Large language model trained on clinical oncology data predicts cancer progression
Open accessAbstract
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.
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Cites
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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.
- Findingown data
Woollie achieved an overall AUROC of 0.88 on UCSF data.
“On UCSF data, it achieved an overall AUROC of 0.88”
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 MSK 33B achieved overall accuracy 0.90 in binary classification of cancer progression across all disease sites in the rad_imp test.
“Woollie MSK 33B showed even greater efficacy, achieving an overall accuracy of 0.90”
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
A modest performance improvement was noted between the 33B and 65B models.
“Nevertheless, a modest performance improvement was noted in this scaling trend when comparing the 33B and 65B models, both pre-trained on datasets of identical size (1.4 trillion tokens).”
Quote in the paperNot a substantial claim - Findingown data
Larger models significantly outperform smaller ones.
“Our scaling studies indicate that larger models significantly outperform smaller ones.”
Quote in the paperNot a substantial claim - Findingown data
For the 33B models, micro-averaged AUROC escalated from 0.80 to 0.97.
“For the 33B models, it escalated from 0.80 to 0.97”
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
The 7B model is three times faster than the 33B model.
“Specifically, the 7B model is three times faster than the 33B model (Supplementary Table 2).”
Quote in the paperSubstantial claim - Findingcitation
Woollie plausibly identified the most frequent sites of metastatic involvement otherwise known to be associated with the evaluated cancers (e.g., brain or bone metastases among the breast cancer cohort or hepatic metastases for colorectal cancer).
“Notably, Woollie plausibly identified the most frequent sites of metastatic involvement that are otherwise known to be associated with the evaluated cancers (e.g., brain or bone metastases among the cohort with breast cancer or hepatic metastases for those with colorectal cancer32,33).”
Quote in the paperNot a substantial claim0 of 2 sources checked- cites [32] Kennecke, H. et al. Metastatic behavior of breast cancer subtypes. J. Clin. Oncol. 28, 3271–3277, https://doi.org/10.1200/jco.2009.25.9820 (2010). source
Not checked in the free run.
- cites [33] Patanaphan, V. & Salazar, O. M. Colorectal cancer: metastatic patterns and prognosis. South Med. J. 86, 38–41 (1993). source
Not checked in the free run.
- Findingown data
Woollie MSK models were particularly effective in detecting pancreatic cancer, achieving AUROC 0.98 and accuracy 0.92.
“These models were particularly effective in detecting pancreatic cancer, achieving an AUROC of 0.98 and an accuracy of 0.92”
Quote in the paperNot a substantial 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
No significant differences in performance were observed across demographic groups defined by Age, Birth sex, and Race (p-values > 0.1).
“No significant differences in performance were observed across these demographic groups (p-values > 0.1).”
Quote in the paperSubstantial claim- Rests on an assumption: The datasets from MSK and UCSF differ in the sociodemographic composition of their patient populations.
- Findingnone given
Woollie All models' performance remains significantly lower than that of the Woollie models.
“However, their performance remains significantly lower than that of the Woollie models.”
Quote in the paperNot a substantial claim - Findingown data
Woollie MSK 33B had high precision in detecting lung cancer progression at 0.99.
“with high precision in detecting lung cancer progression at 0.99.”
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 models significantly outperformed Llama models in medical domain tests PubMedQA, MedMCQA, and USMLE.
“In the medical domain, the Woollie models significantly outperformed the Llama models in tests such as PubMedQA, MedMCQA, and USMLE.”
Quote in the paperSubstantial claim - Findingown data
The inclusion of oncology domain knowledge from radiology impression has enhanced the model's performance on standard medical benchmarks like PubMedQA.
“The inclusion of oncology domain knowledge from radiology impression has also enhanced the model’s performance on standard medical benchmarks like PubMedQA (Fig. 4b).”
Quote in the paperNot a substantial claim - Findingown data
Knowledge transfer between proprietary data and standard benchmarks is not evident.
“Knowledge transfer between proprietary data and standard benchmarks is not evident.”
Quote in the paperSubstantial claim - Findingnone given
The stacked alignment approach has shown the ability to prevent catastrophic forgetting, ensuring the model retains comprehensive capabilities while specializing in medical knowledge.
“This approach has shown the ability in preventing catastrophic forgetting, ensuring the model retains comprehensive capabilities while specializing in medical knowledge.”
Quote in the paperSubstantial claim - Findingown data
Woollie MSK 33B showed a slight decrease in AUROC on the UCSF dataset (0.88 compared to 0.89 for the 7B model).
“While the Woollie MSK 33B model outperformed the 7B model on the MSK dataset, it showed a slight decrease in AUROC on the UCSF dataset (0.88 compared to 0.89 for the 7B model).”
Quote in the paperNot a substantial 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
After alignments, all models confirmed expected scaling benefits.
“After alignments, all models confirmed the expected scaling benefits.”
Quote in the paperNot a substantial claim - Findingown data
The improvements in medical benchmark accuracy after MSK fine-tuning were statistically significant (p < 0.001).
“These improvements were statistically significant (p < 0.001).”
Quote in the paperNot a substantial claim - Findingown data
Woollie All models (7B, 13B, and 33B) demonstrate higher accuracy compared to their corresponding Llama models.
“The Woollie All models (7B, 13B, and 33B) demonstrate higher accuracy compared to their corresponding Llama models.”
Quote in the paperNot a substantial claim - Findingown data
Woollie has effectively learned and utilizes local features to inform its classifications.
“The results demonstrate that the model has effectively learned and utilizes local features to inform its classifications (Supplementary Figs. 4, 5, Supplementary Note 3).”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [34] Ribeiro, M. T., Singh, S. & Guestrin, C. in Proceedings of the 22nd ACM SIGKDD international conference on knowledge discovery and data mining. 1135–1144.
Not checked in the free run.
- Findingown data
Micro-averaged AUROC for the 7B models increased from 0.63 to 0.93 compared to Llama.
“The micro-averaged AUROC for the 7B models saw a significant increase from 0.63 to 0.93 comparing to Llama.”
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.
- Findingreasoning
The overall performance remains remarkable when encountering new datasets.
“While some performance degradation is expected when encountering new datasets, the overall performance remains remarkable.”
Quote in the paperSubstantial claim- Rests on an assumption: Some performance degradation is expected when encountering new datasets.
- Findingreasoning
Larger models like the 33B are impacted by their complexity, resulting in slower inference times.
“Larger models like the 33B, while powerful, are impacted by their complexity, resulting in slower inference times.”
Quote in the paperSubstantial claim - Findingown data
Comparison among Llama, Woollie Foundation, Woollie Medicine, and Woollie models demonstrates incremental performance improvements across various benchmarks.
“A comparison among Llama, Woollie Foundation, Woollie Medicine, and Woollie models clearly demonstrates incremental performance improvements across various benchmarks”
Quote in the paperSubstantial claim - Findingown data
In the Woollie model, PubMedQA accuracy improved with size: 0.72 for 7B, 0.74 for 13B, 0.80 for 33B, and 0.81 for 65B.
“For example, in the Woollie model, the accuracy on PubMedQA improved with size: 0.72 for 7B, 0.74 for 13B, 0.80 for 33B, and 0.81 for 65B”
Quote in the paperNot a substantial claim - Findingown data
In detecting lung cancer progression on UCSF, the models achieved AUROC 0.95 and accuracy 0.88.
“Notably, in detecting lung cancer progression, the models achieved an AUROC of 0.95 and an accuracy of 0.88”
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
In 33B model evaluations, Woollie 33B achieved accuracy 0.43 on MMLU versus 0.40 for Woollie All 33B.
“For instance, in the 33B model evaluations, Woollie 33B achieved an accuracy of 0.43 on MMLU, compared to 0.40 for Woollie All 33B.”
Quote in the paperSubstantial claim - Findingown data
The stacked alignment strategy effectively addressed the challenge of "catastrophic forgetting," which often occurs when LLMs transition between domains.
“This stacked alignment strategy effectively addressed the challenge of “catastrophic forgetting,” which often occurs when LLMs transition between domains.”
Quote in the paperSubstantial claim - Findingown data
The results reveal a significant performance gap, with the stacked alignment models demonstrating superior performance.
“The results reveal a significant performance gap, with the stacked alignment models demonstrating superior performance (Fig. 2b, Supplementary Fig. 1b).”
Quote in the paperSubstantial claim - Interpretationown data
Woollie is the first oncology-specific LLM validated across institutions.
“As the first oncology specific LLM validated across institutions, Woollie demonstrates high accuracy and consistency across cancer types”
Quote in the paperSubstantial claim - Interpretationown data
Catastrophic forgetting is mitigated in Woollie models through the stacked alignment strategy.
“Catastrophic forgetting26, a common issue where an LLM loses previously learned knowledge during fine-tuning, is mitigated in Woollie models through the stacked alignment strategy.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [26] Luo, Y. et al. An empirical study of catastrophic forgetting in large language models during continual fine-tuning. Preprint at https://arxiv.org/html/2308.08747v3 (2023).
Not checked in the free run.
- Premisecitation
Closed-source LLMs have notable performance deficiencies in healthcare environments.
“Privacy concerns have hampered the adoption of closed-source LLMs in clinical settings, compounded by studies indicating notable performance deficiencies in these models within healthcare environments9.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [9] Chen, S. et al. Use of artificial intelligence chatbots for cancer treatment information. JAMA Oncol. https://doi.org/10.1001/jamaoncol.2023.2954 (2023) source
Not checked in the free run.
- Interpretationown data
The stacked alignment strategy effectively counteracts catastrophic forgetting.
“These results suggest that the stacked alignment strategy effectively counteracts the problem of catastrophic forgetting.”
Quote in the paperSubstantial claim - Study design and conductown data
Smaller sample sizes within certain age and race subgroups limit the ability to fully exclude the possibility of performance variation.
“However, smaller sample sizes within certain age and race subgroups limit our ability to fully exclude the possibility of performance variation.”
Quote in the paperSubstantial claim - Interpretationown data
The 7B model's efficiency and faster inference times make it significantly more practical and feasible for deployment in a clinical environment as oncologist assistant.
“7B model’s efficiency and faster inference times make it significantly more practical and feasible for deployment in a clinical environment as oncologist assistant.”
Quote in the paperSubstantial claim - Interpretationown data
Beyond a certain point, the scaling law in aligned models may be more influenced by data quality than quantity alone.
“This observation indicates that beyond a certain point, the scaling law in aligned models may be more influenced by data quality than quantity alone.”
Quote in the paperNot a substantial claim - Interpretationown data
The performance comparison between stacked aligned Woollie models, not stacked aligned Woollie All models, and baseline Llama models provides further evidence of the significant impact of the alignment strategy on performance, particularly on proprietary datasets not exposed during pretraining.
“The performance comparison between the “stacked aligned” Woollie models, “not stacked aligned” Woollie All models, and baseline Llama models provides further evidence of the significant impact of the alignment strategy on performance, particularly on proprietary datasets that were not exposed during pretraining.”
Quote in the paperSubstantial claim - Interpretationown data
Radiology impression narratives appear largely independent of demographic factors.
“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.
- Interpretationreasoning
It is possible to align and fine-tune LLMs within the oncology domain without losing prior knowledge.
“It is possible to align and fine-tune LLMs within the oncology domain without losing prior knowledge.”
Quote in the paperSubstantial claim - Interpretationown data
The alignment's effectiveness is contingent upon the quality of the baseline model's pre-training.
“The trend suggested that the alignment’s effectiveness is contingent upon the quality of the baseline model’s pre-training—the more robust the baseline, the better the performance of the aligned models.”
Quote in the paperSubstantial claim - Interpretationreasoning
The high AUROC scores, alignment with oncological knowledge, and localized explainability analyses using LIME strongly suggest that hallucination has been significantly minimized in our use cases.
“The high AUROC scores, alignment with oncological knowledge, and localized explainability analyses using LIME strongly suggest that hallucination has been significantly minimized in our use cases.”
Quote in the paperSubstantial claim - Interpretationown data
These local features play a key role in identifying cancer progression.
“These local features, which play a key role in identifying cancer progression, demonstrate the model’s understanding of cancer biology and align with human interpretation.”
Quote in the paperSubstantial claim - Study design and conductown data
The MSK radiology impressions were thoroughly reviewed and labeled by radiologists into five categories indicating cancer progression.
“These radiology impressions, gathered from MSK30, were thoroughly reviewed and labeled by radiologists with five categories indicating cancer progression”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [30] Jee, J. et al. Automated annotation for large-scale clinicogenomic models of lung cancer treatment response and overall survival. Cancer Res. 83, 5721–5721 (2023). source
Not checked in the free run.
- Interpretationown data
The model's understanding of cancer biology aligns with human interpretation.
“These local features, which play a key role in identifying cancer progression, demonstrate the model’s understanding of cancer biology and align with human interpretation.”
Quote in the paperSubstantial claim - Study design and conductnone given
The radiology impression data from the MSK patient cohort does not include protected health information (PHI).
“The radiology impression data from the MSK patient cohort does not include protected health information (PHI).”
Quote in the paperSubstantial claim - Study design and conductown data
The maximum input token window of 2048 tokens was sufficient to accommodate the full radiology impression during training.
“We used an optimized prompting strategy (Supplementary Note 5, Supplementary Fig. 7) with a maximum input token window of 2048 tokens, which was sufficient to accommodate the full radiology impression during training (Supplementary Fig. 9).”
Quote in the paperNot a substantial claim - Interpretationreasoning
The Woollie MSK models, trained on a non-PHI dataset, do not contain any knowledge of individual patient private information.
“The Woollie MSK models, trained on a non-PHI dataset, do not contain any knowledge of individual patient private information.”
Quote in the paperSubstantial claim
- 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 givenWoollie 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 claimMay combine two claims.
Findingnone givenWoollie 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 claimMay combine two claims.
Findingown dataFor 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataStylistic 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 claimMay combine two claims.
Findingown dataWhen 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 dataThe 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 claimMay combine two claims.
FindingreasoningThe 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 claimMay combine two claims.
Findingown dataWoollie 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 dataWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.
FindingreasoningWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 dataAlthough 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 dataWoollie 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 dataWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 claimMay combine two claims.
Findingown dataLlama 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 claimProbably not a substantial claim: may not pass S2 (checkable).
FindingreasoningBy 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 claimMay combine two claims.
Findingown dataOn 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 claimMay combine two claims.
Findingown dataAs 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 claimMay combine two claims.
Findingown dataWoollie 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 claimMay combine two claims.
Findingown dataWoollie 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 dataLarger 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 claimMay combine two claims.
Findingown dataOn 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 claimMay combine two claims.
Findingown dataModel 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 claimMay combine two claims.
Findingown dataThe 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 claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingown dataThe 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 claimMay combine two claims.
FindingreasoningPerformance 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 claimMay combine two claims.
Findingown dataExamination 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 claimProbably not a substantial claim: may not pass S4 (based). May combine two claims.
Findingnone givenTraining 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Findingown dataOut 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 claimProbably not a substantial claim: may not pass S4 (based).
InterpretationreasoningHigh 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 claimMay combine two claims.
PremisecitationSpecialized 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 givenConfiguring 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationnone givenReliance 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 claimProbably not a substantial claim: may not pass S2 (checkable). May combine two claims.
InterpretationreasoningWoollie'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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataThe 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 claimMay combine two claims.
Interpretationown dataWoollie'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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationOur 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 dataDespite 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 claimClassified as probably not a substantial claim. May combine two claims.
InterpretationreasoningUsing 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 claimMay combine two claims.
Interpretationown dataWoollie 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).
InterpretationreasoningThese 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 claimMay combine two claims.
Interpretationown dataModels 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 claimClassified as probably not a substantial claim. May combine two claims.
InterpretationreasoningAligning 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 claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based). May combine two claims.
InterpretationreasoningWoollie'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 claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
InterpretationreasoningThe 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.
InterpretationreasoningThe 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
InterpretationreasoningUnderrepresentation 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).
InterpretationreasoningChoosing 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 claimMay combine two claims.
InterpretationreasoningThe 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 claimClassified as probably not a substantial claim.
InterpretationreasoningPredictions 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 claimClassified as probably not a substantial claim. May combine two claims.
InterpretationreasoningCombining 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 claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Study design and conductnone givenAll 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 claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
Interpretationnone givenThis 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningAUROC 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 claimProbably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductcitationThe 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 dataDuring 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 claimProbably not a substantial claim: may not pass S2 (checkable). May combine two claims.
InterpretationreasoningOnce 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 claimClassified as probably not a substantial claim. May combine two claims.
PremisecitationHDBSCAN 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).
InterpretationcitationThis 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.
InterpretationreasoningOnce 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 claimClassified as probably not a substantial claim.
Study design and conductnone givenThe radiologist has manually annotated the dataset.
“The radiologist has manually annotated the dataset.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim.
PremisereasoningAUROC 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 claimProbably not a substantial claim: may not pass S2 (checkable), S3 (load-bearing), S4 (based).
InterpretationreasoningThis 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.
InterpretationreasoningThese 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.
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.”
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].”
From Artificial Intelligence in Clinical Oncology: From Productivity Enhancement to Creative Discovery (2025) · cites this paper as [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
MinorThe 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.
“The micro-averaged AUROC for the 7B models saw a significant increase from 0.63 to 0.93 comparing to Llama.”
“This approach involves generating an ROC curve for each class by comparing it against all other classes combined, computing the AUROC for each curve, and then averaging these values to obtain a single representative score.”
MSK patient count differs by one
MinorThe 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.
“38,719 radiology impressions from 3401 patients”
“38,719 radiology impression notes from 3402 patients”
UCSF cancer types are described as different from MSK's
MinorThe three UCSF cancer types are all included in the paper's list of MSK cancer types, rather than being different from them.
“focusing on lung, breast, and prostate cancers—different from those in the MSK dataset.”
“five types of cancer: lung, breast, pancreatic, prostate, and colorectal.”
Woollie 33B PubMedQA accuracy is reported inconsistently
MinorThe 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.
“Woollie 33B achieved an accuracy of 0.79, significantly outperforming Woollie All 33B at 0.70.”
“on the PubMedQA benchmark, the Woollie 33B model achieved an accuracy of 0.7980”
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Training language models to follow instructions with human feedback
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InfluentialLlama 2: Open Foundation and Fine-Tuned Chat Models
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Metastatic Behavior of Breast Cancer Subtypes
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“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 47 .”
Scaling Instruction-Finetuned Language Models
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A large language model for electronic health records
Yang, X., Chen, A., PourNejatian, N., Shin, H. C., Smith, K. E., Parisien, C., Compas, C., Martin, C., Costa, A. B., Flores, M. G., et al. (2022) · npj Digital Medicine · doi:10.1038/s41746-022-00742-2 · Cited by 847 · cited 1× · see citing works
“In the medical domain, numerous studies have demonstrated the improved performance of domain-speci fi c foundation LLMs, including BioMedLM 13 , BioGPT 14 , GatorTron 15 , MedPaLM 16 , MedPalM2 17 , and BioMistral 18 .”
HellaSwag: Can a Machine Really Finish Your Sentence?
Zellers, R., Holtzman, A., Bisk, Y., Farhadi, A., & Choi, Y. (2019) · Proceedings of the 57th Annual Meeting of the Association for Computational Linguistics · doi:10.18653/v1/p19-1472 · Cited by 830 · see citing works
PubMedQA: A Dataset for Biomedical Research Question Answering
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“For the medical domain, our dataset selection was as follows: (1) PubMedQA 43 (link), which challenges models to generate answers from NIH PubMed abstracts to be compared with expert-curated responses, covering a broad spectrum of biomedical topics.”
C-Pack: Packed Resources For General Chinese Embeddings
Xiao, S., Liu, Z., Zhang, P., Muennighoff, N., Lian, D., & Nie, J.-Y. (2024) · Proceedings of the 47th International ACM SIGIR Conference on Research and Development in Information Retrieval · doi:10.1145/3626772.3657878 · Cited by 523 · see citing works
QLoRA: Efficient Finetuning of Quantized LLMs
Dettmers, T., Pagnoni, A., Holtzman, A., & Zettlemoyer, L. (2023) · arXiv · doi:10.48550/arxiv.2305.14314 · Cited by 507 · see citing works
Measuring Massive Multitask Language Understanding
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“In non-medical benchmarks such as OpenbookQA 21 , LogiQA 22 , and MMLU 23 , particularly in conversation-centric tests like COQA 24 and HellaSWAG 25 , the larger Woollie models (13B, 33B, and 65B) outperformed their Llama equivalents, with the 65B model showing the most signi fi cant advantage (Fig.”
BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains
Labrak, Y., Bazoge, A., Morin, E., Gourraud, P.-A., Rouvier, M., & Dufour, R. (2024) · Findings of the Association for Computational Linguistics ACL 2024 · doi:10.18653/v1/2024.findings-acl.348 · Cited by 269 · see citing works
Evaluating ChatGPT as an Adjunct for Radiologic Decision-Making
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“Initial explorations of large language models (LLMs) such as ChatGPT in healthcare 4,5 have yielded promising results across numerous medical fi elds 6 – 8 .”
Use of Artificial Intelligence Chatbots for Cancer Treatment Information
Chen, S., Kann, B. H., Foote, M. B., Aerts, H. J. W. L., Savova, G. K., Mak, R. H., & Bitterman, D. S. (2023) · JAMA Oncology · doi:10.1001/jamaoncol.2023.2954 · Cited by 251 · see citing works
A question-entailment approach to question answering
Abacha, A. B., & Demner‐Fushman, D. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3119-4 · Cited by 221 · see citing works
Will ChatGPT transform healthcare?
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LogiQA: A Challenge Dataset for Machine Reading Comprehension with Logical Reasoning
Jian, L., Cui, L., Liu, H., Huang, D., Wang, Y., & Zhang, Y. (2020) · International Joint Conference on Artificial Intelligence · doi:10.24963/ijcai.2020/501 · Cited by 209 · see citing works
Applicability of ChatGPT in Assisting to Solve Higher Order Problems in Pathology
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An Empirical Study of Catastrophic Forgetting in Large Language Models During Continual Fine-Tuning
Luo, Y., Yang, Z., Meng, F., Li, Y., Zhou, J., & Zhang, Y. (2025) · IEEE Transactions on Audio, Speech and Language Processing · doi:10.1109/taslpro.2025.3606231 · Cited by 136 · see citing works
An Empirical Study of Catastrophic Forgetting in Large Language Models During Continual Fine-tuning
Luo, Y., Yang, Z., Meng, F., Li, Y., Zhou, J., & Zhang, Y. (2023) · arXiv · doi:10.48550/arxiv.2308.08747 · Cited by 135 · cited 1× · see citing works
“Catastrophicforgetting 26 , a common issue where an LLM loses previously learned knowledge during fi ne-tuning, is mitigated in Woollie models through the stacked alignment strategy.”
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“This collection is a subset of the AACR Project GENIE Biopharma Collaborative (BPC) dataset 45,46 .”
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Research works printed but not linked: 12
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Cited by
Sorted by citations
Large language models for clinical decision support in gastroenterology and hepatology
Wiest, I. C., Bhat, M., Clusmann, J., Schneider, C. V., Jiang, X., & Kather, J. N. (2025) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-025-01108-1 · Cited by 33 · see citing works
“Zhu et al. trained a custom LLM on 39,319 radiology notes from about 4,000 patients with cancer, and found that the LLM was able to predict cancer progression with high predictive value 145 .”
Large Language Models in Lung Cancer: Systematic Review
Zhong, R., Chen, S., Li, Z., Gao, T., Su, Y., Zhang, W., Liu, D., Gao, L., & Hu, K. (2025) · Journal of Medical Internet Research · doi:10.2196/74177 · Cited by 11 · see citing works
“…with LC, found that a fine-tuned BERT model using annotated data achieved a higher F 1 -score than an instruction-based LLM. Similarly, Zhu et al [78] developed an open-source, oncology-specific LLM using a stacked alignment and fine-tuning process, which outperformed ChatGPT on medical…”
Incorporating large language models as clinical decision support in oncology: the Woollie model
Heydari, K., Enichen, E. J., Li, B., & Kvedar, J. C. (2025) · npj Digital Medicine · doi:10.1038/s41746-025-01941-3 · Cited by 8 · see citing works
Artificial Intelligence in Clinical Oncology: From Productivity Enhancement to Creative Discovery
Kuno, M., Osumi, H., Udagawa, S., Yoshikawa, K., Ooki, A., Shinozaki, E., Ishikawa, T., Oba, J., Yamaguchi, K., & Sakurada, K. (2025) · Current Oncology · doi:10.3390/curroncol32110588 · Cited by 7 · see citing works
Large Language Models in Colorectal Cancer Care and Clinical Decision Support: Systematic Review
Tian, J., Lou, Q., Wang, X., xuhangying, Mei, H., & Yu, Y. (2026) · Journal of Medical Internet Research · doi:10.2196/89862 · Cited by 4 · see citing works
“Their probabilistic structure allows them to synthesize vast, disparate datasets and infer latent correlations that traditional algorithms might overlook [72].”
Zitu, M. M., Manne, A., Zhu, Y., Rahat, W. B., & Binkheder, S. (2025) · Pharmacy · doi:10.3390/pharmacy13060176 · Cited by 4 · see citing works
“We include empirical studies that applied LLMs (encoder-only transformers, encoder–decoder models, and decoder-only/generative LLMs) as well as techniques such as citation-enforced RAG [21,32].”
Clinical decision support in hematological malignancies using a case-grounded AI agent
Zoller, J., Kalz, M., Wu, X., Cuntz, S., Kruk, L., Kehl, N., Michel, J. J., Funk, C. M., Richter, S., Tix, T., et al. (2026) · Nature Medicine · doi:10.1038/s41591-026-04494-4 · Cited by 5 · see citing works
Qi, X. S., Wang, Y., Yang, X., Ren, L., Liu, W., Benedict, S., Xiao, Y., Xing, L., & Naqa, I. M. E. (2026) · Medical Physics · doi:10.1002/mp.70616 · Cited by 2 · see citing works
“However, the emergence of data-driven techniques, particularly AI and generative AI has changed the landscape of outcome modeling in oncology including radiation therapy, 103,106–108 as will be discussed next.”
InfluentialMittal, P., Sharma, S., Solanki, S., Kumar, L., Haripriya, R., & Beg, R. (2026) · Discover Artificial Intelligence · doi:10.1007/s44163-026-01279-z · Cited by 3 · see citing works
“Zhu et al. [4] show improved cancer progression prediction using oncology-trained LLMs, while Wu and Tang [8] leverage LLMs for single-cell RNA-sequencing annotation.”
Phaterpekar, T., Zeng, Z., Mali, Y., Leung, B., Ho, C., Ng, R. T., Bates, A. T., & Nunez, J.-J. (2026) · ESMO Real World Data and Digital Oncology · doi:10.1016/j.esmorw.2026.100703 · Cited by 1 · see citing works
“25 To our knowledge, no work has applied these models to oncology consultation notes.”
Precision oncology: from large language models to multi-agent systems
Guo, X., Chen, J., Zhang, Y., Zhang, X., Lu, J., Qin, Q., Chen, J., Gao, X., & Wang, J. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1828507 · Cited by 3 · see citing works
“It demonstrates superior performance over general-purpose large language models across multiple tasks, supporting more ef fi cient identi fi cation of disease progression in oncologic practice (77).”
Viculin, I., Vrdoljak, J., Tomić, K., Canjko, I., Čerina, D., Ćurin, M., Bošković, L., Družijanić, Z., Vuković, B., Dunkić, N., et al. (2026) · Journal of Medical Internet Research · doi:10.2196/91733 · Cited by 2 · see citing works
“Early explorations suggest these LLMs can yield promising results across diverse medical tasks [1].”
Kayira, A. B., Elyazori, H. R. A., Lybarger, K., Walter, F. M., Chelala, C., & Funston, G. (2026) · JMIR AI · doi:10.2196/73481 · Cited by 1 · see citing works
“In contrast, approaches that predict outcomes directly from unstructured text without an explicit IE step are often less transparent, constrain the incorporation of domain knowledge, and are typically optimized for a single task [155].”
Global trends and emerging frontiers of large language models in cancer research
Tian, D., Xie, Z., Hu, Z., Yang, Z., Tian, H., Chen, Y., Zhao, H., Du, S., Wang, F., Zhang, L., et al. (2026) · Digital Health · doi:10.1177/20552076261458966 · Cited by 2 · see citing works
“19 Representative examples illustrate the breadth of this approach.”
Evaluation of ChatGPT-4o’s and DeepSeek R1’s responses to urological problems: a comparative study
Lu, H., Zhang, Y., Wang, Z., Zhao, Y., Liu, J., Qiu, D., & Zhang, Y. (2026) · BMC Urology · doi:10.1186/s12894-026-02228-9 · Cited by 2 · see citing works
“Several studies have evaluated the reasoning capabilities of models like GPT-4 in various medical domains [7, 17], including general internal medicine [3], oncology [18], and radiology [19].”
Corso, F., Zec, A., Favali, M., Ligero, M., Hilgers, L., Invernizzi, L. M., Mazzeo, L., Morales, A. M., Müller‐Franzes, G. A., Machado, I. P., et al. (2026) · Cell Reports Medicine · doi:10.1016/j.xcrm.2026.102966 · Cited by 2 · see citing works
Anil, S., Srinivas, B., Liu, B., et al. (2025) · Research Square · doi:10.21203/rs.3.rs-7329357/v1
Self-citationViculin, I., Vrdoljak, J., Tomić, K., et al. (2026) · doi:10.2196/preprints.91733
Dickerson, J. C., McClure, M. B., Shaw, M. L., Reitsma, M. B., Dalal, N., Curtis, C. N., Kurian, A. W., & Caswell-Jin, J. L. (2026) · medRxiv · doi:10.64898/2026.03.23.26349012
Virtual medicine: medical AI in human health and diseases
Zhang, C., Wang, F.-X., Tang, X., Li, J.-L., Ding, N., Hong, Y., Song, P., Bai, L., & Su, J. (2026) · Military Medical Research · doi:10.1016/j.mmr.2026.100012 · Cited by 1 · see citing works
Masood, F. (2026) · Journal of Psychosocial Oncology · doi:10.1080/07347332.2026.2649035
Mouheb, K., Pomp, A. C., Manenti, A., de Haan, R., Faghir, F., Martens, J., Seelaar, H., Mattace-Raso, F. U. S., Vernooij, M. W., Wolters, F. J., et al. (2026) · European Radiology · doi:10.1007/s00330-026-12821-z
“For instance, Zhu et al. showed that an oncology-specific LLM outperformed LLaMA 3 in predicting cancer progression [37], yet Liu et al. [38] found that, without task-specific fine-tuning, general-purpose LLaMA 3.1 8B outperformed Llama-3-8B-UltraMedical on structuring radiology and pathology…”
InfluentialThe Rise of Conversational Modeling in Predictive Oncology
Ręka, F., Dziwak, P., Minch, B., et al. (2026) · Lecture notes in computer science · doi:10.1007/978-3-032-29921-5_26
“Trained on vast bodies of biomedical literature, these models have internalized how biological mechanisms are described, interconnected, and operationalized across disciplines [4, 3, 20, 17, 5].”
Generative small language models in clinical NLP: applications, adaptation, and evaluation
Türkmen, H. (2026) · PeerJ Computer Science · doi:10.7717/peerj-cs.4000
Artificial intelligence in oncology: linking biological discovery to clinical utility
Kuchana, S. K., Alahari, N. V., Kode, R., Jalapu, K. R., & Alahari, S. K. (2026) · Molecular Cancer · doi:10.1186/s12943-026-02771-x
Zhang, W.-Z., Feng, Z.-R., Liu, Y.-T., Zhong, R.-K., Chen, S.-Y., Li, Z.-X., Li, B.-Y., Liu, D.-N., Gao, L., & Hu, K.-W. (2026) · Frontiers in Oncology · doi:10.3389/fonc.2026.1915669
Hsu, E., Lu, S.-C., Ebrahimi, S., Beinart, N. I., Ostos-Mendoza, K. C., Deswal, A. M., Roberts, K. E., Kell, T., Jin, S., & Palaskas, N. L. (2026) · European Heart Journal - Digital Health · doi:10.1093/ehjdh/ztag145
Artificial intelligence for tumor board simulation among HPV positive oropharynx cancer patients
Su, A. Y., Patel, N. D., Beiriger, J., Bellamkonda, N., Bestourous, D. E., Farlow, J. L., Xu, A. Y., Ni, A., Cannon, R. B., Monroe, M. M., et al. (2026) · American Journal of Otolaryngology · doi:10.1016/j.amjoto.2026.104958
Worth, J. E., Perez, A., Wu, D. J., Brodeur, P. G., Tat, E., Manrai, A. K., Wu, D., Walton, C., McCoy, L. G., Jain, P., et al. (2026) · BMJ Digital Health & AI · doi:10.1136/bmjdh-2026-000113 · Cited by 1 · see citing works
- 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
- ORCID
- Venue
- npj Digital Medicine
- Published
- 2025-07-02
- Volume
- 8
- Issue
- 1
- Pages
- 397-397
- ISSN
- 2398-6352 (ISSN-L)
- PMC
- PMC12223279
- OpenAlex
- W4411919356
- Semantic Scholar
- 0c5e45ee2b8c11202a06273e037440a301bc7e6c
- Cited by
- 30
- References
- 37
- Citations by year
- 2026: 25 · 2025: 5
- FWCI
- 7.22
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- 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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