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Cited by 233Artificial Intelligence in Healthcare and EducationMachine Learning in HealthcareArtificial Intelligence in Healthcare

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Benchmark evaluation of DeepSeek large language models in clinical decision-making

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Sandmann, Sarah, Hegselmann, Stefan, Fujarski, Michael, Bickmann, Lucas, Wild, Benjamin, Eils, Roland, Varghese, Julian·2025·Nature Medicine
DOI 10.1038/s41591-025-03727-2PMC PMC12353792
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Abstract

Large language models (LLMs) are increasingly transforming medical applications. However, proprietary models such as GPT-4o face significant barriers to clinical adoption because they cannot be deployed on site within healthcare institutions, making them noncompliant with stringent privacy regulations. Recent advancements in open-source LLMs such as DeepSeek models offer a promising alternative because they allow efficient fine-tuning on local data in hospitals with advanced information technology infrastructure. Here, to demonstrate the clinical utility of DeepSeek-V3 and DeepSeek-R1, we benchmarked their performance on clinical decision support tasks against proprietary LLMs, including GPT-4o and Gemini-2.0 Flash Thinking Experimental. Using 125 patient cases with sufficient statistical power, covering a broad range of frequent and rare diseases, we found that DeepSeek models perform equally well and in some cases better than proprietary LLMs. Our study demonstrates that open-source LLMs can provide a scalable pathway for secure model training enabling real-world medical applications in accordance with data privacy and healthcare regulations.

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Fig. 1 Model performance for diagnosis tasks. a–d, Bubble plots showing the results of the 125 pairwise comparisons on a 5-point Likert scale for GPT-4o versus DeepSeek-R1 (a) (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 0.3085, V = 378, 95% CI −3.13 × 10−7 to infinity, estimate 0.25); GPT-4o versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 7.89 × 10−6, V = 1,576, 95% CI 0.5 to infinity, estimate 0.75) (b); DeepSeek-R1 versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 5.73 × 10−5, V = 1,515, 95% CI 0.5 to infinity, estimate 0.5) (c); and DeepSeek-R1 versus DeepSeek-V3 (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 1, V = 307, 95% CI −0.25 to infinity, estimate 1.97 × 10−5) (d). e, Violin plots comparing the Likert scores of GPT-4o, DeepSeek-R1, DeepSeek-V3 and Gem2FTE with those of GPT-4, GPT-3.5 and Google in our previous study (n.s., not significant; ***P < 0.001; significance levels visualizing the results of statistical tests performed in a–d). Explorative comparison of the n = 110 cases analyzed by all seven models with the n = 15 newly added cases shows that the performance scores align well (one-sided unpaired Mann–Whitney test, alternative = greater; GPT-4o: pGPT-4o 0.5441, W = 813.5, 95% CI −1.84 × 10−5 to infinity, estimate −4.99 × 10−5; DeepSeek-R1: pDeepSeek-R1 0.7710, W = 740, 95% CI 3.75 × 10−5 to infinity, estimate −2.16 × 10−5; DeepSeek-V3: pDeepSeek-V3 0.6678, W = 775.5, 95% CI −7.45 × 10−5 to infinity, estimate 5.91 × 10−5; Gem2FTE: pGem2FTE 0.9899, W = 540, 95% CI −0.5 to infinity, estimate −3.51 × 10−5). f, The cumulative frequency of the Likert scores for GPT-4o, DeepSeek-R1, DeepSeek-V3, Gem2FTE and GPT-4.
Fig. 1 Model performance for diagnosis tasks. a–d, Bubble plots showing the results of the 125 pairwise comparisons on a 5-point Likert scale for GPT-4o versus DeepSeek-R1 (a) (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 0.3085, V = 378, 95% CI −3.13 × 10−7 to infinity, estimate 0.25); GPT-4o versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 7.89 × 10−6, V = 1,576, 95% CI 0.5 to infinity, estimate 0.75) (b); DeepSeek-R1 versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 5.73 × 10−5, V = 1,515, 95% CI 0.5 to infinity, estimate 0.5) (c); and DeepSeek-R1 versus DeepSeek-V3 (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 4, adjusted P = 1, V = 307, 95% CI −0.25 to infinity, estimate 1.97 × 10−5) (d). e, Violin plots comparing the Likert scores of GPT-4o, DeepSeek-R1, DeepSeek-V3 and Gem2FTE with those of GPT-4, GPT-3.5 and Google in our previous study (n.s., not significant; ***P < 0.001; significance levels visualizing the results of statistical tests performed in a–d). Explorative comparison of the n = 110 cases analyzed by all seven models with the n = 15 newly added cases shows that the performance scores align well (one-sided unpaired Mann–Whitney test, alternative = greater; GPT-4o: pGPT-4o 0.5441, W = 813.5, 95% CI −1.84 × 10−5 to infinity, estimate −4.99 × 10−5; DeepSeek-R1: pDeepSeek-R1 0.7710, W = 740, 95% CI 3.75 × 10−5 to infinity, estimate −2.16 × 10−5; DeepSeek-V3: pDeepSeek-V3 0.6678, W = 775.5, 95% CI −7.45 × 10−5 to infinity, estimate 5.91 × 10−5; Gem2FTE: pGem2FTE 0.9899, W = 540, 95% CI −0.5 to infinity, estimate −3.51 × 10−5). f, The cumulative frequency of the Likert scores for GPT-4o, DeepSeek-R1, DeepSeek-V3, Gem2FTE and GPT-4.CC BY-NC-ND · PubMed Central
Fig. 2 Model performance for treatment recommendation tasks. a–c, Bubble plots showing the results of the 125 pairwise comparisons on a 5-point Likert scale for GPT-4o versus DeepSeek-R1 (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.1522, V = 771.5, 95% CI −6.88 × 10−5 to infinity, estimate 0.25) (a); GPT-4o versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.0016, V = 1154, 95% CI 0.2501 to infinity, estimate 0.5) (b); DeepSeek-R1 versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.0235, V = 1,124, 95% CI 4.21 × 10−6 to infinity, estimate 0.5) (c). d, Violin plots comparing the Likert scores of GPT-4o, DeepSeek-R1 and Gem2FTE with GPT-4 and GPT-3.5 (n.s., not significant; *P < 0.05; significance levels visualizing the results of statistical tests performed in a–c). Explorative comparison of the n = 110 cases analyzed by all seven models with the n = 15 newly added cases shows that the performance scores align well (one-sided unpaired Mann–Whitney test, alternative = greater; GPT-4o: pGPT-4o 0.1460, W = 955, 95% CI −5.38 × 10−5 to infinity, estimate 3.16 × 10−5; DeepSeek-R1: pDeepSeek-R1 0.5256, W = 817.5, 95% CI −1.46 × 10−5 to infinity, estimate −1.73 × 10−5; Gem2FTE: pGem2FTE 0.4591, W = 838.5, 95% CI −9.54 × 10−6 to infinity, estimate −6.10 × 10−5). e, The cumulative frequency of Likert scores for GPT-4o, DeepSeek-R1, Gem2FTE and GPT-4.
Fig. 2 Model performance for treatment recommendation tasks. a–c, Bubble plots showing the results of the 125 pairwise comparisons on a 5-point Likert scale for GPT-4o versus DeepSeek-R1 (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.1522, V = 771.5, 95% CI −6.88 × 10−5 to infinity, estimate 0.25) (a); GPT-4o versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.0016, V = 1154, 95% CI 0.2501 to infinity, estimate 0.5) (b); DeepSeek-R1 versus Gem2FTE (one-sided paired Mann–Whitney test with continuity correction, alternative = greater, Bonferroni correction with k = 3, adjusted P = 0.0235, V = 1,124, 95% CI 4.21 × 10−6 to infinity, estimate 0.5) (c). d, Violin plots comparing the Likert scores of GPT-4o, DeepSeek-R1 and Gem2FTE with GPT-4 and GPT-3.5 (n.s., not significant; *P < 0.05; significance levels visualizing the results of statistical tests performed in a–c). Explorative comparison of the n = 110 cases analyzed by all seven models with the n = 15 newly added cases shows that the performance scores align well (one-sided unpaired Mann–Whitney test, alternative = greater; GPT-4o: pGPT-4o 0.1460, W = 955, 95% CI −5.38 × 10−5 to infinity, estimate 3.16 × 10−5; DeepSeek-R1: pDeepSeek-R1 0.5256, W = 817.5, 95% CI −1.46 × 10−5 to infinity, estimate −1.73 × 10−5; Gem2FTE: pGem2FTE 0.4591, W = 838.5, 95% CI −9.54 × 10−6 to infinity, estimate −6.10 × 10−5). e, The cumulative frequency of Likert scores for GPT-4o, DeepSeek-R1, Gem2FTE and GPT-4.CC BY-NC-ND · PubMed Central
Extended Data Fig. 1 Visual abstract.
Extended Data Fig. 1 Visual abstract.CC BY-NC-ND · PubMed Central
Extended Data Fig. 2 Summarized model performances for diagnosis and treatment recommendation tasks. Histograms showing the performance of GPT-4o, DeepSeek-R1, Gemini-2.0 Flash Thinking Experimental (Gem2FTE) and DeepSeek-V3 considering diagnosis and treatment, rated with Likert scores. Five points represent the highest possible level of accuracy as assessed by the expert. The red line indicates the mean performance of each model.
Extended Data Fig. 2 Summarized model performances for diagnosis and treatment recommendation tasks. Histograms showing the performance of GPT-4o, DeepSeek-R1, Gemini-2.0 Flash Thinking Experimental (Gem2FTE) and DeepSeek-V3 considering diagnosis and treatment, rated with Likert scores. Five points represent the highest possible level of accuracy as assessed by the expert. The red line indicates the mean performance of each model.CC BY-NC-ND · PubMed Central

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  1. Bonferroni, C. E. Teoria statistica delle classi e calcolo delle probabilita. Pubblicazioni del R. Istituto Super. di Sci. Economiche e Commericiali di Firenze 8, 3–62 (1936).

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Metadata

Authors
Sandmann, S., Hegselmann, S., Fujarski, M., Bickmann, L., Wild, B., Eils, R., & Varghese, J.
Affiliations
  • University of Münster (DE)
  • Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
  • Shanghai Medical College of Fudan University (CN)
  • Otto-von-Guericke-Universität Magdeburg (DE)
Corresponding author
Eils, Roland
ORCID
Venue
Nature Medicine
Publisher
Springer Science and Business Media LLC
Published
2025-04-23
Volume
31
Issue
8
Pages
2546-2549
ISSN
  • 1078-8956 (ISSN-L)
  • 1546-170X
DOI
10.1038/s41591-025-03727-2
PMC
PMC12353792
OpenAlex
W4409695426
Cited by
233
References
20
Citations by year
2026: 171 · 2025: 62
FWCI
55.69
Type
journal article
Language
en
Open access
Licence
Locations
  • Nature Medicine (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
Funders
  • Deutsche Forschungsgemeinschaft (SFB 1470)
  • National Natural Science Foundation of China (W2441025)
  • Bundesministerium für Bildung und Forschung (01KX2121)
Topics
  • Health Sciences › Medicine › Health Informatics › Artificial Intelligence in Healthcare and Education
  • Physical Sciences › Computer Science › Artificial Intelligence › Machine Learning in Healthcare
  • Health Sciences › Health Professions › Health Information Management › Artificial Intelligence in Healthcare
Keywords
DeepSeek, open-source large language models, clinical decision support, benchmarking, GPT-4o, Gemini, DeepSeek-V3, DeepSeek-R1, data privacy, rare diseases, clinical adoption
MeSH terms
Clinical Decision-Making, Large Language Models, Humans, Benchmarking, Decision Support Systems, Clinical

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