Performance of DeepSeek-R1, ChatGPT (GPT-o3-mini), and Gemini 2.0 Flash on German Medical Multiple-Choice Questions: Comparative Evaluation
Bibliographic record
Abstract
BACKGROUND: Despite the transformative potential of artificial intelligence (AI)-based chatbots in medicine, their implementation is hindered by data privacy and security concerns. DeepSeek offers a conceivable solution through its capability for local offline operations. However, as of 2025, it remains unclear whether DeepSeek can achieve an accuracy comparable to that of conventional, cloud-based AI chatbots. OBJECTIVE: This study aims to evaluate whether DeepSeek, an AI-based chatbot capable of offline operation, achieves answer accuracy on medical multiple-choice questions (MCQs) comparable to that of leading chatbots (ie, ChatGPT and Gemini) on German medical MCQs, thereby assessing its potential as a privacy-preserving alternative for clinical use. METHODS: A total of 200 interdisciplinary MCQs from the German Progress Test Medicine were administered to ChatGPT (GPT-o3-mini), DeepSeek (DeepSeek-R1), and Gemini (Gemini 2.0 Flash). Accuracy was defined as the proportion of correctly solved questions. Overall differences among the 3 models were tested with the Cochran Q test, while pairwise comparisons were conducted using the McNemar test. Subgroup analyses were performed by medical domain (Fisher exact test) and question length (Wilcoxon rank-sum test). An a priori power analysis indicated a minimum sample size of 195 questions. RESULTS: All 3 chatbots surpassed the conventional passing threshold of 60%, with accuracies of 96% (192/200) for DeepSeek, 94% (188/200) for Gemini, and 92.5% (185/200) for ChatGPT. The overall difference among models was not statistically significant (P=.10) nor were pairwise comparisons. However, incorrect responses were significantly associated with longer question length for DeepSeek (P=.049) and ChatGPT (P=.04) but not for Gemini. No significant differences in performance were observed across clinical versus preclinical domains or medical specialties (all P>.05). CONCLUSIONS: Overall, DeepSeek demonstrates outstanding performance on German medical MCQs comparable to the widely used chatbots ChatGPT and Gemini. Similar to ChatGPT, DeepSeek's performance declined with increasing question length, highlighting verbosity as a persistent challenge for large language models. While DeepSeek's offline capability and lower operational costs are advantageous, its safe and reliable application in clinical contexts requires further investigation.
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.008 | 0.032 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.001 |
| Science and technology studies | 0.000 | 0.001 |
| Scholarly communication | 0.001 | 0.002 |
| Open science | 0.001 | 0.002 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.004 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".