We annotate PubMed Central paragraphs for document type, domain, and educational quality using a two-stage pipeline: Llama-3.1-70B labels 400K paragraphs, then a fine-tuned XLM-RoBERTa propagates annotations to the full corpus. This paragraph-level approach captures content diversity within scientific articles that document-level labels miss. The resulting Biomed-Enriched corpus contains 2M clinical case paragraphs, providing a publicly available alternative to restricted clinical datasets. For decoders, continual pretraining experiments enable targeted improvements, with clinical upsampling boosting performance by 4 points on MMLU ProfMed and educational filtering improving MedQA and MedMCQA by ~1 point. Combinations of these techniques led to faster convergence, reaching the same performance with a third of training tokens. For encoders, our best recipe matches BioClinical-ModernBERT on 11 tasks (77.3% vs 77.1% F1) while using 2.5x fewer tokens and only public data.

Standardized benchmarks have become the dominant metric for measuring progress in large language models, yet their validity is increasingly compromised by data contamination and the unclear relationship between benchmark scores and genuine language understanding. We introduce Gaperon, a suite of fully open bilingual (French-English) language models designed as an experimental testbed to investigate evaluation dynamics under realistic training conditions. Our study makes three core contributions. First, we demonstrate mismatches between benchmark performance and generation quality: models that excel on benchmarks may underperform in qualitative text generation, and vice versa. Second, through our deliberately contaminated Gaperon-Garlic variant, we show that competitive benchmark scores can be recovered via late-stage contamination with only moderate degradation of generation quality, and surprisingly, such contamination also improves performance on held-out benchmarks. Third, we provide empirical evidence that widely used neural quality filters, particularly those trained to favor instructional or educational content, amplify benchmark contamination in pretraining corpora, with the DCLM classifier systematically ranking benchmark samples in the top-5 percentiles of samples. We release all models, data mixtures, checkpoints, and evaluation code to support reproducibility and further investigation.

Clinical data in hospitals are increasingly accessible for research through clinical data warehouses. However these documents are unstructured and it is therefore necessary to extract information from medical reports to conduct clinical studies. Transfer learning with BERT-like models such as CamemBERT has allowed major advances for French, especially for named entity recognition. However, these models are trained for plain language and are less efficient on biomedical data. Addressing this gap, we introduce CamemBERT-bio, a dedicated French biomedical model derived from a new public French biomedical dataset. Through continual pre-training of the original CamemBERT, CamemBERT-bio achieves an improvement of 2.54 points of F1-score on average across various biomedical named entity recognition tasks, reinforcing the potential of continual pre-training as an equally proficient yet less computationally intensive alternative to training from scratch. Additionally, we highlight the importance of using a standard evaluation protocol that provides a clear view of the current state-of-the-art for French biomedical models.

Nous présentons les 3 expériences menées par l’équipe ALMAnaCH - Arkhn et leurs résultats pour le DÉfi Fouille de Textes (DEFT) 2023. Les scores sont encourageants mais suggèrent surtout de nouveaux éléments à prendre en compte pour réussir ce défi. Nous avons exploré différentes approches avec des modèles de tailles variables et modélisé la tâche de différentes manières (classification multi-labels, implication textuelle, séquence à séquence). Nous n’avons pas observé des gains de performance significatifs. Nos expériences semblent montrer la nécessité de l’utilisation de bases de connaissances externes pour obtenir de bons résultats sur ce type de tâche.

Les données cliniques dans les hôpitaux sont de plus en plus accessibles pour la recherche à travers les entrepôts de données de santé, cependant ces documents sont non-structurés. Il est donc nécessaire d’extraire les informations des comptes-rendus médicaux. L’utilisation du transfert d’apprentissage grâce à des modèles de type BERT comme CamemBERT ont permis des avancées majeures, notamment pour la reconnaissance d’entités nommées. Cependant, ces modèles sont entraînés pour le langage courant et sont moins performants sur des données biomédicales. C’est pourquoi nous proposons un nouveau jeu de données biomédical public français sur lequel nous avons poursuivi le pré-entraînement de CamemBERT. Ainsi, nous présentons une première version de CamemBERT-bio, un modèle public spécialisé pour le domaine biomédical français qui montre un gain de 2,54 points de F-mesure en moyenne sur différents jeux d’évaluations de reconnaissance d’entités nommées biomédicales.