This work explores the effectiveness of employing Clinical BERT for Relation Extraction (RE) tasks in medical texts within an Active Learning (AL) framework. Our main objective is to optimize RE in medical texts through AL while examining the trade-offs between performance and computation time, comparing it with alternative methods like Random Forest and BiLSTM networks. Comparisons extend to feature engineering requirements, performance metrics, and considerations of annotation costs, including AL step times and annotation rates. The utilization of AL strategies aligns with our broader goal of enhancing the efficiency of relation classification models, particularly when dealing with the challenges of annotating complex medical texts in a Human-in-the-Loop (HITL) setting. The results indicate that uncertainty-based sampling achieves comparable performance with significantly fewer annotated samples across three categories of supervised learning methods, thereby reducing annotation costs for clinical and biomedical corpora. While Clinical BERT exhibits clear performance advantages across two different corpora, the trade-off involves longer computation times in interactive annotation processes. In real-world applications, where practical feasibility and timely results are crucial, optimizing this trade-off becomes imperative.

Clinical Named Entity Recognition (NER) is essential for extracting important medical insights from clinical narratives. Given the challenges in obtaining expert training datasets for real-world clinical applications related to data protection regulations and the lack of standardised entity types, this work represents a collaborative initiative aimed at building a German clinical NER system with a focus on addressing these obstacles effectively. In response to the challenge of training data scarcity, we propose a Conditional Relevance Learning (CRL) approach in low-resource transfer learning scenarios. CRL effectively leverages a pre-trained language model and domain-specific open resources, enabling the acquisition of a robust base model tailored for clinical NER tasks, particularly in the face of changing label sets. This flexibility empowers the implementation of a Multilayered Semantic Annotation (MSA) schema in our NER system, capable of organizing a diverse array of entity types, thus significantly boosting the NER system’s adaptability and utility across various clinical domains. In the case study, we demonstrate how our NER system can be applied to overcome resource constraints and comply with data privacy regulations. Lacking prior training on in-domain data, feedback from expert users in respective domains is essential in identifying areas for system refinement. Future work will focus on the integration of expert feedback to improve system performance in specific clinical contexts.

Information extraction from clinical text has the potential to facilitate clinical research and personalized clinical care, but annotating large amounts of data for each set of target tasks is prohibitive. We present a German medical Named Entity Recognition (NER) system capable of cross-domain knowledge transferring. The system builds on a pre-trained German language model and a token-level binary classifier, employing semantic types sourced from the Unified Medical Language System (UMLS) as entity labels to identify corresponding entity spans within the input text. To enhance the system’s performance and robustness, we pre-train it using a medical literature corpus that incorporates UMLS semantic term annotations. We evaluate the system’s effectiveness on two German annotated datasets obtained from different clinics in zero- and few-shot settings. The results show that our approach outperforms task-specific Condition Random Fields (CRF) classifiers in terms of accuracy. Our work contributes to developing robust and transparent German medical NER models that can support the extraction of information from various clinical texts.

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.

In this work we propose an approach for generating statements that explicate implicit knowledge connecting sentences in text. We make use of pre-trained language models which we refine by fine-tuning them on specifically prepared corpora that we enriched with implicit information, and by constraining them with relevant concepts and connecting commonsense knowledge paths. Manual and automatic evaluation of the generations shows that by refining language models as proposed, we can generate coherent and grammatically sound sentences that explicate implicit knowledge which connects sentence pairs in texts – on both in-domain and out-of-domain test data.