Shift- and stretch-invariant non-negative matrix factorization with an application to brain tissue delineation in emission tomography data

Dynamic neuroimaging data, such as emission tomography measurements of radiotracer transport in blood or cerebrospinal fluid, often exhibit diffusion-like properties. These introduce distance-dependent temporal delays, scale-differences, and stretching effects that limit the effectiveness of conventional linear modeling and decomposition methods. To address this, we present the shift- and stretch-invariant non-negative matrix factorization framework. Our approach estimates both integer and non-integer temporal shifts as well as temporal stretching, all implemented in the frequency domain, where shifts correspond to phase modifications, and where stretching is handled via zero-padding or truncation. The model is implemented in PyTorch (https://github.com/anders-s-olsen/shiftstretchNMF). We demonstrate on synthetic data and brain emission tomography data that the model is able to account for stretching to provide more detailed characterization of brain tissue structure.

Classification of Radiological Text in Small and Imbalanced Datasets in a Non-English Language

Natural language processing (NLP) in the medical domain can underperform in real-world applications involving small datasets in a non-English language with few labeled samples and imbalanced classes. There is yet no consensus on how to approach this problem. We evaluated a set of NLP models including BERT-like transformers, few-shot learning with sentence transformers (SetFit), and prompted large language models (LLM), using three datasets of radiology reports on magnetic resonance images of epilepsy patients in Danish, a low-resource language. Our results indicate that BERT-like models pretrained in the target domain of radiology reports currently offer the optimal performances for this scenario. Notably, the SetFit and LLM models underperformed compared to BERT-like models, with LLM performing the worst. Importantly, none of the models investigated was sufficiently accurate to allow for text classification without any supervision. However, they show potential for data filtering, which could reduce the amount of manual labeling required.