AI-Driven MRI-based Brain Tumour Segmentation Benchmarking

Medical image segmentation has greatly aided medical diagnosis, with U-Net based architectures and nnU-Net providing state-of-the-art performance. There have been numerous general promptable models and medical variations introduced in recent years, but there is currently a lack of evaluation and comparison of these models across a variety of prompt qualities on a common medical dataset. This research uses Segment Anything Model (SAM), Segment Anything Model 2 (SAM 2), MedSAM, SAM-Med-3D, and nnU-Net to obtain zero-shot inference on the BraTS 2023 adult glioma and pediatrics dataset across multiple prompt qualities for both points and bounding boxes. Several of these models exhibit promising Dice scores, particularly SAM and SAM 2 achieving scores of up to 0.894 and 0.893, respectively when given extremely accurate bounding box prompts which exceeds nnU-Net's segmentation performance. However, nnU-Net remains the dominant medical image segmentation network due to the impracticality of providing highly accurate prompts to the models. The model and prompt evaluation, as well as the comparison, are extended through fine-tuning SAM, SAM 2, MedSAM, and SAM-Med-3D on the pediatrics dataset. The improvements in point prompt performance after fine-tuning are substantial and show promise for future investigation, but are unable to achieve better segmentation than bounding boxes or nnU-Net.

Edge-Enhanced Dilated Residual Attention Network for Multimodal Medical Image Fusion

Multimodal medical image fusion is a crucial task that combines complementary information from different imaging modalities into a unified representation, thereby enhancing diagnostic accuracy and treatment planning. While deep learning methods, particularly Convolutional Neural Networks (CNNs) and Transformers, have significantly advanced fusion performance, some of the existing CNN-based methods fall short in capturing fine-grained multiscale and edge features, leading to suboptimal feature integration. Transformer-based models, on the other hand, are computationally intensive in both the training and fusion stages, making them impractical for real-time clinical use. Moreover, the clinical application of fused images remains unexplored. In this paper, we propose a novel CNN-based architecture that addresses these limitations by introducing a Dilated Residual Attention Network Module for effective multiscale feature extraction, coupled with a gradient operator to enhance edge detail learning. To ensure fast and efficient fusion, we present a parameter-free fusion strategy based on the weighted nuclear norm of softmax, which requires no additional computations during training or inference. Extensive experiments, including a downstream brain tumor classification task, demonstrate that our approach outperforms various baseline methods in terms of visual quality, texture preservation, and fusion speed, making it a possible practical solution for real-world clinical applications. The code will be released at https://github.com/simonZhou86/en_dran.

Tumor Location-weighted MRI-Report Contrastive Learning: A Framework for Improving the Explainability of Pediatric Brain Tumor Diagnosis

Despite the promising performance of convolutional neural networks (CNNs) in brain tumor diagnosis from magnetic resonance imaging (MRI), their integration into the clinical workflow has been limited. That is mainly due to the fact that the features contributing to a model's prediction are unclear to radiologists and hence, clinically irrelevant, i.e., lack of explainability. As the invaluable sources of radiologists' knowledge and expertise, radiology reports can be integrated with MRI in a contrastive learning (CL) framework, enabling learning from image-report associations, to improve CNN explainability. In this work, we train a multimodal CL architecture on 3D brain MRI scans and radiology reports to learn informative MRI representations. Furthermore, we integrate tumor location, salient to several brain tumor analysis tasks, into this framework to improve its generalizability. We then apply the learnt image representations to improve explainability and performance of genetic marker classification of pediatric Low-grade Glioma, the most prevalent brain tumor in children, as a downstream task. Our results indicate a Dice score of 31.1% between the model's attention maps and manual tumor segmentation (as an explainability measure) with test classification performance of 87.7%, significantly outperforming the baselines. These enhancements can build trust in our model among radiologists, facilitating its integration into clinical practices for more efficient tumor diagnosis.

Opportunities for Persian Digital Humanities Research with Artificial Intelligence Language Models; Case Study: Forough Farrokhzad

This study explores the integration of advanced Natural Language Processing (NLP) and Artificial Intelligence (AI) techniques to analyze and interpret Persian literature, focusing on the poetry of Forough Farrokhzad. Utilizing computational methods, we aim to unveil thematic, stylistic, and linguistic patterns in Persian poetry. Specifically, the study employs AI models including transformer-based language models for clustering of the poems in an unsupervised framework. This research underscores the potential of AI in enhancing our understanding of Persian literary heritage, with Forough Farrokhzad's work providing a comprehensive case study. This approach not only contributes to the field of Persian Digital Humanities but also sets a precedent for future research in Persian literary studies using computational techniques.

Improving Pediatric Low-Grade Neuroepithelial Tumors Molecular Subtype Identification Using a Novel AUROC Loss Function for Convolutional Neural Networks

Pediatric Low-Grade Neuroepithelial Tumors (PLGNT) are the most common pediatric cancer type, accounting for 40% of brain tumors in children, and identifying PLGNT molecular subtype is crucial for treatment planning. However, the gold standard to determine the PLGNT subtype is biopsy, which can be impractical or dangerous for patients. This research improves the performance of Convolutional Neural Networks (CNNs) in classifying PLGNT subtypes through MRI scans by introducing a loss function that specifically improves the model's Area Under the Receiver Operating Characteristic (ROC) Curve (AUROC), offering a non-invasive diagnostic alternative. In this study, a retrospective dataset of 339 children with PLGNT (143 BRAF fusion, 71 with BRAF V600E mutation, and 125 non-BRAF) was curated. We employed a CNN model with Monte Carlo random data splitting. The baseline model was trained using binary cross entropy (BCE), and achieved an AUROC of 86.11% for differentiating BRAF fusion and BRAF V600E mutations, which was improved to 87.71% using our proposed AUROC loss function (p-value 0.045). With multiclass classification, the AUROC improved from 74.42% to 76. 59% (p-value 0.0016).

Generating 3D Brain Tumor Regions in MRI using Vector-Quantization Generative Adversarial Networks

Medical image analysis has significantly benefited from advancements in deep learning, particularly in the application of Generative Adversarial Networks (GANs) for generating realistic and diverse images that can augment training datasets. However, the effectiveness of such approaches is often limited by the amount of available data in clinical settings. Additionally, the common GAN-based approach is to generate entire image volumes, rather than solely the region of interest (ROI). Research on deep learning-based brain tumor classification using MRI has shown that it is easier to classify the tumor ROIs compared to the entire image volumes. In this work, we present a novel framework that uses vector-quantization GAN and a transformer incorporating masked token modeling to generate high-resolution and diverse 3D brain tumor ROIs that can be directly used as augmented data for the classification of brain tumor ROI. We apply our method to two imbalanced datasets where we augment the minority class: (1) the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2019 dataset to generate new low-grade glioma (LGG) ROIs to balance with high-grade glioma (HGG) class; (2) the internal pediatric LGG (pLGG) dataset tumor ROIs with BRAF V600E Mutation genetic marker to balance with BRAF Fusion genetic marker class. We show that the proposed method outperforms various baseline models in both qualitative and quantitative measurements. The generated data was used to balance the data in the brain tumor types classification task. Using the augmented data, our approach surpasses baseline models by 6.4% in AUC on the BraTS 2019 dataset and 4.3% in AUC on our internal pLGG dataset. The results indicate the generated tumor ROIs can effectively address the imbalanced data problem. Our proposed method has the potential to facilitate an accurate diagnosis of rare brain tumors using MRI scans.

Using Large Text-to-Image Models with Structured Prompts for Skin Disease Identification: A Case Study

This paper investigates the potential usage of large text-to-image (LTI) models for the automated diagnosis of a few skin conditions with rarity or a serious lack of annotated datasets. As the input to the LTI model, we provide the targeted instantiation of a generic but succinct prompt structure designed upon careful observations of the conditional narratives from the standard medical textbooks. In this regard, we pave the path to utilizing accessible textbook descriptions for automated diagnosis of conditions with data scarcity through the lens of LTI models. Experiments show the efficacy of the proposed framework, including much better localization of the infected regions. Moreover, it has the immense possibility for generalization across the medical sub-domains, not only to mitigate the data scarcity issue but also to debias automated diagnostics from the all-pervasive racial biases.

Automating Cobb Angle Measurement for Adolescent Idiopathic Scoliosis using Instance Segmentation

Scoliosis is a three-dimensional deformity of the spine, most often diagnosed in childhood. It affects 2-3% of the population, which is approximately seven million people in North America. Currently, the reference standard for assessing scoliosis is based on the manual assignment of Cobb angles at the site of the curvature center. This manual process is time consuming and unreliable as it is affected by inter- and intra-observer variance. To overcome these inaccuracies, machine learning (ML) methods can be used to automate the Cobb angle measurement process. This paper proposes to address the Cobb angle measurement task using YOLACT, an instance segmentation model. The proposed method first segments the vertebrae in an X-Ray image using YOLACT, then it tracks the important landmarks using the minimum bounding box approach. Lastly, the extracted landmarks are used to calculate the corresponding Cobb angles. The model achieved a Symmetric Mean Absolute Percentage Error (SMAPE) score of 10.76%, demonstrating the reliability of this process in both vertebra localization and Cobb angle measurement.

A Comprehensive Study of Radiomics-based Machine Learning for Fibrosis Detection

Objectives: Early detection of liver fibrosis can help cure the disease or prevent disease progression. We perform a comprehensive study of machine learning-based fibrosis detection in CT images using radiomic features to develop a non-invasive approach to fibrosis detection. Methods: Two sets of radiomic features were extracted from spherical ROIs in CT images of 182 patients who underwent simultaneous liver biopsy and CT examinations, one set corresponding to biopsy locations and another distant from biopsy locations. Combinations of contrast, normalization, machine learning model, feature selection method, bin width, and kernel radius were investigated, each of which were trained and evaluated 100 times with randomized development and test cohorts. The best settings were evaluated based on their mean test AUC and the best features were determined based on their frequency among the best settings. Results: Logistic regression models with NC images normalized using Gamma correction with $\gamma = 1.5$ performed best for fibrosis detection. Boruta was the best for radiomic feature selection method. Training a model using these optimal settings and features consisting of first order energy, first order kurtosis, and first order skewness, resulted in a model that achieved mean test AUCs of 0.7549 and 0.7166 on biopsy-based and non-biopsy ROIs respectively, outperforming a baseline and best models found during the initial study. Conclusions: Logistic regression models trained on radiomic features from NC images normalized using Gamma correction with $\gamma = 1.5$ that underwent Boruta feature selection are effective for liver fibrosis detection. Energy, kurtosis, and skewness are particularly effective features for fibrosis detection.

A novel GAN-based paradigm for weakly supervised brain tumor segmentation of MR images

Segmentation of regions of interest (ROIs) for identifying abnormalities is a leading problem in medical imaging. Using Machine Learning (ML) for this problem generally requires manually annotated ground-truth segmentations, demanding extensive time and resources from radiologists. This work presents a novel weakly supervised approach that utilizes binary image-level labels, which are much simpler to acquire, to effectively segment anomalies in medical Magnetic Resonance (MR) images without ground truth annotations. We train a binary classifier using these labels and use it to derive seeds indicating regions likely and unlikely to contain tumors. These seeds are used to train a generative adversarial network (GAN) that converts cancerous images to healthy variants, which are then used in conjunction with the seeds to train a ML model that generates effective segmentations. This method produces segmentations that achieve Dice coefficients of 0.7903, 0.7868, and 0.7712 on the MICCAI Brain Tumor Segmentation (BraTS) 2020 dataset for the training, validation, and test cohorts respectively. We also propose a weakly supervised means of filtering the segmentations, removing a small subset of poorer segmentations to acquire a large subset of high quality segmentations. The proposed filtering further improves the Dice coefficients to up to 0.8374, 0.8232, and 0.8136 for training, validation, and test, respectively.