Magnetic Resonance Imaging Feature-Based Subtyping and Model Ensemble for Enhanced Brain Tumor Segmentation

Accurate and automatic segmentation of brain tumors in multi-parametric magnetic resonance imaging (mpMRI) is essential for quantitative measurements, which play an increasingly important role in clinical diagnosis and prognosis. The International Brain Tumor Segmentation (BraTS) Challenge 2024 offers a unique benchmarking opportunity, including various types of brain tumors in both adult and pediatric populations, such as pediatric brain tumors (PED), meningiomas (MEN-RT) and brain metastases (MET), among others. Compared to previous editions, BraTS 2024 has implemented changes to substantially increase clinical relevance, such as refined tumor regions for evaluation. We propose a deep learning-based ensemble approach that integrates state-of-the-art segmentation models. Additionally, we introduce innovative, adaptive pre- and post-processing techniques that employ MRI-based radiomic analyses to differentiate tumor subtypes. Given the heterogeneous nature of the tumors present in the BraTS datasets, this approach enhances the precision and generalizability of segmentation models. On the final testing sets, our method achieved mean lesion-wise Dice similarity coefficients of 0.926, 0.801, and 0.688 for the whole tumor in PED, MEN-RT, and MET, respectively. These results demonstrate the effectiveness of our approach in improving segmentation performance and generalizability for various brain tumor types.

Adult Glioma Segmentation in Sub-Saharan Africa using Transfer Learning on Stratified Finetuning Data

Gliomas, a kind of brain tumor characterized by high mortality, present substantial diagnostic challenges in low- and middle-income countries, particularly in Sub-Saharan Africa. This paper introduces a novel approach to glioma segmentation using transfer learning to address challenges in resource-limited regions with minimal and low-quality MRI data. We leverage pre-trained deep learning models, nnU-Net and MedNeXt, and apply a stratified fine-tuning strategy using the BraTS2023-Adult-Glioma and BraTS-Africa datasets. Our method exploits radiomic analysis to create stratified training folds, model training on a large brain tumor dataset, and transfer learning to the Sub-Saharan context. A weighted model ensembling strategy and adaptive post-processing are employed to enhance segmentation accuracy. The evaluation of our proposed method on unseen validation cases on the BraTS-Africa 2024 task resulted in lesion-wise mean Dice scores of 0.870, 0.865, and 0.926, for enhancing tumor, tumor core, and whole tumor regions and was ranked first for the challenge. Our approach highlights the ability of integrated machine-learning techniques to bridge the gap between the medical imaging capabilities of resource-limited countries and established developed regions. By tailoring our methods to a target population's specific needs and constraints, we aim to enhance diagnostic capabilities in isolated environments. Our findings underscore the importance of approaches like local data integration and stratification refinement to address healthcare disparities, ensure practical applicability, and enhance impact.

Model Ensemble for Brain Tumor Segmentation in Magnetic Resonance Imaging

Segmenting brain tumors in multi-parametric magnetic resonance imaging enables performing quantitative analysis in support of clinical trials and personalized patient care. This analysis provides the potential to impact clinical decision-making processes, including diagnosis and prognosis. In 2023, the well-established Brain Tumor Segmentation (BraTS) challenge presented a substantial expansion with eight tasks and 4,500 brain tumor cases. In this paper, we present a deep learning-based ensemble strategy that is evaluated for newly included tumor cases in three tasks: pediatric brain tumors (PED), intracranial meningioma (MEN), and brain metastases (MET). In particular, we ensemble outputs from state-of-the-art nnU-Net and Swin UNETR models on a region-wise basis. Furthermore, we implemented a targeted post-processing strategy based on a cross-validated threshold search to improve the segmentation results for tumor sub-regions. The evaluation of our proposed method on unseen test cases for the three tasks resulted in lesion-wise Dice scores for PED: 0.653, 0.809, 0.826; MEN: 0.876, 0.867, 0.849; and MET: 0.555, 0.6, 0.58; for the enhancing tumor, tumor core, and whole tumor, respectively. Our method was ranked first for PED, third for MEN, and fourth for MET, respectively.

Data Alchemy: Mitigating Cross-Site Model Variability Through Test Time Data Calibration

Deploying deep learning-based imaging tools across various clinical sites poses significant challenges due to inherent domain shifts and regulatory hurdles associated with site-specific fine-tuning. For histopathology, stain normalization techniques can mitigate discrepancies, but they often fall short of eliminating inter-site variations. Therefore, we present Data Alchemy, an explainable stain normalization method combined with test time data calibration via a template learning framework to overcome barriers in cross-site analysis. Data Alchemy handles shifts inherent to multi-site data and minimizes them without needing to change the weights of the normalization or classifier networks. Our approach extends to unseen sites in various clinical settings where data domain discrepancies are unknown. Extensive experiments highlight the efficacy of our framework in tumor classification in hematoxylin and eosin-stained patches. Our explainable normalization method boosts classification tasks' area under the precision-recall curve(AUPR) by 0.165, 0.545 to 0.710. Additionally, Data Alchemy further reduces the multisite classification domain gap, by improving the 0.710 AUPR an additional 0.142, elevating classification performance further to 0.852, from 0.545. Our Data Alchemy framework can popularize precision medicine with minimal operational overhead by allowing for the seamless integration of pre-trained deep learning-based clinical tools across multiple sites.

Harvesting Private Medical Images in Federated Learning Systems with Crafted Models

Federated learning (FL) allows a set of clients to collaboratively train a machine-learning model without exposing local training samples. In this context, it is considered to be privacy-preserving and hence has been adopted by medical centers to train machine-learning models over private data. However, in this paper, we propose a novel attack named MediLeak that enables a malicious parameter server to recover high-fidelity patient images from the model updates uploaded by the clients. MediLeak requires the server to generate an adversarial model by adding a crafted module in front of the original model architecture. It is published to the clients in the regular FL training process and each client conducts local training on it to generate corresponding model updates. Then, based on the FL protocol, the model updates are sent back to the server and our proposed analytical method recovers private data from the parameter updates of the crafted module. We provide a comprehensive analysis for MediLeak and show that it can successfully break the state-of-the-art cryptographic secure aggregation protocols, designed to protect the FL systems from privacy inference attacks. We implement MediLeak on the MedMNIST and COVIDx CXR-4 datasets. The results show that MediLeak can nearly perfectly recover private images with high recovery rates and quantitative scores. We further perform downstream tasks such as disease classification with the recovered data, where our results show no significant performance degradation compared to using the original training samples.

D-Rax: Domain-specific Radiologic assistant leveraging multi-modal data and eXpert model predictions

Large vision language models (VLMs) have progressed incredibly from research to applicability for general-purpose use cases. LLaVA-Med, a pioneering large language and vision assistant for biomedicine, can perform multi-modal biomedical image and data analysis to provide a natural language interface for radiologists. While it is highly generalizable and works with multi-modal data, it is currently limited by well-known challenges that exist in the large language model space. Hallucinations and imprecision in responses can lead to misdiagnosis which currently hinder the clinical adaptability of VLMs. To create precise, user-friendly models in healthcare, we propose D-Rax -- a domain-specific, conversational, radiologic assistance tool that can be used to gain insights about a particular radiologic image. In this study, we enhance the conversational analysis of chest X-ray (CXR) images to support radiological reporting, offering comprehensive insights from medical imaging and aiding in the formulation of accurate diagnosis. D-Rax is achieved by fine-tuning the LLaVA-Med architecture on our curated enhanced instruction-following data, comprising of images, instructions, as well as disease diagnosis and demographic predictions derived from MIMIC-CXR imaging data, CXR-related visual question answer (VQA) pairs, and predictive outcomes from multiple expert AI models. We observe statistically significant improvement in responses when evaluated for both open and close-ended conversations. Leveraging the power of state-of-the-art diagnostic models combined with VLMs, D-Rax empowers clinicians to interact with medical images using natural language, which could potentially streamline their decision-making process, enhance diagnostic accuracy, and conserve their time.

Lung-CADex: Fully automatic Zero-Shot Detection and Classification of Lung Nodules in Thoracic CT Images

Lung cancer has been one of the major threats to human life for decades. Computer-aided diagnosis can help with early lung nodul detection and facilitate subsequent nodule characterization. Large Visual Language models (VLMs) have been found effective for multiple downstream medical tasks that rely on both imaging and text data. However, lesion level detection and subsequent diagnosis using VLMs have not been explored yet. We propose CADe, for segmenting lung nodules in a zero-shot manner using a variant of the Segment Anything Model called MedSAM. CADe trains on a prompt suite on input computed tomography (CT) scans by using the CLIP text encoder through prefix tuning. We also propose, CADx, a method for the nodule characterization as benign/malignant by making a gallery of radiomic features and aligning image-feature pairs through contrastive learning. Training and validation of CADe and CADx have been done using one of the largest publicly available datasets, called LIDC. To check the generalization ability of the model, it is also evaluated on a challenging dataset, LUNGx. Our experimental results show that the proposed methods achieve a sensitivity of 0.86 compared to 0.76 that of other fully supervised methods.The source code, datasets and pre-processed data can be accessed using the link:

Zero-Shot Pediatric Tuberculosis Detection in Chest X-Rays using Self-Supervised Learning

Tuberculosis (TB) remains a significant global health challenge, with pediatric cases posing a major concern. The World Health Organization (WHO) advocates for chest X-rays (CXRs) for TB screening. However, visual interpretation by radiologists can be subjective, time-consuming and prone to error, especially in pediatric TB. Artificial intelligence (AI)-driven computer-aided detection (CAD) tools, especially those utilizing deep learning, show promise in enhancing lung disease detection. However, challenges include data scarcity and lack of generalizability. In this context, we propose a novel self-supervised paradigm leveraging Vision Transformers (ViT) for improved TB detection in CXR, enabling zero-shot pediatric TB detection. We demonstrate improvements in TB detection performance ($\sim$12.7% and $\sim$13.4% top AUC/AUPR gains in adults and children, respectively) when conducting self-supervised pre-training when compared to fully-supervised (i.e., non pre-trained) ViT models, achieving top performances of 0.959 AUC and 0.962 AUPR in adult TB detection, and 0.697 AUC and 0.607 AUPR in zero-shot pediatric TB detection. As a result, this work demonstrates that self-supervised learning on adult CXRs effectively extends to challenging downstream tasks such as pediatric TB detection, where data are scarce.

Quantitative Metrics for Benchmarking Medical Image Harmonization

Image harmonization is an important preprocessing strategy to address domain shifts arising from data acquired using different machines and scanning protocols in medical imaging. However, benchmarking the effectiveness of harmonization techniques has been a challenge due to the lack of widely available standardized datasets with ground truths. In this context, we propose three metrics: two intensity harmonization metrics and one anatomy preservation metric for medical images during harmonization, where no ground truths are required. Through extensive studies on a dataset with available harmonization ground truth, we demonstrate that our metrics are correlated with established image quality assessment metrics. We show how these novel metrics may be applied to real-world scenarios where no harmonization ground truth exists. Additionally, we provide insights into different interpretations of the metric values, shedding light on their significance in the context of the harmonization process. As a result of our findings, we advocate for the adoption of these quantitative harmonization metrics as a standard for benchmarking the performance of image harmonization techniques.

Harmonization Across Imaging Locations(HAIL): One-Shot Learning for Brain MRI

For machine learning-based prognosis and diagnosis of rare diseases, such as pediatric brain tumors, it is necessary to gather medical imaging data from multiple clinical sites that may use different devices and protocols. Deep learning-driven harmonization of radiologic images relies on generative adversarial networks (GANs). However, GANs notoriously generate pseudo structures that do not exist in the original training data, a phenomenon known as "hallucination". To prevent hallucination in medical imaging, such as magnetic resonance images (MRI) of the brain, we propose a one-shot learning method where we utilize neural style transfer for harmonization. At test time, the method uses one image from a clinical site to generate an image that matches the intensity scale of the collaborating sites. Our approach combines learning a feature extractor, neural style transfer, and adaptive instance normalization. We further propose a novel strategy to evaluate the effectiveness of image harmonization approaches with evaluation metrics that both measure image style harmonization and assess the preservation of anatomical structures. Experimental results demonstrate the effectiveness of our method in preserving patient anatomy while adjusting the image intensities to a new clinical site. Our general harmonization model can be used on unseen data from new sites, making it a valuable tool for real-world medical applications and clinical trials.