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Model Card for MedGENIE-fid-flan-t5-base-medmcqa

MedGENIE comprises a collection of language models designed to utilize generated contexts, rather than retrieved ones, for addressing multiple-choice open-domain questions in the medical field. Specifically, MedGENIE-fid-flan-t5-base-medmcqa is a fusion-in-decoder (FID) model based on flan-t5-base, trained on the MedMCQA dataset and grounded on artificial contexts generated by PMC-LLaMA-13B. This model achieves performance levels comparable to state-of-the-art (SOTA) larger models on both MedMCQA and MMLU-Medical benchmarks.

Model description


At the time of release (February 2024), MedGENIE-fid-flan-t5-base-medmcqa outcompetes many fine-tuned and few-shot versions of 7B models on MedMCQA. Moreover, it emerges as the leading model on MMLU-Medical, a compilation of 9 medical subsets from MMLU, following Zephyr-β (7B) augmented with MedWiki.

Model Ground (Source) Learning Params MedMCQA MMLU-medical AVG (↓)
MEDITRON (Chen et al.) Fine-tuned 7B 59.2 55.6 57.4
VOD (Liévin et al. 2023) R (MedWiki) Fine-tuned 220M 58.3 56.8 57.6
Zephyr-β R (MedWiki) 2-shot 7B 47.0 66.7 56.9
MedGENIE-FID-Flan-T5 G (PMC-LLaMA) Fine-tuned 250M 52.1 59.9 56.0
PMC-LLaMA (Chen et al.) Fine-tuned 7B 51.4 59.7 55.6
LLaMA-2 (Chen et al.) Fine-tuned 7B 54.4 56.3 55.4
Zephyr-β (Chen et al.) 2-shot 7B 43.4 60.7 52.1
Mistral-Instruct R (MedWiki) 2-shot 7B 44.3 58.5 51.4
Mistral-Instruct (Chen et al.) 3-shot 7B 40.2 55.8 48.0
LLaMA-2-chat 2-shot 7B 35.0 49.3 42.2
LLaMA-2-chat R (MedWiki) 2-shot 7B 37.2 52.0 44.6

Training hyperparameters

The following hyperparameters were used during training:

  • learning_rate: 5e-05
  • n_context: 5
  • per_gpu_batch_size: 2
  • accumulation_steps: 2
  • total_steps: 182,816
  • eval_freq: 22,852
  • optimizer: AdamW
  • scheduler: linear
  • weight_decay: 0.01
  • warmup_ratio: 0.1
  • text_maxlength: 600

Bias, Risk and Limitation

Our model is trained on artificially generated contextual documents, which might inadvertently magnify inherent biases and depart from clinical and societal norms. This could lead to the spread of convincing medical misinformation. To mitigate this risk, we recommend a cautious approach: domain experts should manually review any output before real-world use. This ethical safeguard is crucial to prevent the dissemination of potentially erroneous or misleading information, particularly within clinical and scientific circles.


If you find MedGENIE-fid-flan-t5-base-medmcqa is useful in your work, please cite it with:

      title={To Generate or to Retrieve? On the Effectiveness of Artificial Contexts for Medical Open-Domain Question Answering}, 
      author={Giacomo Frisoni and Alessio Cocchieri and Alex Presepi and Gianluca Moro and Zaiqiao Meng},
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Dataset used to train disi-unibo-nlp/MedGENIE-fid-flan-t5-base-medmcqa

Collection including disi-unibo-nlp/MedGENIE-fid-flan-t5-base-medmcqa