Jan Trienes


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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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Guidance in Radiology Report Summarization: An Empirical Evaluation and Error Analysis
Jan Trienes | Paul Youssef | Jörg Schlötterer | Christin Seifert
Proceedings of the 16th International Natural Language Generation Conference

Automatically summarizing radiology reports into a concise impression can reduce the manual burden of clinicians and improve the consistency of reporting. Previous work aimed to enhance content selection and factuality through guided abstractive summarization. However, two key issues persist. First, current methods heavily rely on domain-specific resources to extract the guidance signal, limiting their transferability to domains and languages where those resources are unavailable. Second, while automatic metrics like ROUGE show progress, we lack a good understanding of the errors and failure modes in this task. To bridge these gaps, we first propose a domain-agnostic guidance signal in form of variable-length extractive summaries. Our empirical results on two English benchmarks demonstrate that this guidance signal improves upon unguided summarization while being competitive with domain-specific methods. Additionally, we run an expert evaluation of four systems according to a taxonomy of 11 fine-grained errors. We find that the most pressing differences between automatic summaries and those of radiologists relate to content selection including omissions (up to 52%) and additions (up to 57%). We hypothesize that latent reporting factors and corpus-level inconsistencies may limit models to reliably learn content selection from the available data, presenting promising directions for future work.


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Patient-friendly Clinical Notes: Towards a new Text Simplification Dataset
Jan Trienes | Jörg Schlötterer | Hans-Ulrich Schildhaus | Christin Seifert
Proceedings of the Workshop on Text Simplification, Accessibility, and Readability (TSAR-2022)

Automatic text simplification can help patients to better understand their own clinical notes. A major hurdle for the development of clinical text simplification methods is the lack of high quality resources. We report ongoing efforts in creating a parallel dataset of professionally simplified clinical notes. Currently, this corpus consists of 851 document-level simplifications of German pathology reports. We highlight characteristics of this dataset and establish first baselines for paragraph-level simplification.