Deep learning and abstractive summarisation for radiological reports: an empirical study for adapting the PEGASUS models' family with scarce data

Regardless of the rapid development of artificial intelligence, abstractive summarisation is still challenging for sensitive and data-restrictive domains like medicine. With the increasing number of imaging, the relevance of automated tools for complex medical text summarisation is expected to become highly relevant. In this paper, we investigated the adaptation via fine-tuning process of a non-domain-specific abstractive summarisation encoder-decoder model family, and gave insights to practitioners on how to avoid over- and underfitting. We used PEGASUS and PEGASUS-X, on a medium-sized radiological reports public dataset. For each model, we comprehensively evaluated two different checkpoints with varying sizes of the same training data. We monitored the models' performances with lexical and semantic metrics during the training history on the fixed-size validation set. PEGASUS exhibited different phases, which can be related to epoch-wise double-descent, or peak-drop-recovery behaviour. For PEGASUS-X, we found that using a larger checkpoint led to a performance detriment. This work highlights the challenges and risks of fine-tuning models with high expressivity when dealing with scarce training data, and lays the groundwork for future investigations into more robust fine-tuning strategies for summarisation models in specialised domains.

Large Language Models-Enabled Digital Twins for Precision Medicine in Rare Gynecological Tumors

Rare gynecological tumors (RGTs) present major clinical challenges due to their low incidence and heterogeneity. The lack of clear guidelines leads to suboptimal management and poor prognosis. Molecular tumor boards accelerate access to effective therapies by tailoring treatment based on biomarkers, beyond cancer type. Unstructured data that requires manual curation hinders efficient use of biomarker profiling for therapy matching. This study explores the use of large language models (LLMs) to construct digital twins for precision medicine in RGTs. Our proof-of-concept digital twin system integrates clinical and biomarker data from institutional and published cases (n=21) and literature-derived data (n=655 publications with n=404,265 patients) to create tailored treatment plans for metastatic uterine carcinosarcoma, identifying options potentially missed by traditional, single-source analysis. LLM-enabled digital twins efficiently model individual patient trajectories. Shifting to a biology-based rather than organ-based tumor definition enables personalized care that could advance RGT management and thus enhance patient outcomes.

GottBERT: a pure German Language Model

Lately, pre-trained language models advanced the field of natural language processing (NLP). The introduction of Bidirectional Encoders for Transformers (BERT) and its optimized version RoBERTa have had significant impact and increased the relevance of pre-trained models. First, research in this field mainly started on English data followed by models trained with multilingual text corpora. However, current research shows that multilingual models are inferior to monolingual models. Currently, no German single language RoBERTa model is yet published, which we introduce in this work (GottBERT). The German portion of the OSCAR data set was used as text corpus. In an evaluation we compare its performance on the two Named Entity Recognition (NER) tasks Conll 2003 and GermEval 2014 as well as on the text classification tasks GermEval 2018 (fine and coarse) and GNAD with existing German single language BERT models and two multilingual ones. GottBERT was pre-trained related to the original RoBERTa model using fairseq. All downstream tasks were trained using hyperparameter presets taken from the benchmark of German BERT. The experiments were setup utilizing FARM. Performance was measured by the $F_{1}$ score. GottBERT was successfully pre-trained on a 256 core TPU pod using the RoBERTa BASE architecture. Even without extensive hyper-parameter optimization, in all NER and one text classification task, GottBERT already outperformed all other tested German and multilingual models. In order to support the German NLP field, we publish GottBERT under the AGPLv3 license.