Hadas Ben-Atya

Hadas Ben-Atya, Moti Freiman

Estimating $T_2$ relaxation time distributions from multi-echo $T_2$-weighted MRI ($T_2W$) data can provide valuable biomarkers for assessing inflammation, demyelination, edema, and cartilage composition in various pathologies, including neurodegenerative disorders, osteoarthritis, and tumors. Deep neural network (DNN) based methods have been proposed to address the complex inverse problem of estimating $T_2$ distributions from MRI data, but they are not yet robust enough for clinical data with low Signal-to-Noise ratio (SNR) and are highly sensitive to distribution shifts such as variations in echo-times (TE) used during acquisition. Consequently, their application is hindered in clinical practice and large-scale multi-institutional trials with heterogeneous acquisition protocols. We propose a physically-primed DNN approach, called $P_2T_2$, that incorporates the signal decay forward model in addition to the MRI signal into the DNN architecture to improve the accuracy and robustness of $T_2$ distribution estimation. We evaluated our $P_2T_2$ model in comparison to both DNN-based methods and classical methods for $T_2$ distribution estimation using 1D and 2D numerical simulations along with clinical data. Our model improved the baseline model's accuracy for low SNR levels ($SNR<80$) which are common in the clinical setting. Further, our model achieved a $\sim$35\% improvement in robustness against distribution shifts in the acquisition process compared to previously proposed DNN models. Finally, Our $P_2T_2$ model produces the most detailed Myelin-Water fraction maps compared to baseline approaches when applied to real human MRI data. Our $P_2T_2$ model offers a reliable and precise means of estimating $T_2$ distributions from MRI data and shows promise for use in large-scale multi-institutional trials with heterogeneous acquisition protocols.

Zvi Badash, Hadas Ben-Atya, Naama Gavrielov et al.

Extracting structured clinical information from radiology reports is challenging, especially in low-resource languages. This is pronounced in Crohn's disease, with sparsely represented multi-organ findings. We developed Hierarchical Structured Matching Prediction BERT (HSMP-BERT), a prompt-based model for extraction from Hebrew radiology text. In an administrative database study, we analyzed 9,683 reports from Crohn's patients imaged 2010-2023 across Israeli providers. A subset of 512 reports was radiologist-annotated for findings across six gastrointestinal organs and 15 pathologies, yielding 90 structured labels per subject. Multilabel-stratified split (66% train+validation; 33% test), preserving label prevalence. Performance was evaluated with accuracy, F1, Cohen's $κ$, AUC, PPV, NPV, and recall. On 24 organ-finding combinations with $>$15 positives, HSMP-BERT achieved mean F1 0.83$\pm$0.08 and $κ$ 0.65$\pm$0.17, outperforming the SMP zero-shot baseline (F1 0.49$\pm$0.07, $κ$ 0.06$\pm$0.07) and standard fine-tuning (F1 0.30$\pm$0.27, $κ$ 0.27$\pm$0.34; paired t-test $p < 10^{-7}$). Hierarchical inference cuts runtime 5.1$\times$ vs. traditional inference. Applied to all reports, it revealed associations among ileal wall thickening, stenosis, and pre-stenotic dilatation, plus age- and sex-specific trends in inflammatory findings. HSMP-BERT offers a scalable solution for structured extraction in radiology, enabling population-level analysis of Crohn's disease and demonstrating AI's potential in low-resource settings.

Hadas Ben-Atya, Naama Gavrielov, Zvi Badash et al.

Reliable extraction of structured data from radiology reports using Large Language Models (LLMs) remains challenging, especially for complex, non-English texts like Hebrew. This study introduces an agent-based uncertainty-aware approach to improve the trustworthiness of LLM predictions in medical applications. We analyzed 9,683 Hebrew radiology reports from Crohn's disease patients (from 2010 to 2023) across three medical centers. A subset of 512 reports was manually annotated for six gastrointestinal organs and 15 pathological findings, while the remaining reports were automatically annotated using HSMP-BERT. Structured data extraction was performed using Llama 3.1 (Llama 3-8b-instruct) with Bayesian Prompt Ensembles (BayesPE), which employed six semantically equivalent prompts to estimate uncertainty. An Agent-Based Decision Model integrated multiple prompt outputs into five confidence levels for calibrated uncertainty and was compared against three entropy-based models. Performance was evaluated using accuracy, F1 score, precision, recall, and Cohen's Kappa before and after filtering high-uncertainty cases. The agent-based model outperformed the baseline across all metrics, achieving an F1 score of 0.3967, recall of 0.6437, and Cohen's Kappa of 0.3006. After filtering high-uncertainty cases (greater than or equal to 0.5), the F1 score improved to 0.4787, and Kappa increased to 0.4258. Uncertainty histograms demonstrated clear separation between correct and incorrect predictions, with the agent-based model providing the most well-calibrated uncertainty estimates. By incorporating uncertainty-aware prompt ensembles and an agent-based decision model, this approach enhances the performance and reliability of LLMs in structured data extraction from radiology reports, offering a more interpretable and trustworthy solution for high-stakes medical applications.

Hadas Ben-Atya, Ori Rajchert, Liran Goshen et al.

Automatic brain tumor segmentation from Magnetic Resonance Imaging (MRI) data plays an important role in assessing tumor response to therapy and personalized treatment stratification.Manual segmentation is tedious and subjective.Deep-learning-based algorithms for brain tumor segmentation have the potential to provide objective and fast tumor segmentation.However, the training of such algorithms requires large datasets which are not always available. Data augmentation techniques may reduce the need for large datasets.However current approaches are mostly parametric and may result in suboptimal performance.We introduce two non-parametric methods of data augmentation for brain tumor segmentation: the mixed structure regularization (MSR) and shuffle pixels noise (SPN).We evaluated the added value of the MSR and SPN augmentation on the brain tumor segmentation (BraTS) 2018 challenge dataset with the encoder-decoder nnU-Net architecture as the segmentation algorithm.Both MSR and SPN improve the nnU-Net segmentation accuracy compared to parametric Gaussian noise augmentation.Mean dice score increased from 80% to 82% and p-values=0.0022, 0.0028 when comparing MSR to non-parametric augmentation for the tumor core and whole tumor experiments respectively.The proposed MSR and SPN augmentations have the potential to improve neural-networks performance in other tasks as well.