Pierre-Antoine Gourraud

Yanis Labrak, Adrien Bazoge, Richard Dufour et al.

In recent years, pre-trained language models (PLMs) achieve the best performance on a wide range of natural language processing (NLP) tasks. While the first models were trained on general domain data, specialized ones have emerged to more effectively treat specific domains. In this paper, we propose an original study of PLMs in the medical domain on French language. We compare, for the first time, the performance of PLMs trained on both public data from the web and private data from healthcare establishments. We also evaluate different learning strategies on a set of biomedical tasks. In particular, we show that we can take advantage of already existing biomedical PLMs in a foreign language by further pre-train it on our targeted data. Finally, we release the first specialized PLMs for the biomedical field in French, called DrBERT, as well as the largest corpus of medical data under free license on which these models are trained.

Yanis Labrak, Adrien Bazoge, Richard Dufour et al.

This paper introduces FrenchMedMCQA, the first publicly available Multiple-Choice Question Answering (MCQA) dataset in French for medical domain. It is composed of 3,105 questions taken from real exams of the French medical specialization diploma in pharmacy, mixing single and multiple answers. Each instance of the dataset contains an identifier, a question, five possible answers and their manual correction(s). We also propose first baseline models to automatically process this MCQA task in order to report on the current performances and to highlight the difficulty of the task. A detailed analysis of the results showed that it is necessary to have representations adapted to the medical domain or to the MCQA task: in our case, English specialized models yielded better results than generic French ones, even though FrenchMedMCQA is in French. Corpus, models and tools are available online.

Yanis Labrak, Adrien Bazoge, Emmanuel Morin et al.

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.

Adrien Bazoge, Josselin Corvellec, Sofiane Djillali Sid-Ahmed et al.

Large language models (LLMs) are increasingly explored for clinical decision support, yet most evaluations are conducted in English, leaving their reliability in other languages uncertain. Here we evaluate the impact of prompting language on diagnostic reasoning and final diagnosis accuracy by comparing English and French performance across five LLMs (o3, DeepSeek-R1, GPT-4-Turbo, Llama-3.1-405B-Instruct, and BioMistral-7B). A total of 180 clinical vignettes covering 16 medical specialties were assessed by two physicians using an 18-point scale evaluating both diagnosis accuracy and reasoning quality. Four of the five models performed better in English (mean difference 0.37-0.91, adjusted p < 0.05), with the gap spanning multiple aspects of reasoning, including differential diagnosis, logical structure, and internal validity. o3 was the only model showing no overall language effect. These findings demonstrate that prompting language remains a critical determinant of LLM clinical performance, with implications for equitable linguistico-cultural deployment worldwide.

Trung Hieu Ngo, Adrien Bazoge, Solen Quiniou et al.

Large Language Models (LLMs) excel in Natural Language Processing (NLP) tasks, but they often propagate biases embedded in their training data, which is potentially impactful in sensitive domains like healthcare. While existing benchmarks evaluate biases related to individual social determinants of health (SDoH) such as gender or ethnicity, they often overlook interactions between these factors and lack context-specific assessments. This study investigates bias in LLMs by probing the relationships between gender and other SDoH in French patient records. Through a series of experiments, we found that embedded stereotypes can be probed using SDoH input and that LLMs rely on embedded stereotypes to make gendered decisions, suggesting that evaluating interactions among SDoH factors could usefully complement existing approaches to assessing LLM performance and bias.

Yanis Labrak, Adrien Bazoge, Oumaima El Khettari et al.

The biomedical domain has sparked a significant interest in the field of Natural Language Processing (NLP), which has seen substantial advancements with pre-trained language models (PLMs). However, comparing these models has proven challenging due to variations in evaluation protocols across different models. A fair solution is to aggregate diverse downstream tasks into a benchmark, allowing for the assessment of intrinsic PLMs qualities from various perspectives. Although still limited to few languages, this initiative has been undertaken in the biomedical field, notably English and Chinese. This limitation hampers the evaluation of the latest French biomedical models, as they are either assessed on a minimal number of tasks with non-standardized protocols or evaluated using general downstream tasks. To bridge this research gap and account for the unique sensitivities of French, we present the first-ever publicly available French biomedical language understanding benchmark called DrBenchmark. It encompasses 20 diversified tasks, including named-entity recognition, part-of-speech tagging, question-answering, semantic textual similarity, and classification. We evaluate 8 state-of-the-art pre-trained masked language models (MLMs) on general and biomedical-specific data, as well as English specific MLMs to assess their cross-lingual capabilities. Our experiments reveal that no single model excels across all tasks, while generalist models are sometimes still competitive.

Adrien Bazoge, Emmanuel Morin, Beatrice Daille et al.

Recently, pretrained language models based on BERT have been introduced for the French biomedical domain. Although these models have achieved state-of-the-art results on biomedical and clinical NLP tasks, they are constrained by a limited input sequence length of 512 tokens, which poses challenges when applied to clinical notes. In this paper, we present a comparative study of three adaptation strategies for long-sequence models, leveraging the Longformer architecture. We conducted evaluations of these models on 16 downstream tasks spanning both biomedical and clinical domains. Our findings reveal that further pre-training an English clinical model with French biomedical texts can outperform both converting a French biomedical BERT to the Longformer architecture and pre-training a French biomedical Longformer from scratch. The results underscore that long-sequence French biomedical models improve performance across most downstream tasks regardless of sequence length, but BERT based models remain the most efficient for named entity recognition tasks.

Adrien Bazoge, Pacôme Constant dit Beaufils, Mohammed Hmitouch et al.

Social determinants of health (SDoH) significantly influence health outcomes, shaping disease progression, treatment adherence, and health disparities. However, their documentation in structured electronic health records (EHRs) is often incomplete or missing. This study presents an approach based on large language models (LLMs) for extracting 13 SDoH categories from French clinical notes. We trained Flan-T5-Large on annotated social history sections from clinical notes at Nantes University Hospital, France. We evaluated the model at two levels: (i) identification of SDoH categories and associated values, and (ii) extraction of detailed SDoH with associated temporal and quantitative information. The model performance was assessed across four datasets, including two that we publicly release as open resources. The model achieved strong performance for identifying well-documented categories such as living condition, marital status, descendants, job, tobacco, and alcohol use (F1 score > 0.80). Performance was lower for categories with limited training data or highly variable expressions, such as employment status, housing, physical activity, income, and education. Our model identified 95.8% of patients with at least one SDoH, compared to 2.8% for ICD-10 codes from structured EHR data. Our error analysis showed that performance limitations were linked to annotation inconsistencies, reliance on English-centric tokenizer, and reduced generalizability due to the model being trained on social history sections only. These results demonstrate the effectiveness of NLP in improving the completeness of real-world SDoH data in a non-English EHR system.