PubMedQA
Harbor: pendingPubMedQA is a novel biomedical question answering (QA) dataset collected from PubMed abstracts.
- Samples
- 500
- Released
- 2019
- Scores
- 12
Medical exam Q&A benchmark
Available in EleutherAI lm-evaluation-harness as task family medqa (2 tasks).
$ npm i -g lettokenburn-cli$ ltb bench pull medqa
External harness. pip install lm-eval && lm_eval --model <hf|vllm|openai-chat-completions> --model_args <model args> --tasks medqa_4options (lm-evaluation-harness task family 'medqa') https://github.com/EleutherAI/lm-evaluation-harness
Runs happen on your machine with your own subscription; only the score summary is pushed. CLI docs
| Harness | Source | Confidence | Link | |||
|---|---|---|---|---|---|---|
| GPT-4 | 90.2 | N/A | Independent | medium | Nov 28, 2023 | arxiv.org |
| Med-PaLM 2 | 85.4 | N/A | Independent | medium | May 16, 2023 | arxiv.org |
| Med-PaLM 2 | 79.7 | N/A | Independent | medium | May 16, 2023 | arxiv.org |
| Flan-PaLM | 67.6 | N/A | Independent | medium | Dec 26, 2022 | arxiv.org |
| Codex 5-shot CoT | 60.2 | N/A | Independent | medium | Jul 17, 2022 | arxiv.org |
| llama 2 | 59.2 | N/A | Independent | medium | Nov 27, 2023 | arxiv.org |
| GPT-Neo | 33.3 | N/A | Independent | medium | Dec 26, 2022 | arxiv.org |
| BLOOM | 23.3 | N/A | Independent | medium | Nov 16, 2022 | arxiv.org |
Every number links to where it was published. Low-confidence rows are muted and need per-cell verification.
From "What Disease Does This Patient Have? A Large-Scale Open Domain Question Answering Dataset from Medical Exams" (Jin et al.), MedQA is an open domain question answering dataset composed of questions from professional medical board exams.
From Jin et al., "to comply with fair use of law ,we shuffle the order of answer options and randomly delete one of the wrong options for each question for USMLE and MCMLE datasets, which results in four options with one right option and three wrong options". We use the 4-options, English subset ("US") of the dataset, which contains 12,723 questions.
The following is an example from the dataset:
{ "question": "A 23-year-old pregnant woman at 22 weeks gestation presents with burning upon urination. She states it started 1 day ago and has been worsening despite drinking more water and taking cranberry extract. She otherwise feels well and is followed by a doctor for her pregnancy. Her temperature is 97.7°F (36.5°C), blood pressure is 122/77 mmHg, pulse is 80/min, respirations are 19/min, and oxygen saturation is 98% on room air. Physical exam is notable for an absence of costovertebral angle tenderness and a gravid uterus. Which of the following is the best treatment for this patient?", "answer": "Nitrofurantoin", "options": { "A": "Ampicillin", "B": "Ceftriaxone", "C": "Ciprofloxacin", "D": "Doxycycline", "E": "Nitrofurantoin" }, "meta_info": "step2&3", "answer_idx": "E" }
Paper: https://arxiv.org/abs/2009.13081 Code: https://github.com/jind11/MedQA
@article{jin2020disease, title={What Disease does this Patient Have? A Large-scale Open Domain Question Answering Dataset from Medical Exams}, author={Jin, Di and Pan, Eileen and Oufattole, Nassim and Weng, Wei-Hung and Fang, Hanyi and Szolovits, Peter}, journal={arXiv preprint arXiv:2009.13081}, year={2020} }