Challenge: Clinical data in hospitals are unstructured and therefore need to be extracted from medical reports to conduct clinical studies.
Approach: They propose a dedicated French biomedical model based on a public French biomedicine dataset.
Outcome: The proposed model improves 2.54 points of F1-score on biomedical named entity recognition tasks.

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A Benchmark Evaluation of Clinical Named Entity Recognition in French (2024.lrec-main)

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Challenge: Masked Language Models (MLMs) have shown strong performance on many NLP tasks.
Approach: They evaluate masked language models for biomedical French on the task of clinical named entity recognition using gold-standard corpora.
Outcome: The proposed model outperforms standard models on the task of clinical named entity recognition in biomedical French while remaining lighter than current models.
CamemBERT: a Tasty French Language Model (2020.acl-main)

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Challenge: Pretrained language models are now ubiquitous in Natural Language Processing, but their use in other languages is limited.
Approach: They propose to train monolingual Transformer-based model for other languages using web crawled data instead of Wikipedia data and a relatively small web crawl dataset leads to better results.
Outcome: The proposed model performs as well as those obtained using larger datasets.
Comprehensive Study on German Language Models for Clinical and Biomedical Text Understanding (2024.lrec-main)

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Challenge: Pre-trained language models can struggle in specialized domains such as medicine . existing generalpurpose pre-tried models can be used and refined through further pre-training on domainspecific unlabeled data.
Approach: They pre-trained German medical language models on 2.4B tokens from translated public data and 3B token of German clinical data.
Outcome: The proposed models outperform clinical models on various downstream tasks in germany . the authors show that continuous pre-training can match or exceed clinical models trained from scratch .
Data-Efficient French Language Modeling with CamemBERTa (2023.findings-acl)

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Challenge: Recent advances in NLP have significantly improved the performance of language models on a variety of tasks.
Approach: They introduce a French DeBERTa model that builds upon the DeBERTAV3 architecture and training objective and evaluate its performance on a variety of French downstream tasks and datasets.
Outcome: The proposed model outperforms BERT-based models on most tasks given the same amount of training tokens and trained on 30% of its input tokens.
DrBERT: A Robust Pre-trained Model in French for Biomedical and Clinical domains (2023.acl-long)

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Challenge: Recent studies have shown that pre-trained language models improve performance on a wide range of NLP tasks.
Approach: They propose to use pre-trained language models to train medical domains on French language to compare performance with specialized ones.
Outcome: The proposed models can take advantage of existing biomedical models in a foreign language by further pre-training them on our targeted data.
Re-train or Train from Scratch? Comparing Pre-training Strategies of BERT in the Medical Domain (2022.lrec-1)

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Challenge: Recent years have witnessed the widespread use of transfer learning techniques in Natural Language Processing (NLP)
Approach: They train BERT models from scratch using many configurations involving general and medical corpora.
Outcome: The initial corpus only has a weak influence when these are further pre-trained on a medical corpus.
Transfer Learning in Biomedical Named Entity Recognition: An Evaluation of BERT in the PharmaCoNER task (D19-57)

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Challenge: Existing methods for natural language processing are labor-intensive and skill-dependent . Currently, most biomedical natural language tasks focus on English documents .
Approach: They introduce a BERT benchmark to facilitate the research of PharmaCoNER task . they evaluate two baselines based on Multilingual BERT and BioBERT on the corpus .
Outcome: The proposed task is based on multilingual BERT and BioBERT on the PharmaCoNER corpus.
DrBenchmark: A Large Language Understanding Evaluation Benchmark for French Biomedical Domain (2024.lrec-main)

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Challenge: Existing benchmarks for pre-trained language models are limited to only a few languages . a limited number of tasks are evaluated on non-standardized protocols .
Approach: They propose to aggregate diverse downstream tasks into a benchmark to assess PLMs' qualities . they evaluate 8 pre-trained masked language models on general and biomedical-specific data .
Outcome: The proposed benchmark assesses pre-trained language models on 20 diversified tasks.
An Empirical Investigation Towards Efficient Multi-Domain Language Model Pre-training (2020.emnlp-main)

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Challenge: Pre-training large language models is a standard practice in the natural language processing community.
Approach: They propose to use elastic weight consolidation to mitigate catastrophic forgetting when pre-trained large language models are evaluated on generic benchmarks.
Outcome: The proposed model achieves state-of-the-art on out-of domain tasks with minimal pre-training . elastic weight consolidation provides best overall scores yielding only a 0.33% drop in performance across seven generic tasks while remaining competitive in bio-medical tasks.
OpenBioNER: Lightweight Open-Domain Biomedical Named Entity Recognition Through Entity Type Description (2025.findings-naacl)

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Challenge: Biomedical Named Entity Recognition (BioNER) is a computationally expensive and limited tool . specialized 7B NER LLMs and GPT-4o can't match textual spans with entity types .
Approach: They propose a lightweight BERT-based cross-encoder architecture that can identify any biomedical entity using only its description.
Outcome: The proposed system outperforms existing models that match textual spans with entity types rather than descriptions on biomedical benchmarks.

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