Towards evaluating and building versatile large language models for medicine
Open accessAbstract
In this study, we present MedS-Bench, a comprehensive benchmark to evaluate large language models (LLMs) in clinical contexts, MedS-Bench, spanning 11 high-level clinical tasks. We evaluate nine leading LLMs, e.g., MEDITRON, Llama 3, Mistral, GPT-4, Claude-3.5, etc. and found that most models struggle with these complex tasks. To address these limitations, we developed MedS-Ins, a large-scale instruction-tuning dataset for medicine. MedS-Ins comprises 58 medically oriented language corpora, totaling 5M instances with 19K instructions, across 122 tasks. To demonstrate the dataset's utility, we conducted a proof-of-concept experiment by performing instruction tuning on a lightweight, open-source medical language model. The resulting model, MMedIns-Llama 3, significantly outperformed existing models on various clinical tasks. To promote further advancements, we have made MedS-Ins fully accessible and invite the research community to contribute to its expansion. Additionally, we have launched a dynamic leaderboard for MedS-Bench, to track the development progress of medical LLMs.
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Written from the paper’s full text.
TL;DR
The paper introduces MedS-Bench, an 11-task clinical benchmark showing that leading LLMs struggle beyond multiple-choice QA, and MedS-Ins, a 5M-instance medical instruction-tuning dataset. Instruction tuning an 8B open-source medical model on MedS-Ins yields MMedIns-Llama 3, which outperforms GPT-4 and Claude-3.5 on many evaluated clinical tasks.
Key findings
- MedS-Bench covers 11 high-level clinical task categories, 28 datasets, and 52 distinct tasks; most evaluated LLMs struggled on complex clinical tasks despite strong MCQA performance.
- MedS-Ins contains 58 medically oriented language corpora, 5M instances, 19K instructions, 122 tasks, 19 task categories, and five text domains.
- MMedIns-Llama 3 achieved average scores of 63.9 on multilingual MCQA, 46.82/48.38 BLEU/ROUGE on text summarization, 83.77 accuracy on information extraction, 34.43/37.47 on concept explanation, 46.90/34.54 on rationale, 79.29 F1 on NER, 98.47 on SEER treatment planning, 97.53 on DDXPlus diagnosis, 63.35 average on MIMIC4ED clinical outcome prediction, and 86.66 macro-F1 on HoC classification.
- On fact verification and NLI, MMedIns-Llama 3 reached 97.08 on PubMedQA Answer Verification, 79.55 on PUBLICHEALTH Health Fact Verification, 86.71 on MedNLI discriminative entailment, and 23.52/25.17 BLEU/ROUGE on MedNLI generative entailment; it slightly trailed GPT-4 and Llama 3 on EMBS Justification Verification with 12.71/14.65.
Methods
- MedS-Bench was built from 28 existing datasets reformatted into instruction-prompted QA with hand-crafted task definitions; nine mainstream LLMs were evaluated, using 3-shot prompting except MCQA, which used zero-shot, with around 1500 test cases sampled per benchmark due to proprietary-model costs.
- MedS-Ins was constructed by filtering medical-related tasks from Super-NaturalInstructions and prompting existing BioNLP datasets into a unified free-form QA format, yielding 5M instances, 19K instructions, and 122 tasks.
- MMedIns-Llama 3 was trained by supervised instruction tuning from the medical-knowledge-enhanced MMed-Llama 3 base model for 5 epochs on 32 Ascend910B for 383.5 hours, with max length 2048, global batch size 128, and learning rate 1e-5.
Limitations
- The paper states MedS-Bench covers only 11 clinical tasks, omits some mainstream LLMs, and cannot replace final evaluation in actual clinical settings; MedS-Ins remains incomplete, may miss practical medical scenarios, and has not yet shown emergent generalization to unseen clinical tasks.
- The paper states the work is primarily English and plans multilingual expansion; the model has not undergone extensive clinical validation or human-preference safety alignment.
- Evident from the text: many baseline results are borrowed from other works rather than uniformly re-evaluated, evaluation used sampled test cases for cost reasons, and GPT-4 was excluded from rationale evaluation because the MMedBench rationale component was primarily constructed using GPT-4 outputs.
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 21 cited sources checked · 0 supported · 0 flagged
- Findingown data
MedS-Ins is the first comprehensive instruction tuning dataset for medicine.
“construct the first, comprehensive instruction tuning dataset for medicine, MedS-Ins.”
Quote in the paperSubstantial claim- Rests on an assumption: The 58 source datasets are of sufficient quality and diversity to produce a comprehensive medical instruction dataset.
- Findingown data
MMedIns-Llama 3 achieved the highest accuracy score as InternLM 2 on PubMedQA Answer Verification.
“MMedIns-Llama 3 continues surpassing existing models, achieving the highest accuracy score as InternLM 2, excelling in PubMedQA Answer Verification and HealthFact Verification while in EMBS, MMedIns-Llama 3 slightly falls behind the GPT-4 and Llama 3 with 12.71/14.65 in BLEU and ROUGE, which we treat as future work for further improvement.”
Quote in the paperSubstantial claim - Findingown data
Most evaluated large language models struggle with complex clinical tasks, even when using few-shot prompting.
“most models struggle with these complex tasks.”
- Also stated in: § Introduction · hedged
“Our findings indicate that even the most advanced LLMs struggle with complex clinical tasks, even when utilizing few-shot prompting”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
- Also stated in: § Introduction · hedged
- Findingown data
On rationale tasks, MMedIns-Llama 3 achieves the best overall average BLEU-1/ROUGE-1 scores of 46.90/34.54 across all languages.
“our final model, MMedIns-Llama 3, demonstrated the best overall performance with average BLEU-1/ROUGE-1 scores of 46.90/34.54 across all languages”
Quote in the paperSubstantial claim - Findingown data
Qwen 2 achieved a macro-F1 score of 40.29 on the HoC multi-label classification task.
“Llama 3 and Qwen 2 show moderate performance, with macro-F1 scores of 38.37 and 40.29, respectively.”
Quote in the paperNot a substantial claim
- Findingown data
Med42-v2 achieved a macro-F1 score of 47.87 on the HoC multi-label classification task.
“Among open-source models, Med42-v2, the latest medical LLM that underwent comprehensive supervised fine-tuning and preference optimization, performs well among the open-source models, achieving a macro-F1 score of 47.87.”
Quote in the paperNot a substantial claim - Findingown data
MMedIns-Llama 3 significantly outperformed existing models on various clinical tasks.
“MMedIns-Llama 3, significantly outperformed existing models on various clinical tasks.”
Quote in the paperSubstantial claim - Findingown data
Open-source large language models underperform closed-source large language models on diagnosis, treatment planning, and clinical outcome prediction tasks.
“Overall, the open-source LLMs underperform the closed-source LLMs in these tasks.”
Quote in the paperSubstantial claim - Findingown data
GPT-4 achieved a macro-F1 score of 68.06 on the HoC multi-label classification task.
“GPT-4 and Claude-3.5 perform well on this task, with GPT-4 achieving a macro-F1 score of 68.06 and Claude-3.5 slightly worse at 66.74.”
Quote in the paperNot a substantial claim - Findingown data
Llama 3 and GPT-4 showed comparable performance on the EBMS benchmark, with average BLEU/ROUGE scores of 16.52/16.49 and 16.28/16.27 respectively.
“In the EBMS benchmark, Llama 3 and GPT-4 show comparable performance, with average BLEU/ROUGE score of 16.52/16.49 and 16.28/16.27.”
Quote in the paperNot a substantial claim - Findingown data
Llama 3 demonstrated the highest consistency with the reference ground truth among open-source models on the MedNLI generative task, achieving BLEU 21.31 and ROUGE 22.75.
“In the generative task, Llama 3 demonstrates the highest consistency with the reference ground truth, achieving scores of 21.31 for BLEU and 22.75 for ROUGE among the open-source models.”
Quote in the paperNot a substantial claim - Findingown data
MMedIns-Llama 3 excelled in HealthFact Verification.
“MMedIns-Llama 3 continues surpassing existing models, achieving the highest accuracy score as InternLM 2, excelling in PubMedQA Answer Verification and HealthFact Verification while in EMBS, MMedIns-Llama 3 slightly falls behind the GPT-4 and Llama 3 with 12.71/14.65 in BLEU and ROUGE, which we treat as future work for further improvement.”
Quote in the paperSubstantial claim - Findingown data
Claude-3.5 achieved a macro-F1 score of 66.74 on the HoC multi-label classification task.
“GPT-4 and Claude-3.5 perform well on this task, with GPT-4 achieving a macro-F1 score of 68.06 and Claude-3.5 slightly worse at 66.74.”
Quote in the paperNot a substantial claim - Findingown data
MedS-Ins integrates a broader range of medical text sources, encompassing five primary text domains and 19 task categories.
“In contrast, MedS-Ins integrates a broader range of medical text sources, encompassing five primary text domains and 19 task categories, as illustrated in Fig. 2d.”
Quote in the paperSubstantial claim - Findingown data
MMedIns-Llama 3 surpasses leading closed-source models, including GPT-4 and Claude-3.5, across a wide range of clinical tasks.
“MMedIns-Llama 3, for the first time, showing the effectiveness of training on diverse medical tasks through instruction tuning, enabling open-source medical LLMs to surpass leading closed-source models, including GPT-4 and Claude-3.5, across a wide range of clinical tasks.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
- Findingown data
GPT-4 achieved a macro-Recall of 80.23 on the HoC multi-label classification task.
“Both models show strong recall capabilities, particularly GPT-4, which achieves a macro-Recall of 80.23, underscoring its proficiency in identifying relevant labels.”
Quote in the paperNot a substantial claim - Findingnone given
The run-time differences between various LLM series (like Mistral vs. Llama 3) are not significant.
“Generally, the run-time differences between various LLM series (like Mistral vs. Llama 3) are not significant.”
Quote in the paperNot a substantial claim - Findingown data
On multiple-choice question-answering benchmarks, MMedIns-Llama 3 achieves an average accuracy of 63.9, significantly surpassing GPT-3.5.
“Our proposed model, MMedIns-Llama 3, although not primarily trained on multi-choice questions, still shows notable improvement, achieving an average accuracy of 63.9 across different benchmarks, significantly surpassing GPT-3.5.”
Quote in the paperSubstantial claim - Findingown data
GPT-4 performed well on the MedNLI generative task, achieving BLEU/ROUGE scores of 27.09/23.71.
“Similarly, GPT-4 also performs well in the generative task format, resulting in 27.09/23.71 scores while Claude-3.5 is not ideal in this task.”
Quote in the paperNot a substantial claim - Findingown data
InternLM 2 achieved the highest score among open-source LLMs on the MedNLI discriminative task, scoring 84.67.
“InternLM 2 achieves the highest scores among the open-source LLMs, scoring 84.67.”
Quote in the paperNot a substantial claim - Findingown data
MMedIns-Llama 3 slightly fell behind GPT-4 and Llama 3 on EMBS with BLEU/ROUGE scores of 12.71/14.65.
“MMedIns-Llama 3 continues surpassing existing models, achieving the highest accuracy score as InternLM 2, excelling in PubMedQA Answer Verification and HealthFact Verification while in EMBS, MMedIns-Llama 3 slightly falls behind the GPT-4 and Llama 3 with 12.71/14.65 in BLEU and ROUGE, which we treat as future work for further improvement.”
Quote in the paperNot a substantial claim - Findingown data
Qwen 2 and Med42-v2 achieved second-best performance of 82.00 and 77.57 among open-source LLMs on the MedNLI discriminative task.
“Qwen 2 and Med42-v2 also show second-best performance of 82.00 and 77.57 among the open-source LLMs”
Quote in the paperNot a substantial claim - Findingown data
MedS-Ins is a large-scale instruction-tuning dataset for medicine comprising 58 medically oriented language corpora, totaling 5M instances with 19K instructions across 122 tasks.
“MedS-Ins comprises 58 medically oriented language corpora, totaling 5M instances with 19K instructions, across 122 tasks.”
- Also stated in: § Results · plain
“MedS-Ins, with the data collected from 5 distinct text sources and 19 task categories, 122 distinct clinical tasks.”
Quote in the paperSubstantial claim- Rests on an assumption: The 58 source datasets are of sufficient quality and diversity to produce a comprehensive medical instruction dataset.
- Also stated in: § Results · plain
- Findingown data
Llama 3 achieved a macro-F1 score of 38.37 on the HoC multi-label classification task.
“Llama 3 and Qwen 2 show moderate performance, with macro-F1 scores of 38.37 and 40.29, respectively.”
Quote in the paperNot a substantial claim - Findingown data
Baichuan 2 achieved a macro-F1 score of 23.76 on the HoC multi-label classification task.
“Baichuan and MEDITRON rank the lowest in this task, with macro-F1 scores of 23.76 and 23.70, respectively.”
Quote in the paperNot a substantial claim - Findingown data
InternLM 2 achieved the highest accuracy on PubMedQA Answer Verification with a score of 99.23.
“InternLM 2 achieves the highest accuracy on PubMedQA Answer Verification with scores of 99.23.”
Quote in the paperNot a substantial claim - Findingown data
MEDITRON achieved a macro-F1 score of 23.70 on the HoC multi-label classification task.
“Baichuan and MEDITRON rank the lowest in this task, with macro-F1 scores of 23.76 and 23.70, respectively.”
Quote in the paperNot a substantial claim - Findingnone given
MMedIns-Llama 3 has not yet undergone extensive clinical validation.
“Forth, our model has not yet undergone extensive clinical validation.”
Quote in the paperSubstantial claim - Study design and conductreasoning
The use of accuracy as a metric is appropriate for diagnosis, treatment planning, and clinical outcome prediction because each dataset simplifies the original problem into a closed-set choice.
“Here, the use of accuracy as a metric is appropriate in this generative prediction problem, as each of these datasets simplifies the original problem into a closed-set choice.”
Quote in the paperSubstantial claim - Premisecitation
Current benchmarks largely focus on multiple-choice problems.
“Current benchmarks, which largely focus on multiple-choice problems2,7,8, fail to adequately reflect the practical utility of LLMs in real-world clinical scenarios.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [2] Singhal, K. et al. Towards expert-level medical question answering with large language models. arXiv preprint arXiv:2305.09617 (2023).
Not checked in the free run.
- cites [7] Wu, C. et al. Pmc-llama: toward building open-source language models for medicine. Journal of the American Medical Informatics Association ocae045 (2024). source
Not checked in the free run.
- cites [8] Chen, Z. et al. Meditron-70b: Scaling medical pretraining for large language models. arXiv preprint arXiv:2311.16079 (2023).
Not checked in the free run.
- Premisecitation
Large language models have demonstrated poor comprehension of ICD codes.
“LLMs have demonstrated poor comprehension of ICD codes4”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [4] Soroush, A. et al. Large language models are poor medical coders—benchmarking of medical code querying. NEJM AI 1, AIdbp2300040 (2024). source
Not checked in the free run.
- Interpretationreasoning
The scores on diagnosis, treatment planning, and clinical outcome prediction remain insufficient for reliable clinical use.
“Despite these results, the scores remain insufficient for reliable clinical use.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
- Interpretationown data
Instruction tuning on MedS-Ins significantly enhances the alignment of open-source medical LLMs with clinical demands.
“On the model front, we demonstrate that by conducting instruction tuning on MedS-Ins, we can significantly enhance the alignment of open-source medical LLMs with clinical demands.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks reflects clinical capabilities.
- Premisecitation
Large language models have produced inaccurate predictions related to clinical procedures.
“produced inaccurate predictions related to clinical procedures5”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [5] Hager, P. et al. Evaluation and mitigation of the limitations of large language models in clinical decision-making. Nature Medicine 1–10 (2024).
Not checked in the free run.
- Interpretationcitation
The current limited number of tasks may explain why the models have not yet exhibited emergent abilities to generalize to unseen clinical tasks.
“The current limited number of tasks may explain why we have not yet observed the models exhibiting emergent abilities to generalize to unseen clinical tasks, a capability seen in LLMs trained on thousands of diverse tasks in the general domain17,22.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [17] Wang, Y. et al. Super-naturalinstructions: Generalization via declarative instructions on 1600+ nlp tasks. In Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing (pp. 5085-5109). source
Not checked in the free run.
- cites [22] Longpre, S. et al. The flan collection: Designing data and methods for effective instruction tuning. In International Conference on Machine Learning (pp. 22631-22648). PMLR.
Not checked in the free run.
- Interpretationcitation
MMedIns-Llama 3's superior multilingual rationale performance is likely due to its base language model (MMed-Llama 3) being initially developed to be multilingual.
“This superior performance is likely due to the fact that our base language model (MMed-Llama 3) was initially developed to be multilingual19.”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [19] Qiu, P. et al. Towards building multilingual language model for medicine. Nature Communications 15.1 (2024): 8384. source
Not checked in the free run.
- Interpretationreasoning
MedS-Bench provides clinicians and researchers with a detailed understanding of where large language models excel and where they fall short in medical tasks.
“This benchmark provides clinicians and researchers with a detailed understanding of where LLMs excel and where they fall short in medical tasks.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
- Interpretationown data
MMedIns-Llama 3 is the first model showing the effectiveness of training on diverse medical tasks through instruction tuning.
“MMedIns-Llama 3, for the first time, showing the effectiveness of training on diverse medical tasks through instruction tuning”
Quote in the paperSubstantial claim - Interpretationown data
MMedIns-Llama 3 is the most effective model for the HoC multi-label classification task.
“These results highlight MMedIns-Llama 3’s superior ability to accurately classify and recall multiple labels, making it the most effective model for this complex task.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks reflects clinical capabilities.
- Premisecitation
Large language models have misinterpreted Electronic Health Record (EHR) data.
“misinterpreted Electronic Health Record (EHR) data6”
Quote in the paperSubstantial claim0 of 1 sources checked- cites [6] Fleming, S. L. et al. Medalign: A clinician-generated dataset for instruction following with electronic medical records. In Proceedings of the AAAI Conference on Artificial Intelligence, 38, 22021–22030 (2024). source
Not checked in the free run.
- Study design and conductreasoning
GPT-4 was excluded from the rationale evaluation because the rationale component of the MMedBench dataset was primarily constructed using GPT-4 outputs, which could introduce bias and unfair comparisons.
“It is important to note that GPT-4 was excluded from this evaluation, because the rationale component of the MMedBench dataset was primarily constructed using GPT-4 outputs, which could introduce bias and bring unfair comparisons.”
Quote in the paperSubstantial claim - Interpretationreasoning
Current benchmarks fail to adequately reflect the practical utility of large language models in real-world clinical scenarios.
“Current benchmarks, which largely focus on multiple-choice problems2,7,8, fail to adequately reflect the practical utility of LLMs in real-world clinical scenarios.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [2] Singhal, K. et al. Towards expert-level medical question answering with large language models. arXiv preprint arXiv:2305.09617 (2023).
Not checked in the free run.
- cites [7] Wu, C. et al. Pmc-llama: toward building open-source language models for medicine. Journal of the American Medical Informatics Association ocae045 (2024). source
Not checked in the free run.
- cites [8] Chen, Z. et al. Meditron-70b: Scaling medical pretraining for large language models. arXiv preprint arXiv:2311.16079 (2023).
Not checked in the free run.
- Rests on an assumption: Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
- Interpretationown data
MMedIns-Llama 3 outperforms existing LLMs, including GPT-4 and Claude-3.5, across a range of medical benchmarks covering different text sources.
“As evidenced by the results, our model outperforms existing LLMs, including GPT-4, Claude-3.5, across a range of medical benchmarks, covering different text sources.”
Quote in the paperSubstantial claim- Rests on an assumption: Performance on MedS-Bench tasks reflects clinical capabilities.
- Premisecitation
Med42-v2 is a suite of clinical LLMs built on the Llama 3 architecture and fine-tuned with specialized clinical data.
“Med42-v214 is a suite of clinical LLMs built on the Llama 3 architecture and fine-tuned with specialized clinical data.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [14] Christophe, C., Kanithi, P. K., Raha, T., Khan, S. & Pimentel, M. A. Med42-v2: A suite of clinical llms. arXiv preprint arXiv:2408.06142 (2024).
Not checked in the free run.
- Premisecitation
Further auto-regressive training on medical-related corpus can inject medical knowledge into models, allowing them to perform better in different downstream tasks.
“We take the same approach as our previous work7,19, which have shown that further auto-regressive training on medical-elated corpus can inject medical knowledge into the models, thus allowing them to perform better in different downstream tasks.”
Quote in the paperSubstantial claim0 of 2 sources checked- cites [7] Wu, C. et al. Pmc-llama: toward building open-source language models for medicine. Journal of the American Medical Informatics Association ocae045 (2024). source
Not checked in the free run.
- cites [19] Qiu, P. et al. Towards building multilingual language model for medicine. Nature Communications 15.1 (2024): 8384. source
Not checked in the free run.
- May combine two claims. 22
- Classified as probably not a substantial claim. 9
May combine two claims.
Findingown dataMed42-v2 achieved 79.54 on PUBLICHEALTH, the best among open-source models, just behind GPT-4 with 78.60.
“On PUBLICHEALTH, Med42-v2 achieves 79.54, which is the best among all the open-source models, just behind GPT-4 with 78.60.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataMMedIns-Llama 3 achieved the highest scores across all metrics on the HoC multi-label classification task, with a macro-Precision of 89.59, a macro-Recall of 85.58, and a macro-F1 score of 86.66.
“Our MMedIns-Llama 3 clearly outperforms all other models, achieving the highest scores across all metrics, with a macro-Precision of 89.59, a macro-Recall of 85.58, and a macro-F1 score of 86.66.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataMedS-Ins tokens are distributed across five text domains: exams 7%, clinical texts 35%, academic papers 13%, medical knowledge bases 43%, and daily conversations 2%.
“7% of the tokens in our dataset are from the exams.”
- Also stated in: § Results · plain
“35% of the tokens in our dataset are from clinical texts.”
- Also stated in: § Results · plain
“43% of the tokens in our dataset are from medical knowledge.”
Quote in the paperNot a substantial claim- Also stated in: § Results · plain
May combine two claims.
Findingown dataMMedIns-Llama 3 excelled in the MedNLI generative task, with BLEU/ROUGE scores of 23.52/25.17, outperforming other models except GPT-4.
“MMedIns-Llama 3 also excels in the generative task, with BLEU/ROUGE scores of 23.52/25.17, outperforming other models except the GPT-4.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOn medical concept explanation, MMedIns-Llama 3 achieves the highest average BLEU/ROUGE scores of 34.43/37.47, significantly outperforming other models.
“Our final model, MMedIns-Llama 3, significantly outperforms the other ones across all concept explanation tasks, particularly in Health Fact Explanation (30.50/28.53) and BioLORD Concept Explanation (38.12/43.90), and achieving the highest average scores of 34.43/37.47.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.
Findingnone givenMedS-Bench currently covers only 11 clinical tasks, which does not fully encompass the complexity of all clinical scenarios.
“First, MedS-Bench currently covers only 11 clinical tasks, which does not fully encompass the complexity of all clinical scenarios.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataMedS-Bench is a comprehensive benchmark for evaluating large language models in clinical contexts, extending beyond multiple-choice question answering to include 11 high-level clinical task categories derived from 28 existing datasets.
“we present MedS-Bench, a comprehensive benchmark to evaluate large language models (LLMs) in clinical contexts, MedS-Bench, spanning 11 high-level clinical tasks.”
- Also stated in: § Results · plain
“MedS-Bench encompasses 11 high-level clinical task categories, derived from 28 existing datasets”
Quote in the paperSubstantial claim- Rests on an assumption: The selected 11 clinical task categories in MedS-Bench adequately represent real-world clinical demands.
- Also stated in: § Results · plain
May combine two claims.
Findingown dataInternLM 2 exhibited high recall but struggled with precision on the HoC multi-label classification task, resulting in a lower F1 score.
“These models, especially InternLM 2, exhibit high recall but struggle with precision, resulting in lower F1 scores.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataMedS-Ins has 19 task categories, including the 11 categories in MedS-Bench and additional categories such as Intent Identification, Translation, Word Relation Classification, Text Retrieval, Sentence Composition Analysis, Wrong Candidate Generation, Dialogue, and Text Completion, with MCQA extended to general Question Answering.
“These 19 task categories include but are not limited to, the 11 categories in the MedS-Bench benchmark.”
- Also stated in: § Results · plain
“The additional categories encompass a range of linguistic and analytical tasks essential for comprehensive medical language processing, including Intent Identification, Translation, Word Relation Classification, Text Retrieval, Sentence Composition Analysis, Wrong Candidate Generation, Dialogue, and Text Completion and the MCQA category is extended to general Question Answering, which also include”
Quote in the paperSubstantial claim- Also stated in: § Results · plain
May combine two claims.
Findingown dataEight of the task categories require the model to recall knowledge from the model, while the remaining three require fact retrieval from the given context.
“eight of the task categories require the model to recall knowledge from the model, while the remaining three require fact retrieval from the given context.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataGPT-4 and Claude-3.5 achieved accuracy scores of 86.63 and 82.14 respectively on the MedNLI discriminative task.
“For the closed-source LLMs, GPT-4 and Claude-3.5 all show relatively high scores, with 86.63 and 82.14 accuracy scores respectively.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataOn named entity recognition tasks, MMedIns-Llama 3 achieves an average F1-Score of 79.29, significantly outperforming all other models.
“Our model, MMedIns-Llama 3, significantly outperforms all other models, achieving an average F1-Score of 79.29.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOn information extraction, MMedIns-Llama 3 achieves the best overall average score of 83.77, surpassing InternLM 2 by 4.66 points.
“Our proposed model, MMedIns-Llama 3, demonstrates the best overall performance, achieving an average score of 83.77, surpassing InternLM 2 by 4.66 points.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataMMedIns-Llama 3 achieved the highest accuracy in the MedNLI discriminative task, scoring 86.71, comparable with GPT-4.
“MMedIns-Llama 3 achieves the highest accuracy in the discriminative task, scoring 86.71, comparable with GPT-4.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOn text summarization, MMedIns-Llama 3 achieves average BLEU/ROUGE scores of 46.82/48.38, significantly outperforming other models.
“Our model (MMedIns-Llama 3), trained on the medical-specific instruction dataset (MedS-Ins), significantly outperforms the others, achieving average scores of 46.82/48.38.”
Quote in the paperSubstantial claimMay combine two claims.
Findingown dataOn clinical decision support tasks, MMedIns-Llama 3 achieves 98.47 accuracy in treatment planning, 97.53 in diagnosis, and an average accuracy of 63.35 in clinical outcome prediction.
“MMedIns-Llama 3 demonstrate superior accuracy in clinical decision support tasks, with a 98.47 accuracy score in treatment planning, 97.53 in diagnosis, and an average accuracy of 63.35 (mean on the scores of Hospitalization, 72h ED Revisit, and Critical Triage) in clinical outcome prediction.”
Quote in the paperSubstantial claimProbably not a substantial claim: may not pass S4 (based).
Findingown dataOpen-source models struggle to complete zero-shot evaluation.
“we evaluate all models in few-shot settings, as we observe that open-source models struggle to complete zero-shot evaluation.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataBy filtering instruction datasets in the general domain, they collected 37 tasks, for a total of 75373 samples.
“Finally, by filtering instruction datasets in the general domain, we collect 37 tasks, for a total of 75373 samples.”
Quote in the paperNot a substantial claimMay combine two claims.
Findingown dataThrough the procedure, they prompted an extra 85 tasks into a unified free-form question-answering format, combined with filtered data, resulting in a total of 5M instances with 19K instructions, covering 122 tasks, termed MedS-Ins.
“Through the above procedure, we prompt an extra 85 tasks into a unified free-form question-answering format, combined with the filtered data, resulting in a totaling 5M instances with 19K instructions, covering 122 tasks, termed as MedS-Ins”
Quote in the paperSubstantial claimMay combine two claims.
PremisecitationLarge language models have achieved high scores on multiple-choice question-answering benchmarks in healthcare and have successfully passed the UMLS examination.
“LLMs have achieved high scores on multiple-choice question-answering (MCQA) benchmarks in healthcare, and successfully passed the UMLS examination, as noted by Singhal et al.1,2.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites Singhal et al.1,2
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
Study design and conductreasoningAround 1500 test cases per benchmark were randomly sampled to manage cost constraints.
“we randomly sampled around 1500 test cases per benchmark to manage the cost constraints.”
Quote in the paperNot a substantial claim- Rests on an assumption: The randomly sampled around 1500 test cases per benchmark are representative of the full benchmark.
Probably not a substantial claim: may not pass S2 (checkable), S4 (based).
InterpretationreasoningThe diversity of task categories in MedS-Ins guarantees a comprehensive understanding of the potential medical applications.
“The diversity of task categories ranging from common question answering and dialogue to various downstream clinical tasks—guarantees a comprehensive understanding of the potential medical applications.”
Quote in the paperNot a substantial claim- Rests on an assumption: The 58 source datasets are of sufficient quality and diversity to produce a comprehensive medical instruction dataset.
Probably not a substantial claim: may not pass S3 (load-bearing).
Interpretationown dataThe significant proportion of clinical texts in MedS-Ins ensures that the instruction tuning data aligns closely with clinical demands.
“Notably, the significant proportion of clinical texts ensures that the instruction tuning data aligns closely with clinical demands.”
Quote in the paperNot a substantial claim- Rests on an assumption: The 58 source datasets are of sufficient quality and diversity to produce a comprehensive medical instruction dataset.
May combine two claims.
Interpretationown dataExisting LLMs perform exceptionally well on MCQA benchmarks but struggle to align with actual clinical practice, particularly in tasks such as treatment planning and explanation.
“Our results reveal that while existing LLMs perform exceptionally well on MCQA benchmarks, they struggle to align with the actual clinical practice, particularly in tasks such as treatment planning and explanation.”
Quote in the paperSubstantial claimClassified as probably not a substantial claim. May combine two claims.
Study design and conductcitationAll results were obtained using a 3-shot prompting strategy except for MCQA tasks, where a zero-shot prompting setting was used to align with previous studies.
“All results presented here were obtained using a 3-shot prompting strategy (more details in the “Evaluation Settings” section in Supplementary), except for MCQA tasks, where we used a zero-shot prompting setting to align with previous studies7,8,19.”
Quote in the paperSubstantial claim0 of 3 sources checked- cites [7] Wu, C. et al. Pmc-llama: toward building open-source language models for medicine. Journal of the American Medical Informatics Association ocae045 (2024). source
Not checked in the free run.
- cites [8] Chen, Z. et al. Meditron-70b: Scaling medical pretraining for large language models. arXiv preprint arXiv:2311.16079 (2023).
Not checked in the free run.
- cites [19] Qiu, P. et al. Towards building multilingual language model for medicine. Nature Communications 15.1 (2024): 8384. source
Not checked in the free run.
Probably not a substantial claim: may not pass S3 (load-bearing).
PremisecitationLarge language models have shown expert-level performance in clinical text summarization when appropriate prompting strategies are employed.
“LLMs have shown expert-level performance in clinical text summarization when appropriate prompting strategies are employed3.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [3] Van Veen, D. et al. Adapted large language models can outperform medical experts in clinical text summarization. Nat. Med. 30, 1134–1142 (2024). source
Not checked in the free run.
Probably not a substantial claim: may not pass S4 (based).
Interpretationnone givenMedS-Ins has been shown to significantly improve LLMs on clinical tasks.
“which has shown to significantly improve the LLMs on clinical tasks.”
Quote in the paperNot a substantial claim- Rests on an assumption: Performance on MedS-Bench tasks reflects clinical capabilities.
May combine two claims.
PremisecitationMEDITRON is a large-scale medical LLM, further pre-trained on Llama 2, leveraging 21.1M medical papers, guidelines for further pre-training, and supervised finetuning on different MCQA datasets with context and chain-of-thought prompt styles.
“MEDITRON8 is a large-scale medical LLM, further pre-trained on Llama 2. It leverages 21.1M medical papers, guidelines for further pre-training, and supervised finetuning on different MCQA datasets with context and chain-of-thought prompt styles.”
Quote in the paperNot a substantial claim0 of 1 sources checked- cites [8] Chen, Z. et al. Meditron-70b: Scaling medical pretraining for large language models. arXiv preprint arXiv:2311.16079 (2023).
Not checked in the free run.
Classified as probably not a substantial claim.
Interpretationnone givenThe benchmark cannot replace the final stage of evaluating LLMs in actual clinical settings to ensure their safety.
“while our benchmark is more comprehensive and clinically relevant than previous MCQA benchmarks, it cannot replace the final stage of evaluating LLMs in actual clinical settings to ensure their safety.”
Quote in the paperSubstantial claim
The paper relies on this without support.
The selected 11 clinical task categories in MedS-Bench adequately represent real-world clinical demands.
“Current benchmarks, which largely focus on multiple-choice problems2,7,8, fail to adequately reflect the practical utility of LLMs in real-world clinical scenarios.”
“MedS-Bench encompasses 11 high-level clinical task categories, derived from 28 existing datasets”
The paper relies on this without support.
The randomly sampled around 1500 test cases per benchmark are representative of the full benchmark.
“we randomly sampled around 1500 test cases per benchmark to manage the cost constraints.”
The paper relies on this without support.
Performance on MedS-Bench tasks is indicative of practical utility in real-world clinical scenarios.
“This benchmark provides clinicians and researchers with a detailed understanding of where LLMs excel and where they fall short in medical tasks.”
The paper relies on this without support.
The 58 source datasets are of sufficient quality and diversity to produce a comprehensive medical instruction dataset.
“MedS-Ins comprises 58 medically oriented language corpora, totaling 5M instances with 19K instructions, across 122 tasks.”
The paper relies on this without support.
Existing medical LLM benchmarks are narrow (focused on MCQA) and risk overlooking broader clinical capabilities.
“The development of medical LLMs has largely relied on benchmarks focused on multiple-choice question answering (MCQA). However, this narrow evaluation framework risks overlooking the broader capabilities required for LLMs in various clinical scenarios.”
The paper relies on this without support.
Previous instruction tuning datasets neglected texts generated from real clinical practice.
“Previous efforts have focused primarily on constructing question-answer pairs from daily conversations, exams, or academic papers, often neglecting the texts generated from real clinical practice.”
The paper relies on this without support.
Performance on MedS-Bench tasks reflects clinical capabilities.
“our benchmark is expected to serve as an experimental arena for assessing the performance of different LLMs, offering a more accurate reflection of their clinical capabilities”
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?
These frameworks typically focus on narrow clinical scenarios (1-28 datasets), rely on limited data sources or synthetic data, and assess primarily accuracy without comprehensive taxonomy validation or deployment considerations.
“However, these frameworks typically focus on narrow clinical scenarios (1–28 datasets), rely on limited data sources or synthetic data, and assess primarily accuracy without comprehensive taxonomy validation or deployment considerations.”
From Holistic evaluation of large language models for medical tasks with MedHELM (2026) · cites this paper as [19]
Recent medical benchmarking efforts have begun addressing some limitations: HEALTHBENCH incorporates physician-developed rubrics, ClinicBench advances multimodal evaluation, and automated frameworks explore LLM-as-a-Judge strategies for EHR summarization.
“Recent medical benchmarking efforts (Extended Data Table 8) have begun addressing some limitations: HEALTHBENCH10 incorporates physician-developed rubrics for health conversations, ClinicBench18,19 advances multimodal evaluation, and automated frameworks explore LLM-as-a-Judge strategies for EHR summarization19–26.”
From Holistic evaluation of large language models for medical tasks with MedHELM (2026) · cites this paper as [19]
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.
Mistral's MCQA average does not match its eight scores
MinorThe eight reported accuracies average 59.625, not 49.1.
Reported 49.1 · recomputed 59.625
“| Mistral | 7B | 50.8 | 48.2 | 75.4 | 71.1 | 44.7 | 48.7 | 74.2 | 63.9 | 49.1 |”
Med42-v2's PUBLICHEALTH score and ranking conflict with Table 8
MinorThe prose reports 79.54 and calls it the best open-source result. Table 8 instead reports 78.54 for Med42-v2 and 79.55 for MMedIns-Llama 3.
“On PUBLICHEALTH, Med42-v2 achieves 79.54, which is the best among all the open-source models, just behind GPT-4 with 78.60.”
“| Med42-v2 | 8B | 73.23 | 78.54 | 15.63/15.86 | 77.57 | 12.24/15.29 | | Baichuan 2 | 7B | 79.38 | 47.98 | 14.97/15.99 | 53.94 | 14.99/17.27 | | MMedIns-Llama 3 | 8B | 97.08 | 79.55 | 12.71/14.65 | 86.71 | 23.52/25.17 |”
The benchmark lists 12 task categories but says it has 11
MinorThe enumerated list contains 12 categories, counting Explanation and Rationale separately, whereas the text says MedS-Bench encompasses 11.
“MedS-Bench encompasses 11 high-level clinical task categories, derived from 28 existing datasets, as illustrated in Fig. 1.”
“The task categories we considered include: Multi-choice Question Answering, Text Summarization, Information Extraction, Explanation, Rationale, Named Entity Recognition, Diagnosis, Treatment Planning, Clinical Outcome Prediction, Text Classification, Fact Verification, and Natural Language Inference.”
InternLM 2 does not lead intervention extraction
MinorAlthough InternLM 2 scores 74.42 on intervention extraction, Table 3 gives Llama 3 a higher score of 79.07.
“InternLM 2 leads in both Intervention and Outcome Extraction, with scores of 74.42 and 69.77, respectively.”
“| Llama 3 | 8B | 58.14 | 79.07 | 58.14 | 69.57 | 95.93 | 72.17 |”
MMedIns-Llama 3 does not match InternLM 2 on PubMedQA verification
MinorThe prose describes its accuracy as the highest, alongside InternLM 2, but Table 8 reports 97.08 for MMedIns-Llama 3 versus 99.23 for InternLM 2.
“MMedIns-Llama 3 continues surpassing existing models, achieving the highest accuracy score as InternLM 2, excelling in PubMedQA Answer Verification and HealthFact Verification”
“| InternLM 2 | 7B | 99.23 | 76.94 | 8.75/14.69 | 84.67 | 15.84/19.01 |”
No citation lists for this paper
No citation lists for this paper yet — checked again daily.
References 20 · Cited by 52
Research works printed but not linked: 6
- Wang, Y. et al. Super-naturalinstructions: Generalization via declarative instructions on 1600+ nlp tasks. In 2022 Conference on Empirical Methods in Natural Language Processing, EMNLP 2022 (2022). · DOI · Paper page
- Longpre, S. et al. The flan collection: Designing data and methods for effective instruction tuning. In International Conference on Machine Learning (pp. 22631-22648). PMLR.
- Tom, K. et al. Findings of the 2023 conference on machine translation (wmt23): Llms are here but not quite there yet. In WMT23-Eighth Conference on Machine Translation, 198–216 (2023).
- Zhang, W., Aljunied, M., Gao, C., Chia, Y. K. & Bing, L. M3exam: A multilingual, multimodal, multilevel benchmark for examining large language models. Adv. Neural Inf. Process. Syst. 36, 5484–5505 (2023).
- Zhou, C. et al. Lima: Less is more for alignment. Advances in Neural Information Processing Systems 36 (2024).
- Lu, K. et al. # instag: Instruction tagging for analyzing supervised fine-tuning of large language models. In The Twelfth International Conference on Learning Representations (2023).
- Authors
- Wu, C., Qiu, P., Liu, J., Gu, H., Li, N., Zhang, Y., Wang, Y., & Xie, W.
- Affiliations
- Shanghai Jiao Tong University (CN)
- China Mobile (China) (CN)
- Corresponding author
- Wang, Yanfeng
- Xie, Weidi
- Venue
- npj Digital Medicine
- Published
- 2025-01-27
- Volume
- 8
- Issue
- 1
- Pages
- 58-58
- ISSN
- 2398-6352 (ISSN-L)
- PMC
- PMC11770143
- OpenAlex
- W4406829669
- Cited by
- 52
- References
- 20
- Citations by year
- 2026: 37 · 2025: 15
- FWCI
- 12.52
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- npj Digital Medicine (publishedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- arXiv (Cornell University) (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- arXiv (Cornell University) (cc-by)
- Funders
- Science and Technology Commission of Shanghai Municipality (18DZ2270700)
- 111 plan (BP0719010)
- State Key Laboratory of UHD Video and Audio Production and Presentation
- National Key R&D Program of China (2022ZD0160702)
- Topics
- Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
- Physical Sciences › Computer Science › Artificial Intelligence › Topic Modeling
- Physical Sciences › Computer Science › Computer Vision and Pattern Recognition › Multimodal Machine Learning Applications
- Keywords
- large language models, clinical language models, benchmark, instruction tuning, clinical tasks, leaderboards
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.
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Classified by jev-1.13-20260917 (gold-guideline-v0.2) on 2026-10-06.
Statistics and arithmetic are recomputed, not judged.
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