Henning Schäfer


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Comprehensive Study on German Language Models for Clinical and Biomedical Text Understanding
Ahmad Idrissi-Yaghir | Amin Dada | Henning Schäfer | Kamyar Arzideh | Giulia Baldini | Jan Trienes | Max Hasin | Jeanette Bewersdorff | Cynthia S. Schmidt | Marie Bauer | Kaleb E. Smith | Jiang Bian | Yonghui Wu | Jörg Schlötterer | Torsten Zesch | Peter A. Horn | Christin Seifert | Felix Nensa | Jens Kleesiek | Christoph M. Friedrich
Proceedings of the 2024 Joint International Conference on Computational Linguistics, Language Resources and Evaluation (LREC-COLING 2024)

Recent advances in natural language processing (NLP) can be largely attributed to the advent of pre-trained language models such as BERT and RoBERTa. While these models demonstrate remarkable performance on general datasets, they can struggle in specialized domains such as medicine, where unique domain-specific terminologies, domain-specific abbreviations, and varying document structures are common. This paper explores strategies for adapting these models to domain-specific requirements, primarily through continuous pre-training on domain-specific data. We pre-trained several German medical language models on 2.4B tokens derived from translated public English medical data and 3B tokens of German clinical data. The resulting models were evaluated on various German downstream tasks, including named entity recognition (NER), multi-label classification, and extractive question answering. Our results suggest that models augmented by clinical and translation-based pre-training typically outperform general domain models in medical contexts. We conclude that continuous pre-training has demonstrated the ability to match or even exceed the performance of clinical models trained from scratch. Furthermore, pre-training on clinical data or leveraging translated texts have proven to be reliable methods for domain adaptation in medical NLP tasks.


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Cross-Language Transfer of High-Quality Annotations: Combining Neural Machine Translation with Cross-Linguistic Span Alignment to Apply NER to Clinical Texts in a Low-Resource Language
Henning Schäfer | Ahmad Idrissi-Yaghir | Peter Horn | Christoph Friedrich
Proceedings of the 4th Clinical Natural Language Processing Workshop

In this work, cross-linguistic span prediction based on contextualized word embedding models is used together with neural machine translation (NMT) to transfer and apply the state-of-the-art models in natural language processing (NLP) to a low-resource language clinical corpus. Two directions are evaluated: (a) English models can be applied to translated texts to subsequently transfer the predicted annotations to the source language and (b) existing high-quality annotations can be transferred beyond translation and then used to train NLP models in the target language. Effectiveness and loss of transmission is evaluated using the German Berlin-Tübingen-Oncology Corpus (BRONCO) dataset with transferred external data from NCBI disease, SemEval-2013 drug-drug interaction (DDI) and i2b2/VA 2010 data. The use of English models for translated clinical texts has always involved attempts to take full advantage of the benefits associated with them (large pre-trained biomedical word embeddings). To improve advances in this area, we provide a general-purpose pipeline to transfer any annotated BRAT or CoNLL format to various target languages. For the entity class medication, good results were obtained with 0.806 F1-score after re-alignment. Limited success occurred in the diagnosis and treatment class with results just below 0.5 F1-score due to differences in annotation guidelines.