Marta Bianca Maria Ranzini

Vignesh Kumar Kembu, Pierandrea Morandini, Marta Bianca Maria Ranzini et al.

Large Language Models (LLMs) have become a key topic in AI and NLP, transforming sectors like healthcare, finance, education, and marketing by improving customer service, automating tasks, providing insights, improving diagnostics, and personalizing learning experiences. Information extraction from clinical records is a crucial task in digital healthcare. Although traditional NLP techniques have been used for this in the past, they often fall short due to the complexity, variability of clinical language, and high inner semantics in the free clinical text. Recently, Large Language Models (LLMs) have become a powerful tool for better understanding and generating human-like text, making them highly effective in this area. In this paper, we explore the ability of open-source multilingual LLMs to understand EHRs (Electronic Health Records) in Italian and help extract information from them in real-time. Our detailed experimental campaign on comorbidity extraction from EHR reveals that some LLMs struggle in zero-shot, on-premises settings, and others show significant variation in performance, struggling to generalize across various diseases when compared to native pattern matching and manual annotations.

Marta B. M. Ranzini, Lucas Fidon, Sébastien Ourselin et al.

In fetal Magnetic Resonance Imaging, Super Resolution Reconstruction (SRR) algorithms are becoming popular tools to obtain high-resolution 3D volume reconstructions from low-resolution stacks of 2D slices, acquired at different orientations. To be effective, these algorithms often require accurate segmentation of the region of interest, such as the fetal brain in suspected pathological cases. In the case of Spina Bifida, Ebner, Wang et al. (NeuroImage, 2020) combined their SRR algorithm with a 2-step segmentation pipeline (2D localisation followed by a 2D segmentation network). However, if the localisation step fails, the second network is not able to recover a correct brain mask, thus requiring manual corrections for an effective SRR. In this work, we aim at improving the fetal brain segmentation for SRR in Spina Bifida. We hypothesise that a well-trained single-step UNet can achieve accurate performance, avoiding the need of a 2-step approach. We propose a new tool for fetal brain segmentation called MONAIfbs, which takes advantage of the Medical Open Network for Artificial Intelligence (MONAI) framework. Our network is based on the dynamic UNet (dynUNet), an adaptation of the nnU-Net framework. When compared to the original 2-step approach proposed in Ebner-Wang, and the same Ebner-Wang approach retrained with the expanded dataset available for this work, the dynUNet showed to achieve higher performance using a single step only. It also showed to reduce the number of outliers, as only 28 stacks obtained Dice score less than 0.9, compared to 68 for Ebner-Wang and 53 Ebner-Wang expanded. The proposed dynUNet model thus provides an improvement of the state-of-the-art fetal brain segmentation techniques, reducing the need for manual correction in automated SRR pipelines. Our code and our trained model are made publicly available at https://github.com/gift-surg/MONAIfbs.

Aldo Marzullo, Marta Bianca Maria Ranzini

Zero-shot anomaly detection (ZSAD) offers potential for identifying anomalies in medical imaging without task-specific training. In this paper, we evaluate CLIP-based models, originally developed for industrial tasks, on brain tumor detection using the BraTS-MET dataset. Our analysis examines their ability to detect medical-specific anomalies with no or minimal supervision, addressing the challenges posed by limited data annotation. While these models show promise in transferring general knowledge to medical tasks, their performance falls short of the precision required for clinical use. Our findings highlight the need for further adaptation before CLIP-based models can be reliably applied to medical anomaly detection.

Kerstin Kläser, Pawel Markiewicz, Marta Ranzini et al.

Attenuation correction is an essential requirement of positron emission tomography (PET) image reconstruction to allow for accurate quantification. However, attenuation correction is particularly challenging for PET-MRI as neither PET nor magnetic resonance imaging (MRI) can directly image tissue attenuation properties. MRI-based computed tomography (CT) synthesis has been proposed as an alternative to physics based and segmentation-based approaches that assign a population-based tissue density value in order to generate an attenuation map. We propose a novel deep fully convolutional neural network that generates synthetic CTs in a recursive manner by gradually reducing the residuals of the previous network, increasing the overall accuracy and generalisability, while keeping the number of trainable parameters within reasonable limits. The model is trained on a database of 20 pre-acquired MRI/CT pairs and a four-fold random bootstrapped validation with a 80:20 split is performed. Quantitative results show that the proposed framework outperforms a state-of-the-art atlas-based approach decreasing the Mean Absolute Error (MAE) from 131HU to 68HU for the synthetic CTs and reducing the PET reconstruction error from 14.3% to 7.2%.