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BioMistral-7B-DARE

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metadata
language:
  - en
  - fr
  - nl
  - es
  - it
  - pl
  - ro
  - de
license: apache-2.0
library_name: transformers
tags:
  - mergekit
  - merge
  - dare
  - medical
  - biology
base_model:
  - BioMistral/BioMistral-7B
  - mistralai/Mistral-7B-Instruct-v0.1
datasets:
  - pubmed
pipeline_tag: text-generation
model-index:
  - name: BioMistral-7B-DARE
    results:
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: AI2 Reasoning Challenge (25-Shot)
          type: ai2_arc
          config: ARC-Challenge
          split: test
          args:
            num_few_shot: 25
        metrics:
          - type: acc_norm
            value: 58.28
            name: normalized accuracy
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: HellaSwag (10-Shot)
          type: hellaswag
          split: validation
          args:
            num_few_shot: 10
        metrics:
          - type: acc_norm
            value: 79.87
            name: normalized accuracy
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: MMLU (5-Shot)
          type: cais/mmlu
          config: all
          split: test
          args:
            num_few_shot: 5
        metrics:
          - type: acc
            value: 57.34
            name: accuracy
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: TruthfulQA (0-shot)
          type: truthful_qa
          config: multiple_choice
          split: validation
          args:
            num_few_shot: 0
        metrics:
          - type: mc2
            value: 55.61
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: Winogrande (5-shot)
          type: winogrande
          config: winogrande_xl
          split: validation
          args:
            num_few_shot: 5
        metrics:
          - type: acc
            value: 76.09
            name: accuracy
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard
      - task:
          type: text-generation
          name: Text Generation
        dataset:
          name: GSM8k (5-shot)
          type: gsm8k
          config: main
          split: test
          args:
            num_few_shot: 5
        metrics:
          - type: acc
            value: 15.01
            name: accuracy
        source:
          url: >-
            https://huggingface.co/spaces/HuggingFaceH4/open_llm_leaderboard?query=BioMistral/BioMistral-7B-DARE
          name: Open LLM Leaderboard

BioMistral-7B-mistral7instruct-dare

This is a merge of pre-trained language models created using mergekit.

Merge Details

Merge Method

This model was merged using the DARE TIES merge method using mistralai/Mistral-7B-Instruct-v0.1 as a base.

Models Merged

The following models were included in the merge:

Configuration

The following YAML configuration was used to produce this model:


models:
  - model: mistralai/Mistral-7B-Instruct-v0.1
    # No parameters necessary for base model
  - model: BioMistral/BioMistral-7B
    parameters:
      density: 0.5
      weight: 0.5
merge_method: dare_ties
base_model: mistralai/Mistral-7B-Instruct-v0.1
parameters:
  int8_mask: true
dtype: bfloat16

drawing

BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains

Abstract:

Large Language Models (LLMs) have demonstrated remarkable versatility in recent years, offering potential applications across specialized domains such as healthcare and medicine. Despite the availability of various open-source LLMs tailored for health contexts, adapting general-purpose LLMs to the medical domain presents significant challenges. In this paper, we introduce BioMistral, an open-source LLM tailored for the biomedical domain, utilizing Mistral as its foundation model and further pre-trained on PubMed Central. We conduct a comprehensive evaluation of BioMistral on a benchmark comprising 10 established medical question-answering (QA) tasks in English. We also explore lightweight models obtained through quantization and model merging approaches. Our results demonstrate BioMistral's superior performance compared to existing open-source medical models and its competitive edge against proprietary counterparts. Finally, to address the limited availability of data beyond English and to assess the multilingual generalization of medical LLMs, we automatically translated and evaluated this benchmark into 7 other languages. This marks the first large-scale multilingual evaluation of LLMs in the medical domain. Datasets, multilingual evaluation benchmarks, scripts, and all the models obtained during our experiments are freely released.

Advisory Notice! Although BioMistral is intended to encapsulate medical knowledge sourced from high-quality evidence, it hasn't been tailored to effectively, safely, or suitably convey this knowledge within professional parameters for action. We advise refraining from utilizing BioMistral in medical contexts unless it undergoes thorough alignment with specific use cases and undergoes further testing, notably including randomized controlled trials in real-world medical environments. BioMistral 7B may possess inherent risks and biases that have not yet been thoroughly assessed. Additionally, the model's performance has not been evaluated in real-world clinical settings. Consequently, we recommend using BioMistral 7B strictly as a research tool and advise against deploying it in production environments for natural language generation or any professional health and medical purposes.

1. BioMistral models

BioMistral is a suite of Mistral-based further pre-trained open source models suited for the medical domains and pre-trained using textual data from PubMed Central Open Access (CC0, CC BY, CC BY-SA, and CC BY-ND). All the models are trained using the CNRS (French National Centre for Scientific Research) Jean Zay French HPC.

Model Name Base Model Model Type Sequence Length Download
BioMistral-7B Mistral-7B-Instruct-v0.1 Further Pre-trained 2048 HuggingFace
BioMistral-7B-DARE Mistral-7B-Instruct-v0.1 Merge DARE 2048 HuggingFace
BioMistral-7B-TIES Mistral-7B-Instruct-v0.1 Merge TIES 2048 HuggingFace
BioMistral-7B-SLERP Mistral-7B-Instruct-v0.1 Merge SLERP 2048 HuggingFace

2. Quantized Models

Base Model Method q_group_size w_bit version VRAM GB Time Download
BioMistral-7B FP16/BF16 15.02 x1.00 HuggingFace
BioMistral-7B AWQ 128 4 GEMM 4.68 x1.41 HuggingFace
BioMistral-7B AWQ 128 4 GEMV 4.68 x10.30 HuggingFace
BioMistral-7B BnB.4 4 5.03 x3.25 HuggingFace
BioMistral-7B BnB.8 8 8.04 x4.34 HuggingFace
BioMistral-7B-DARE AWQ 128 4 GEMM 4.68 x1.41 HuggingFace
BioMistral-7B-TIES AWQ 128 4 GEMM 4.68 x1.41 HuggingFace
BioMistral-7B-SLERP AWQ 128 4 GEMM 4.68 x1.41 HuggingFace

2. Using BioMistral

You can use BioMistral with Hugging Face's Transformers library as follow.

Loading the model and tokenizer :

from transformers import AutoModel, AutoTokenizer

tokenizer = AutoTokenizer.from_pretrained("BioMistral/BioMistral-7B")
model = AutoModel.from_pretrained("BioMistral/BioMistral-7B")

3. Supervised Fine-tuning Benchmark

Clinical KG Medical Genetics Anatomy Pro Medicine College Biology College Medicine MedQA MedQA 5 opts PubMedQA MedMCQA Avg.
BioMistral 7B 59.9 64.0 56.5 60.4 59.0 54.7 50.6 42.8 77.5 48.1 57.3
Mistral 7B Instruct 62.9 57.0 55.6 59.4 62.5 57.2 42.0 40.9 75.7 46.1 55.9
BioMistral 7B Ensemble 62.8 62.7 57.5 63.5 64.3 55.7 50.6 43.6 77.5 48.8 58.7
BioMistral 7B DARE 62.3 67.0 55.8 61.4 66.9 58.0 51.1 45.2 77.7 48.7 59.4
BioMistral 7B TIES 60.1 65.0 58.5 60.5 60.4 56.5 49.5 43.2 77.5 48.1 57.9
BioMistral 7B SLERP 62.5 64.7 55.8 62.7 64.8 56.3 50.8 44.3 77.8 48.6 58.8
MedAlpaca 7B 53.1 58.0 54.1 58.8 58.1 48.6 40.1 33.7 73.6 37.0 51.5
PMC-LLaMA 7B 24.5 27.7 35.3 17.4 30.3 23.3 25.5 20.2 72.9 26.6 30.4
MediTron-7B 41.6 50.3 46.4 27.9 44.4 30.8 41.6 28.1 74.9 41.3 42.7
BioMedGPT-LM-7B 51.4 52.0 49.4 53.3 50.7 49.1 42.5 33.9 76.8 37.6 49.7
GPT-3.5 Turbo 1106* 74.71 74.00 65.92 72.79 72.91 64.73 57.71 50.82 72.66 53.79 66.0

Supervised Fine-Tuning (SFT) performance of BioMistral 7B models compared to baselines, measured by accuracy (↑) and averaged across 3 random seeds of 3-shot. DARE, TIES, and SLERP are model merging strategies that combine BioMistral 7B and Mistral 7B Instruct. Best model in bold, and second-best underlined. *GPT-3.5 Turbo performances are reported from the 3-shot results without SFT.

Citation BibTeX

Arxiv : https://arxiv.org/abs/2402.10373

@misc{labrak2024biomistral,
      title={BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains}, 
      author={Yanis Labrak and Adrien Bazoge and Emmanuel Morin and Pierre-Antoine Gourraud and Mickael Rouvier and Richard Dufour},
      year={2024},
      eprint={2402.10373},
      archivePrefix={arXiv},
      primaryClass={cs.CL}
}

CAUTION! Both direct and downstream users need to be informed about the risks, biases, and constraints inherent in the model. While the model can produce natural language text, our exploration of its capabilities and limitations is just beginning. In fields such as medicine, comprehending these limitations is crucial. Hence, we strongly advise against deploying this model for natural language generation in production or for professional tasks in the realm of health and medicine.

Open LLM Leaderboard Evaluation Results

Detailed results can be found here

Metric Value
Avg. 57.03
AI2 Reasoning Challenge (25-Shot) 58.28
HellaSwag (10-Shot) 79.87
MMLU (5-Shot) 57.34
TruthfulQA (0-shot) 55.61
Winogrande (5-shot) 76.09
GSM8k (5-shot) 15.01