a substantial claim: may not pass S2 (checkable). May combine two claims.

    Interpretationreasoning

    Once fine-tuned, an LLM can serve multiple functions across various subspecialties, making it an invaluable tool for oncology clinics and research.

    “Once fine-tuned, an LLM can serve multiple functions across various subspecialties, making it an invaluable tool for oncology clinics and research.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim. May combine two claims.

    Premisecitation

    HDBSCAN is adept at clustering outputs from LLMs due to its ability to manage clusters with varied densities, autonomously identify the number of clusters, and filter out noise as outlier data.

    “HDBSCAN is adept at clustering outputs from LLMs due to its ability to manage clusters with varied densities, autonomously identify the number of clusters, and filter out noise as outlier data.”
    Quote in the paperSubstantial claim0 of 1 sources checked
    • cites [54] Campello, R., Moulavi, D. & Sander, J. (2013). Density-Based Clustering Based on Hierarchical Density Estimates. 7819, 160–172. https://doi.org/10.1007/978-3-642-37456-2_14. source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing).

    Interpretationcitation

    This decline may be attributed to the model nearing its maximum context size, causing it to lose focus on content in the middle of the sequence.

    “This decline may be attributed to the model nearing its maximum context size, causing it to lose focus on content in the middle of the sequence47.”
    Quote in the paperNot a substantial claim0 of 1 sources checked
    • cites [47] Liu, N. F. et al. Lost in the middle: how language models use long contexts. Trans. Assoc. Computational Linguist. 12, 157–173 (2024). source

      Not checked in the free run.

  • Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

    Interpretationreasoning

    Once downloaded to a local environment, the model can function without an external network connection, allowing it to be used on PHI data while ensuring the dataset remains secure and does not transmit outside the system.

    “Once downloaded to a local environment, the model can function without an external network connection, allowing it to be used on PHI data while ensuring the dataset remains secure and does not transmit outside the system.”
    Quote in the paperNot a substantial claim
  • Classified as probably not a substantial claim.

    Study design and conductnone given

    The radiologist has manually annotated the dataset.

    “The radiologist has manually annotated the dataset.”
    Quote in the paperSubstantial claim
  • Classified as probably not a substantial claim.

    Premisereasoning

    AUROC is effective in handling imbalanced datasets by focusing on true positive and false positive rates rather than absolute counts.

    “Furthermore, AUROC is effective in handling imbalanced datasets by focusing on true positive and false positive rates rather than absolute counts, providing a balanced evaluation even when class distributions are uneven.”
    Quote in the paperSubstantial claim
  • Probably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).

    Interpretationreasoning

    This capability is essential for oncological tasks where clinicians or researchers require precise answers to questions about tumor progression, diagnostic accuracy, or treatment efficacy based on imaging data.

    “This capability is essential for oncological tasks where clinicians or researchers require precise answers to questions about tumor progression, diagnostic accuracy, or treatment efficacy based on imaging data.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: OpenAssistant is a Q&A dataset that trains the model to respond effectively to specific and often domain-specific queries.
  • Probably not a substantial claim: may not pass S2 (checkable), S4 (based). May combine two claims.

    Interpretationreasoning

    These skills translate directly into the ability to parse nuanced medical terminology, infer progression or stability.

    “These skills translate directly into the ability to parse nuanced medical terminology, infer progression or stability.”
    Quote in the paperNot a substantial claim
    • Rests on an assumption: OpenAssistant is a Q&A dataset that trains the model to respond effectively to specific and often domain-specific queries.
68 of 68
  • The paper relies on this without support.

    Radiology impression notes contain sufficient information to determine cancer progression.

    “For oncologists, the impression section of radiology reports provides comprehensive insights into tumor location, size, and changes over time—critical factors for determining cancer staging and guiding treatment strategies.”
  • The paper relies on this without support.

    The radiologist-assigned progression labels are a valid reference standard for cancer progression.

    “These radiology impressions, gathered from MSK30, were thoroughly reviewed and labeled by radiologists with five categories indicating cancer progression”
  • The paper relies on this without support.

    Performance on retrospective radiology impression datasets is indicative of potential clinical utility as real-time assistants for oncologists.

    “this study was driven by the potential use case of deploying LLMs as real-time assistants for oncologists while they enter patient information into electronic health record systems.”
  • The paper relies on this without support.

    LLM performance in real-world oncology data has not been extensively studied.

    “This aspect of LLM performance, especially in real-world oncology data, has not been extensively studied.”
  • The paper relies on this without support.

    The datasets from MSK and UCSF differ in the sociodemographic composition of their patient populations.

    “The datasets from MSK and UCSF differ in the sociodemographic composition of their patient populations, making it important to evaluate the model’s generalizability across subgroups defined by “Age”, “Birth sex”, and “Race”.”
  • The paper relies on this without support.

    The use of human-curated labels helps transfer sentiment, contextual understanding, and domain knowledge into the LLM.

    “While the use of human-curated labels helps transfer sentiment, contextual understanding, and domain knowledge into the LLM, the specific impact of such uncertain phrasing has not been systematically studied and warrants dedicated investigation, which was beyond the scope of this work.”
  • The paper relies on this without support.

    OpenAssistant is a Q&A dataset that trains the model to respond effectively to specific and often domain-specific queries.

    “OpenAssistant is the Q&A datasets that train the model to respond effectively to specific and often domain-specific queries.”
  • The paper relies on this without support.

    Some performance degradation is expected when encountering new datasets.

    “While some performance degradation is expected when encountering new datasets, the overall performance remains remarkable.”
8 of 8

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • Woollie, an oncology-specific LLM, achieved an AUROC of 0.97 for progression prediction on internal validation and 0.88 on external validation at UCSF.

    “trained on real-world data from Memorial Sloan Kettering Cancer Center across lung, breast, prostate, pancreatic, and colorectal cancers, it achieved an area under the receiver operating characteristic curve (AUROC) of 0.97 for progression prediction, with external validation at University of California, San Francisco (UCSF) showing an AUROC of 0.88 [50].”

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

Each contradiction between two passages listed here was confirmed by an independent check.

  • Five-class AUROC averaging method conflicts with reported micro-average

    Minor

    The results call the five-label AUROC micro-averaged, while the Methods describe calculating an AUROC for each class and averaging those values. Averaging class-level AUROCs is not a micro-average.

  • MSK patient count differs by one

    Minor

    The MSK radiology impression dataset is described as containing 3401 patients here, but elsewhere the same 38,719-report dataset is said to contain 3402 patients.

  • UCSF cancer types are described as different from MSK's

    Minor

    The three UCSF cancer types are all included in the paper's list of MSK cancer types, rather than being different from them.

  • Woollie 33B PubMedQA accuracy is reported inconsistently

    Minor

    The same model's PubMedQA accuracy is given as 0.79 and, later, 0.7980. The latter rounds to 0.80, not 0.79, at two decimal places.

4 of 4

Cites

Flagged first, then by citations

1 of the 37 references couldn’t be matched to a known paper.

Research works printed but not linked: 12

  1. Eloundou, T., Manning, S., Mishkin, P. & Rock, D. Gpts are gpts: an early look at the labor market impact potential of large language models. Preprint at https://arxiv.org/abs/2303.10130 (2023). · arXiv
  2. Nori, H., King, N., McKinney, S. M., Carignan, D. & Horvitz, E. Capabilities of gpt-4 on medical challenge problems. Preprint at https://arxiv.org/abs/2303.13375 (2023). · arXiv
  3. Bolton, E. et al. Biomedlm: A 2.7 b parameter language model trained on biomedical text. Preprint at https://arxiv.org/abs/2403.18421 (2024). · arXiv
  4. Pal, A., Logesh, K. U. & Malaikannan, S. Medmcqa: A large-scale multi-subject multi-choice dataset for medical domain question answering. Conference on health, inference, and learning. (PMLR, 2022).
  5. Mihaylov, T., Clark, P., Khot, T. & Sabharwal, A. in Conference on Empirical Methods in Natural Language Processing.
  6. Achiam, J. et al. Gpt-4 technical report. Preprint at https://arxiv.org/abs/2303.08774 (2023). · arXiv
  7. Blei, D. M., Ng, A. Y. & Jordan, M. I. Latent dirichlet allocation. J. Mach. Learn. Res. 3, 993–1022 (2003).
  8. Ribeiro, M. T., Singh, S. & Guestrin, C. in Proceedings of the 22nd ACM SIGKDD international conference on knowledge discovery and data mining. 1135–1144.
  9. Dettmers, T., Pagnoni, A., Holtzman, A. & Zettlemoyer, L. Qlora: Efficient finetuning of quantized LLMs. In Advances in neural information processing Systems 36 (NIPS, 2024).
  10. Liu, Y. RoBERTa: a robustly optimized bert pretraining approach. Preprint at https://arxiv.org/abs/1907.11692 (2019). · arXiv
  11. Honnibal, M., Montani, I., Van Landeghem, S. & Boyd, A. spaCy: industrial-strength natural language processing in python. https://arxiv.org/abs/1907.11692 (2020). · arXiv
  12. Grootendorst, M. BERTopic: Neural topic modeling with a class-based TF-IDF procedure. Preprint at https://arxiv.org/abs/2203.05794 (2022). · arXiv

Cited by

Sorted by citations

Authors
Zhu, M., Lin, H., Jiang, J., Jinia, A. J., Jee, J., Pichotta, K., Waters, M., Rose, D., Schultz, N., Chalise, S., Valleru, L., Morin, O., Moran, J., Deasy, J. O., Pilai, S., Nichols, C., Riely, G., Braunstein, L. Z., & Li, A.
Affiliations
  • Memorial Sloan Kettering Cancer Center (US)
  • University of California, San Francisco (US)
Corresponding author
  • Braunstein, Lior Z.
  • Li, Anyi
Venue
npj Digital Medicine
Published
2025-07-02
Volume
8
Issue
1
Pages
397-397
ISSN
2398-6352 (ISSN-L)
OpenAlex
W4411919356
Cited by
30
References
37
Citations by year
2026: 25 · 2025: 5
FWCI
7.22
Type
journal article
Language
en
Open access
Locations
  • npj Digital Medicine (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
U.S. Department of Health & Human Services | NIH | National Cancer Institute (P30 CA008748)
Topics
  • Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
  • Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
  • Physical Sciences › Computer Science › Artificial Intelligence › AI in cancer detection
Keywords
large language models, tumor progression prediction, external validation, lung cancer, breast cancer, prostate cancer, pancreatic cancer, colorectal cancer, clinical natural language processing, open-source AI models

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Claims read by deepseek-v4.1-flash under definition version 3 (extract-v3) on 2026-10-07.

Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-07.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

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