Jens Kleesiek


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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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IKIM at MEDIQA-M3G 2024: Multilingual Visual Question-Answering for Dermatology through VLM Fine-tuning and LLM Translations
Marie Bauer | Amin Dada | Constantin Seibold | Jens Kleesiek
Proceedings of the 6th Clinical Natural Language Processing Workshop

This paper presents our solution to the MEDIQA-M3G Challenge at NAACL-ClinicalNLP 2024. We participated in all three languages, ranking first in Chinese and Spanish and third in English. Our approach utilizes LLaVA-med, an open-source, medical vision-language model (VLM) for visual question-answering in Chinese, and Mixtral-8x7B-instruct, a Large Language Model (LLM) for a subsequent translation into English and Spanish. In addition to our final method, we experiment with alternative approaches: Training three different models for each language instead of translating the results from one model, using different combinations and numbers of input images, and additional training on publicly available data that was not part of the original challenge training set.


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On the Impact of Cross-Domain Data on German Language Models
Amin Dada | Aokun Chen | Cheng Peng | Kaleb Smith | Ahmad Idrissi-Yaghir | Constantin Seibold | Jianning Li | Lars Heiliger | Christoph Friedrich | Daniel Truhn | Jan Egger | Jiang Bian | Jens Kleesiek | Yonghui Wu
Findings of the Association for Computational Linguistics: EMNLP 2023

Traditionally, large language models have been either trained on general web crawls or domain-specific data. However, recent successes of generative large language models, have shed light on the benefits of cross-domain datasets. To examine the significance of prioritizing data diversity over quality, we present a German dataset comprising texts from five domains, along with another dataset aimed at containing high-quality data. Through training a series of models ranging between 122M and 750M parameters on both datasets, we conduct a comprehensive benchmark on multiple downstream tasks. Our findings demonstrate that the models trained on the cross-domain dataset outperform those trained on quality data alone, leading to improvements up to 4.45% over the previous state-of-the-art.


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Fine-tuning BERT Models for Summarizing German Radiology Findings
Siting Liang | Klaus Kades | Matthias Fink | Peter Full | Tim Weber | Jens Kleesiek | Michael Strube | Klaus Maier-Hein
Proceedings of the 4th Clinical Natural Language Processing Workshop

Writing the conclusion section of radiology reports is essential for communicating the radiology findings and its assessment to physician in a condensed form. In this work, we employ a transformer-based Seq2Seq model for generating the conclusion section of German radiology reports. The model is initialized with the pretrained parameters of a German BERT model and fine-tuned in our downstream task on our domain data. We proposed two strategies to improve the factual correctness of the model. In the first method, next to the abstractive learning objective, we introduce an extraction learning objective to train the decoder in the model to both generate one summary sequence and extract the key findings from the source input. The second approach is to integrate the pointer mechanism into the transformer-based Seq2Seq model. The pointer network helps the Seq2Seq model to choose between generating tokens from the vocabulary or copying parts from the source input during generation. The results of the automatic and human evaluations show that the enhanced Seq2Seq model is capable of generating human-like radiology conclusions and that the improved models effectively reduce the factual errors in the generations despite the small amount of training data.